subject:"Re\: Using multi\-processor for model

Re: Using multi-processor for model_free

2016-10-27 Thread Edward d'Auvergne

On 10 October 2016 at 23:12, Mahdi, Sam  wrote:
> Hi Edward,
>
> Wanted to update you a prior problem I had. So I ran relax with multiple
> processors and single processor with the same data set, and obtained
> identical data on my computer. So the previous issue I had with missing data
> I don't think is related to relax itself. Just wanted to let you know.

This is great to hear.  The relax test suite is a gold standard which
shows that this should always be the case.  Though there are a few
extremely minor differences when using different operating systems and
32 vs. 64-bit systems, the code paths for running on the multi and
uni-processors is identical.  This is thanks to Gary Thompson's great
design of the multi-processor system :)

Regards,

Edward

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Re: Using multi-processor for model_free

2016-10-10 Thread Mahdi, Sam

Hi Edward,

Wanted to update you a prior problem I had. So I ran relax with multiple
processors and single processor with the same data set, and obtained
identical data on my computer. So the previous issue I had with missing
data I don't think is related to relax itself. Just wanted to let you know.

Sincerely,
Sam

On Thu, Oct 6, 2016 at 3:05 PM, Mahdi, Sam 
wrote:

> Hi Edward,
>
> I was talking to the developer of mpi4py, and he said that mpi4py should
> work with both, even if you have both of them installed, by loading the
> appropriate module (openmpi or mpich) I should be able to run mpi4py. He
> said he suspects there was probably a problem with the installation of
> openmpi itself (improper compilation, or the package itself was improperly
> configured itself). Regardless, it finally works Thanks to both of you for
> your help with relax and my multi-processor problem.
>
> Sincerely,
> Sam
>
> On Thu, Oct 6, 2016 at 2:39 PM, Edward d'Auvergne 
> wrote:
>
>> On Thursday, 6 October 2016, Mahdi, Sam 
>> wrote:
>>
>>> Hi Troels and Edward,
>>>
>>> I was able to get relax working on a multi-processor platform finally. I
>>> tried using the mpich instead of openmpi.
>>> module load mpi/mpich-x86_64
>>> mpirun -np 7 ./relax --multi='mpi4py'
>>>
>>> and it loaded up relax with 1 master and 7 slaves. I don't exactly
>>> understand why openmpi doesn't work. I have gotten both from the package
>>> list, and installed them directly., and I have mpi4py for both mpich and
>>> openmpi (I also got these from the package list and installed directly),
>>> but this seemed to finally get it to work.
>>>
>>
>> Hi Sam,
>>
>> This sounds like a classic software clash, with OpenMPI loosing out to
>> MPICH with respect to mpi4py.  Maybe uninstalling all MPI packages and just
>> having openmpi and python-mpi4py would have solved this.  Anyway, as long
>> as something works, that's all that is needed.  Thank you Troels for all of
>> your help!
>>
>> Regards,
>>
>> Edward
>>
>
>
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Re: Using multi-processor for model_free

2016-10-06 Thread Mahdi, Sam

Hi Edward,

I was talking to the developer of mpi4py, and he said that mpi4py should
work with both, even if you have both of them installed, by loading the
appropriate module (openmpi or mpich) I should be able to run mpi4py. He
said he suspects there was probably a problem with the installation of
openmpi itself (improper compilation, or the package itself was improperly
configured itself). Regardless, it finally works Thanks to both of you for
your help with relax and my multi-processor problem.

Sincerely,
Sam

On Thu, Oct 6, 2016 at 2:39 PM, Edward d'Auvergne 
wrote:

> On Thursday, 6 October 2016, Mahdi, Sam  wrote:
>
>> Hi Troels and Edward,
>>
>> I was able to get relax working on a multi-processor platform finally. I
>> tried using the mpich instead of openmpi.
>> module load mpi/mpich-x86_64
>> mpirun -np 7 ./relax --multi='mpi4py'
>>
>> and it loaded up relax with 1 master and 7 slaves. I don't exactly
>> understand why openmpi doesn't work. I have gotten both from the package
>> list, and installed them directly., and I have mpi4py for both mpich and
>> openmpi (I also got these from the package list and installed directly),
>> but this seemed to finally get it to work.
>>
>
> Hi Sam,
>
> This sounds like a classic software clash, with OpenMPI loosing out to
> MPICH with respect to mpi4py.  Maybe uninstalling all MPI packages and just
> having openmpi and python-mpi4py would have solved this.  Anyway, as long
> as something works, that's all that is needed.  Thank you Troels for all of
> your help!
>
> Regards,
>
> Edward
>
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Re: Using multi-processor for model_free

2016-10-05 Thread Mahdi, Sam

Ok. Thank you both by the way. You guys have been incredibly helpful, and
sorry I bothered you guys so much. I'll still attempt to troubleshoot this
and potentially fix it. When I find out what the solution is, I will let
you guys know.
Thank you.

Sincerely,
Sam

On Wed, Oct 5, 2016 at 3:10 PM, Troels Emtekær Linnet  wrote:

> I think there is nothing more to do here.
>
> Call the nearest computer wizard,
> and give a round of beer.
>
> Best Troels
>
>
> Den onsdag den 5. oktober 2016 skrev Mahdi, Sam  >:
>
>> But i already have mpi4py installed from the package list.
>>
>> On Wed, Oct 5, 2016 at 2:43 PM, Troels Emtekær Linnet <
>> tlin...@nmr-relax.com> wrote:
>>
>>> Hi Sam.
>>>
>>> Akk you PI to run this:
>>>
>>> sudo -- sh -c 'setenv MPICC /usr/lib64/openmpi-1.10/bin/mpicc; pip
>>> install mpi4py'
>>> or
>>> sudo -i
>>> setenv MPICC /usr/lib64/openmpi-1.10/bin/mpicc
>>> pip install mpi4py
>>>
>>>
>>> Where '/usr/lib64/openmpi-1.10/bin/mpicc' should be the path to mpicc.
>>>
>>> Find the path with:
>>> which mpicc
>>>
>>> Look here:
>>> https://mpi4py.scipy.org/docs/usrman/install.html
>>>
>>> Under:
>>> "Using pip or easy_install"
>>>
>>> You need to tell where the mpicc is with the environment, so mpi4py can
>>> be compiled correctly.
>>>
>>> Note: Setting the environment in BASH and TCSH is different!
>>>
>>> BASH:
>>> sudo -- sh -c 'env MPICC=/usr/lib64/openmpi-1.10/bin/mpicc; pip install
>>> mpi4py'
>>>
>>> TCSH:
>>> sudo -- sh -c 'setenv MPICC /usr/lib64/openmpi-1.10/bin/mpicc; pip
>>> install mpi4py'
>>>
>>>
>>>
>>>
>>>
>>> 2016-10-05 23:31 GMT+02:00 Mahdi, Sam :
>>>
 Hi Edward,

 I installed mpi4py and OpenMPI both from the fedora packages. I had a
 mpi4py that I downloaded via the site itself, and compiled it, but I wasn't
 able to install it so I deleted it. The command
 mpirun --np 5 python -c "import mpi4py; from mpi4py import MPI;
 print('Mpi4py %s process %d of %d on %s.'%(mpi4py._version_,MPI>COM
 M_WORLD.Get_rank(),MPI>COMM_WORLD.Get_size(),MPI.Get_process
 or_name()))"

 gave no output. These are the mpi packages I have installed
 Openmpi:
 openmpi-1.7.3-1.fc.20(64-bit)
 openmpi-devel-1.7.3-1.fc20(64bit)
 pypar-openmpi-2.1.5_108_3.fc.20(64bit)
 python3-mpi4py-1.3.1-1.fc20(64bit)

 Mpi4py
 mpi4py-common-1.3.1-1.fc20
 mpi4py-mpich-1.3.1-1.fc20
 mpi4py-openmpi-1.3.1-1.fc20
 python3-mpi4py-mpich-1.3.1-1.fc20
 python3-mpi4py-openmpi-1.3.1-1.fc20

 Could you reccomend which packages specifically I should install? I
 could just tell my PI to remove all the openmpi and mpi4py programs, and
 download the specific 2 that do work (if there is a problem with having
 different mpi's and mpi4py's)

 All of these were installed from the fedora packages themselves. Also
 the locate mpi list gave me a massive output (I assume this is because I
 have 5 programs that use mpi)
 Sincerely,
 Sam

 On Wed, Oct 5, 2016 at 2:09 PM, Edward d'Auvergne  wrote:

> On 5 October 2016 at 22:01, Mahdi, Sam 
> wrote:
> > Hi Troels,
> >
> > The mpirun --np 2 gave no output, so I had to abort the command, but
> here is
> > the output.
> > crowlab: [~]> python -c "import mpi4py; print mpi4py.__version__"
> > 1.3.1
> > crowlab: [~]> mpirun --np 2 python -c "from mpi4py import MPI; print
> > MPI.COMM_WORLD.Get_rank()"
> > ^Ccrowlab: [~]>
>
> Hi Sam,
>
> This result I'm pretty sure shows that mpi4py is not functioning
> correctly - i.e. there is an installation problem.  This is what you
> should see:
>
> [edward@localhost ~]$ mpirun --np 2 python -c "from mpi4py import MPI;
> print MPI.COMM_WORLD.Get_rank()"
> 0
> 1
> [edward@localhost ~]$
>
> Note the printout of 0 and 1.  Maybe try the following:
>
> [edward@localhost ~]$ mpirun --np 5 python -c "import mpi4py; from
> mpi4py import MPI; print('Mpi4py %s process %d of %d on %s.'
> %(mpi4py.__version__,
> MPI.COMM_WORLD.Get_rank(),MPI.COMM_WORLD.Get_size(),
> MPI.Get_processor_name()))"
> Mpi4py 1.3.1 process 0 of 5 on localhost.localdomain.
> Mpi4py 1.3.1 process 1 of 5 on localhost.localdomain.
> Mpi4py 1.3.1 process 4 of 5 on localhost.localdomain.
> Mpi4py 1.3.1 process 2 of 5 on localhost.localdomain.
> Mpi4py 1.3.1 process 3 of 5 on localhost.localdomain.
> [edward@localhost ~]$
>
> If you don't see a printout here, then clearly mpi4py and OpenMPI are
> not working together correctly.  Without a printout, your mpi4py is
> FUBAR.  Are you using the default OpenMPI and mpi4py packages form
> fedora, and you don't have any backports or other non-standard sources
> set up for your RPMs?  Do you have any user installed MPI

Re: Using multi-processor for model_free

2016-10-05 Thread Troels Emtekær Linnet

I think there is nothing more to do here.

Call the nearest computer wizard,
and give a round of beer.

Best Troels

Den onsdag den 5. oktober 2016 skrev Mahdi, Sam :

> But i already have mpi4py installed from the package list.
>
> On Wed, Oct 5, 2016 at 2:43 PM, Troels Emtekær Linnet <
> tlin...@nmr-relax.com
> > wrote:
>
>> Hi Sam.
>>
>> Akk you PI to run this:
>>
>> sudo -- sh -c 'setenv MPICC /usr/lib64/openmpi-1.10/bin/mpicc; pip
>> install mpi4py'
>> or
>> sudo -i
>> setenv MPICC /usr/lib64/openmpi-1.10/bin/mpicc
>> pip install mpi4py
>>
>>
>> Where '/usr/lib64/openmpi-1.10/bin/mpicc' should be the path to mpicc.
>>
>> Find the path with:
>> which mpicc
>>
>> Look here:
>> https://mpi4py.scipy.org/docs/usrman/install.html
>>
>> Under:
>> "Using pip or easy_install"
>>
>> You need to tell where the mpicc is with the environment, so mpi4py can
>> be compiled correctly.
>>
>> Note: Setting the environment in BASH and TCSH is different!
>>
>> BASH:
>> sudo -- sh -c 'env MPICC=/usr/lib64/openmpi-1.10/bin/mpicc; pip install
>> mpi4py'
>>
>> TCSH:
>> sudo -- sh -c 'setenv MPICC /usr/lib64/openmpi-1.10/bin/mpicc; pip
>> install mpi4py'
>>
>>
>>
>>
>>
>> 2016-10-05 23:31 GMT+02:00 Mahdi, Sam > >:
>>
>>> Hi Edward,
>>>
>>> I installed mpi4py and OpenMPI both from the fedora packages. I had a
>>> mpi4py that I downloaded via the site itself, and compiled it, but I wasn't
>>> able to install it so I deleted it. The command
>>> mpirun --np 5 python -c "import mpi4py; from mpi4py import MPI;
>>> print('Mpi4py %s process %d of %d on %s.'%(mpi4py._version_,MPI>COM
>>> M_WORLD.Get_rank(),MPI>COMM_WORLD.Get_size(),MPI.Get_processor_name()))"
>>>
>>> gave no output. These are the mpi packages I have installed
>>> Openmpi:
>>> openmpi-1.7.3-1.fc.20(64-bit)
>>> openmpi-devel-1.7.3-1.fc20(64bit)
>>> pypar-openmpi-2.1.5_108_3.fc.20(64bit)
>>> python3-mpi4py-1.3.1-1.fc20(64bit)
>>>
>>> Mpi4py
>>> mpi4py-common-1.3.1-1.fc20
>>> mpi4py-mpich-1.3.1-1.fc20
>>> mpi4py-openmpi-1.3.1-1.fc20
>>> python3-mpi4py-mpich-1.3.1-1.fc20
>>> python3-mpi4py-openmpi-1.3.1-1.fc20
>>>
>>> Could you reccomend which packages specifically I should install? I
>>> could just tell my PI to remove all the openmpi and mpi4py programs, and
>>> download the specific 2 that do work (if there is a problem with having
>>> different mpi's and mpi4py's)
>>>
>>> All of these were installed from the fedora packages themselves. Also
>>> the locate mpi list gave me a massive output (I assume this is because I
>>> have 5 programs that use mpi)
>>> Sincerely,
>>> Sam
>>>
>>> On Wed, Oct 5, 2016 at 2:09 PM, Edward d'Auvergne >> > wrote:
>>>
 On 5 October 2016 at 22:01, Mahdi, Sam > wrote:
 > Hi Troels,
 >
 > The mpirun --np 2 gave no output, so I had to abort the command, but
 here is
 > the output.
 > crowlab: [~]> python -c "import mpi4py; print mpi4py.__version__"
 > 1.3.1
 > crowlab: [~]> mpirun --np 2 python -c "from mpi4py import MPI; print
 > MPI.COMM_WORLD.Get_rank()"
 > ^Ccrowlab: [~]>

 Hi Sam,

 This result I'm pretty sure shows that mpi4py is not functioning
 correctly - i.e. there is an installation problem.  This is what you
 should see:

 [edward@localhost ~]$ mpirun --np 2 python -c "from mpi4py import MPI;
 print MPI.COMM_WORLD.Get_rank()"
 0
 1
 [edward@localhost ~]$

 Note the printout of 0 and 1.  Maybe try the following:

 [edward@localhost ~]$ mpirun --np 5 python -c "import mpi4py; from
 mpi4py import MPI; print('Mpi4py %s process %d of %d on %s.'
 %(mpi4py.__version__,
 MPI.COMM_WORLD.Get_rank(),MPI.COMM_WORLD.Get_size(),
 MPI.Get_processor_name()))"
 Mpi4py 1.3.1 process 0 of 5 on localhost.localdomain.
 Mpi4py 1.3.1 process 1 of 5 on localhost.localdomain.
 Mpi4py 1.3.1 process 4 of 5 on localhost.localdomain.
 Mpi4py 1.3.1 process 2 of 5 on localhost.localdomain.
 Mpi4py 1.3.1 process 3 of 5 on localhost.localdomain.
 [edward@localhost ~]$

 If you don't see a printout here, then clearly mpi4py and OpenMPI are
 not working together correctly.  Without a printout, your mpi4py is
 FUBAR.  Are you using the default OpenMPI and mpi4py packages form
 fedora, and you don't have any backports or other non-standard sources
 set up for your RPMs?  Do you have any user installed MPI or mpi4py
 software around?  If you type:

 $ locate mpi

 What do you see?  For me this is pretty clearly an installation problem.

 Regards,

 Edward

>>>
>>>
>>
>
___
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Re: Using multi-processor for model_free

2016-10-05 Thread Mahdi, Sam

But i already have mpi4py installed from the package list.

On Wed, Oct 5, 2016 at 2:43 PM, Troels Emtekær Linnet  wrote:

> Hi Sam.
>
> Akk you PI to run this:
>
> sudo -- sh -c 'setenv MPICC /usr/lib64/openmpi-1.10/bin/mpicc; pip
> install mpi4py'
> or
> sudo -i
> setenv MPICC /usr/lib64/openmpi-1.10/bin/mpicc
> pip install mpi4py
>
>
> Where '/usr/lib64/openmpi-1.10/bin/mpicc' should be the path to mpicc.
>
> Find the path with:
> which mpicc
>
> Look here:
> https://mpi4py.scipy.org/docs/usrman/install.html
>
> Under:
> "Using pip or easy_install"
>
> You need to tell where the mpicc is with the environment, so mpi4py can be
> compiled correctly.
>
> Note: Setting the environment in BASH and TCSH is different!
>
> BASH:
> sudo -- sh -c 'env MPICC=/usr/lib64/openmpi-1.10/bin/mpicc; pip install
> mpi4py'
>
> TCSH:
> sudo -- sh -c 'setenv MPICC /usr/lib64/openmpi-1.10/bin/mpicc; pip
> install mpi4py'
>
>
>
>
>
> 2016-10-05 23:31 GMT+02:00 Mahdi, Sam :
>
>> Hi Edward,
>>
>> I installed mpi4py and OpenMPI both from the fedora packages. I had a
>> mpi4py that I downloaded via the site itself, and compiled it, but I wasn't
>> able to install it so I deleted it. The command
>> mpirun --np 5 python -c "import mpi4py; from mpi4py import MPI;
>> print('Mpi4py %s process %d of %d on %s.'%(mpi4py._version_,MPI>COM
>> M_WORLD.Get_rank(),MPI>COMM_WORLD.Get_size(),MPI.Get_processor_name()))"
>>
>> gave no output. These are the mpi packages I have installed
>> Openmpi:
>> openmpi-1.7.3-1.fc.20(64-bit)
>> openmpi-devel-1.7.3-1.fc20(64bit)
>> pypar-openmpi-2.1.5_108_3.fc.20(64bit)
>> python3-mpi4py-1.3.1-1.fc20(64bit)
>>
>> Mpi4py
>> mpi4py-common-1.3.1-1.fc20
>> mpi4py-mpich-1.3.1-1.fc20
>> mpi4py-openmpi-1.3.1-1.fc20
>> python3-mpi4py-mpich-1.3.1-1.fc20
>> python3-mpi4py-openmpi-1.3.1-1.fc20
>>
>> Could you reccomend which packages specifically I should install? I could
>> just tell my PI to remove all the openmpi and mpi4py programs, and download
>> the specific 2 that do work (if there is a problem with having different
>> mpi's and mpi4py's)
>>
>> All of these were installed from the fedora packages themselves. Also the
>> locate mpi list gave me a massive output (I assume this is because I have 5
>> programs that use mpi)
>> Sincerely,
>> Sam
>>
>> On Wed, Oct 5, 2016 at 2:09 PM, Edward d'Auvergne 
>> wrote:
>>
>>> On 5 October 2016 at 22:01, Mahdi, Sam 
>>> wrote:
>>> > Hi Troels,
>>> >
>>> > The mpirun --np 2 gave no output, so I had to abort the command, but
>>> here is
>>> > the output.
>>> > crowlab: [~]> python -c "import mpi4py; print mpi4py.__version__"
>>> > 1.3.1
>>> > crowlab: [~]> mpirun --np 2 python -c "from mpi4py import MPI; print
>>> > MPI.COMM_WORLD.Get_rank()"
>>> > ^Ccrowlab: [~]>
>>>
>>> Hi Sam,
>>>
>>> This result I'm pretty sure shows that mpi4py is not functioning
>>> correctly - i.e. there is an installation problem.  This is what you
>>> should see:
>>>
>>> [edward@localhost ~]$ mpirun --np 2 python -c "from mpi4py import MPI;
>>> print MPI.COMM_WORLD.Get_rank()"
>>> 0
>>> 1
>>> [edward@localhost ~]$
>>>
>>> Note the printout of 0 and 1.  Maybe try the following:
>>>
>>> [edward@localhost ~]$ mpirun --np 5 python -c "import mpi4py; from
>>> mpi4py import MPI; print('Mpi4py %s process %d of %d on %s.'
>>> %(mpi4py.__version__,
>>> MPI.COMM_WORLD.Get_rank(),MPI.COMM_WORLD.Get_size(),
>>> MPI.Get_processor_name()))"
>>> Mpi4py 1.3.1 process 0 of 5 on localhost.localdomain.
>>> Mpi4py 1.3.1 process 1 of 5 on localhost.localdomain.
>>> Mpi4py 1.3.1 process 4 of 5 on localhost.localdomain.
>>> Mpi4py 1.3.1 process 2 of 5 on localhost.localdomain.
>>> Mpi4py 1.3.1 process 3 of 5 on localhost.localdomain.
>>> [edward@localhost ~]$
>>>
>>> If you don't see a printout here, then clearly mpi4py and OpenMPI are
>>> not working together correctly.  Without a printout, your mpi4py is
>>> FUBAR.  Are you using the default OpenMPI and mpi4py packages form
>>> fedora, and you don't have any backports or other non-standard sources
>>> set up for your RPMs?  Do you have any user installed MPI or mpi4py
>>> software around?  If you type:
>>>
>>> $ locate mpi
>>>
>>> What do you see?  For me this is pretty clearly an installation problem.
>>>
>>> Regards,
>>>
>>> Edward
>>>
>>
>>
>
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Re: Using multi-processor for model_free

2016-10-05 Thread Mahdi, Sam

Hi Edward,

I installed mpi4py and OpenMPI both from the fedora packages. I had a
mpi4py that I downloaded via the site itself, and compiled it, but I wasn't
able to install it so I deleted it. The command
mpirun --np 5 python -c "import mpi4py; from mpi4py import MPI;
print('Mpi4py %s process %d of %d on
%s.'%(mpi4py._version_,MPI>COMM_WORLD.Get_rank(),MPI>COMM_WORLD.Get_size(),MPI.Get_processor_name()))"

gave no output. These are the mpi packages I have installed
Openmpi:
openmpi-1.7.3-1.fc.20(64-bit)
openmpi-devel-1.7.3-1.fc20(64bit)
pypar-openmpi-2.1.5_108_3.fc.20(64bit)
python3-mpi4py-1.3.1-1.fc20(64bit)

Mpi4py
mpi4py-common-1.3.1-1.fc20
mpi4py-mpich-1.3.1-1.fc20
mpi4py-openmpi-1.3.1-1.fc20
python3-mpi4py-mpich-1.3.1-1.fc20
python3-mpi4py-openmpi-1.3.1-1.fc20

Could you reccomend which packages specifically I should install? I could
just tell my PI to remove all the openmpi and mpi4py programs, and download
the specific 2 that do work (if there is a problem with having different
mpi's and mpi4py's)

All of these were installed from the fedora packages themselves. Also the
locate mpi list gave me a massive output (I assume this is because I have 5
programs that use mpi)
Sincerely,
Sam

On Wed, Oct 5, 2016 at 2:09 PM, Edward d'Auvergne 
wrote:

> On 5 October 2016 at 22:01, Mahdi, Sam  wrote:
> > Hi Troels,
> >
> > The mpirun --np 2 gave no output, so I had to abort the command, but
> here is
> > the output.
> > crowlab: [~]> python -c "import mpi4py; print mpi4py.__version__"
> > 1.3.1
> > crowlab: [~]> mpirun --np 2 python -c "from mpi4py import MPI; print
> > MPI.COMM_WORLD.Get_rank()"
> > ^Ccrowlab: [~]>
>
> Hi Sam,
>
> This result I'm pretty sure shows that mpi4py is not functioning
> correctly - i.e. there is an installation problem.  This is what you
> should see:
>
> [edward@localhost ~]$ mpirun --np 2 python -c "from mpi4py import MPI;
> print MPI.COMM_WORLD.Get_rank()"
> 0
> 1
> [edward@localhost ~]$
>
> Note the printout of 0 and 1.  Maybe try the following:
>
> [edward@localhost ~]$ mpirun --np 5 python -c "import mpi4py; from
> mpi4py import MPI; print('Mpi4py %s process %d of %d on %s.'
> %(mpi4py.__version__,
> MPI.COMM_WORLD.Get_rank(),MPI.COMM_WORLD.Get_size(),
> MPI.Get_processor_name()))"
> Mpi4py 1.3.1 process 0 of 5 on localhost.localdomain.
> Mpi4py 1.3.1 process 1 of 5 on localhost.localdomain.
> Mpi4py 1.3.1 process 4 of 5 on localhost.localdomain.
> Mpi4py 1.3.1 process 2 of 5 on localhost.localdomain.
> Mpi4py 1.3.1 process 3 of 5 on localhost.localdomain.
> [edward@localhost ~]$
>
> If you don't see a printout here, then clearly mpi4py and OpenMPI are
> not working together correctly.  Without a printout, your mpi4py is
> FUBAR.  Are you using the default OpenMPI and mpi4py packages form
> fedora, and you don't have any backports or other non-standard sources
> set up for your RPMs?  Do you have any user installed MPI or mpi4py
> software around?  If you type:
>
> $ locate mpi
>
> What do you see?  For me this is pretty clearly an installation problem.
>
> Regards,
>
> Edward
>
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Re: Using multi-processor for model_free

2016-10-05 Thread Edward d'Auvergne

On 5 October 2016 at 22:01, Mahdi, Sam  wrote:
> Hi Troels,
>
> The mpirun --np 2 gave no output, so I had to abort the command, but here is
> the output.
> crowlab: [~]> python -c "import mpi4py; print mpi4py.__version__"
> 1.3.1
> crowlab: [~]> mpirun --np 2 python -c "from mpi4py import MPI; print
> MPI.COMM_WORLD.Get_rank()"
> ^Ccrowlab: [~]>

Hi Sam,

This result I'm pretty sure shows that mpi4py is not functioning
correctly - i.e. there is an installation problem.  This is what you
should see:

[edward@localhost ~]$ mpirun --np 2 python -c "from mpi4py import MPI;
print MPI.COMM_WORLD.Get_rank()"
0
1
[edward@localhost ~]$

Note the printout of 0 and 1.  Maybe try the following:

[edward@localhost ~]$ mpirun --np 5 python -c "import mpi4py; from
mpi4py import MPI; print('Mpi4py %s process %d of %d on %s.'
%(mpi4py.__version__,
MPI.COMM_WORLD.Get_rank(),MPI.COMM_WORLD.Get_size(),
MPI.Get_processor_name()))"
Mpi4py 1.3.1 process 0 of 5 on localhost.localdomain.
Mpi4py 1.3.1 process 1 of 5 on localhost.localdomain.
Mpi4py 1.3.1 process 4 of 5 on localhost.localdomain.
Mpi4py 1.3.1 process 2 of 5 on localhost.localdomain.
Mpi4py 1.3.1 process 3 of 5 on localhost.localdomain.
[edward@localhost ~]$

If you don't see a printout here, then clearly mpi4py and OpenMPI are
not working together correctly.  Without a printout, your mpi4py is
FUBAR.  Are you using the default OpenMPI and mpi4py packages form
fedora, and you don't have any backports or other non-standard sources
set up for your RPMs?  Do you have any user installed MPI or mpi4py
software around?  If you type:

$ locate mpi

What do you see?  For me this is pretty clearly an installation problem.

Regards,

Edward

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Re: Using multi-processor for model_free

2016-10-05 Thread Troels Emtekær Linnet

Hi Sam.

One thing that bothers me, is that
---
python -c "import mpi4py; print mpi4py.__version__"
---
shows version 1.3.

In the "relax -i" , you uploaded, it says:
mpi4py True 2.0.0
 /home/crowlab/.local/lib/python2.7/site-packages/mpi4py

So, lets check this.

Do this in terminal: 3 small lines, and then one big line.
---
python -c "import mpi4py; print mpi4py.__version__"

mpirun --np 2 python -c "import sys; print('%s'%sys.version_info)"

mpirun --np 2 python -c "import mpi4py; print mpi4py.__version__"

mpirun --np 2 python -c "import mpi4py; from mpi4py import MPI;
print('Mpi4py %s process %d of %d on %s.' %(mpi4py.__version__,
MPI.COMM_WORLD.Get_rank(),MPI.COMM_WORLD.Get_size(),
MPI.Get_processor_name()))"
---

And in the end (we have done it before, lets try again):
---
# NOTE: Use the FULL path to relax. Not the alias function. This is
important
mpirun --np 2 /home/tlinnet/relax-4.0.2/relax --multi='mpi4py' -v
mpirun --np 2 /home/tlinnet/relax-4.0.2/relax --multi='mpi4py' -i

# If this does not work, please provide
relax -v
relax -i
---

Best
Troels

2016-10-04 21:15 GMT+02:00 Mahdi, Sam :

> Hi Troels,
>
> So I ran the script, here is the output. But I got no output for mpirun
> -np 2 python -c "import mpi4py" command.
> crowlab: [~]> which relax
> relax:  aliased to /home/crowlab/relax-4.0.2/relax
> crowlab: [~]> #!/bin/tcsh
> /bin/tcsh: Event not found.
> crowlab: [~]> echo 'http://svn.gna.org/viewcvs/*
> checkout*/relax/trunk/devel_scripts/openmpi_test_install_tcsh.sh'
> http://svn.gna.org/viewcvs/*checkout*/relax/trunk/devel_
> scripts/openmpi_test_install_tcsh.sh
> crowlab: [~]> echo 'Source the commands with: source
> openmpi_test_install_tcsh.sh'
> Source the commands with: source openmpi_test_install_tcsh.sh
> crowlab: [~]> echo ""
>
> crowlab: [~]> set A="'"
> crowlab: [~]> echo "This is functions to test openmpi, python and
> openmpi." echo ""
> This is functions to test openmpi, python and openmpi. echo
> crowlab: [~]>
> crowlab: [~]> echo "Shell is: $SHELL"; echo ""
> Shell is: /bin/tcsh
>
> crowlab: [~]>
> crowlab: [~]> echo "> which mpirun"; which mpirun; echo ""
> > which mpirun
> /usr/lib64/openmpi/bin/mpirun
>
> crowlab: [~]>
> crowlab: [~]> echo "> module avail"; module avail; echo ""
> > module avail
>
>  /usr/share/Modules/modulefiles
> 
> dot module-git  module-info modules nulluse.own
>
> --- /etc/modulefiles
> ---
> mpi/mpich-x86_64   mpi/openmpi-x86_64 mpich-x86_64
>
> crowlab: [~]>
> crowlab: [~]> echo "> lscpu"; lscpu; echo ""
> > lscpu
> Architecture:  x86_64
> CPU op-mode(s):32-bit, 64-bit
> Byte Order:Little Endian
> CPU(s):8
> On-line CPU(s) list:   0-7
> Thread(s) per core:2
> Core(s) per socket:4
> Socket(s): 1
> NUMA node(s):  1
> Vendor ID: GenuineIntel
> CPU family:6
> Model: 58
> Model name:Intel(R) Core(TM) i7-3770S CPU @ 3.10GHz
> Stepping:  9
> CPU MHz:   1600.011
> CPU max MHz:   3900.
> CPU min MHz:   1600.
> BogoMIPS:  6186.25
> Virtualization:VT-x
> L1d cache: 32K
> L1i cache: 32K
> L2 cache:  256K
> L3 cache:  8192K
> NUMA node0 CPU(s): 0-7
>
> crowlab: [~]>
> crowlab: [~]> echo "> mpirun --version"; mpirun --version;echo ""
> > mpirun --version
> mpirun (Open MPI) 1.7.3
>
> Report bugs to http://www.open-mpi.org/community/help/
>
> crowlab: [~]>
> crowlab: [~]> echo "> mpirun --report-bindings -np 2 echo $A hello world
> $A"; mpirun --report-bindings -np 2 echo "hello world"; echo ""
> > mpirun --report-bindings -np 2 echo ' hello world '
> hello world
> hello world
>
> crowlab: [~]>
> crowlab: [~]> echo "> mpirun --report-bindings -np 2 python -c $A print
> "\""hello"\"" $A"; mpirun --report-bindings -np 2 python -c "print $A hello
> $A"; echo ""
> > mpirun --report-bindings -np 2 python -c ' print "hello" '
>  hello
>  hello
>
> crowlab: [~]>
> crowlab: [~]> echo "> mpirun --report-bindings -np 2 python --version";
> mpirun --report-bindings -np 2 python --version; echo ""
> > mpirun --report-bindings -np 2 python --version
> Python 2.7.5
> Python 2.7.5
>
> crowlab: [~]>
> crowlab: [~]> echo "> mpirun --report-bindings -np 2 /usr/bin/env python
> --version"; mpirun --report-bindings -np 2 /usr/bin/env python --version;
> echo ""
> > mpirun --report-bindings -np 2 /usr/bin/env python --version
> Python 2.7.5
> Python 2.7.5
>
> crowlab: [~]> echo "Testing python, mpi4py and mpirun"; python --version;
> /usr/bin/env python --version; python -c "import mpi4py; print
> mpi4py.__version__"
> Testing python, mpi4py and mpirun
> Python 2.7.5
> Python 2.7.5
> 1.3.1
> crowlab: [~]>
> crowlab: [~]> mpirun -np 2 python -c

Re: Using multi-processor for model_free

2016-10-04 Thread Mahdi, Sam

Hi Troels,

So I ran the script, here is the output. But I got no output for mpirun -np
2 python -c "import mpi4py" command.
crowlab: [~]> which relax
relax:  aliased to /home/crowlab/relax-4.0.2/relax
crowlab: [~]> #!/bin/tcsh
/bin/tcsh: Event not found.
crowlab: [~]> echo '
http://svn.gna.org/viewcvs/*checkout*/relax/trunk/devel_scripts/openmpi_test_install_tcsh.sh
'
http://svn.gna.org/viewcvs/*checkout*/relax/trunk/devel_scripts/openmpi_test_install_tcsh.sh
crowlab: [~]> echo 'Source the commands with: source
openmpi_test_install_tcsh.sh'
Source the commands with: source openmpi_test_install_tcsh.sh
crowlab: [~]> echo ""

crowlab: [~]> set A="'"
crowlab: [~]> echo "This is functions to test openmpi, python and openmpi."
echo ""
This is functions to test openmpi, python and openmpi. echo
crowlab: [~]>
crowlab: [~]> echo "Shell is: $SHELL"; echo ""
Shell is: /bin/tcsh

crowlab: [~]>
crowlab: [~]> echo "> which mpirun"; which mpirun; echo ""
> which mpirun
/usr/lib64/openmpi/bin/mpirun

crowlab: [~]>
crowlab: [~]> echo "> module avail"; module avail; echo ""
> module avail

 /usr/share/Modules/modulefiles

dot module-git  module-info modules nulluse.own

--- /etc/modulefiles
---
mpi/mpich-x86_64   mpi/openmpi-x86_64 mpich-x86_64

crowlab: [~]>
crowlab: [~]> echo "> lscpu"; lscpu; echo ""
> lscpu
Architecture:  x86_64
CPU op-mode(s):32-bit, 64-bit
Byte Order:Little Endian
CPU(s):8
On-line CPU(s) list:   0-7
Thread(s) per core:2
Core(s) per socket:4
Socket(s): 1
NUMA node(s):  1
Vendor ID: GenuineIntel
CPU family:6
Model: 58
Model name:Intel(R) Core(TM) i7-3770S CPU @ 3.10GHz
Stepping:  9
CPU MHz:   1600.011
CPU max MHz:   3900.
CPU min MHz:   1600.
BogoMIPS:  6186.25
Virtualization:VT-x
L1d cache: 32K
L1i cache: 32K
L2 cache:  256K
L3 cache:  8192K
NUMA node0 CPU(s): 0-7

crowlab: [~]>
crowlab: [~]> echo "> mpirun --version"; mpirun --version;echo ""
> mpirun --version
mpirun (Open MPI) 1.7.3

Report bugs to http://www.open-mpi.org/community/help/

crowlab: [~]>
crowlab: [~]> echo "> mpirun --report-bindings -np 2 echo $A hello world
$A"; mpirun --report-bindings -np 2 echo "hello world"; echo ""
> mpirun --report-bindings -np 2 echo ' hello world '
hello world
hello world

crowlab: [~]>
crowlab: [~]> echo "> mpirun --report-bindings -np 2 python -c $A print
"\""hello"\"" $A"; mpirun --report-bindings -np 2 python -c "print $A hello
$A"; echo ""
> mpirun --report-bindings -np 2 python -c ' print "hello" '
 hello
 hello

crowlab: [~]>
crowlab: [~]> echo "> mpirun --report-bindings -np 2 python --version";
mpirun --report-bindings -np 2 python --version; echo ""
> mpirun --report-bindings -np 2 python --version
Python 2.7.5
Python 2.7.5

crowlab: [~]>
crowlab: [~]> echo "> mpirun --report-bindings -np 2 /usr/bin/env python
--version"; mpirun --report-bindings -np 2 /usr/bin/env python --version;
echo ""
> mpirun --report-bindings -np 2 /usr/bin/env python --version
Python 2.7.5
Python 2.7.5

crowlab: [~]> echo "Testing python, mpi4py and mpirun"; python --version;
/usr/bin/env python --version; python -c "import mpi4py; print
mpi4py.__version__"
Testing python, mpi4py and mpirun
Python 2.7.5
Python 2.7.5
1.3.1
crowlab: [~]>
crowlab: [~]> mpirun -np 2 python -c "import mpi4py; from mpi4py import
MPI; print($A Mpi4py %s process %d of %d on %s.$A %(mpi4py.__version__,
MPI.COMM_WORLD.Get_rank(),MPI.COMM_WORLD.Get_size(),
MPI.Get_processor_name()))"


Sincerely,
Sam


On Mon, Oct 3, 2016 at 11:14 PM, Troels Emtekær Linnet <
tlin...@nmr-relax.com> wrote:

> Hi Sam.
>
> Please try not to use the tilde.
> Use the full path instead.
> Sometimes the expansion of tilde can give problems.
>
> The module command looks right.
>
> Then start a new terminal.
> Try write: which relax
>
> And also paste in these command: Open the link in a browser.
>
>
> http://svn.gna.org/viewcvs/*checkout*/relax/trunk/devel_
> scripts/openmpi_test_install_tcsh.sh?content-type=text%2Fplain
>
> Best Troels
>
>
> Den tirsdag den 4. oktober 2016 skrev Mahdi, Sam <
> sam.mahdi@my.csun.edu>:
>
>> Hi Troels,
>>
>> So did you want me to simply put something like this?
>> alias relax '~/relax-4.0.2/relax'
>>
>> module load mpi/openmpi-x86_64
>>
>> And when you say run the mpirun, did you want me to rerun this script:
>> source openmpi_test_install.sh
>>
>> Sincerely,
>> Sam
>>
>>
>> On Mon, Oct 3, 2016 at 10:29 PM, Troels Emtekær Linnet <
>> tlin...@nmr-relax.com> wrote:
>>
>>> Hi Sam.
>>>
>>> Please modify the file.
>>> Remove the old two alias to relax, and make a new alias to the newest
>>> version of relax.
>>>
>>> You could/should also include the module load command here.

Re: Using multi-processor for model_free

2016-10-03 Thread Mahdi, Sam

Hi Troels,

So did you want me to simply put something like this?
alias relax '~/relax-4.0.2/relax'

module load mpi/openmpi-x86_64

And when you say run the mpirun, did you want me to rerun this script:
source openmpi_test_install.sh

Sincerely,
Sam


On Mon, Oct 3, 2016 at 10:29 PM, Troels Emtekær Linnet <
tlin...@nmr-relax.com> wrote:

> Hi Sam.
>
> Please modify the file.
> Remove the old two alias to relax, and make a new alias to the newest
> version of relax.
>
> You could/should also include the module load command here.
>
> Then open a new terminal.
> Try again with mpirun, etc.
>
> Den mandag den 3. oktober 2016 skrev Mahdi, Sam  >:
>
>> Hi Troels,
>>
>> So it was the tcshrc here was the output
>> lias rm 'rm -i'
>> alias cp 'cp -i'
>> alias mv 'mv -i'
>>
>> setenv NMR_CONT CORRECT_ALL
>> setenv GLOVEDIR ~/glove
>>
>> if (-e /usr/local/NMRPipe/com/nmrInit.linux9.com) then
>> source /usr/local/NMRPipe/com/nmrInit.linux9.com
>> endif
>>
>> set PATH = ($PATH /usr/local/java:$GLOVEDIR/bin)
>>
>> alias relax '/usr/local/relax-1.3.10/relax -g'
>>
>> alias csi '/usr/local//csi'
>>
>> alias nvj '/usr/local/bin/NMRViewJ'
>>
>> alias pymol '/usr/local/pymol/pymol.exe'
>>
>> alias nessy '/usr/local/nessy/nessy'
>>
>> alias relax '/usr/local/Relax/relax-2.2.5/relax -g'
>> #set prompt="crowlab >"
>>
>> alias naccess '/usr/local/Naccess/naccess2.1.1/naccess'
>>
>> if( ${?prompt} ) then
>>   alias setprompt 'set prompt = "crowlab: [%c]> "'
>>   alias cwdcmd 'setprompt'
>>   setprompt
>>endif
>>
>> Also, the 2nd command gave me no responce.
>> crowlab: [~]> alias get 'set noglob; wget http://svn.gna.org/viewcvs/*ch
>> eckout*/relax/trunk/devel_scripts/openmpi_test_install_tcsh.sh;unset
>> noglob'
>> crowlab: [~]>
>>
>>
>> On Mon, Oct 3, 2016 at 9:32 AM, Troels Emtekær Linnet <
>> tlin...@nmr-relax.com> wrote:
>>
>>> Hi Sam.
>>>
>>> I know your problem. :)
>>> It is the same for me. Getting hang of a system admin for our lab
>>> computers, and then to convince him/her
>>> to fix stuff is not easy.
>>>
>>> Thats why I test on Google Cloud.
>>> There I can get access to a multi core computer, and mess with it.
>>>
>>> But it only has a set of standard images. And Fedora is not one of them.
>>>
>>> But we can try to have a look at your personal shell setup.
>>> Can you display your login script?:
>>>
>>> One of these should be the right one.
>>> ---
>>> cat $HOME/.cshrc
>>> cat $HOME/.login,
>>> cat $HOME/.tcshrc
>>> ---
>>>
>>> And now try as well:
>>> ---
>>> alias get 'set noglob; wget http://svn.gna.org/viewcvs/*ch
>>> eckout*/relax/trunk/devel_scripts/openmpi_test_install_tcsh.sh;unset
>>> noglob'
>>> get
>>>
>>> # Source functions
>>> source openmpi_test_install_tcsh.sh
>>> testopenmpi
>>> -
>>>
>>> 2016-10-03 18:13 GMT+02:00 Mahdi, Sam :
>>>
 Hi Troels,

 It will be a bit difficult for me to attempt to update, remove, or
 install any packages since I am not root user, which means I'd have to wait
 for my PI to come and install/remove packages or programs. Anything
 regarding installing programs on a user basis I can do (such as installing
 relax), but I can not for example, install mpi4py. I can download it, untar
  it, even compile it using the mpicc wrapper, but I cannot install it. I
 know we discussed the potential problem could be because I have 2 version
 of relax on my system. Could you try to potentially download another
 version of relax (the other one I have is 2.2.5) and the older version of
 openmpi, and attempt to run it then? It would be a lot easier for me to
 directly tell my PI to simply remove a file, or update one, then to attempt
 to troubleshoot with them.

 Sincerely,
 Sam

 On Mon, Oct 3, 2016 at 8:58 AM, Troels Emtekær Linnet <
 tlin...@nmr-relax.com> wrote:

> Hi Sam.
>
> I can get relax to run and work on redhat/centos version 6.
>
> I have updated a deployment script for this:
> http://wiki.nmr-relax.com/Run_relax_at_Google_Cloud_Computin
> g#Install_packages_at_server
>
> Please have a look here:
> http://svn.gna.org/viewcvs/relax/trunk/devel_scripts/deploy_scripts/
>
> and specific:
> http://svn.gna.org/viewcvs/*checkout*/relax/trunk/devel_scri
> pts/deploy_scripts/deploy_google_computing_redhat_6_86_x64_u
> pgrade_python.sh?content-type=text%2Fplain
>
> This is for centos 6, which should get very close to fedora 20.
>
> For centos 6, the openmpi is version 1.8. And you have 1.7.3
>
> So, the only difference I can see is the openmpi version.
> Can you upgrade this?
>
> --
> [tlinnet@instance-1 ~]$ relax_4.0.2 -i
>
>
>
> relax 4.0.2
>
>   Molecular dynamics by NMR data analysis
>
>

Re: Using multi-processor for model_free

2016-10-03 Thread Troels Emtekær Linnet

Hi Sam.

Please modify the file.
Remove the old two alias to relax, and make a new alias to the newest
version of relax.

You could/should also include the module load command here.

Then open a new terminal.
Try again with mpirun, etc.

Den mandag den 3. oktober 2016 skrev Mahdi, Sam :

> Hi Troels,
>
> So it was the tcshrc here was the output
> lias rm 'rm -i'
> alias cp 'cp -i'
> alias mv 'mv -i'
>
> setenv NMR_CONT CORRECT_ALL
> setenv GLOVEDIR ~/glove
>
> if (-e /usr/local/NMRPipe/com/nmrInit.linux9.com) then
> source /usr/local/NMRPipe/com/nmrInit.linux9.com
> endif
>
> set PATH = ($PATH /usr/local/java:$GLOVEDIR/bin)
>
> alias relax '/usr/local/relax-1.3.10/relax -g'
>
> alias csi '/usr/local//csi'
>
> alias nvj '/usr/local/bin/NMRViewJ'
>
> alias pymol '/usr/local/pymol/pymol.exe'
>
> alias nessy '/usr/local/nessy/nessy'
>
> alias relax '/usr/local/Relax/relax-2.2.5/relax -g'
> #set prompt="crowlab >"
>
> alias naccess '/usr/local/Naccess/naccess2.1.1/naccess'
>
> if( ${?prompt} ) then
>   alias setprompt 'set prompt = "crowlab: [%c]> "'
>   alias cwdcmd 'setprompt'
>   setprompt
>endif
>
> Also, the 2nd command gave me no responce.
> crowlab: [~]> alias get 'set noglob; wget http://svn.gna.org/viewcvs/*
> checkout*/relax/trunk/devel_scripts/openmpi_test_install_tcsh.sh;unset
> noglob'
> crowlab: [~]>
>
>
> On Mon, Oct 3, 2016 at 9:32 AM, Troels Emtekær Linnet <
> tlin...@nmr-relax.com
> > wrote:
>
>> Hi Sam.
>>
>> I know your problem. :)
>> It is the same for me. Getting hang of a system admin for our lab
>> computers, and then to convince him/her
>> to fix stuff is not easy.
>>
>> Thats why I test on Google Cloud.
>> There I can get access to a multi core computer, and mess with it.
>>
>> But it only has a set of standard images. And Fedora is not one of them.
>>
>> But we can try to have a look at your personal shell setup.
>> Can you display your login script?:
>>
>> One of these should be the right one.
>> ---
>> cat $HOME/.cshrc
>> cat $HOME/.login,
>> cat $HOME/.tcshrc
>> ---
>>
>> And now try as well:
>> ---
>> alias get 'set noglob; wget http://svn.gna.org/viewcvs/*ch
>> eckout*/relax/trunk/devel_scripts/openmpi_test_install_tcsh.sh;unset
>> noglob'
>> get
>>
>> # Source functions
>> source openmpi_test_install_tcsh.sh
>> testopenmpi
>> -
>>
>> 2016-10-03 18:13 GMT+02:00 Mahdi, Sam > >:
>>
>>> Hi Troels,
>>>
>>> It will be a bit difficult for me to attempt to update, remove, or
>>> install any packages since I am not root user, which means I'd have to wait
>>> for my PI to come and install/remove packages or programs. Anything
>>> regarding installing programs on a user basis I can do (such as installing
>>> relax), but I can not for example, install mpi4py. I can download it, untar
>>>  it, even compile it using the mpicc wrapper, but I cannot install it. I
>>> know we discussed the potential problem could be because I have 2 version
>>> of relax on my system. Could you try to potentially download another
>>> version of relax (the other one I have is 2.2.5) and the older version of
>>> openmpi, and attempt to run it then? It would be a lot easier for me to
>>> directly tell my PI to simply remove a file, or update one, then to attempt
>>> to troubleshoot with them.
>>>
>>> Sincerely,
>>> Sam
>>>
>>> On Mon, Oct 3, 2016 at 8:58 AM, Troels Emtekær Linnet <
>>> tlin...@nmr-relax.com
>>> > wrote:
>>>
 Hi Sam.

 I can get relax to run and work on redhat/centos version 6.

 I have updated a deployment script for this:
 http://wiki.nmr-relax.com/Run_relax_at_Google_Cloud_Computin
 g#Install_packages_at_server

 Please have a look here:
 http://svn.gna.org/viewcvs/relax/trunk/devel_scripts/deploy_scripts/

 and specific:
 http://svn.gna.org/viewcvs/*checkout*/relax/trunk/devel_scri
 pts/deploy_scripts/deploy_google_computing_redhat_6_86_x64_u
 pgrade_python.sh?content-type=text%2Fplain

 This is for centos 6, which should get very close to fedora 20.

 For centos 6, the openmpi is version 1.8. And you have 1.7.3

 So, the only difference I can see is the openmpi version.
 Can you upgrade this?

 --
 [tlinnet@instance-1 ~]$ relax_4.0.2 -i



 relax 4.0.2

   Molecular dynamics by NMR data analysis

  Copyright (C) 2001-2006 Edward d'Auvergne
  Copyright (C) 2006-2016 the relax development
 team

 This is free software which you are welcome to modify and redistribute
 under the conditions of the
 GNU General Public License (GPL).  This program, including all modules,
 is

Re: Using multi-processor for model_free

2016-10-03 Thread Troels Emtekær Linnet

Hi Sam.

I know your problem. :)
It is the same for me. Getting hang of a system admin for our lab
computers, and then to convince him/her
to fix stuff is not easy.

Thats why I test on Google Cloud.
There I can get access to a multi core computer, and mess with it.

But it only has a set of standard images. And Fedora is not one of them.

But we can try to have a look at your personal shell setup.
Can you display your login script?:

One of these should be the right one.
---
cat $HOME/.cshrc
cat $HOME/.login,
cat $HOME/.tcshrc
---

And now try as well:
---
alias get 'set noglob; wget
http://svn.gna.org/viewcvs/*checkout*/relax/trunk/devel_scripts/openmpi_test_install_tcsh.sh;unset
noglob'
get

# Source functions
source openmpi_test_install_tcsh.sh
testopenmpi
-

2016-10-03 18:13 GMT+02:00 Mahdi, Sam :

> Hi Troels,
>
> It will be a bit difficult for me to attempt to update, remove, or install
> any packages since I am not root user, which means I'd have to wait for my
> PI to come and install/remove packages or programs. Anything regarding
> installing programs on a user basis I can do (such as installing relax),
> but I can not for example, install mpi4py. I can download it, untar  it,
> even compile it using the mpicc wrapper, but I cannot install it. I know we
> discussed the potential problem could be because I have 2 version of relax
> on my system. Could you try to potentially download another version of
> relax (the other one I have is 2.2.5) and the older version of openmpi, and
> attempt to run it then? It would be a lot easier for me to directly tell my
> PI to simply remove a file, or update one, then to attempt to troubleshoot
> with them.
>
> Sincerely,
> Sam
>
> On Mon, Oct 3, 2016 at 8:58 AM, Troels Emtekær Linnet <
> tlin...@nmr-relax.com> wrote:
>
>> Hi Sam.
>>
>> I can get relax to run and work on redhat/centos version 6.
>>
>> I have updated a deployment script for this:
>> http://wiki.nmr-relax.com/Run_relax_at_Google_Cloud_Computin
>> g#Install_packages_at_server
>>
>> Please have a look here:
>> http://svn.gna.org/viewcvs/relax/trunk/devel_scripts/deploy_scripts/
>>
>> and specific:
>> http://svn.gna.org/viewcvs/*checkout*/relax/trunk/devel_scri
>> pts/deploy_scripts/deploy_google_computing_redhat_6_86_x64_
>> upgrade_python.sh?content-type=text%2Fplain
>>
>> This is for centos 6, which should get very close to fedora 20.
>>
>> For centos 6, the openmpi is version 1.8. And you have 1.7.3
>>
>> So, the only difference I can see is the openmpi version.
>> Can you upgrade this?
>>
>> --
>> [tlinnet@instance-1 ~]$ relax_4.0.2 -i
>>
>>
>>
>> relax 4.0.2
>>
>>   Molecular dynamics by NMR data analysis
>>
>>  Copyright (C) 2001-2006 Edward d'Auvergne
>>  Copyright (C) 2006-2016 the relax development
>> team
>>
>> This is free software which you are welcome to modify and redistribute
>> under the conditions of the
>> GNU General Public License (GPL).  This program, including all modules,
>> is licensed under the GPL
>> and comes with absolutely no warranty.  For details type 'GPL' within the
>> relax prompt.
>>
>> Assistance in using the relax prompt and scripting interface can be
>> accessed by typing 'help' within
>> the prompt.
>>
>> Processor fabric:  Uni-processor.
>>
>>
>> Hardware information:
>> Machine: x86_64
>> Processor:   x86_64
>> Processor name:  Intel(R) Xeon(R) CPU @ 2.50GHz
>> Endianness:  little
>> Total RAM size:  3426 Mb
>> Total swap size: 0 Mb
>>
>> Operating system information:
>> System:  Linux
>> Release: 2.6.32-642.4.2.el6.x86_64
>> Version: #1 SMP Tue Aug 23 19:58:13 UTC 2016
>> GNU/Linux version:   CentOS 6.8 Final
>> Distribution:centos 6.8 Final
>> Full platform string:Linux-2.6.32-642.4.2.el6.x86_
>> 64-x86_64-with-centos-6.8-Final
>>
>> Python information:
>> Architecture:64bit ELF
>> Python version:  2.7.8
>> Python branch:
>> Python build:default, May 15 2016 12:46:09
>> Python compiler: GCC 4.4.7 20120313 (Red Hat 4.4.7-16)
>> Libc version:glibc 2.2.5
>> Python implementation:   CPython
>> Python revision:
>> Python executable:   /opt/rh/python27/root/usr/bin/python
>> Python flags:sys.flags(debug=0, py3k_warning=0,
>> division_warning=0, division_new=0, inspect=0, interactive=0, optimize=0,
>> dont_write_bytecode=0, no_user_site=0, no_site=0, ignore_environment=0,
>> tabcheck=0, verbose=0, unicode=0, bytes_warning=0, hash_randomization=0)
>> Python float info:   sys.float_info(max=1.7976931348623157e+308,
>> max_exp=1024, max_10_exp=308, min=2.2250738585072014e-308, min_exp=-1021,
>> min_10_exp=-307, dig=15,

Re: Using multi-processor for model_free

2016-10-03 Thread Mahdi, Sam

Hi Troels,

It will be a bit difficult for me to attempt to update, remove, or install
any packages since I am not root user, which means I'd have to wait for my
PI to come and install/remove packages or programs. Anything regarding
installing programs on a user basis I can do (such as installing relax),
but I can not for example, install mpi4py. I can download it, untar  it,
even compile it using the mpicc wrapper, but I cannot install it. I know we
discussed the potential problem could be because I have 2 version of relax
on my system. Could you try to potentially download another version of
relax (the other one I have is 2.2.5) and the older version of openmpi, and
attempt to run it then? It would be a lot easier for me to directly tell my
PI to simply remove a file, or update one, then to attempt to troubleshoot
with them.

Sincerely,
Sam

On Mon, Oct 3, 2016 at 8:58 AM, Troels Emtekær Linnet  wrote:

> Hi Sam.
>
> I can get relax to run and work on redhat/centos version 6.
>
> I have updated a deployment script for this:
> http://wiki.nmr-relax.com/Run_relax_at_Google_Cloud_
> Computing#Install_packages_at_server
>
> Please have a look here:
> http://svn.gna.org/viewcvs/relax/trunk/devel_scripts/deploy_scripts/
>
> and specific:
> http://svn.gna.org/viewcvs/*checkout*/relax/trunk/devel_
> scripts/deploy_scripts/deploy_google_computing_redhat_6_86_
> x64_upgrade_python.sh?content-type=text%2Fplain
>
> This is for centos 6, which should get very close to fedora 20.
>
> For centos 6, the openmpi is version 1.8. And you have 1.7.3
>
> So, the only difference I can see is the openmpi version.
> Can you upgrade this?
>
> --
> [tlinnet@instance-1 ~]$ relax_4.0.2 -i
>
>
>
> relax 4.0.2
>
>   Molecular dynamics by NMR data analysis
>
>  Copyright (C) 2001-2006 Edward d'Auvergne
>  Copyright (C) 2006-2016 the relax development team
>
> This is free software which you are welcome to modify and redistribute
> under the conditions of the
> GNU General Public License (GPL).  This program, including all modules, is
> licensed under the GPL
> and comes with absolutely no warranty.  For details type 'GPL' within the
> relax prompt.
>
> Assistance in using the relax prompt and scripting interface can be
> accessed by typing 'help' within
> the prompt.
>
> Processor fabric:  Uni-processor.
>
>
> Hardware information:
> Machine: x86_64
> Processor:   x86_64
> Processor name:  Intel(R) Xeon(R) CPU @ 2.50GHz
> Endianness:  little
> Total RAM size:  3426 Mb
> Total swap size: 0 Mb
>
> Operating system information:
> System:  Linux
> Release: 2.6.32-642.4.2.el6.x86_64
> Version: #1 SMP Tue Aug 23 19:58:13 UTC 2016
> GNU/Linux version:   CentOS 6.8 Final
> Distribution:centos 6.8 Final
> Full platform string:Linux-2.6.32-642.4.2.el6.x86_
> 64-x86_64-with-centos-6.8-Final
>
> Python information:
> Architecture:64bit ELF
> Python version:  2.7.8
> Python branch:
> Python build:default, May 15 2016 12:46:09
> Python compiler: GCC 4.4.7 20120313 (Red Hat 4.4.7-16)
> Libc version:glibc 2.2.5
> Python implementation:   CPython
> Python revision:
> Python executable:   /opt/rh/python27/root/usr/bin/python
> Python flags:sys.flags(debug=0, py3k_warning=0,
> division_warning=0, division_new=0, inspect=0, interactive=0, optimize=0,
> dont_write_bytecode=0, no_user_site=0, no_site=0, ignore_environment=0,
> tabcheck=0, verbose=0, unicode=0, bytes_warning=0, hash_randomization=0)
> Python float info:   sys.float_info(max=1.7976931348623157e+308,
> max_exp=1024, max_10_exp=308, min=2.2250738585072014e-308, min_exp=-1021,
> min_10_exp=-307, dig=15, mant_dig=53, epsilon=2.220446049250313e-16,
> radix=2, rounds=1)
> Python module path:  ['/home/tlinnet/relax-4.0.2',
> '/usr/lib64/python2.6/site-packages/openmpi', 
> '/usr/lib64/python2.6/site-packages/wx-2.8-gtk2-unicode',
> '/opt/rh/python27/root/usr/lib64/python27.zip',
> '/opt/rh/python27/root/usr/lib64/python2.7', 
> '/opt/rh/python27/root/usr/lib64/python2.7/plat-linux2',
> '/opt/rh/python27/root/usr/lib64/python2.7/lib-tk',
> '/opt/rh/python27/root/usr/lib64/python2.7/lib-old',
> '/opt/rh/python27/root/usr/lib64/python2.7/lib-dynload',
> '/opt/rh/python27/root/usr/lib64/python2.7/site-packages',
> '/opt/rh/python27/root/usr/lib/python2.7/site-packages']
>
> Python packages and modules (most are optional):
>
> Name   InstalledVersionPath
>
> minfx  True 1.0.12
> /home/tlinnet/relax-4.0.2/minfx
> bmrblibTrue 1.0.4
>  /home/tlinnet/relax-4.0.2/bmrblib
> numpy

Re: Using multi-processor for model_free

2016-10-03 Thread Troels Emtekær Linnet

Hi Sam.

I can get relax to run and work on redhat/centos version 6.

I have updated a deployment script for this:
http://wiki.nmr-relax.com/Run_relax_at_Google_Cloud_Computing#Install_packages_at_server

Please have a look here:
http://svn.gna.org/viewcvs/relax/trunk/devel_scripts/deploy_scripts/

and specific:
http://svn.gna.org/viewcvs/*checkout*/relax/trunk/devel_scripts/deploy_scripts/deploy_google_computing_redhat_6_86_x64_upgrade_python.sh?content-type=text%2Fplain

This is for centos 6, which should get very close to fedora 20.

For centos 6, the openmpi is version 1.8. And you have 1.7.3

So, the only difference I can see is the openmpi version.
Can you upgrade this?

--
[tlinnet@instance-1 ~]$ relax_4.0.2 -i



relax 4.0.2

  Molecular dynamics by NMR data analysis

 Copyright (C) 2001-2006 Edward d'Auvergne
 Copyright (C) 2006-2016 the relax development team

This is free software which you are welcome to modify and redistribute
under the conditions of the
GNU General Public License (GPL).  This program, including all modules, is
licensed under the GPL
and comes with absolutely no warranty.  For details type 'GPL' within the
relax prompt.

Assistance in using the relax prompt and scripting interface can be
accessed by typing 'help' within
the prompt.

Processor fabric:  Uni-processor.


Hardware information:
Machine: x86_64
Processor:   x86_64
Processor name:  Intel(R) Xeon(R) CPU @ 2.50GHz
Endianness:  little
Total RAM size:  3426 Mb
Total swap size: 0 Mb

Operating system information:
System:  Linux
Release: 2.6.32-642.4.2.el6.x86_64
Version: #1 SMP Tue Aug 23 19:58:13 UTC 2016
GNU/Linux version:   CentOS 6.8 Final
Distribution:centos 6.8 Final
Full platform string:
 Linux-2.6.32-642.4.2.el6.x86_64-x86_64-with-centos-6.8-Final

Python information:
Architecture:64bit ELF
Python version:  2.7.8
Python branch:
Python build:default, May 15 2016 12:46:09
Python compiler: GCC 4.4.7 20120313 (Red Hat 4.4.7-16)
Libc version:glibc 2.2.5
Python implementation:   CPython
Python revision:
Python executable:   /opt/rh/python27/root/usr/bin/python
Python flags:sys.flags(debug=0, py3k_warning=0,
division_warning=0, division_new=0, inspect=0, interactive=0, optimize=0,
dont_write_bytecode=0, no_user_site=0, no_site=0, ignore_environment=0,
tabcheck=0, verbose=0, unicode=0, bytes_warning=0, hash_randomization=0)
Python float info:   sys.float_info(max=1.7976931348623157e+308,
max_exp=1024, max_10_exp=308, min=2.2250738585072014e-308, min_exp=-1021,
min_10_exp=-307, dig=15, mant_dig=53, epsilon=2.220446049250313e-16,
radix=2, rounds=1)
Python module path:  ['/home/tlinnet/relax-4.0.2',
'/usr/lib64/python2.6/site-packages/openmpi',
'/usr/lib64/python2.6/site-packages/wx-2.8-gtk2-unicode',
'/opt/rh/python27/root/usr/lib64/python27.zip',
'/opt/rh/python27/root/usr/lib64/python2.7',
'/opt/rh/python27/root/usr/lib64/python2.7/plat-linux2',
'/opt/rh/python27/root/usr/lib64/python2.7/lib-tk',
'/opt/rh/python27/root/usr/lib64/python2.7/lib-old',
'/opt/rh/python27/root/usr/lib64/python2.7/lib-dynload',
'/opt/rh/python27/root/usr/lib64/python2.7/site-packages',
'/opt/rh/python27/root/usr/lib/python2.7/site-packages']

Python packages and modules (most are optional):

Name   InstalledVersionPath

minfx  True 1.0.12
/home/tlinnet/relax-4.0.2/minfx
bmrblibTrue 1.0.4
 /home/tlinnet/relax-4.0.2/bmrblib
numpy  True 1.7.1
 /opt/rh/python27/root/usr/lib64/python2.7/site-packages/numpy
scipy  True 0.12.1
/opt/rh/python27/root/usr/lib64/python2.7/site-packages/scipy
wxPython   True 2.8.12.0 (gtk2-unicode)
 /usr/lib64/python2.6/site-packages/wx-2.8-gtk2-unicode/wx
matplotlib True 1.5.3
 /opt/rh/python27/root/usr/lib64/python2.7/site-packages/matplotlib
mpi4py True 2.0.0
 /opt/rh/python27/root/usr/lib64/python2.7/site-packages/mpi4py
epydoc True 3.0.1
 /opt/rh/python27/root/usr/lib/python2.7/site-packages/epydoc
optparse   True 1.5.3
 /opt/rh/python27/root/usr/lib64/python2.7/optparse.pyc
readline   True
 /opt/rh/python27/root/usr/lib64/python2.7/lib-dynload/readline.so
profileTrue
 /opt/rh/python27/root/usr/lib64/python2.7/profile.pyc
bz2True
 /opt/rh/python27/root/usr/lib64/python2.7/lib-dynload/bz2.so
gzip   True
 /opt/rh/python27/root/usr/lib64/python2.7/gzip.pyc
io True
 /opt/rh/python27/root/usr/lib64/python2.7/io.pyc
xmlTrue

Re: Using multi-processor for model_free

2016-10-02 Thread Mahdi, Sam

Hi Troels,

Here is the output
source openmpi_test_install.sh
http://svn.gna.org/viewcvs/*checkout*/relax/trunk/devel_scripts/openmpi_test_install.sh
Source the commands with: source openmpi_test_install.sh
Then do: testopenmpi

function: Command not found.
This is functions to test openmpi, python and openmpi.

Shell is: /bin/tcsh

> which mpirun
mpirun: Command not found.

> module avail

 /usr/share/Modules/modulefiles

dot module-git  module-info modules nulluse.own

--- /etc/modulefiles
---
mpi/mpich-x86_64   mpi/openmpi-x86_64 mpich-x86_64

> lscpu
Architecture:  x86_64
CPU op-mode(s):32-bit, 64-bit
Byte Order:Little Endian
CPU(s):8
On-line CPU(s) list:   0-7
Thread(s) per core:2
Core(s) per socket:4
Socket(s): 1
NUMA node(s):  1
Vendor ID: GenuineIntel
CPU family:6
Model: 58
Model name:Intel(R) Core(TM) i7-3770S CPU @ 3.10GHz
Stepping:  9
CPU MHz:   3653.640
CPU max MHz:   3900.
CPU min MHz:   1600.
BogoMIPS:  6186.25
Virtualization:VT-x
L1d cache: 32K
L1i cache: 32K
L2 cache:  256K
L3 cache:  8192K
NUMA node0 CPU(s): 0-7

> mpirun --version
mpirun: Command not found.

> mpirun --report-bindings -np 2 echo "hello world"
mpirun: Command not found.

A=": Command not found.
A: Undefined variable.


The reason the mpi commands didn't work, is becaues openmpi was not
loaded.  I modified your script (added: module load mpi/openmpi-x86_64) and
then got this output

source openmpi_test_install.sh
http://svn.gna.org/viewcvs/*checkout*/relax/trunk/devel_scripts/openmpi_test_install.sh
Source the commands with: source openmpi_test_install.sh
Then do: testopenmpi

function: Command not found.
This is functions to test openmpi, python and openmpi.

Shell is: /bin/tcsh

> which mpirun
/usr/lib64/openmpi/bin/mpirun

> module avail

 /usr/share/Modules/modulefiles

dot module-git  module-info modules nulluse.own

--- /etc/modulefiles
---
mpi/mpich-x86_64   mpi/openmpi-x86_64 mpich-x86_64

> lscpu
Architecture:  x86_64
CPU op-mode(s):32-bit, 64-bit
Byte Order:Little Endian
CPU(s):8
On-line CPU(s) list:   0-7
Thread(s) per core:2
Core(s) per socket:4
Socket(s): 1
NUMA node(s):  1
Vendor ID: GenuineIntel
CPU family:6
Model: 58
Model name:Intel(R) Core(TM) i7-3770S CPU @ 3.10GHz
Stepping:  9
CPU MHz:   3733.320
CPU max MHz:   3900.
CPU min MHz:   1600.
BogoMIPS:  6186.25
Virtualization:VT-x
L1d cache: 32K
L1i cache: 32K
L2 cache:  256K
L3 cache:  8192K
NUMA node0 CPU(s): 0-7

> mpirun --version
mpirun (Open MPI) 1.7.3

Report bugs to http://www.open-mpi.org/community/help/

> mpirun --report-bindings -np 2 echo "hello world"
hello world
hello world

A=": Command not found.
A: Undefined variable.

As to why the report bindings on python didn't work. I don't know what the
A command means, so I don't know what happened there.

Sincerely,
Sam


On Sun, Oct 2, 2016 at 4:16 PM, Troels Emtekær Linnet  wrote:

> Hi Sam.
>
> Can you try this in your terminal.
> I am trying to write a script, which should check at users setup mpirun.
>
> --
>
> URL=http://svn.gna.org/viewcvs/*checkout*/relax/
> trunk/devel_scripts/openmpi_test_install.sh
> wget $URL
>
> # Source functions
> source openmpi_test_install.sh
> testopenmpi
>
> 2016-10-01 0:22 GMT+02:00 Troels Emtekær Linnet :
>
>> Hi Sam.
>>
>> Can you try:
>> mpirun --version
>>
>> Thanks
>>
>> 2016-10-01 0:00 GMT+02:00 Mahdi, Sam :
>>
>>> Hi Troels,
>>>
>>> Here is a list of the packages I got off of the fedora package list
>>> Openmpi:
>>> openmpi-1.7.3-1.fc.20(64-bit)
>>> openmpi-devel-1.7.3-1.fc20(64bit)
>>> pypar-openmpi-2.1.5_108_3.fc.20(64bit)
>>> python3-mpi4py-1.3.1-1.fc20(64bit)
>>>
>>> Mpi4py
>>> mpi4py-common-1.3.1-1.fc20
>>> mpi4py-mpich-1.3.1-1.fc20
>>> mpi4py-openmpi-1.3.1-1.fc20
>>> python3-mpi4py-mpich-1.3.1-1.fc20
>>> python3-mpi4py-openmpi-1.3.1-1.fc20
>>>
>>> Note: I now know the mpich is extra and pointless. I only use the
>>> openmpi when I load my modules. I have not compiled or configured anything
>>> with these packages. I just installed them directly from the package list.
>>> If you need any more info on what is installed on these computers let me
>>> know!
>>>
>>> Sincerely,
>>> Sam
>>>
>>>
>>> On Fri, Sep 30,

Re: Using multi-processor for model_free

2016-10-02 Thread Troels Emtekær Linnet

Hi Sam.

Can you try this in your terminal.
I am trying to write a script, which should check at users setup mpirun.

--

URL=
http://svn.gna.org/viewcvs/*checkout*/relax/trunk/devel_scripts/openmpi_test_install.sh
wget $URL

# Source functions
source openmpi_test_install.sh
testopenmpi

2016-10-01 0:22 GMT+02:00 Troels Emtekær Linnet :

> Hi Sam.
>
> Can you try:
> mpirun --version
>
> Thanks
>
> 2016-10-01 0:00 GMT+02:00 Mahdi, Sam :
>
>> Hi Troels,
>>
>> Here is a list of the packages I got off of the fedora package list
>> Openmpi:
>> openmpi-1.7.3-1.fc.20(64-bit)
>> openmpi-devel-1.7.3-1.fc20(64bit)
>> pypar-openmpi-2.1.5_108_3.fc.20(64bit)
>> python3-mpi4py-1.3.1-1.fc20(64bit)
>>
>> Mpi4py
>> mpi4py-common-1.3.1-1.fc20
>> mpi4py-mpich-1.3.1-1.fc20
>> mpi4py-openmpi-1.3.1-1.fc20
>> python3-mpi4py-mpich-1.3.1-1.fc20
>> python3-mpi4py-openmpi-1.3.1-1.fc20
>>
>> Note: I now know the mpich is extra and pointless. I only use the openmpi
>> when I load my modules. I have not compiled or configured anything with
>> these packages. I just installed them directly from the package list. If
>> you need any more info on what is installed on these computers let me know!
>>
>> Sincerely,
>> Sam
>>
>>
>> On Fri, Sep 30, 2016 at 2:23 PM, Troels Emtekær Linnet <
>> tlin...@nmr-relax.com> wrote:
>>
>>> Hi Sam.
>>>
>>> I am trying to setup myself on Google Cloud Platform.
>>>
>>> Here I setting up for a Redhat 6 distro, in hope it gets close to Fedora
>>> 20.
>>>
>>> I am currently making a deployment script.
>>>
>>> The process is written here:
>>> http://wiki.nmr-relax.com/Run_relax_at_Google_Cloud_Computin
>>> g#Install_packages_at_server
>>>
>>> But that is a little old, since the configurations has changed a little
>>> since 2015.
>>> And the last deployment script is for Ubuntu.
>>>
>>> Getting the packages right is a pain ;)
>>>
>>> Let me return when I know some more.
>>>
>>>
>>>
>>> 2016-09-30 23:03 GMT+02:00 Mahdi, Sam :
>>>
 Hi Troels,

 I attempted the full path
 mpirun -np 5 ~/relax-4.0.2/relax --multi="mpi4py" -v
 and still got the same result. No output.

 Sincerely,
 Sam

 On Fri, Sep 30, 2016 at 11:43 AM, Troels Emtekær Linnet <
 tlin...@nmr-relax.com> wrote:

> Hi Sam.
>
> Hm. Alright.
>
> But to rule it out in my head, can you try this:
>
> mpirun -np 5 /home/users/software/relax-4.0.2/relax --multi="mpi4py"
> -v
>
> Or similar destination path.
> But please try the full path.
>
> Best
> Troels
>
> 2016-09-30 19:47 GMT+02:00 Mahdi, Sam :
>
>> I get the same results with the full path mpirun -np 5
>> ~/relax-4.0.2/relax --multi="mpi4py" -v
>> Still no output.
>>
>> Sincerely,
>> Sam
>>
>> On Fri, Sep 30, 2016 at 10:39 AM, Troels Emtekær Linnet <
>> tlin...@nmr-relax.com> wrote:
>>
>>> Sam.
>>>
>>> All points to:
>>> "./relax"   is NOT calling relax in the current folder.
>>>
>>> It is because the command "mpirun" is running it.
>>>
>>> Please provide the FULL path to relax.
>>>
>>> I think I have written this before. ;)
>>>
>>> Best
>>> Troels
>>>
>>>
>>> 2016-09-30 19:24 GMT+02:00 Mahdi, Sam :
>>>
 Sorry, you're right, I re-ran the mpirun -np 5 ./relax
 --multi="mpi4py" -v
 and got no output. So I'm just curious for the other computers I
 download
 openmpi in, just installing it and compiling it isn't enough? There
 are
 some configurations you have to make to have it run on relax?

 Sincerely,
 Sam

 On Fri, Sep 30, 2016 at 10:17 AM, Edward d'Auvergne <
 edw...@nmr-relax.com>
 wrote:

 > On 30 September 2016 at 19:12, Mahdi, Sam <
 sam.mahdi@my.csun.edu>
 > wrote:
 > > Hi Edward,
 > >
 > > So I ran the the mpirun commands you suggested. The echo world
 works
 > fine. I
 > > get the same results you did. For the relax one, this is the
 output I
 > > recieved
 > >  [~/relax-4.0.2]> mpirun -np 5 ./relax --multi="mpi4py" -v
 relax 4.0.2
 > > Usage: relax [options] [script_file]
 > >
 > > RelaxError: incorrect number of arguments
 >
 > Have a close look at my original text:
 >
 > [edward@localhost ~]$ mpirun -np 5 /data/relax/tags/4.0.2/relax
 > --multi="mpi4py" -v
 > relax 4.0.2
 > [edward@localhost ~]$
 >
 > Note how "relax 4.0.2" is on a different line - that is the relax
 > output, not the command line input.  Try again without that text.
 >
 >
 > > RelaxError: ambiguous option: --v

Re: Using multi-processor for model_free

2016-09-30 Thread Troels Emtekær Linnet

Hi Sam.

Can you try:
mpirun --version

Thanks

2016-10-01 0:00 GMT+02:00 Mahdi, Sam :

> Hi Troels,
>
> Here is a list of the packages I got off of the fedora package list
> Openmpi:
> openmpi-1.7.3-1.fc.20(64-bit)
> openmpi-devel-1.7.3-1.fc20(64bit)
> pypar-openmpi-2.1.5_108_3.fc.20(64bit)
> python3-mpi4py-1.3.1-1.fc20(64bit)
>
> Mpi4py
> mpi4py-common-1.3.1-1.fc20
> mpi4py-mpich-1.3.1-1.fc20
> mpi4py-openmpi-1.3.1-1.fc20
> python3-mpi4py-mpich-1.3.1-1.fc20
> python3-mpi4py-openmpi-1.3.1-1.fc20
>
> Note: I now know the mpich is extra and pointless. I only use the openmpi
> when I load my modules. I have not compiled or configured anything with
> these packages. I just installed them directly from the package list. If
> you need any more info on what is installed on these computers let me know!
>
> Sincerely,
> Sam
>
>
> On Fri, Sep 30, 2016 at 2:23 PM, Troels Emtekær Linnet <
> tlin...@nmr-relax.com> wrote:
>
>> Hi Sam.
>>
>> I am trying to setup myself on Google Cloud Platform.
>>
>> Here I setting up for a Redhat 6 distro, in hope it gets close to Fedora
>> 20.
>>
>> I am currently making a deployment script.
>>
>> The process is written here:
>> http://wiki.nmr-relax.com/Run_relax_at_Google_Cloud_Computin
>> g#Install_packages_at_server
>>
>> But that is a little old, since the configurations has changed a little
>> since 2015.
>> And the last deployment script is for Ubuntu.
>>
>> Getting the packages right is a pain ;)
>>
>> Let me return when I know some more.
>>
>>
>>
>> 2016-09-30 23:03 GMT+02:00 Mahdi, Sam :
>>
>>> Hi Troels,
>>>
>>> I attempted the full path
>>> mpirun -np 5 ~/relax-4.0.2/relax --multi="mpi4py" -v
>>> and still got the same result. No output.
>>>
>>> Sincerely,
>>> Sam
>>>
>>> On Fri, Sep 30, 2016 at 11:43 AM, Troels Emtekær Linnet <
>>> tlin...@nmr-relax.com> wrote:
>>>
 Hi Sam.

 Hm. Alright.

 But to rule it out in my head, can you try this:

 mpirun -np 5 /home/users/software/relax-4.0.2/relax --multi="mpi4py" -v

 Or similar destination path.
 But please try the full path.

 Best
 Troels

 2016-09-30 19:47 GMT+02:00 Mahdi, Sam :

> I get the same results with the full path mpirun -np 5
> ~/relax-4.0.2/relax --multi="mpi4py" -v
> Still no output.
>
> Sincerely,
> Sam
>
> On Fri, Sep 30, 2016 at 10:39 AM, Troels Emtekær Linnet <
> tlin...@nmr-relax.com> wrote:
>
>> Sam.
>>
>> All points to:
>> "./relax"   is NOT calling relax in the current folder.
>>
>> It is because the command "mpirun" is running it.
>>
>> Please provide the FULL path to relax.
>>
>> I think I have written this before. ;)
>>
>> Best
>> Troels
>>
>>
>> 2016-09-30 19:24 GMT+02:00 Mahdi, Sam :
>>
>>> Sorry, you're right, I re-ran the mpirun -np 5 ./relax
>>> --multi="mpi4py" -v
>>> and got no output. So I'm just curious for the other computers I
>>> download
>>> openmpi in, just installing it and compiling it isn't enough? There
>>> are
>>> some configurations you have to make to have it run on relax?
>>>
>>> Sincerely,
>>> Sam
>>>
>>> On Fri, Sep 30, 2016 at 10:17 AM, Edward d'Auvergne <
>>> edw...@nmr-relax.com>
>>> wrote:
>>>
>>> > On 30 September 2016 at 19:12, Mahdi, Sam <
>>> sam.mahdi@my.csun.edu>
>>> > wrote:
>>> > > Hi Edward,
>>> > >
>>> > > So I ran the the mpirun commands you suggested. The echo world
>>> works
>>> > fine. I
>>> > > get the same results you did. For the relax one, this is the
>>> output I
>>> > > recieved
>>> > >  [~/relax-4.0.2]> mpirun -np 5 ./relax --multi="mpi4py" -v relax
>>> 4.0.2
>>> > > Usage: relax [options] [script_file]
>>> > >
>>> > > RelaxError: incorrect number of arguments
>>> >
>>> > Have a close look at my original text:
>>> >
>>> > [edward@localhost ~]$ mpirun -np 5 /data/relax/tags/4.0.2/relax
>>> > --multi="mpi4py" -v
>>> > relax 4.0.2
>>> > [edward@localhost ~]$
>>> >
>>> > Note how "relax 4.0.2" is on a different line - that is the relax
>>> > output, not the command line input.  Try again without that text.
>>> >
>>> >
>>> > > RelaxError: ambiguous option: --v (--verification-tests,
>>> --version?)
>>> >
>>> > This is because the double-dash to single-dash conversion is only
>>> in
>>> > the HTML version of the relax manual, and not emails.  Run "relax
>>> -h"
>>> > to see a description of this option.
>>> >
>>> >
>>> > > Also, the reason its ./relax is because I have relax 2.2.5
>>> installed,
>>> > and I
>>> > > have that set up as an Alias, so if I just type relax, it'll
>>> open up
>>> > relax
>>> > > 2.2.5. So I went to the actual

Re: Using multi-processor for model_free

2016-09-30 Thread Troels Emtekær Linnet

Hi Sam.

I am trying to setup myself on Google Cloud Platform.

Here I setting up for a Redhat 6 distro, in hope it gets close to Fedora 20.

I am currently making a deployment script.

The process is written here:
http://wiki.nmr-relax.com/Run_relax_at_Google_Cloud_Computing#Install_packages_at_server

But that is a little old, since the configurations has changed a little
since 2015.
And the last deployment script is for Ubuntu.

Getting the packages right is a pain ;)

Let me return when I know some more.



2016-09-30 23:03 GMT+02:00 Mahdi, Sam :

> Hi Troels,
>
> I attempted the full path
> mpirun -np 5 ~/relax-4.0.2/relax --multi="mpi4py" -v
> and still got the same result. No output.
>
> Sincerely,
> Sam
>
> On Fri, Sep 30, 2016 at 11:43 AM, Troels Emtekær Linnet <
> tlin...@nmr-relax.com> wrote:
>
>> Hi Sam.
>>
>> Hm. Alright.
>>
>> But to rule it out in my head, can you try this:
>>
>> mpirun -np 5 /home/users/software/relax-4.0.2/relax --multi="mpi4py" -v
>>
>> Or similar destination path.
>> But please try the full path.
>>
>> Best
>> Troels
>>
>> 2016-09-30 19:47 GMT+02:00 Mahdi, Sam :
>>
>>> I get the same results with the full path mpirun -np 5
>>> ~/relax-4.0.2/relax --multi="mpi4py" -v
>>> Still no output.
>>>
>>> Sincerely,
>>> Sam
>>>
>>> On Fri, Sep 30, 2016 at 10:39 AM, Troels Emtekær Linnet <
>>> tlin...@nmr-relax.com> wrote:
>>>
 Sam.

 All points to:
 "./relax"   is NOT calling relax in the current folder.

 It is because the command "mpirun" is running it.

 Please provide the FULL path to relax.

 I think I have written this before. ;)

 Best
 Troels


 2016-09-30 19:24 GMT+02:00 Mahdi, Sam :

> Sorry, you're right, I re-ran the mpirun -np 5 ./relax
> --multi="mpi4py" -v
> and got no output. So I'm just curious for the other computers I
> download
> openmpi in, just installing it and compiling it isn't enough? There are
> some configurations you have to make to have it run on relax?
>
> Sincerely,
> Sam
>
> On Fri, Sep 30, 2016 at 10:17 AM, Edward d'Auvergne <
> edw...@nmr-relax.com>
> wrote:
>
> > On 30 September 2016 at 19:12, Mahdi, Sam  >
> > wrote:
> > > Hi Edward,
> > >
> > > So I ran the the mpirun commands you suggested. The echo world
> works
> > fine. I
> > > get the same results you did. For the relax one, this is the
> output I
> > > recieved
> > >  [~/relax-4.0.2]> mpirun -np 5 ./relax --multi="mpi4py" -v relax
> 4.0.2
> > > Usage: relax [options] [script_file]
> > >
> > > RelaxError: incorrect number of arguments
> >
> > Have a close look at my original text:
> >
> > [edward@localhost ~]$ mpirun -np 5 /data/relax/tags/4.0.2/relax
> > --multi="mpi4py" -v
> > relax 4.0.2
> > [edward@localhost ~]$
> >
> > Note how "relax 4.0.2" is on a different line - that is the relax
> > output, not the command line input.  Try again without that text.
> >
> >
> > > RelaxError: ambiguous option: --v (--verification-tests,
> --version?)
> >
> > This is because the double-dash to single-dash conversion is only in
> > the HTML version of the relax manual, and not emails.  Run "relax -h"
> > to see a description of this option.
> >
> >
> > > Also, the reason its ./relax is because I have relax 2.2.5
> installed,
> > and I
> > > have that set up as an Alias, so if I just type relax, it'll open
> up
> > relax
> > > 2.2.5. So I went to the actual relax-4.0.2. directory instead of
> > indicating
> > > its path and just typed ./relax. (By I, I mean the administrator
> of this
> > > computer, I do not have root access to this computer).
> >
> > You should set your alias to the relax-4.0.2 version instead.  The
> > 2.2.5 version is very, very old, and many bugs have been fixed since
> > then.
> >
> > Regards,
> >
> > Edward
> >
> ___
> relax (http://www.nmr-relax.com)
>
> This is the relax-users mailing list
> relax-users@gna.org
>
> To unsubscribe from this list, get a password
> reminder, or change your subscription options,
> visit the list information page at
> https://mail.gna.org/listinfo/relax-users
>


>>>
>>
>
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Re: Using multi-processor for model_free

2016-09-30 Thread Mahdi, Sam

Hi Troels,

I attempted the full path
mpirun -np 5 ~/relax-4.0.2/relax --multi="mpi4py" -v
and still got the same result. No output.

Sincerely,
Sam

On Fri, Sep 30, 2016 at 11:43 AM, Troels Emtekær Linnet <
tlin...@nmr-relax.com> wrote:

> Hi Sam.
>
> Hm. Alright.
>
> But to rule it out in my head, can you try this:
>
> mpirun -np 5 /home/users/software/relax-4.0.2/relax --multi="mpi4py" -v
>
> Or similar destination path.
> But please try the full path.
>
> Best
> Troels
>
> 2016-09-30 19:47 GMT+02:00 Mahdi, Sam :
>
>> I get the same results with the full path mpirun -np 5
>> ~/relax-4.0.2/relax --multi="mpi4py" -v
>> Still no output.
>>
>> Sincerely,
>> Sam
>>
>> On Fri, Sep 30, 2016 at 10:39 AM, Troels Emtekær Linnet <
>> tlin...@nmr-relax.com> wrote:
>>
>>> Sam.
>>>
>>> All points to:
>>> "./relax"   is NOT calling relax in the current folder.
>>>
>>> It is because the command "mpirun" is running it.
>>>
>>> Please provide the FULL path to relax.
>>>
>>> I think I have written this before. ;)
>>>
>>> Best
>>> Troels
>>>
>>>
>>> 2016-09-30 19:24 GMT+02:00 Mahdi, Sam :
>>>
 Sorry, you're right, I re-ran the mpirun -np 5 ./relax --multi="mpi4py"
 -v
 and got no output. So I'm just curious for the other computers I
 download
 openmpi in, just installing it and compiling it isn't enough? There are
 some configurations you have to make to have it run on relax?

 Sincerely,
 Sam

 On Fri, Sep 30, 2016 at 10:17 AM, Edward d'Auvergne <
 edw...@nmr-relax.com>
 wrote:

 > On 30 September 2016 at 19:12, Mahdi, Sam 
 > wrote:
 > > Hi Edward,
 > >
 > > So I ran the the mpirun commands you suggested. The echo world works
 > fine. I
 > > get the same results you did. For the relax one, this is the output
 I
 > > recieved
 > >  [~/relax-4.0.2]> mpirun -np 5 ./relax --multi="mpi4py" -v relax
 4.0.2
 > > Usage: relax [options] [script_file]
 > >
 > > RelaxError: incorrect number of arguments
 >
 > Have a close look at my original text:
 >
 > [edward@localhost ~]$ mpirun -np 5 /data/relax/tags/4.0.2/relax
 > --multi="mpi4py" -v
 > relax 4.0.2
 > [edward@localhost ~]$
 >
 > Note how "relax 4.0.2" is on a different line - that is the relax
 > output, not the command line input.  Try again without that text.
 >
 >
 > > RelaxError: ambiguous option: --v (--verification-tests, --version?)
 >
 > This is because the double-dash to single-dash conversion is only in
 > the HTML version of the relax manual, and not emails.  Run "relax -h"
 > to see a description of this option.
 >
 >
 > > Also, the reason its ./relax is because I have relax 2.2.5
 installed,
 > and I
 > > have that set up as an Alias, so if I just type relax, it'll open up
 > relax
 > > 2.2.5. So I went to the actual relax-4.0.2. directory instead of
 > indicating
 > > its path and just typed ./relax. (By I, I mean the administrator of
 this
 > > computer, I do not have root access to this computer).
 >
 > You should set your alias to the relax-4.0.2 version instead.  The
 > 2.2.5 version is very, very old, and many bugs have been fixed since
 > then.
 >
 > Regards,
 >
 > Edward
 >
 ___
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 relax-users@gna.org

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 reminder, or change your subscription options,
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 https://mail.gna.org/listinfo/relax-users

>>>
>>>
>>
>
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Re: Using multi-processor for model_free

2016-09-30 Thread Troels Emtekær Linnet

Hi Sam.

Hm. Alright.

But to rule it out in my head, can you try this:

mpirun -np 5 /home/users/software/relax-4.0.2/relax --multi="mpi4py" -v

Or similar destination path.
But please try the full path.

Best
Troels

2016-09-30 19:47 GMT+02:00 Mahdi, Sam :

> I get the same results with the full path mpirun -np 5 ~/relax-4.0.2/relax
> --multi="mpi4py" -v
> Still no output.
>
> Sincerely,
> Sam
>
> On Fri, Sep 30, 2016 at 10:39 AM, Troels Emtekær Linnet <
> tlin...@nmr-relax.com> wrote:
>
>> Sam.
>>
>> All points to:
>> "./relax"   is NOT calling relax in the current folder.
>>
>> It is because the command "mpirun" is running it.
>>
>> Please provide the FULL path to relax.
>>
>> I think I have written this before. ;)
>>
>> Best
>> Troels
>>
>>
>> 2016-09-30 19:24 GMT+02:00 Mahdi, Sam :
>>
>>> Sorry, you're right, I re-ran the mpirun -np 5 ./relax --multi="mpi4py"
>>> -v
>>> and got no output. So I'm just curious for the other computers I download
>>> openmpi in, just installing it and compiling it isn't enough? There are
>>> some configurations you have to make to have it run on relax?
>>>
>>> Sincerely,
>>> Sam
>>>
>>> On Fri, Sep 30, 2016 at 10:17 AM, Edward d'Auvergne <
>>> edw...@nmr-relax.com>
>>> wrote:
>>>
>>> > On 30 September 2016 at 19:12, Mahdi, Sam 
>>> > wrote:
>>> > > Hi Edward,
>>> > >
>>> > > So I ran the the mpirun commands you suggested. The echo world works
>>> > fine. I
>>> > > get the same results you did. For the relax one, this is the output I
>>> > > recieved
>>> > >  [~/relax-4.0.2]> mpirun -np 5 ./relax --multi="mpi4py" -v relax
>>> 4.0.2
>>> > > Usage: relax [options] [script_file]
>>> > >
>>> > > RelaxError: incorrect number of arguments
>>> >
>>> > Have a close look at my original text:
>>> >
>>> > [edward@localhost ~]$ mpirun -np 5 /data/relax/tags/4.0.2/relax
>>> > --multi="mpi4py" -v
>>> > relax 4.0.2
>>> > [edward@localhost ~]$
>>> >
>>> > Note how "relax 4.0.2" is on a different line - that is the relax
>>> > output, not the command line input.  Try again without that text.
>>> >
>>> >
>>> > > RelaxError: ambiguous option: --v (--verification-tests, --version?)
>>> >
>>> > This is because the double-dash to single-dash conversion is only in
>>> > the HTML version of the relax manual, and not emails.  Run "relax -h"
>>> > to see a description of this option.
>>> >
>>> >
>>> > > Also, the reason its ./relax is because I have relax 2.2.5 installed,
>>> > and I
>>> > > have that set up as an Alias, so if I just type relax, it'll open up
>>> > relax
>>> > > 2.2.5. So I went to the actual relax-4.0.2. directory instead of
>>> > indicating
>>> > > its path and just typed ./relax. (By I, I mean the administrator of
>>> this
>>> > > computer, I do not have root access to this computer).
>>> >
>>> > You should set your alias to the relax-4.0.2 version instead.  The
>>> > 2.2.5 version is very, very old, and many bugs have been fixed since
>>> > then.
>>> >
>>> > Regards,
>>> >
>>> > Edward
>>> >
>>> ___
>>> relax (http://www.nmr-relax.com)
>>>
>>> This is the relax-users mailing list
>>> relax-users@gna.org
>>>
>>> To unsubscribe from this list, get a password
>>> reminder, or change your subscription options,
>>> visit the list information page at
>>> https://mail.gna.org/listinfo/relax-users
>>>
>>
>>
>
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Re: Using multi-processor for model_free

2016-09-30 Thread Edward d'Auvergne

On 30 September 2016 at 19:47, Mahdi, Sam  wrote:
> I get the same results with the full path mpirun -np 5 ~/relax-4.0.2/relax
> --multi="mpi4py" -v
> Still no output.

The reason is because either OpenMPI or mpi4py are not working.  If
you compiled OpenMPI, then you'll have to compile mpi4py against that
self-compiled version of MPI.  Having multiple versions of MPI on the
system might be problematic, unless you know how to set your
environmental variables correctly for compilation and linking.  If you
cannot run the mpi4py demo that comes with the mpi4py source code,
then you do not have it set up correctly.  If you need help setting up
mpi4py for Python, please see the "Discussion and Support" section at
https://pythonhosted.org/mpi4py/ .  I don't think anyone on the relax
mailing lists have experience with broken mpi4py installations and can
help you fix this.

Regards,

Edward

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Re: Using multi-processor for model_free

2016-09-30 Thread Troels Emtekær Linnet

Sam.

All points to:
"./relax"   is NOT calling relax in the current folder.

It is because the command "mpirun" is running it.

Please provide the FULL path to relax.

I think I have written this before. ;)

Best
Troels


2016-09-30 19:24 GMT+02:00 Mahdi, Sam :

> Sorry, you're right, I re-ran the mpirun -np 5 ./relax --multi="mpi4py" -v
> and got no output. So I'm just curious for the other computers I download
> openmpi in, just installing it and compiling it isn't enough? There are
> some configurations you have to make to have it run on relax?
>
> Sincerely,
> Sam
>
> On Fri, Sep 30, 2016 at 10:17 AM, Edward d'Auvergne 
> wrote:
>
> > On 30 September 2016 at 19:12, Mahdi, Sam 
> > wrote:
> > > Hi Edward,
> > >
> > > So I ran the the mpirun commands you suggested. The echo world works
> > fine. I
> > > get the same results you did. For the relax one, this is the output I
> > > recieved
> > >  [~/relax-4.0.2]> mpirun -np 5 ./relax --multi="mpi4py" -v relax 4.0.2
> > > Usage: relax [options] [script_file]
> > >
> > > RelaxError: incorrect number of arguments
> >
> > Have a close look at my original text:
> >
> > [edward@localhost ~]$ mpirun -np 5 /data/relax/tags/4.0.2/relax
> > --multi="mpi4py" -v
> > relax 4.0.2
> > [edward@localhost ~]$
> >
> > Note how "relax 4.0.2" is on a different line - that is the relax
> > output, not the command line input.  Try again without that text.
> >
> >
> > > RelaxError: ambiguous option: --v (--verification-tests, --version?)
> >
> > This is because the double-dash to single-dash conversion is only in
> > the HTML version of the relax manual, and not emails.  Run "relax -h"
> > to see a description of this option.
> >
> >
> > > Also, the reason its ./relax is because I have relax 2.2.5 installed,
> > and I
> > > have that set up as an Alias, so if I just type relax, it'll open up
> > relax
> > > 2.2.5. So I went to the actual relax-4.0.2. directory instead of
> > indicating
> > > its path and just typed ./relax. (By I, I mean the administrator of
> this
> > > computer, I do not have root access to this computer).
> >
> > You should set your alias to the relax-4.0.2 version instead.  The
> > 2.2.5 version is very, very old, and many bugs have been fixed since
> > then.
> >
> > Regards,
> >
> > Edward
> >
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Re: Using multi-processor for model_free

2016-09-30 Thread Mahdi, Sam

Sorry, you're right, I re-ran the mpirun -np 5 ./relax --multi="mpi4py" -v
and got no output. So I'm just curious for the other computers I download
openmpi in, just installing it and compiling it isn't enough? There are
some configurations you have to make to have it run on relax?

Sincerely,
Sam

On Fri, Sep 30, 2016 at 10:17 AM, Edward d'Auvergne 
wrote:

> On 30 September 2016 at 19:12, Mahdi, Sam 
> wrote:
> > Hi Edward,
> >
> > So I ran the the mpirun commands you suggested. The echo world works
> fine. I
> > get the same results you did. For the relax one, this is the output I
> > recieved
> >  [~/relax-4.0.2]> mpirun -np 5 ./relax --multi="mpi4py" -v relax 4.0.2
> > Usage: relax [options] [script_file]
> >
> > RelaxError: incorrect number of arguments
>
> Have a close look at my original text:
>
> [edward@localhost ~]$ mpirun -np 5 /data/relax/tags/4.0.2/relax
> --multi="mpi4py" -v
> relax 4.0.2
> [edward@localhost ~]$
>
> Note how "relax 4.0.2" is on a different line - that is the relax
> output, not the command line input.  Try again without that text.
>
>
> > RelaxError: ambiguous option: --v (--verification-tests, --version?)
>
> This is because the double-dash to single-dash conversion is only in
> the HTML version of the relax manual, and not emails.  Run "relax -h"
> to see a description of this option.
>
>
> > Also, the reason its ./relax is because I have relax 2.2.5 installed,
> and I
> > have that set up as an Alias, so if I just type relax, it'll open up
> relax
> > 2.2.5. So I went to the actual relax-4.0.2. directory instead of
> indicating
> > its path and just typed ./relax. (By I, I mean the administrator of this
> > computer, I do not have root access to this computer).
>
> You should set your alias to the relax-4.0.2 version instead.  The
> 2.2.5 version is very, very old, and many bugs have been fixed since
> then.
>
> Regards,
>
> Edward
>
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Re: Using multi-processor for model_free

2016-09-30 Thread Edward d'Auvergne

On 30 September 2016 at 19:12, Mahdi, Sam  wrote:
> Hi Edward,
>
> So I ran the the mpirun commands you suggested. The echo world works fine. I
> get the same results you did. For the relax one, this is the output I
> recieved
>  [~/relax-4.0.2]> mpirun -np 5 ./relax --multi="mpi4py" -v relax 4.0.2
> Usage: relax [options] [script_file]
>
> RelaxError: incorrect number of arguments

Have a close look at my original text:

[edward@localhost ~]$ mpirun -np 5 /data/relax/tags/4.0.2/relax
--multi="mpi4py" -v
relax 4.0.2
[edward@localhost ~]$

Note how "relax 4.0.2" is on a different line - that is the relax
output, not the command line input.  Try again without that text.


> RelaxError: ambiguous option: --v (--verification-tests, --version?)

This is because the double-dash to single-dash conversion is only in
the HTML version of the relax manual, and not emails.  Run "relax -h"
to see a description of this option.


> Also, the reason its ./relax is because I have relax 2.2.5 installed, and I
> have that set up as an Alias, so if I just type relax, it'll open up relax
> 2.2.5. So I went to the actual relax-4.0.2. directory instead of indicating
> its path and just typed ./relax. (By I, I mean the administrator of this
> computer, I do not have root access to this computer).

You should set your alias to the relax-4.0.2 version instead.  The
2.2.5 version is very, very old, and many bugs have been fixed since
then.

Regards,

Edward

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Re: Using multi-processor for model_free

2016-09-30 Thread Edward d'Auvergne

On 30 September 2016 at 19:03, Mahdi, Sam  wrote:
> Hi Edward,
>
> So the GUI problems came from relax 2.2.5 The actual output is big, so I
> will only post where the errors started
> relax> monte_carlo.error_analysis()
>
> relax> results.write(file='devnull', dir='pipe_name', compress_type=1,
> force=True)
> Opening the null device file for writing.
> Traceback (most recent call last):

[snip]

> "/usr/local/Relax/relax-2.2.5/test_suite/system_tests/scripts/n_state_model/paramag_centre_fit.py",
> line 121, in 
> print("A:\n" % cdp.align_tensors[0])
> TypeError: not all arguments converted during string formatting

[snip]

> That was for relax 2.2.5

These issues were fixed a long, long time ago ;)


> This is the output for relax 4.0.2 It seemed to run and finish, but it gave
> a bunch of errors that stated
> (python:28738): IBUS-WARNING **: Create input context failed: Timeout was
> reached.
>
> This warning basically takes up the entire terminal. Followed by this

These issues are with your Ibus input system, which I guess you have
set up for a few Indian languages on top of English, interacting with
wxPython (again a Fedora configuration issue).  Those are wxPython
messages which are not related to relax.  You should run the wxPython
demos and see if you can type with different Ibus languages, and see
if you get these same Ibus warnings.  No need to report back here
about that though - it would be of more benefit to report this
upstream to Fedora.

Regards,

Edward

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Re: Using multi-processor for model_free

2016-09-30 Thread Mahdi, Sam

Hi Edward,

So the GUI problems came from relax 2.2.5 The actual output is big, so I
will only post where the errors started
relax> monte_carlo.error_analysis()

relax> results.write(file='devnull', dir='pipe_name', compress_type=1,
force=True)
Opening the null device file for writing.
Traceback (most recent call last):
  File
"/usr/local/Relax/relax-2.2.5/test_suite/system_tests/n_state_model.py",
line 733, in test_paramag_centre_fit
self.script_exec(status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'n_state_model'+sep+'paramag_centre_fit.py')
  File
"/usr/local/Relax/relax-2.2.5/test_suite/system_tests/base_classes.py",
line 65, in script_exec
self.interpreter.run(script_file=script)
  File "/usr/local/Relax/relax-2.2.5/prompt/interpreter.py", line 278, in
run
return run_script(intro=self.__intro_string, local=locals(),
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script, raise_relax_error=self.__raise_relax_error)
  File "/usr/local/Relax/relax-2.2.5/prompt/interpreter.py", line 585, in
run_script
return console.interact(intro, local, script_file, quit,
show_script=show_script, raise_relax_error=raise_relax_error)
  File "/usr/local/Relax/relax-2.2.5/prompt/interpreter.py", line 468, in
interact_script
exec_script(script_file, local)
  File "/usr/local/Relax/relax-2.2.5/prompt/interpreter.py", line 341, in
exec_script
runpy.run_module(module, globals)
  File "/usr/lib64/python2.7/runpy.py", line 180, in run_module
fname, loader, pkg_name)
  File "/usr/lib64/python2.7/runpy.py", line 72, in _run_code
exec code in run_globals
  File
"/usr/local/Relax/relax-2.2.5/test_suite/system_tests/scripts/n_state_model/paramag_centre_fit.py",
line 121, in 
print("A:\n" % cdp.align_tensors[0])
TypeError: not all arguments converted during string formatting

--
Ran 284 tests in 279.175s

FAILED (errors=1)
##
# Unit tests #
##


.E.EE...E
==
ERROR: test_read_protein_noe_data
(test_suite.unit_tests._generic_fns.test_sequence.Test_sequence)
Test the reading of the amino acid sequence out of a protein NOE data file.
--
Traceback (most recent call last):
  File
"/usr/local/Relax/relax-2.2.5/test_suite/unit_tests/sequence_testing_base.py",
line 130, in test_read_protein_noe_data
self.sequence_fns.read(file='Ap4Aase.Noe.600.bz2',
dir=status.install_path+sep+'test_suite'+sep+'shared_data'+sep+'relaxation_data',
res_num_col=1, res_name_col=2)
  File "/usr/local/Relax/relax-2.2.5/generic_fns/sequence.py", line 339, in
read
for mol_name, res_num, res_name, spin_num, spin_name in
read_spin_data(file=file, dir=dir, file_data=file_data,
spin_id_col=spin_id_col, mol_name_col=mol_name_col,
res_num_col=res_num_col, res_name_col=res_name_col,
spin_num_col=spin_num_col, spin_name_col=spin_name_col, sep=sep,
spin_id=spin_id):
  File "/usr/local/Relax/relax-2.2.5/relax_io.py", line 533, in
read_spin_data
file_data = extract_data(file, dir)
  File "/usr/local/Relax/relax-2.2.5/relax_io.py", line 141, in extract_data
file = open_read_file(file_name=file, dir=dir)
  File "/usr/local/Relax/relax-2.2.5/relax_io.py", line 345, in
open_read_file
compress_type, file_path = determine_compression(file_path)
  File "/usr/local/Relax/relax-2.2.5/relax_io.py", line 112, in
determine_compression
raise RelaxFileError(file_path)
RelaxFileError: RelaxError: The file
'/usr/local/Relax/relax-2.2.5/test_suite/shared_data/relaxation_data/Ap4Aase.Noe.600.bz2'
does not exist.

Re: Using multi-processor for model_free

2016-09-30 Thread Edward d'Auvergne

On 30 September 2016 at 17:37, Mahdi, Sam  wrote:
> Hi Edward,
>
> I also wanted to add, for running a multi-processor platform problem. I
> installed openmpi from the fedora package list, not from the site itself. I
> installed both openmpi, mpi4py, and the openmpi devel. I did not modify
> anything. I can also successfully open relax using mpirun in a single
> processor mode (as in I can load the module, and do mpirun relax and it'll
> work). Do I actually have to do some modifications to openmpi for relax? The
> other computer I was able to successfully run multi-processor on, already
> had openmpi installed and set up, so I only downloaded mpi4py on that
> computer. So I don't know what their setting or configuration was.

Hi Sam,

This sounds like a Fedora OpenMPI misconfiguration.  I guess on the
computer that you see no output with relax, you would also see no
output with:

[edward@localhost ~]$ mpirun -np 5 echo "hello"
hello
hello
hello
hello
hello
[edward@localhost ~]$

In any case, this has nothing to do with relax.  And without a local
login to your computer, there is not much anyone can do about it.  Do
you have a system administrator there who can help you?  Oh, another
good and quick test is:

[edward@localhost ~]$ mpirun -np 5 /data/relax/tags/4.0.2/relax
--multi="mpi4py" -v
relax 4.0.2
[edward@localhost ~]$

You should only see a single version number printed.  This tests both
your OpenMPI configuration and the mpi4py Python package.  If you do
not see these exact same results, you have some configuration work in
front of you ;)

Regards,

Edward

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Re: Using multi-processor for model_free

2016-09-30 Thread Mahdi, Sam

Hi Edward,

I also wanted to add, for running a multi-processor platform problem. I
installed openmpi from the fedora package list, not from the site itself. I
installed both openmpi, mpi4py, and the openmpi devel. I did not modify
anything. I can also successfully open relax using mpirun in a single
processor mode (as in I can load the module, and do mpirun relax and it'll
work). Do I actually have to do some modifications to openmpi for relax?
The other computer I was able to successfully run multi-processor on,
already had openmpi installed and set up, so I only downloaded mpi4py on
that computer. So I don't know what their setting or configuration was.

Sincerely,
Sam

On Fri, Sep 30, 2016 at 8:22 AM, Mahdi, Sam 
wrote:

> Hi Edward,
>
> I have uploaded a bug with the pdb file, the relax data, and the script as
> well. I can upload the original pdb file I recieved from HADDOCK (without
> changing the HN to H). I will attempt to re-run my data again then on both
> computer. Most of the data was the same, but there were some data in from
> one computer, that was virtually non-existent in the other. Also to the
> relax -x error, I believe that was on the relax 2.5 version. I am
> re-running it on the 4.0.2. version.
>
> Sincerely,
> Sam
>
> On Fri, Sep 30, 2016 at 12:04 AM, Edward d'Auvergne 
> wrote:
>
>> On 29 September 2016 at 00:23, Mahdi, Sam 
>> wrote:
>> > Hi Troels,
>> > Update on both proteins: So for protein 1, I can upload all the spins (H
>> > and N), but then I recieve an error. This is the error I recieved for
>> > protein 2 as well. These are both dimer pdb files. Meaning they have 2
>> sets
>> > (set A) and set (B) (e.g.
>> > http://www.rcsb.org/pdb/explore/explore.do?structureId=1DJ8 this pdb
>> > protein has 4 sets, A,B,C, and D ours only have A and B). For both these
>> > proteins I recieve this error
>> >  File "/home/crowlab/relax-4.0.2/multi/processor.py", line 494, in run
>> > self.callback.init_master(self)
>> >   File "/home/crowlab/relax-4.0.2/multi/__init__.py", line 318, in
>> > default_init_master
>> > self.master.run()
>> >   File "/home/crowlab/relax-4.0.2/relax.py", line 199, in run
>> > self.interpreter.run(self.script_file)
>> >   File "/home/crowlab/relax-4.0.2/prompt/interpreter.py", line 279, in
>> run
>> > return run_script(intro=self.__intro_string, local=locals(),
>> > script_file=script_file, show_script=self.__show_script,
>> > raise_relax_error=self.__raise_relax_error)
>> >   File "/home/crowlab/relax-4.0.2/prompt/interpreter.py", line 585, in
>> > run_script
>> > return console.interact(intro, local, script_file,
>> > show_script=show_script, raise_relax_error=raise_relax_error)
>> >   File "/home/crowlab/relax-4.0.2/prompt/interpreter.py", line 484, in
>> > interact_script
>> > exec_script(script_file, local)
>> >   File "/home/crowlab/relax-4.0.2/prompt/interpreter.py", line 363, in
>> > exec_script
>> > runpy.run_module(module, globals)
>> >   File "/usr/lib64/python2.7/runpy.py", line 180, in run_module
>> > fname, loader, pkg_name)
>> >   File "/usr/lib64/python2.7/runpy.py", line 72, in _run_code
>> > exec code in run_globals
>> >   File "/home/crowlab/relax-4.0.2/RGS4_modelfree_sample_script.py",
>> line
>> > 31, in 
>> >
>> > dAuvergne_protocol(pipe_name=name,pipe_bundle=pipe_bundle,di
>> ff_model=DIFF_MODEL,mf_models=MF_MODELS,local_tm_models=
>> LOCAL_TM_MODELS,grid_inc=GRID_INC,min_algor=MIN_ALGOR,mc_
>> sim_num=MC_NUM,conv_loop=CONV_LOOP)
>> >   File "/home/crowlab/relax-4.0.2/auto_analyses/dauvergne_protocol.py",
>> > line 246, in __init__
>> > self.execute()
>> >   File "/home/crowlab/relax-4.0.2/auto_analyses/dauvergne_protocol.py",
>> > line 600, in execute
>> > self.multi_model(local_tm=True)
>> >   File "/home/crowlab/relax-4.0.2/auto_analyses/dauvergne_protocol.py",
>> > line 888, in multi_model
>> > self.interpreter.minimise.grid_search(inc=self.grid_inc)
>> >   File "/home/crowlab/relax-4.0.2/prompt/uf_objects.py", line 225, in
>> > __call__
>> > self._backend(*new_args, **uf_kargs)
>> >   File "/home/crowlab/relax-4.0.2/pipe_control/minimise.py", line 172,
>> in
>> > grid_search
>> > model_lower, model_upper, model_inc = grid_setup(lower, upper, inc,
>> > verbosity=verbosity, skip_preset=skip_preset)
>> >   File "/home/crowlab/relax-4.0.2/pipe_control/minimise.py", line 341,
>> in
>> > grid_setup
>> > elif values[i] in [None, {}, []]:
>> > IndexError: index out of bounds
>> >
>> > Which from my understanding basically means, the co-ordinates of the
>> spins
>> > are out of the acceptable range for relax. I've checked all the
>> > co-ordinates for both, nothing is extreme or outlandish (all within a
>> range
>> > of -20 to 20).
>> > Is relax unable to process pdb files that are dimers (with 2 sets A and
>> > B).? Furthermore, is it unable to process trimers and tetramers?
>>
>> Hi,
>>
>> For the model-free

Re: Using multi-processor for model_free

2016-09-30 Thread Mahdi, Sam

Hi Edward,

I have uploaded a bug with the pdb file, the relax data, and the script as
well. I can upload the original pdb file I recieved from HADDOCK (without
changing the HN to H). I will attempt to re-run my data again then on both
computer. Most of the data was the same, but there were some data in from
one computer, that was virtually non-existent in the other. Also to the
relax -x error, I believe that was on the relax 2.5 version. I am
re-running it on the 4.0.2. version.

Sincerely,
Sam

On Fri, Sep 30, 2016 at 12:04 AM, Edward d'Auvergne 
wrote:

> On 29 September 2016 at 00:23, Mahdi, Sam 
> wrote:
> > Hi Troels,
> > Update on both proteins: So for protein 1, I can upload all the spins (H
> > and N), but then I recieve an error. This is the error I recieved for
> > protein 2 as well. These are both dimer pdb files. Meaning they have 2
> sets
> > (set A) and set (B) (e.g.
> > http://www.rcsb.org/pdb/explore/explore.do?structureId=1DJ8 this pdb
> > protein has 4 sets, A,B,C, and D ours only have A and B). For both these
> > proteins I recieve this error
> >  File "/home/crowlab/relax-4.0.2/multi/processor.py", line 494, in run
> > self.callback.init_master(self)
> >   File "/home/crowlab/relax-4.0.2/multi/__init__.py", line 318, in
> > default_init_master
> > self.master.run()
> >   File "/home/crowlab/relax-4.0.2/relax.py", line 199, in run
> > self.interpreter.run(self.script_file)
> >   File "/home/crowlab/relax-4.0.2/prompt/interpreter.py", line 279, in
> run
> > return run_script(intro=self.__intro_string, local=locals(),
> > script_file=script_file, show_script=self.__show_script,
> > raise_relax_error=self.__raise_relax_error)
> >   File "/home/crowlab/relax-4.0.2/prompt/interpreter.py", line 585, in
> > run_script
> > return console.interact(intro, local, script_file,
> > show_script=show_script, raise_relax_error=raise_relax_error)
> >   File "/home/crowlab/relax-4.0.2/prompt/interpreter.py", line 484, in
> > interact_script
> > exec_script(script_file, local)
> >   File "/home/crowlab/relax-4.0.2/prompt/interpreter.py", line 363, in
> > exec_script
> > runpy.run_module(module, globals)
> >   File "/usr/lib64/python2.7/runpy.py", line 180, in run_module
> > fname, loader, pkg_name)
> >   File "/usr/lib64/python2.7/runpy.py", line 72, in _run_code
> > exec code in run_globals
> >   File "/home/crowlab/relax-4.0.2/RGS4_modelfree_sample_script.py", line
> > 31, in 
> >
> > dAuvergne_protocol(pipe_name=name,pipe_bundle=pipe_bundle,
> diff_model=DIFF_MODEL,mf_models=MF_MODELS,local_tm_
> models=LOCAL_TM_MODELS,grid_inc=GRID_INC,min_algor=MIN_
> ALGOR,mc_sim_num=MC_NUM,conv_loop=CONV_LOOP)
> >   File "/home/crowlab/relax-4.0.2/auto_analyses/dauvergne_protocol.py",
> > line 246, in __init__
> > self.execute()
> >   File "/home/crowlab/relax-4.0.2/auto_analyses/dauvergne_protocol.py",
> > line 600, in execute
> > self.multi_model(local_tm=True)
> >   File "/home/crowlab/relax-4.0.2/auto_analyses/dauvergne_protocol.py",
> > line 888, in multi_model
> > self.interpreter.minimise.grid_search(inc=self.grid_inc)
> >   File "/home/crowlab/relax-4.0.2/prompt/uf_objects.py", line 225, in
> > __call__
> > self._backend(*new_args, **uf_kargs)
> >   File "/home/crowlab/relax-4.0.2/pipe_control/minimise.py", line 172,
> in
> > grid_search
> > model_lower, model_upper, model_inc = grid_setup(lower, upper, inc,
> > verbosity=verbosity, skip_preset=skip_preset)
> >   File "/home/crowlab/relax-4.0.2/pipe_control/minimise.py", line 341,
> in
> > grid_setup
> > elif values[i] in [None, {}, []]:
> > IndexError: index out of bounds
> >
> > Which from my understanding basically means, the co-ordinates of the
> spins
> > are out of the acceptable range for relax. I've checked all the
> > co-ordinates for both, nothing is extreme or outlandish (all within a
> range
> > of -20 to 20).
> > Is relax unable to process pdb files that are dimers (with 2 sets A and
> > B).? Furthermore, is it unable to process trimers and tetramers?
>
> Hi,
>
> For the model-free analysis in relax, as well as all other analyses,
> we have designed the program to try to catch all user input errors and
> to produce a specific RelaxError prior to minimisation explaining
> exactly what went wrong.  An IndexError here simply shows that not all
> erroneous data input has been caught.  Let me go back to your PDB
> file.  You should not edit this file unless you know exactly what you
> are doing, but relax will handle all PDB files.  There is no need to
> rename protons.  You just specify the correct proton name in the input
> script.  I may have missed it as there is a lot of correspondence I
> have to catch up on, but did you upload your script and a truncated
> set of data to the relax bug or support trackers?  Do you have a
> mini-data set (1 or 2 residues) and script that triggers this error?
> If we can reproduce the IndexError, then

Re: Using multi-processor for model_free

2016-09-30 Thread Edward d'Auvergne

On 30 September 2016 at 01:35, Mahdi, Sam  wrote:
> Also, Congrats to Edward!

Thanks :)

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Re: Using multi-processor for model_free

2016-09-30 Thread Edward d'Auvergne

On 28 September 2016 at 22:44, Mahdi, Sam  wrote:
> Hey Troels,
>
> I ran the relax -x and recieve this error at the GUI tests
> =
> = GUI tests =
> =
>
> **
> Gtk:ERROR:gtkfilesystemmodel.c:746:gtk_file_system_model_sort: assertion
> failed: (r == n_visible_rows)
> Abort (core dumped)
> crowlab: [~/relax-4.0.2]>

That is a strange error, but it shouldn't effect you.  It is a minor
problem with your wxPython setup and GTK+ on your system.  It's only
an issue if you are running the GUI and the GUI suddenly crashes on
you.  But again, this problem is not due to relax.

Regards,

Edward

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Re: Using multi-processor for model_free

2016-09-30 Thread Edward d'Auvergne

On 28 September 2016 at 20:32, Troels Emtekær Linnet
 wrote:
> If you get different results, for the same setup, this is not good.
> Not at all !

Hi,

Sorry for not being more involved, I've been in what could be called
paternity leave.  This point is very, very important.  With the same
setup you must absolutely always obtain the same result.  There are
numerical precision differences between operating systems, CPU types,
and Python 2 vs. 3, but this should be very small.

Regards,

Edward

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Re: Using multi-processor for model_free

2016-09-29 Thread Mahdi, Sam

Also, Congrats to Edward!

On Thu, Sep 29, 2016 at 4:11 PM, Mahdi, Sam 
wrote:

> Hi Troels,
>
> I will upload a bug report with the pdb file, the script I use, and the
> data I'm using.
>
> Sincerely,
> Sam
>
> On Thu, Sep 29, 2016 at 2:25 PM, Troels Emtekær Linnet <
> tlin...@nmr-relax.com> wrote:
>
>> Hi Sam.
>>
>> Hm...
>>
>> I had a look in: pipe_control/minimise.py
>>
>> The trouble start with line
>> "elif values[i] in [None, {}, []]:"
>>
>> Where the index "i" is running out of bounds.
>>
>> The index is drawn from range(n).
>> n = len(names)
>> names = api.get_param_names(model_info)
>> values = api.get_param_values(model_info)
>>
>> So "something" is not aligned well in the data structures.
>> It seems that the index of parameter names exceeds parameter values.
>>
>>
>> One guess is, that the selection of
>> * diff_model
>> * mf_models
>> * local_tm_models
>>
>> is not correctly set. But I reach my limit of being able to help you.
>> Edward is the expert here, but he is on paternity leave.
>>
>>
>> Another possibility is that some of the spins are in "select" mode, where
>> they maybe should be in "deselect" mode.
>>
>> Maybe the spins do not carry any data from before, and somehow relax
>> expect this.
>>
>> It's very tricky to figure out!
>>
>> A bug report, some minimum data, and a script which make the bug occur
>> can solve this.
>>
>> Then I can write a systemtest, if it relax which is failing.
>>
>> Best
>> Troels
>>
>>
>>
>>
>> 2016-09-29 0:23 GMT+02:00 Mahdi, Sam :
>>
>>> Hi Troels,
>>> Update on both proteins: So for protein 1, I can upload all the spins (H
>>> and N), but then I recieve an error. This is the error I recieved for
>>> protein 2 as well. These are both dimer pdb files. Meaning they have 2 sets
>>> (set A) and set (B) (e.g. http://www.rcsb.org/pdb/explor
>>> e/explore.do?structureId=1DJ8 this pdb protein has 4 sets, A,B,C, and D
>>> ours only have A and B). For both these proteins I recieve this error
>>>  File "/home/crowlab/relax-4.0.2/multi/processor.py", line 494, in run
>>> self.callback.init_master(self)
>>>   File "/home/crowlab/relax-4.0.2/multi/__init__.py", line 318, in
>>> default_init_master
>>> self.master.run()
>>>   File "/home/crowlab/relax-4.0.2/relax.py", line 199, in run
>>> self.interpreter.run(self.script_file)
>>>   File "/home/crowlab/relax-4.0.2/prompt/interpreter.py", line 279, in
>>> run
>>> return run_script(intro=self.__intro_string, local=locals(),
>>> script_file=script_file, show_script=self.__show_script,
>>> raise_relax_error=self.__raise_relax_error)
>>>   File "/home/crowlab/relax-4.0.2/prompt/interpreter.py", line 585, in
>>> run_script
>>> return console.interact(intro, local, script_file,
>>> show_script=show_script, raise_relax_error=raise_relax_error)
>>>   File "/home/crowlab/relax-4.0.2/prompt/interpreter.py", line 484, in
>>> interact_script
>>> exec_script(script_file, local)
>>>   File "/home/crowlab/relax-4.0.2/prompt/interpreter.py", line 363, in
>>> exec_script
>>> runpy.run_module(module, globals)
>>>   File "/usr/lib64/python2.7/runpy.py", line 180, in run_module
>>> fname, loader, pkg_name)
>>>   File "/usr/lib64/python2.7/runpy.py", line 72, in _run_code
>>> exec code in run_globals
>>>   File "/home/crowlab/relax-4.0.2/RGS4_modelfree_sample_script.py",
>>> line 31, in 
>>> dAuvergne_protocol(pipe_name=name,pipe_bundle=pipe_bundle,di
>>> ff_model=DIFF_MODEL,mf_models=MF_MODELS,local_tm_models=LOCA
>>> L_TM_MODELS,grid_inc=GRID_INC,min_algor=MIN_ALGOR,mc_sim_num
>>> =MC_NUM,conv_loop=CONV_LOOP)
>>>   File "/home/crowlab/relax-4.0.2/auto_analyses/dauvergne_protocol.py",
>>> line 246, in __init__
>>> self.execute()
>>>   File "/home/crowlab/relax-4.0.2/auto_analyses/dauvergne_protocol.py",
>>> line 600, in execute
>>> self.multi_model(local_tm=True)
>>>   File "/home/crowlab/relax-4.0.2/auto_analyses/dauvergne_protocol.py",
>>> line 888, in multi_model
>>> self.interpreter.minimise.grid_search(inc=self.grid_inc)
>>>   File "/home/crowlab/relax-4.0.2/prompt/uf_objects.py", line 225, in
>>> __call__
>>> self._backend(*new_args, **uf_kargs)
>>>   File "/home/crowlab/relax-4.0.2/pipe_control/minimise.py", line 172,
>>> in grid_search
>>> model_lower, model_upper, model_inc = grid_setup(lower, upper, inc,
>>> verbosity=verbosity, skip_preset=skip_preset)
>>>   File "/home/crowlab/relax-4.0.2/pipe_control/minimise.py", line 341,
>>> in grid_setup
>>> elif values[i] in [None, {}, []]:
>>> IndexError: index out of bounds
>>>
>>> Which from my understanding basically means, the co-ordinates of the
>>> spins are out of the acceptable range for relax. I've checked all the
>>> co-ordinates for both, nothing is extreme or outlandish (all within a range
>>> of -20 to 20).
>>> Is relax unable to process pdb files that are dimers (with 2 sets A and
>>> B).? Furthermore, is it unable to process trimers and tetramers?
>>>
>>>

Re: Using multi-processor for model_free

2016-09-29 Thread Mahdi, Sam

Hi Troels,

I will upload a bug report with the pdb file, the script I use, and the
data I'm using.

Sincerely,
Sam

On Thu, Sep 29, 2016 at 2:25 PM, Troels Emtekær Linnet <
tlin...@nmr-relax.com> wrote:

> Hi Sam.
>
> Hm...
>
> I had a look in: pipe_control/minimise.py
>
> The trouble start with line
> "elif values[i] in [None, {}, []]:"
>
> Where the index "i" is running out of bounds.
>
> The index is drawn from range(n).
> n = len(names)
> names = api.get_param_names(model_info)
> values = api.get_param_values(model_info)
>
> So "something" is not aligned well in the data structures.
> It seems that the index of parameter names exceeds parameter values.
>
>
> One guess is, that the selection of
> * diff_model
> * mf_models
> * local_tm_models
>
> is not correctly set. But I reach my limit of being able to help you.
> Edward is the expert here, but he is on paternity leave.
>
>
> Another possibility is that some of the spins are in "select" mode, where
> they maybe should be in "deselect" mode.
>
> Maybe the spins do not carry any data from before, and somehow relax
> expect this.
>
> It's very tricky to figure out!
>
> A bug report, some minimum data, and a script which make the bug occur can
> solve this.
>
> Then I can write a systemtest, if it relax which is failing.
>
> Best
> Troels
>
>
>
>
> 2016-09-29 0:23 GMT+02:00 Mahdi, Sam :
>
>> Hi Troels,
>> Update on both proteins: So for protein 1, I can upload all the spins (H
>> and N), but then I recieve an error. This is the error I recieved for
>> protein 2 as well. These are both dimer pdb files. Meaning they have 2 sets
>> (set A) and set (B) (e.g. http://www.rcsb.org/pdb/explor
>> e/explore.do?structureId=1DJ8 this pdb protein has 4 sets, A,B,C, and D
>> ours only have A and B). For both these proteins I recieve this error
>>  File "/home/crowlab/relax-4.0.2/multi/processor.py", line 494, in run
>> self.callback.init_master(self)
>>   File "/home/crowlab/relax-4.0.2/multi/__init__.py", line 318, in
>> default_init_master
>> self.master.run()
>>   File "/home/crowlab/relax-4.0.2/relax.py", line 199, in run
>> self.interpreter.run(self.script_file)
>>   File "/home/crowlab/relax-4.0.2/prompt/interpreter.py", line 279, in
>> run
>> return run_script(intro=self.__intro_string, local=locals(),
>> script_file=script_file, show_script=self.__show_script,
>> raise_relax_error=self.__raise_relax_error)
>>   File "/home/crowlab/relax-4.0.2/prompt/interpreter.py", line 585, in
>> run_script
>> return console.interact(intro, local, script_file,
>> show_script=show_script, raise_relax_error=raise_relax_error)
>>   File "/home/crowlab/relax-4.0.2/prompt/interpreter.py", line 484, in
>> interact_script
>> exec_script(script_file, local)
>>   File "/home/crowlab/relax-4.0.2/prompt/interpreter.py", line 363, in
>> exec_script
>> runpy.run_module(module, globals)
>>   File "/usr/lib64/python2.7/runpy.py", line 180, in run_module
>> fname, loader, pkg_name)
>>   File "/usr/lib64/python2.7/runpy.py", line 72, in _run_code
>> exec code in run_globals
>>   File "/home/crowlab/relax-4.0.2/RGS4_modelfree_sample_script.py", line
>> 31, in 
>> dAuvergne_protocol(pipe_name=name,pipe_bundle=pipe_bundle,di
>> ff_model=DIFF_MODEL,mf_models=MF_MODELS,local_tm_models=LOCA
>> L_TM_MODELS,grid_inc=GRID_INC,min_algor=MIN_ALGOR,mc_sim_
>> num=MC_NUM,conv_loop=CONV_LOOP)
>>   File "/home/crowlab/relax-4.0.2/auto_analyses/dauvergne_protocol.py",
>> line 246, in __init__
>> self.execute()
>>   File "/home/crowlab/relax-4.0.2/auto_analyses/dauvergne_protocol.py",
>> line 600, in execute
>> self.multi_model(local_tm=True)
>>   File "/home/crowlab/relax-4.0.2/auto_analyses/dauvergne_protocol.py",
>> line 888, in multi_model
>> self.interpreter.minimise.grid_search(inc=self.grid_inc)
>>   File "/home/crowlab/relax-4.0.2/prompt/uf_objects.py", line 225, in
>> __call__
>> self._backend(*new_args, **uf_kargs)
>>   File "/home/crowlab/relax-4.0.2/pipe_control/minimise.py", line 172,
>> in grid_search
>> model_lower, model_upper, model_inc = grid_setup(lower, upper, inc,
>> verbosity=verbosity, skip_preset=skip_preset)
>>   File "/home/crowlab/relax-4.0.2/pipe_control/minimise.py", line 341,
>> in grid_setup
>> elif values[i] in [None, {}, []]:
>> IndexError: index out of bounds
>>
>> Which from my understanding basically means, the co-ordinates of the
>> spins are out of the acceptable range for relax. I've checked all the
>> co-ordinates for both, nothing is extreme or outlandish (all within a range
>> of -20 to 20).
>> Is relax unable to process pdb files that are dimers (with 2 sets A and
>> B).? Furthermore, is it unable to process trimers and tetramers?
>>
>> Sincerely,
>> Sam
>>
>> On Wed, Sep 28, 2016 at 1:44 PM, Mahdi, Sam 
>> wrote:
>>
>>> Hey Troels,
>>>
>>> I ran the relax -x and recieve this error at the GUI tests
>>> =
>>> = GUI tests =
>>>

Re: Using multi-processor for model_free

2016-09-29 Thread Troels Emtekær Linnet

Hi Sam.

Hm...

I had a look in: pipe_control/minimise.py

The trouble start with line
"elif values[i] in [None, {}, []]:"

Where the index "i" is running out of bounds.

The index is drawn from range(n).
n = len(names)
names = api.get_param_names(model_info)
values = api.get_param_values(model_info)

So "something" is not aligned well in the data structures.
It seems that the index of parameter names exceeds parameter values.


One guess is, that the selection of
* diff_model
* mf_models
* local_tm_models

is not correctly set. But I reach my limit of being able to help you.
Edward is the expert here, but he is on paternity leave.


Another possibility is that some of the spins are in "select" mode, where
they maybe should be in "deselect" mode.

Maybe the spins do not carry any data from before, and somehow relax expect
this.

It's very tricky to figure out!

A bug report, some minimum data, and a script which make the bug occur can
solve this.

Then I can write a systemtest, if it relax which is failing.

Best
Troels




2016-09-29 0:23 GMT+02:00 Mahdi, Sam :

> Hi Troels,
> Update on both proteins: So for protein 1, I can upload all the spins (H
> and N), but then I recieve an error. This is the error I recieved for
> protein 2 as well. These are both dimer pdb files. Meaning they have 2 sets
> (set A) and set (B) (e.g. http://www.rcsb.org/pdb/explor
> e/explore.do?structureId=1DJ8 this pdb protein has 4 sets, A,B,C, and D
> ours only have A and B). For both these proteins I recieve this error
>  File "/home/crowlab/relax-4.0.2/multi/processor.py", line 494, in run
> self.callback.init_master(self)
>   File "/home/crowlab/relax-4.0.2/multi/__init__.py", line 318, in
> default_init_master
> self.master.run()
>   File "/home/crowlab/relax-4.0.2/relax.py", line 199, in run
> self.interpreter.run(self.script_file)
>   File "/home/crowlab/relax-4.0.2/prompt/interpreter.py", line 279, in run
> return run_script(intro=self.__intro_string, local=locals(),
> script_file=script_file, show_script=self.__show_script,
> raise_relax_error=self.__raise_relax_error)
>   File "/home/crowlab/relax-4.0.2/prompt/interpreter.py", line 585, in
> run_script
> return console.interact(intro, local, script_file,
> show_script=show_script, raise_relax_error=raise_relax_error)
>   File "/home/crowlab/relax-4.0.2/prompt/interpreter.py", line 484, in
> interact_script
> exec_script(script_file, local)
>   File "/home/crowlab/relax-4.0.2/prompt/interpreter.py", line 363, in
> exec_script
> runpy.run_module(module, globals)
>   File "/usr/lib64/python2.7/runpy.py", line 180, in run_module
> fname, loader, pkg_name)
>   File "/usr/lib64/python2.7/runpy.py", line 72, in _run_code
> exec code in run_globals
>   File "/home/crowlab/relax-4.0.2/RGS4_modelfree_sample_script.py", line
> 31, in 
> dAuvergne_protocol(pipe_name=name,pipe_bundle=pipe_bundle,di
> ff_model=DIFF_MODEL,mf_models=MF_MODELS,local_tm_models=
> LOCAL_TM_MODELS,grid_inc=GRID_INC,min_algor=MIN_ALGOR,mc_
> sim_num=MC_NUM,conv_loop=CONV_LOOP)
>   File "/home/crowlab/relax-4.0.2/auto_analyses/dauvergne_protocol.py",
> line 246, in __init__
> self.execute()
>   File "/home/crowlab/relax-4.0.2/auto_analyses/dauvergne_protocol.py",
> line 600, in execute
> self.multi_model(local_tm=True)
>   File "/home/crowlab/relax-4.0.2/auto_analyses/dauvergne_protocol.py",
> line 888, in multi_model
> self.interpreter.minimise.grid_search(inc=self.grid_inc)
>   File "/home/crowlab/relax-4.0.2/prompt/uf_objects.py", line 225, in
> __call__
> self._backend(*new_args, **uf_kargs)
>   File "/home/crowlab/relax-4.0.2/pipe_control/minimise.py", line 172, in
> grid_search
> model_lower, model_upper, model_inc = grid_setup(lower, upper, inc,
> verbosity=verbosity, skip_preset=skip_preset)
>   File "/home/crowlab/relax-4.0.2/pipe_control/minimise.py", line 341, in
> grid_setup
> elif values[i] in [None, {}, []]:
> IndexError: index out of bounds
>
> Which from my understanding basically means, the co-ordinates of the spins
> are out of the acceptable range for relax. I've checked all the
> co-ordinates for both, nothing is extreme or outlandish (all within a range
> of -20 to 20).
> Is relax unable to process pdb files that are dimers (with 2 sets A and
> B).? Furthermore, is it unable to process trimers and tetramers?
>
> Sincerely,
> Sam
>
> On Wed, Sep 28, 2016 at 1:44 PM, Mahdi, Sam 
> wrote:
>
>> Hey Troels,
>>
>> I ran the relax -x and recieve this error at the GUI tests
>> =
>> = GUI tests =
>> =
>>
>> **
>> Gtk:ERROR:gtkfilesystemmodel.c:746:gtk_file_system_model_sort: assertion
>> failed: (r == n_visible_rows)
>> Abort (core dumped)
>> crowlab: [~/relax-4.0.2]>
>>
>>
>> On Wed, Sep 28, 2016 at 1:30 PM, Mahdi, Sam 
>> wrote:
>>
>>> Hi Troels,
>>>
>>> An update on protein number 1: I have successfully

Re: Using multi-processor for model_free

2016-09-29 Thread Troels Emtekær Linnet

Hi Sam.

Problems with the GUI do not necessary mean a problem.

It could be a problem of wxPython.
Which version do you have? (relax -i )

To find the specific tests that fails, can you do:
> relax --gui-tests --time -t gui_fail.txt

Best
Troels


2016-09-28 22:44 GMT+02:00 Mahdi, Sam :

> Hey Troels,
>
> I ran the relax -x and recieve this error at the GUI tests
> =
> = GUI tests =
> =
>
> **
> Gtk:ERROR:gtkfilesystemmodel.c:746:gtk_file_system_model_sort: assertion
> failed: (r == n_visible_rows)
> Abort (core dumped)
> crowlab: [~/relax-4.0.2]>
>
>
> On Wed, Sep 28, 2016 at 1:30 PM, Mahdi, Sam 
> wrote:
>
>> Hi Troels,
>>
>> An update on protein number 1: I have successfully resolved the problem.
>> Initially the pdb file had HN instead of just H for the backbone hydrogens.
>> So it couldn't read it. I changed all the HN to H. Then I recieved the
>> error
>> RelaxError: Multiple alternate location indicators are present in the PDB
>> file, but the desired coordinate set has not been specified
>> By removing the extra N, all the text for the 3D location (the
>> co-ordinates) for the HN were shifted a space (no longer aligned). Once I
>> aligned them all, relax was able to read all the spins. So its working now.
>> I'm currently running the test suite as well.
>>
>> Sincerely,
>> Sam
>>
>> On Wed, Sep 28, 2016 at 11:45 AM, Troels Emtekær Linnet <
>> tlin...@nmr-relax.com> wrote:
>>
>>> To test the speed difference between script and GUI,
>>> you could try to run the full test-suite through the terminal or
>>> inside the GUI.
>>>
>>> That should give you a clue about time difference.
>>>
>>>
>>> 2016-09-28 20:32 GMT+02:00 Troels Emtekær Linnet 
>>> :
>>>
 If you get different results, for the same setup, this is not good.
 Not at all !

 Have you run the full relax test suite after installation?

 http://wiki.nmr-relax.com/Installation_test

 run it with:
 relax -x

 This takes about 1 Hour to run, and should not be used with multiple
 processors.

 Relax will test itself with thousands of unit tests and system tests,
 and confer that all
 results are the same.

 If the system tests do not pass on each system, something fishy is
 going on.

 This is the best line of defence against "systems" acting weird due to
 software/packages etc. etc.

 Best
 Troels



 2016-09-28 9:44 GMT+02:00 Mahdi, Sam :

> Hi Troels,
>
> I wanted to give a bit of feedback on the results I've obtained
> throughout the few weeks I've been using model free on relax. First off,
> thank you guys (both you and Edward) immensly for your patience and help 
> as
> I attempted to understand and work relax. Secondly, I have noticed a
> difference between using the gui and the terminal (using scripts to run
> relax). I've currently finished about 3 runs using the gui, and 3 runs
> using the terminal (all the same data sets, same pdb files, same settings,
> etc.). The gui takes about a week to finish, where the terminal takes
> approximately 24 hours. I've tried this on 2 proteins, both had the same
> results. The terminal is by far, much faster than the gui. Finally, I've
> run 1 protein on 2 different computers (one using the multi-processor
> platform, and on another computer, single-processor). The data sets were
> all the same, the same pdb file, etc. , but the results I obtained from 
> the
> computers were slightly different. For the most part, most of the
> difference in the data was similar, slightly different, but within the
> error. But there were about 7 or 8 data points that appeared in one run on
> one computer, and were absent in another run on another computer. This
> happened in both the S^2 I analyzed and the Rex.
> I.e. On the fedora 20 (single processor), say I had S^2 values for
> amino acid 24,25 and 26 in the sequence, but not for 28,29, and 30. On the
> fedora 24 (multi-processor), I might be missing a value for amino acid 24,
> but I would have S^2 values for 28,29 and 30. Note the data sets are all
> the same, the pdb files the same, settings the same, I used the same 
> script
> for both. The only difference between these runs is they were run on
> different computer and one was single processor well another was multi.
> I don't know why I obtained different data from 2 different runs, when
> the input was all the same, just on different computers.
> However the S^2 values do make sense. The Rex values were incredibly
> small (1x10^-20), but there are some similarities (in terms of big Rex
> values) between the Rex I obtained from relax, and CPMG data analyzed by
> glove. So I have been able to obtain some

Re: Using multi-processor for model_free

2016-09-28 Thread Mahdi, Sam

Hey Troels,

I ran the relax -x and recieve this error at the GUI tests
=
= GUI tests =
=

**
Gtk:ERROR:gtkfilesystemmodel.c:746:gtk_file_system_model_sort: assertion
failed: (r == n_visible_rows)
Abort (core dumped)
crowlab: [~/relax-4.0.2]>

On Wed, Sep 28, 2016 at 1:30 PM, Mahdi, Sam 
wrote:

> Hi Troels,
>
> An update on protein number 1: I have successfully resolved the problem.
> Initially the pdb file had HN instead of just H for the backbone hydrogens.
> So it couldn't read it. I changed all the HN to H. Then I recieved the
> error
> RelaxError: Multiple alternate location indicators are present in the PDB
> file, but the desired coordinate set has not been specified
> By removing the extra N, all the text for the 3D location (the
> co-ordinates) for the HN were shifted a space (no longer aligned). Once I
> aligned them all, relax was able to read all the spins. So its working now.
> I'm currently running the test suite as well.
>
> Sincerely,
> Sam
>
> On Wed, Sep 28, 2016 at 11:45 AM, Troels Emtekær Linnet <
> tlin...@nmr-relax.com> wrote:
>
>> To test the speed difference between script and GUI,
>> you could try to run the full test-suite through the terminal or
>> inside the GUI.
>>
>> That should give you a clue about time difference.
>>
>>
>> 2016-09-28 20:32 GMT+02:00 Troels Emtekær Linnet :
>>
>>> If you get different results, for the same setup, this is not good.
>>> Not at all !
>>>
>>> Have you run the full relax test suite after installation?
>>>
>>> http://wiki.nmr-relax.com/Installation_test
>>>
>>> run it with:
>>> relax -x
>>>
>>> This takes about 1 Hour to run, and should not be used with multiple
>>> processors.
>>>
>>> Relax will test itself with thousands of unit tests and system tests,
>>> and confer that all
>>> results are the same.
>>>
>>> If the system tests do not pass on each system, something fishy is going
>>> on.
>>>
>>> This is the best line of defence against "systems" acting weird due to
>>> software/packages etc. etc.
>>>
>>> Best
>>> Troels
>>>
>>>
>>>
>>> 2016-09-28 9:44 GMT+02:00 Mahdi, Sam :
>>>
 Hi Troels,

 I wanted to give a bit of feedback on the results I've obtained
 throughout the few weeks I've been using model free on relax. First off,
 thank you guys (both you and Edward) immensly for your patience and help as
 I attempted to understand and work relax. Secondly, I have noticed a
 difference between using the gui and the terminal (using scripts to run
 relax). I've currently finished about 3 runs using the gui, and 3 runs
 using the terminal (all the same data sets, same pdb files, same settings,
 etc.). The gui takes about a week to finish, where the terminal takes
 approximately 24 hours. I've tried this on 2 proteins, both had the same
 results. The terminal is by far, much faster than the gui. Finally, I've
 run 1 protein on 2 different computers (one using the multi-processor
 platform, and on another computer, single-processor). The data sets were
 all the same, the same pdb file, etc. , but the results I obtained from the
 computers were slightly different. For the most part, most of the
 difference in the data was similar, slightly different, but within the
 error. But there were about 7 or 8 data points that appeared in one run on
 one computer, and were absent in another run on another computer. This
 happened in both the S^2 I analyzed and the Rex.
 I.e. On the fedora 20 (single processor), say I had S^2 values for
 amino acid 24,25 and 26 in the sequence, but not for 28,29, and 30. On the
 fedora 24 (multi-processor), I might be missing a value for amino acid 24,
 but I would have S^2 values for 28,29 and 30. Note the data sets are all
 the same, the pdb files the same, settings the same, I used the same script
 for both. The only difference between these runs is they were run on
 different computer and one was single processor well another was multi.
 I don't know why I obtained different data from 2 different runs, when
 the input was all the same, just on different computers.
 However the S^2 values do make sense. The Rex values were incredibly
 small (1x10^-20), but there are some similarities (in terms of big Rex
 values) between the Rex I obtained from relax, and CPMG data analyzed by
 glove. So I have been able to obtain some reasonable data and results from
 model_free using relax.

 Sincerely,
 Sam

 On Mon, Sep 26, 2016 at 2:59 PM, Mahdi, Sam 
 wrote:

> Hi Troels,
>
>
> I have attempted the fix for running on a multi-processor platform by
> creating the script you told me too, and I still got the same result. I
> have uploaded a screenshot that shows again, relax is running in the

Re: Using multi-processor for model_free

2016-09-28 Thread Mahdi, Sam

Hi Troels,

An update on protein number 1: I have successfully resolved the problem.
Initially the pdb file had HN instead of just H for the backbone hydrogens.
So it couldn't read it. I changed all the HN to H. Then I recieved the
error
RelaxError: Multiple alternate location indicators are present in the PDB
file, but the desired coordinate set has not been specified
By removing the extra N, all the text for the 3D location (the
co-ordinates) for the HN were shifted a space (no longer aligned). Once I
aligned them all, relax was able to read all the spins. So its working now.
I'm currently running the test suite as well.

Sincerely,
Sam

On Wed, Sep 28, 2016 at 11:45 AM, Troels Emtekær Linnet <
tlin...@nmr-relax.com> wrote:

> To test the speed difference between script and GUI,
> you could try to run the full test-suite through the terminal or
> inside the GUI.
>
> That should give you a clue about time difference.
>
>
> 2016-09-28 20:32 GMT+02:00 Troels Emtekær Linnet :
>
>> If you get different results, for the same setup, this is not good.
>> Not at all !
>>
>> Have you run the full relax test suite after installation?
>>
>> http://wiki.nmr-relax.com/Installation_test
>>
>> run it with:
>> relax -x
>>
>> This takes about 1 Hour to run, and should not be used with multiple
>> processors.
>>
>> Relax will test itself with thousands of unit tests and system tests, and
>> confer that all
>> results are the same.
>>
>> If the system tests do not pass on each system, something fishy is going
>> on.
>>
>> This is the best line of defence against "systems" acting weird due to
>> software/packages etc. etc.
>>
>> Best
>> Troels
>>
>>
>>
>> 2016-09-28 9:44 GMT+02:00 Mahdi, Sam :
>>
>>> Hi Troels,
>>>
>>> I wanted to give a bit of feedback on the results I've obtained
>>> throughout the few weeks I've been using model free on relax. First off,
>>> thank you guys (both you and Edward) immensly for your patience and help as
>>> I attempted to understand and work relax. Secondly, I have noticed a
>>> difference between using the gui and the terminal (using scripts to run
>>> relax). I've currently finished about 3 runs using the gui, and 3 runs
>>> using the terminal (all the same data sets, same pdb files, same settings,
>>> etc.). The gui takes about a week to finish, where the terminal takes
>>> approximately 24 hours. I've tried this on 2 proteins, both had the same
>>> results. The terminal is by far, much faster than the gui. Finally, I've
>>> run 1 protein on 2 different computers (one using the multi-processor
>>> platform, and on another computer, single-processor). The data sets were
>>> all the same, the same pdb file, etc. , but the results I obtained from the
>>> computers were slightly different. For the most part, most of the
>>> difference in the data was similar, slightly different, but within the
>>> error. But there were about 7 or 8 data points that appeared in one run on
>>> one computer, and were absent in another run on another computer. This
>>> happened in both the S^2 I analyzed and the Rex.
>>> I.e. On the fedora 20 (single processor), say I had S^2 values for amino
>>> acid 24,25 and 26 in the sequence, but not for 28,29, and 30. On the fedora
>>> 24 (multi-processor), I might be missing a value for amino acid 24, but I
>>> would have S^2 values for 28,29 and 30. Note the data sets are all the
>>> same, the pdb files the same, settings the same, I used the same script for
>>> both. The only difference between these runs is they were run on different
>>> computer and one was single processor well another was multi.
>>> I don't know why I obtained different data from 2 different runs, when
>>> the input was all the same, just on different computers.
>>> However the S^2 values do make sense. The Rex values were incredibly
>>> small (1x10^-20), but there are some similarities (in terms of big Rex
>>> values) between the Rex I obtained from relax, and CPMG data analyzed by
>>> glove. So I have been able to obtain some reasonable data and results from
>>> model_free using relax.
>>>
>>> Sincerely,
>>> Sam
>>>
>>>
>>>
>>> On Mon, Sep 26, 2016 at 2:59 PM, Mahdi, Sam 
>>> wrote:
>>>
 Hi Troels,


 I have attempted the fix for running on a multi-processor platform by
 creating the script you told me too, and I still got the same result. I
 have uploaded a screenshot that shows again, relax is running in the
 background, but there is no output for relax, nor can I input any commands.
 The only output I recieve is this:
 Running relax with NP=$NPROC+8|bc in multi-processor mode

 And any command I type in after that gets no response.

 I've also checked the spins via script. For 2 scenarios. Scenario 1-
 All hydrogens are kept as HN and Scenario 2- I change all the HN spins to
 H.
 The output from Scenario one is, it read all the Nitrogen spins

Re: Using multi-processor for model_free

2016-09-28 Thread Troels Emtekær Linnet

To test the speed difference between script and GUI,
you could try to run the full test-suite through the terminal or
inside the GUI.

That should give you a clue about time difference.


2016-09-28 20:32 GMT+02:00 Troels Emtekær Linnet :

> If you get different results, for the same setup, this is not good.
> Not at all !
>
> Have you run the full relax test suite after installation?
>
> http://wiki.nmr-relax.com/Installation_test
>
> run it with:
> relax -x
>
> This takes about 1 Hour to run, and should not be used with multiple
> processors.
>
> Relax will test itself with thousands of unit tests and system tests, and
> confer that all
> results are the same.
>
> If the system tests do not pass on each system, something fishy is going
> on.
>
> This is the best line of defence against "systems" acting weird due to
> software/packages etc. etc.
>
> Best
> Troels
>
>
>
> 2016-09-28 9:44 GMT+02:00 Mahdi, Sam :
>
>> Hi Troels,
>>
>> I wanted to give a bit of feedback on the results I've obtained
>> throughout the few weeks I've been using model free on relax. First off,
>> thank you guys (both you and Edward) immensly for your patience and help as
>> I attempted to understand and work relax. Secondly, I have noticed a
>> difference between using the gui and the terminal (using scripts to run
>> relax). I've currently finished about 3 runs using the gui, and 3 runs
>> using the terminal (all the same data sets, same pdb files, same settings,
>> etc.). The gui takes about a week to finish, where the terminal takes
>> approximately 24 hours. I've tried this on 2 proteins, both had the same
>> results. The terminal is by far, much faster than the gui. Finally, I've
>> run 1 protein on 2 different computers (one using the multi-processor
>> platform, and on another computer, single-processor). The data sets were
>> all the same, the same pdb file, etc. , but the results I obtained from the
>> computers were slightly different. For the most part, most of the
>> difference in the data was similar, slightly different, but within the
>> error. But there were about 7 or 8 data points that appeared in one run on
>> one computer, and were absent in another run on another computer. This
>> happened in both the S^2 I analyzed and the Rex.
>> I.e. On the fedora 20 (single processor), say I had S^2 values for amino
>> acid 24,25 and 26 in the sequence, but not for 28,29, and 30. On the fedora
>> 24 (multi-processor), I might be missing a value for amino acid 24, but I
>> would have S^2 values for 28,29 and 30. Note the data sets are all the
>> same, the pdb files the same, settings the same, I used the same script for
>> both. The only difference between these runs is they were run on different
>> computer and one was single processor well another was multi.
>> I don't know why I obtained different data from 2 different runs, when
>> the input was all the same, just on different computers.
>> However the S^2 values do make sense. The Rex values were incredibly
>> small (1x10^-20), but there are some similarities (in terms of big Rex
>> values) between the Rex I obtained from relax, and CPMG data analyzed by
>> glove. So I have been able to obtain some reasonable data and results from
>> model_free using relax.
>>
>> Sincerely,
>> Sam
>>
>>
>>
>> On Mon, Sep 26, 2016 at 2:59 PM, Mahdi, Sam 
>> wrote:
>>
>>> Hi Troels,
>>>
>>>
>>> I have attempted the fix for running on a multi-processor platform by
>>> creating the script you told me too, and I still got the same result. I
>>> have uploaded a screenshot that shows again, relax is running in the
>>> background, but there is no output for relax, nor can I input any commands.
>>> The only output I recieve is this:
>>> Running relax with NP=$NPROC+8|bc in multi-processor mode
>>>
>>> And any command I type in after that gets no response.
>>>
>>> I've also checked the spins via script. For 2 scenarios. Scenario 1- All
>>> hydrogens are kept as HN and Scenario 2- I change all the HN spins to H.
>>> The output from Scenario one is, it read all the Nitrogen spins
>>> accordingly :
>>> Objects:
>>>   element: 'N'
>>>   isotope: '15N'
>>>   name: 'N'
>>>   num: 1304
>>>   pos: array([ 13.196,  15.218,
>>> 3.192])
>>>   select: True
>>>  hRGS4 178 THR #hRGS4:178@1304
>>> Class containing all the spin system specific data.
>>>
>>>
>>> Objects:
>>>   element: 'N'
>>>   isotope: '15N'
>>>   name: 'N'
>>>   num: 2617
>>>   pos: array([ 22.6960002,  10.683,
>>> -4.15 ])
>>>   select: True
>>>  hRGS4 178 THR #hRGS4:178@2617
>>>
>>> But no hydrogens.
>>>
>>> Scenario 2-  I still recieve the same error.
>>> RelaxError: Multiple alternate location indicators are present in the
>>> PDB file, but the desired coordinate set has not been specified.
>>>
>>> Sincerely,
>>> Sam
>>>
>>> On Mon, Sep 26, 2016 at 2:19 PM, Mahdi, Sam

Re: Using multi-processor for model_free

2016-09-28 Thread Troels Emtekær Linnet

If you get different results, for the same setup, this is not good.
Not at all !

Have you run the full relax test suite after installation?

http://wiki.nmr-relax.com/Installation_test

run it with:
relax -x

This takes about 1 Hour to run, and should not be used with multiple
processors.

Relax will test itself with thousands of unit tests and system tests, and
confer that all
results are the same.

If the system tests do not pass on each system, something fishy is going on.

This is the best line of defence against "systems" acting weird due to
software/packages etc. etc.

Best
Troels



2016-09-28 9:44 GMT+02:00 Mahdi, Sam :

> Hi Troels,
>
> I wanted to give a bit of feedback on the results I've obtained throughout
> the few weeks I've been using model free on relax. First off, thank you
> guys (both you and Edward) immensly for your patience and help as I
> attempted to understand and work relax. Secondly, I have noticed a
> difference between using the gui and the terminal (using scripts to run
> relax). I've currently finished about 3 runs using the gui, and 3 runs
> using the terminal (all the same data sets, same pdb files, same settings,
> etc.). The gui takes about a week to finish, where the terminal takes
> approximately 24 hours. I've tried this on 2 proteins, both had the same
> results. The terminal is by far, much faster than the gui. Finally, I've
> run 1 protein on 2 different computers (one using the multi-processor
> platform, and on another computer, single-processor). The data sets were
> all the same, the same pdb file, etc. , but the results I obtained from the
> computers were slightly different. For the most part, most of the
> difference in the data was similar, slightly different, but within the
> error. But there were about 7 or 8 data points that appeared in one run on
> one computer, and were absent in another run on another computer. This
> happened in both the S^2 I analyzed and the Rex.
> I.e. On the fedora 20 (single processor), say I had S^2 values for amino
> acid 24,25 and 26 in the sequence, but not for 28,29, and 30. On the fedora
> 24 (multi-processor), I might be missing a value for amino acid 24, but I
> would have S^2 values for 28,29 and 30. Note the data sets are all the
> same, the pdb files the same, settings the same, I used the same script for
> both. The only difference between these runs is they were run on different
> computer and one was single processor well another was multi.
> I don't know why I obtained different data from 2 different runs, when the
> input was all the same, just on different computers.
> However the S^2 values do make sense. The Rex values were incredibly small
> (1x10^-20), but there are some similarities (in terms of big Rex values)
> between the Rex I obtained from relax, and CPMG data analyzed by glove. So
> I have been able to obtain some reasonable data and results from model_free
> using relax.
>
> Sincerely,
> Sam
>
>
>
> On Mon, Sep 26, 2016 at 2:59 PM, Mahdi, Sam 
> wrote:
>
>> Hi Troels,
>>
>>
>> I have attempted the fix for running on a multi-processor platform by
>> creating the script you told me too, and I still got the same result. I
>> have uploaded a screenshot that shows again, relax is running in the
>> background, but there is no output for relax, nor can I input any commands.
>> The only output I recieve is this:
>> Running relax with NP=$NPROC+8|bc in multi-processor mode
>>
>> And any command I type in after that gets no response.
>>
>> I've also checked the spins via script. For 2 scenarios. Scenario 1- All
>> hydrogens are kept as HN and Scenario 2- I change all the HN spins to H.
>> The output from Scenario one is, it read all the Nitrogen spins
>> accordingly :
>> Objects:
>>   element: 'N'
>>   isotope: '15N'
>>   name: 'N'
>>   num: 1304
>>   pos: array([ 13.196,  15.218,
>> 3.192])
>>   select: True
>>  hRGS4 178 THR #hRGS4:178@1304
>> Class containing all the spin system specific data.
>>
>>
>> Objects:
>>   element: 'N'
>>   isotope: '15N'
>>   name: 'N'
>>   num: 2617
>>   pos: array([ 22.6960002,  10.683,
>> -4.15 ])
>>   select: True
>>  hRGS4 178 THR #hRGS4:178@2617
>>
>> But no hydrogens.
>>
>> Scenario 2-  I still recieve the same error.
>> RelaxError: Multiple alternate location indicators are present in the PDB
>> file, but the desired coordinate set has not been specified.
>>
>> Sincerely,
>> Sam
>>
>> On Mon, Sep 26, 2016 at 2:19 PM, Mahdi, Sam 
>> wrote:
>>
>>> Hi Troels,
>>>
>>> I have attempted the fix for running on a multi-processor platform by
>>> creating the script you told me too, and I still got the same result. I
>>> have uploaded a screenshot that shows again, relax is running in the
>>> background, but there is no output for relax, nor can I input any commands.
>>> The only output I recieve is this:
>>> Running relax with

Re: Using multi-processor for model_free

2016-09-28 Thread Troels Emtekær Linnet

Another possibility for the "slowness" is "the very well known" that,
printing to screen makes
python slow.

Extremely slow...

And all the minimization information to screen actually slow downs relax
(through python).

For even faster calculations, just "log" the relax output with -l, and do
not "tee" -t and print to screen.
Try skipping all printing to screen.

You lose the ability to follow the process live, but you win in speed !

A possible explanation for the slow GUI, is that printing to screen through
the GUI is a terrible process.
Try to imagine how many "computer layers" the "text" has to travel through,
to arrive in the "GUI screen".
The worst is, it is almost impossible to "really" test.







2016-09-28 9:44 GMT+02:00 Mahdi, Sam :

> Hi Troels,
>
> I wanted to give a bit of feedback on the results I've obtained throughout
> the few weeks I've been using model free on relax. First off, thank you
> guys (both you and Edward) immensly for your patience and help as I
> attempted to understand and work relax. Secondly, I have noticed a
> difference between using the gui and the terminal (using scripts to run
> relax). I've currently finished about 3 runs using the gui, and 3 runs
> using the terminal (all the same data sets, same pdb files, same settings,
> etc.). The gui takes about a week to finish, where the terminal takes
> approximately 24 hours. I've tried this on 2 proteins, both had the same
> results. The terminal is by far, much faster than the gui. Finally, I've
> run 1 protein on 2 different computers (one using the multi-processor
> platform, and on another computer, single-processor). The data sets were
> all the same, the same pdb file, etc. , but the results I obtained from the
> computers were slightly different. For the most part, most of the
> difference in the data was similar, slightly different, but within the
> error. But there were about 7 or 8 data points that appeared in one run on
> one computer, and were absent in another run on another computer. This
> happened in both the S^2 I analyzed and the Rex.
> I.e. On the fedora 20 (single processor), say I had S^2 values for amino
> acid 24,25 and 26 in the sequence, but not for 28,29, and 30. On the fedora
> 24 (multi-processor), I might be missing a value for amino acid 24, but I
> would have S^2 values for 28,29 and 30. Note the data sets are all the
> same, the pdb files the same, settings the same, I used the same script for
> both. The only difference between these runs is they were run on different
> computer and one was single processor well another was multi.
> I don't know why I obtained different data from 2 different runs, when the
> input was all the same, just on different computers.
> However the S^2 values do make sense. The Rex values were incredibly small
> (1x10^-20), but there are some similarities (in terms of big Rex values)
> between the Rex I obtained from relax, and CPMG data analyzed by glove. So
> I have been able to obtain some reasonable data and results from model_free
> using relax.
>
> Sincerely,
> Sam
>
>
>
> On Mon, Sep 26, 2016 at 2:59 PM, Mahdi, Sam 
> wrote:
>
>> Hi Troels,
>>
>>
>> I have attempted the fix for running on a multi-processor platform by
>> creating the script you told me too, and I still got the same result. I
>> have uploaded a screenshot that shows again, relax is running in the
>> background, but there is no output for relax, nor can I input any commands.
>> The only output I recieve is this:
>> Running relax with NP=$NPROC+8|bc in multi-processor mode
>>
>> And any command I type in after that gets no response.
>>
>> I've also checked the spins via script. For 2 scenarios. Scenario 1- All
>> hydrogens are kept as HN and Scenario 2- I change all the HN spins to H.
>> The output from Scenario one is, it read all the Nitrogen spins
>> accordingly :
>> Objects:
>>   element: 'N'
>>   isotope: '15N'
>>   name: 'N'
>>   num: 1304
>>   pos: array([ 13.196,  15.218,
>> 3.192])
>>   select: True
>>  hRGS4 178 THR #hRGS4:178@1304
>> Class containing all the spin system specific data.
>>
>>
>> Objects:
>>   element: 'N'
>>   isotope: '15N'
>>   name: 'N'
>>   num: 2617
>>   pos: array([ 22.6960002,  10.683,
>> -4.15 ])
>>   select: True
>>  hRGS4 178 THR #hRGS4:178@2617
>>
>> But no hydrogens.
>>
>> Scenario 2-  I still recieve the same error.
>> RelaxError: Multiple alternate location indicators are present in the PDB
>> file, but the desired coordinate set has not been specified.
>>
>> Sincerely,
>> Sam
>>
>> On Mon, Sep 26, 2016 at 2:19 PM, Mahdi, Sam 
>> wrote:
>>
>>> Hi Troels,
>>>
>>> I have attempted the fix for running on a multi-processor platform by
>>> creating the script you told me too, and I still got the same result. I
>>> have uploaded a screenshot that shows again, relax is running in the
>>> background, but there is

Re: Using multi-processor for model_free

2016-09-28 Thread Troels Emtekær Linnet

Hi Sam.

Thank you for your valuable feedback!
It makes it more fun to help :)

Can you check if this is not in your script :
http://wiki.nmr-relax.com/Tutorial_for_model-free_analysis_sam_mahdi#Let_us_try_to_execute

# Execution.
 # Change some opt params.# COMMENT THESE OUT FOR REAL CALCULATION.
THIS IS ONLY TO SPEED UP THE PROCESS IN ERROR SEARCHING.
dAuvergne_protocol.opt_func_tol = 1e-5
dAuvergne_protocol.opt_max_iterations = 1000



Best Troels


Den onsdag den 28. september 2016 skrev Mahdi, Sam <
sam.mahdi@my.csun.edu>:

> Hi Troels,
>
> I wanted to give a bit of feedback on the results I've obtained throughout
> the few weeks I've been using model free on relax. First off, thank you
> guys (both you and Edward) immensly for your patience and help as I
> attempted to understand and work relax. Secondly, I have noticed a
> difference between using the gui and the terminal (using scripts to run
> relax). I've currently finished about 3 runs using the gui, and 3 runs
> using the terminal (all the same data sets, same pdb files, same settings,
> etc.). The gui takes about a week to finish, where the terminal takes
> approximately 24 hours. I've tried this on 2 proteins, both had the same
> results. The terminal is by far, much faster than the gui. Finally, I've
> run 1 protein on 2 different computers (one using the multi-processor
> platform, and on another computer, single-processor). The data sets were
> all the same, the same pdb file, etc. , but the results I obtained from the
> computers were slightly different. For the most part, most of the
> difference in the data was similar, slightly different, but within the
> error. But there were about 7 or 8 data points that appeared in one run on
> one computer, and were absent in another run on another computer. This
> happened in both the S^2 I analyzed and the Rex.
> I.e. On the fedora 20 (single processor), say I had S^2 values for amino
> acid 24,25 and 26 in the sequence, but not for 28,29, and 30. On the fedora
> 24 (multi-processor), I might be missing a value for amino acid 24, but I
> would have S^2 values for 28,29 and 30. Note the data sets are all the
> same, the pdb files the same, settings the same, I used the same script for
> both. The only difference between these runs is they were run on different
> computer and one was single processor well another was multi.
> I don't know why I obtained different data from 2 different runs, when the
> input was all the same, just on different computers.
> However the S^2 values do make sense. The Rex values were incredibly small
> (1x10^-20), but there are some similarities (in terms of big Rex values)
> between the Rex I obtained from relax, and CPMG data analyzed by glove. So
> I have been able to obtain some reasonable data and results from model_free
> using relax.
>
> Sincerely,
> Sam
>
>
>
> On Mon, Sep 26, 2016 at 2:59 PM, Mahdi, Sam  > wrote:
>
>> Hi Troels,
>>
>>
>> I have attempted the fix for running on a multi-processor platform by
>> creating the script you told me too, and I still got the same result. I
>> have uploaded a screenshot that shows again, relax is running in the
>> background, but there is no output for relax, nor can I input any commands.
>> The only output I recieve is this:
>> Running relax with NP=$NPROC+8|bc in multi-processor mode
>>
>> And any command I type in after that gets no response.
>>
>> I've also checked the spins via script. For 2 scenarios. Scenario 1- All
>> hydrogens are kept as HN and Scenario 2- I change all the HN spins to H.
>> The output from Scenario one is, it read all the Nitrogen spins
>> accordingly :
>> Objects:
>>   element: 'N'
>>   isotope: '15N'
>>   name: 'N'
>>   num: 1304
>>   pos: array([ 13.196,  15.218,
>> 3.192])
>>   select: True
>>  hRGS4 178 THR #hRGS4:178@1304
>> Class containing all the spin system specific data.
>>
>>
>> Objects:
>>   element: 'N'
>>   isotope: '15N'
>>   name: 'N'
>>   num: 2617
>>   pos: array([ 22.6960002,  10.683,
>> -4.15 ])
>>   select: True
>>  hRGS4 178 THR #hRGS4:178@2617
>>
>> But no hydrogens.
>>
>> Scenario 2-  I still recieve the same error.
>> RelaxError: Multiple alternate location indicators are present in the PDB
>> file, but the desired coordinate set has not been specified.
>>
>> Sincerely,
>> Sam
>>
>> On Mon, Sep 26, 2016 at 2:19 PM, Mahdi, Sam > > wrote:
>>
>>> Hi Troels,
>>>
>>> I have attempted the fix for running on a multi-processor platform by
>>> creating the script you told me too, and I still got the same result. I
>>> have uploaded a screenshot that shows again, relax is running in the
>>> background, but there is no output for relax, nor can I input any commands.
>>> The only output I recieve is this:
>>> Running relax with

Re: Using multi-processor for model_free

2016-09-28 Thread Mahdi, Sam

Hi Troels,

I wanted to give a bit of feedback on the results I've obtained throughout
the few weeks I've been using model free on relax. First off, thank you
guys (both you and Edward) immensly for your patience and help as I
attempted to understand and work relax. Secondly, I have noticed a
difference between using the gui and the terminal (using scripts to run
relax). I've currently finished about 3 runs using the gui, and 3 runs
using the terminal (all the same data sets, same pdb files, same settings,
etc.). The gui takes about a week to finish, where the terminal takes
approximately 24 hours. I've tried this on 2 proteins, both had the same
results. The terminal is by far, much faster than the gui. Finally, I've
run 1 protein on 2 different computers (one using the multi-processor
platform, and on another computer, single-processor). The data sets were
all the same, the same pdb file, etc. , but the results I obtained from the
computers were slightly different. For the most part, most of the
difference in the data was similar, slightly different, but within the
error. But there were about 7 or 8 data points that appeared in one run on
one computer, and were absent in another run on another computer. This
happened in both the S^2 I analyzed and the Rex.
I.e. On the fedora 20 (single processor), say I had S^2 values for amino
acid 24,25 and 26 in the sequence, but not for 28,29, and 30. On the fedora
24 (multi-processor), I might be missing a value for amino acid 24, but I
would have S^2 values for 28,29 and 30. Note the data sets are all the
same, the pdb files the same, settings the same, I used the same script for
both. The only difference between these runs is they were run on different
computer and one was single processor well another was multi.
I don't know why I obtained different data from 2 different runs, when the
input was all the same, just on different computers.
However the S^2 values do make sense. The Rex values were incredibly small
(1x10^-20), but there are some similarities (in terms of big Rex values)
between the Rex I obtained from relax, and CPMG data analyzed by glove. So
I have been able to obtain some reasonable data and results from model_free
using relax.

Sincerely,
Sam

On Mon, Sep 26, 2016 at 2:59 PM, Mahdi, Sam 
wrote:

> Hi Troels,
>
>
> I have attempted the fix for running on a multi-processor platform by
> creating the script you told me too, and I still got the same result. I
> have uploaded a screenshot that shows again, relax is running in the
> background, but there is no output for relax, nor can I input any commands.
> The only output I recieve is this:
> Running relax with NP=$NPROC+8|bc in multi-processor mode
>
> And any command I type in after that gets no response.
>
> I've also checked the spins via script. For 2 scenarios. Scenario 1- All
> hydrogens are kept as HN and Scenario 2- I change all the HN spins to H.
> The output from Scenario one is, it read all the Nitrogen spins
> accordingly :
> Objects:
>   element: 'N'
>   isotope: '15N'
>   name: 'N'
>   num: 1304
>   pos: array([ 13.196,  15.218,   3.192
> ])
>   select: True
>  hRGS4 178 THR #hRGS4:178@1304
> Class containing all the spin system specific data.
>
>
> Objects:
>   element: 'N'
>   isotope: '15N'
>   name: 'N'
>   num: 2617
>   pos: array([ 22.6960002,  10.683,  -4.15
> ])
>   select: True
>  hRGS4 178 THR #hRGS4:178@2617
>
> But no hydrogens.
>
> Scenario 2-  I still recieve the same error.
> RelaxError: Multiple alternate location indicators are present in the PDB
> file, but the desired coordinate set has not been specified.
>
> Sincerely,
> Sam
>
> On Mon, Sep 26, 2016 at 2:19 PM, Mahdi, Sam 
> wrote:
>
>> Hi Troels,
>>
>> I have attempted the fix for running on a multi-processor platform by
>> creating the script you told me too, and I still got the same result. I
>> have uploaded a screenshot that shows again, relax is running in the
>> background, but there is no output for relax, nor can I input any commands.
>> The only output I recieve is this:
>> Running relax with NP=$NPROC+8|bc in multi-processor mode
>>
>> And any command I type in after that gets no response.
>>
>> Sincerely,
>> Sam
>>
>>
>> On Sun, Sep 25, 2016 at 6:43 AM, Troels Emtekær Linnet <
>> tlin...@nmr-relax.com> wrote:
>>
>>> Hi Sam.
>>>
>>> Try to load the pdb file and make a spin_loop over the information.
>>> How does the information look like?
>>> http://wiki.nmr-relax.com/Tutorial_for_model-free_analysis_s
>>> am_mahdi#Check_the_spin_containers_via_script
>>>
>>> Regarding the multiprocessor on your Fedora 20 machine, try to have a
>>> look at the bug.
>>> https://gna.org/bugs/?25084
>>>
>>> -
>>> I suspect there is a mismatch between two installations of relax.
>>> One version of 2.x and one local of 4.x.
>>> Try adding the full path to relax
>>> -
>>>
>>> Try make a run script like this and copy it

Re: Using multi-processor for model_free

2016-09-26 Thread Mahdi, Sam

Hi Troels,


I have attempted the fix for running on a multi-processor platform by
creating the script you told me too, and I still got the same result. I
have uploaded a screenshot that shows again, relax is running in the
background, but there is no output for relax, nor can I input any commands.
The only output I recieve is this:
Running relax with NP=$NPROC+8|bc in multi-processor mode

And any command I type in after that gets no response.

I've also checked the spins via script. For 2 scenarios. Scenario 1- All
hydrogens are kept as HN and Scenario 2- I change all the HN spins to H.
The output from Scenario one is, it read all the Nitrogen spins accordingly
:
Objects:
  element: 'N'
  isotope: '15N'
  name: 'N'
  num: 1304
  pos: array([ 13.196,  15.218,   3.192
])
  select: True
 hRGS4 178 THR #hRGS4:178@1304
Class containing all the spin system specific data.


Objects:
  element: 'N'
  isotope: '15N'
  name: 'N'
  num: 2617
  pos: array([ 22.6960002,  10.683,  -4.15
])
  select: True
 hRGS4 178 THR #hRGS4:178@2617

But no hydrogens.

Scenario 2-  I still recieve the same error.
RelaxError: Multiple alternate location indicators are present in the PDB
file, but the desired coordinate set has not been specified.

Sincerely,
Sam

On Mon, Sep 26, 2016 at 2:19 PM, Mahdi, Sam 
wrote:

> Hi Troels,
>
> I have attempted the fix for running on a multi-processor platform by
> creating the script you told me too, and I still got the same result. I
> have uploaded a screenshot that shows again, relax is running in the
> background, but there is no output for relax, nor can I input any commands.
> The only output I recieve is this:
> Running relax with NP=$NPROC+8|bc in multi-processor mode
>
> And any command I type in after that gets no response.
>
> Sincerely,
> Sam
>
>
> On Sun, Sep 25, 2016 at 6:43 AM, Troels Emtekær Linnet <
> tlin...@nmr-relax.com> wrote:
>
>> Hi Sam.
>>
>> Try to load the pdb file and make a spin_loop over the information.
>> How does the information look like?
>> http://wiki.nmr-relax.com/Tutorial_for_model-free_analysis_
>> sam_mahdi#Check_the_spin_containers_via_script
>>
>> Regarding the multiprocessor on your Fedora 20 machine, try to have a
>> look at the bug.
>> https://gna.org/bugs/?25084
>>
>> -
>> I suspect there is a mismatch between two installations of relax.
>> One version of 2.x and one local of 4.x.
>> Try adding the full path to relax
>> -
>>
>> Try make a run script like this and copy it some where to your PATH
>> myrelax
>> --
>>
>> #!/bin/tcsh -fe
>>
>> # Set the relax version used for this script.
>> set RELAX=/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/relax
>>
>> # Set number of available CPUs.
>> set NPROC=`nproc`
>> set NP=`echo $NPROC + 0 | bc `
>> echo "Running relax with NP=$NP in multi-processor mode"
>>
>> # Run relax in multi processor mode.
>> mpirun -np $NP $RELAX --multi='mpi4py' $argv
>>
>> 2016-09-24 1:03 GMT+02:00 Mahdi, Sam :
>>
>>> Hi Troels,
>>>
>>> Update on Protein number 1: So I was able to successfully run model free
>>> with no problems on my protein (I don't know why it was giving problems
>>> before). The reason it may have been giving issues though is the protein I
>>> am working with forms a dimer at the concentrations we work with (thus the
>>> results I have are for the Dimer form of the protein). The pdb file though
>>> only has a monomer structure though. I have been able to obtain the dimer
>>> pdb file using HADDOCK (docking program), but have come across a few
>>> problems uploading the pdb file.
>>> The initial problem was that all the hydrogens attached to the nitrogen
>>> were HN labeled on the HADDOCK modified pdb file, and model free could not
>>> understand what HN meant, and I would recieve this warning.
>>> RelaxWarning: Cannot determine the element associated with atom 'HN'.
>>>
>>> I could however load up all the Nitrogen, but naturally, with no
>>> hydrogens, it wouldn't be able to calculate any bond vectors between
>>> nitrogen and hydrogen. So I would recieve this error and the program would
>>> close
>>> RelaxError: The spin ID '@H' matches no spins.
>>>
>>> To fix this, I changed all the HN spins, to just H, but then recieved
>>> another error.
>>> RelaxError: Multiple alternate location indicators are present in the
>>> PDB file, but the desired coordinates set has not been specified.
>>>
>>> I don't exactly understand what this error means. Is it saying the
>>> program can't locate the 3D coordinates for the Hydrogen and Nitrogen? If
>>> that is the case, why was it able to before, when it couldn't read any of
>>> the Hydrogen spins. I'm just confused a bit as to what this error means.
>>>
>>> Sincerely,
>>> Sam
>>>
>>> On Wed, Sep 21, 2016 at 3:18 PM, Mahdi, Sam 
>>> wrote:
>>>
 Hi Troels,

 Update on protein number 1. I ran it with only 5 simulations. It took

Re: Using multi-processor for model_free

2016-09-26 Thread Troels Emtekær Linnet

That looks wrong.

NP should be the variable for the number of processors.

I suspect the error is not in relax, but somewhere in your system.

I think I can't help you more from here.
Is there a computer wizard around at your lab?

Best Troels

Den mandag den 26. september 2016 skrev Mahdi, Sam <
sam.mahdi@my.csun.edu>:

> Hi Troels,
>
> I have attempted the fix for running on a multi-processor platform by
> creating the script you told me too, and I still got the same result. I
> have uploaded a screenshot that shows again, relax is running in the
> background, but there is no output for relax, nor can I input any commands.
> The only output I recieve is this:
> Running relax with NP=$NPROC+8|bc in multi-processor mode
>
> And any command I type in after that gets no response.
>
> Sincerely,
> Sam
>
>
> On Sun, Sep 25, 2016 at 6:43 AM, Troels Emtekær Linnet <
> tlin...@nmr-relax.com
> > wrote:
>
>> Hi Sam.
>>
>> Try to load the pdb file and make a spin_loop over the information.
>> How does the information look like?
>> http://wiki.nmr-relax.com/Tutorial_for_model-free_analysis_
>> sam_mahdi#Check_the_spin_containers_via_script
>>
>> Regarding the multiprocessor on your Fedora 20 machine, try to have a
>> look at the bug.
>> https://gna.org/bugs/?25084
>>
>> -
>> I suspect there is a mismatch between two installations of relax.
>> One version of 2.x and one local of 4.x.
>> Try adding the full path to relax
>> -
>>
>> Try make a run script like this and copy it some where to your PATH
>> myrelax
>> --
>>
>> #!/bin/tcsh -fe
>>
>> # Set the relax version used for this script.
>> set RELAX=/sbinlab2/tlinnet/software/NMR-relax/relax_trunk/relax
>>
>> # Set number of available CPUs.
>> set NPROC=`nproc`
>> set NP=`echo $NPROC + 0 | bc `
>> echo "Running relax with NP=$NP in multi-processor mode"
>>
>> # Run relax in multi processor mode.
>> mpirun -np $NP $RELAX --multi='mpi4py' $argv
>>
>> 2016-09-24 1:03 GMT+02:00 Mahdi, Sam > >:
>>
>>> Hi Troels,
>>>
>>> Update on Protein number 1: So I was able to successfully run model free
>>> with no problems on my protein (I don't know why it was giving problems
>>> before). The reason it may have been giving issues though is the protein I
>>> am working with forms a dimer at the concentrations we work with (thus the
>>> results I have are for the Dimer form of the protein). The pdb file though
>>> only has a monomer structure though. I have been able to obtain the dimer
>>> pdb file using HADDOCK (docking program), but have come across a few
>>> problems uploading the pdb file.
>>> The initial problem was that all the hydrogens attached to the nitrogen
>>> were HN labeled on the HADDOCK modified pdb file, and model free could not
>>> understand what HN meant, and I would recieve this warning.
>>> RelaxWarning: Cannot determine the element associated with atom 'HN'.
>>>
>>> I could however load up all the Nitrogen, but naturally, with no
>>> hydrogens, it wouldn't be able to calculate any bond vectors between
>>> nitrogen and hydrogen. So I would recieve this error and the program would
>>> close
>>> RelaxError: The spin ID '@H' matches no spins.
>>>
>>> To fix this, I changed all the HN spins, to just H, but then recieved
>>> another error.
>>> RelaxError: Multiple alternate location indicators are present in the
>>> PDB file, but the desired coordinates set has not been specified.
>>>
>>> I don't exactly understand what this error means. Is it saying the
>>> program can't locate the 3D coordinates for the Hydrogen and Nitrogen? If
>>> that is the case, why was it able to before, when it couldn't read any of
>>> the Hydrogen spins. I'm just confused a bit as to what this error means.
>>>
>>> Sincerely,
>>> Sam
>>>
>>> On Wed, Sep 21, 2016 at 3:18 PM, Mahdi, Sam >> > wrote:
>>>
 Hi Troels,

 Update on protein number 1. I ran it with only 5 simulations. It took a
 while, but it ended up finishing. So I assume its due to bad data simply
 slowing down the process.
 Update on protein number 2. I ran it with only 2 spins as well, and I
 still recieved the same error. I suspect its due to the pdb file. I'm going
 to attempt to use another program to add the hydrogens to my pdb file and
 try again.

 Sincerely,
 Sam

 On Tue, Sep 20, 2016 at 1:31 PM, Mahdi, Sam > wrote:

> Thats weird, I can open it up directly from the link you sent me. I'll
> reupload it
>
> On Tue, Sep 20, 2016 at 12:40 PM, Troels Emtekær Linnet <
> tlin...@nmr-relax.com
> > wrote:
>
>> The file:
>> file #28673:  relax -i data

Re: Using multi-processor for model_free

2016-09-23 Thread Mahdi, Sam

Hi Troels,

Update on Protein number 1: So I was able to successfully run model free
with no problems on my protein (I don't know why it was giving problems
before). The reason it may have been giving issues though is the protein I
am working with forms a dimer at the concentrations we work with (thus the
results I have are for the Dimer form of the protein). The pdb file though
only has a monomer structure though. I have been able to obtain the dimer
pdb file using HADDOCK (docking program), but have come across a few
problems uploading the pdb file.
The initial problem was that all the hydrogens attached to the nitrogen
were HN labeled on the HADDOCK modified pdb file, and model free could not
understand what HN meant, and I would recieve this warning.
RelaxWarning: Cannot determine the element associated with atom 'HN'.

I could however load up all the Nitrogen, but naturally, with no hydrogens,
it wouldn't be able to calculate any bond vectors between nitrogen and
hydrogen. So I would recieve this error and the program would close
RelaxError: The spin ID '@H' matches no spins.

To fix this, I changed all the HN spins, to just H, but then recieved
another error.
RelaxError: Multiple alternate location indicators are present in the PDB
file, but the desired coordinates set has not been specified.

I don't exactly understand what this error means. Is it saying the program
can't locate the 3D coordinates for the Hydrogen and Nitrogen? If that is
the case, why was it able to before, when it couldn't read any of the
Hydrogen spins. I'm just confused a bit as to what this error means.

Sincerely,
Sam

On Wed, Sep 21, 2016 at 3:18 PM, Mahdi, Sam 
wrote:

> Hi Troels,
>
> Update on protein number 1. I ran it with only 5 simulations. It took a
> while, but it ended up finishing. So I assume its due to bad data simply
> slowing down the process.
> Update on protein number 2. I ran it with only 2 spins as well, and I
> still recieved the same error. I suspect its due to the pdb file. I'm going
> to attempt to use another program to add the hydrogens to my pdb file and
> try again.
>
> Sincerely,
> Sam
>
> On Tue, Sep 20, 2016 at 1:31 PM, Mahdi, Sam 
> wrote:
>
>> Thats weird, I can open it up directly from the link you sent me. I'll
>> reupload it
>>
>> On Tue, Sep 20, 2016 at 12:40 PM, Troels Emtekær Linnet <
>> tlin...@nmr-relax.com> wrote:
>>
>>> The file:
>>> file #28673:  relax -i data for 4.0,2 a
>>>
>>> https://gna.org/bugs/download.php?file_id=28673
>>>
>>> Its emtpy?
>>>
>>> 2016-09-20 20:05 GMT+02:00 Mahdi, Sam :
>>>
 Hi Troels,

 I am a bit confused what you are talking about. There is no file
 labeled .?

 On Tue, Sep 20, 2016 at 9:15 AM, Troels Emtekær Linnet <
 tlin...@nmr-relax.com> wrote:

> Hi Sam.
>
> On
> https://gna.org/bugs/?25084
>
> I cannot open the file.?
>
> In the meantime, try to specify the full path to relax. Not just
> ./relax
> but /home/user/xxx/relax
>
> Best
> Troels
>
> 2016-09-19 23:13 GMT+02:00 Mahdi, Sam :
>
>> I just uploaded the 4.0.2 relax -i info. I already have minfx 1.0.12
>> with 4.0.2. But I can't open relax on multi  processor platform for 
>> either
>> version.
>>
>> On Mon, Sep 19, 2016 at 10:47 AM, Troels Emtekær Linnet <
>> tlin...@nmr-relax.com> wrote:
>>
>>> Please upgrade!
>>>
>>> Name   InstalledVersion Current version
>>> minfx  True 1.0.41.0.12
>>>
>>> relax information:
>>> Version: 2.2.5 4.0.2
>>>
>>>
>>> 2016-09-19 19:41 GMT+02:00 Mahdi, Sam :
>>>
 Hi Troels,

 I have uploaded the bug report for the issue with running relax on
 multiple processors on my fedora 20 computer. I will upload the mpirun
 report bindings on the fedora 24 computer later today (that is not my 
 lab
 so I don't have access to it, and the professor is not in yet). If 
 there is
 any more info that is needed please let me know. Thanks again in 
 advance.

 Sincerely,
 Sam

 On Mon, Sep 19, 2016 at 10:24 AM, Mahdi, Sam <
 sam.mahdi@my.csun.edu> wrote:

> Hi Troels,
>
> Thanks for the quick response!
>
> Protein 1: I will attempt to troubleshoot using the advice you
> gave me. The problem occurs write after it indicates its writing a 
> file for
> prolate round_3 (so its about to start it). I will run it again and 
> post
> the output to give you a better idea. I'm pretty sure the output was
> something like this
> Over-fit spin deselection:

Re: Using multi-processor for model_free

2016-09-20 Thread Mahdi, Sam

Thats weird, I can open it up directly from the link you sent me. I'll
reupload it

On Tue, Sep 20, 2016 at 12:40 PM, Troels Emtekær Linnet <
tlin...@nmr-relax.com> wrote:

> The file:
> file #28673:  relax -i data for 4.0,2 a
>
> https://gna.org/bugs/download.php?file_id=28673
>
> Its emtpy?
>
> 2016-09-20 20:05 GMT+02:00 Mahdi, Sam :
>
>> Hi Troels,
>>
>> I am a bit confused what you are talking about. There is no file labeled
>> .?
>>
>> On Tue, Sep 20, 2016 at 9:15 AM, Troels Emtekær Linnet <
>> tlin...@nmr-relax.com> wrote:
>>
>>> Hi Sam.
>>>
>>> On
>>> https://gna.org/bugs/?25084
>>>
>>> I cannot open the file.?
>>>
>>> In the meantime, try to specify the full path to relax. Not just ./relax
>>> but /home/user/xxx/relax
>>>
>>> Best
>>> Troels
>>>
>>> 2016-09-19 23:13 GMT+02:00 Mahdi, Sam :
>>>
 I just uploaded the 4.0.2 relax -i info. I already have minfx 1.0.12
 with 4.0.2. But I can't open relax on multi  processor platform for either
 version.

 On Mon, Sep 19, 2016 at 10:47 AM, Troels Emtekær Linnet <
 tlin...@nmr-relax.com> wrote:

> Please upgrade!
>
> Name   InstalledVersion Current version
> minfx  True 1.0.41.0.12
>
> relax information:
> Version: 2.2.5 4.0.2
>
>
> 2016-09-19 19:41 GMT+02:00 Mahdi, Sam :
>
>> Hi Troels,
>>
>> I have uploaded the bug report for the issue with running relax on
>> multiple processors on my fedora 20 computer. I will upload the mpirun
>> report bindings on the fedora 24 computer later today (that is not my lab
>> so I don't have access to it, and the professor is not in yet). If there 
>> is
>> any more info that is needed please let me know. Thanks again in advance.
>>
>> Sincerely,
>> Sam
>>
>> On Mon, Sep 19, 2016 at 10:24 AM, Mahdi, Sam <
>> sam.mahdi@my.csun.edu> wrote:
>>
>>> Hi Troels,
>>>
>>> Thanks for the quick response!
>>>
>>> Protein 1: I will attempt to troubleshoot using the advice you gave
>>> me. The problem occurs write after it indicates its writing a file for
>>> prolate round_3 (so its about to start it). I will run it again and post
>>> the output to give you a better idea. I'm pretty sure the output was
>>> something like this
>>> Over-fit spin deselection:
>>> No spins have been deselected.
>>> Resetting the minimisation statistics.
>>> But I will double check and send you another email with the actual
>>> output.
>>> Protein 2:
>>> I am using the sample script for dAuvergene protocol. So the only
>>> thing I've changed since my previous run (the one that worked that you
>>> wrote a tutorial for), was the pdb file and the data set I used. The 
>>> thing
>>> I suspected was causing an issue ,was the pdb file since I slightly
>>> modified it, and thats really the only thing different from this run 
>>> versus
>>> the others.
>>>
>>> Also side note, if I were to deselect the spins that I don't have
>>> data for or I have bad data for, that wouldn't change any of the
>>> calculations correct? I never have since I assumed relax would just 
>>> ignore
>>> all the amino acids I don't have data for, but it may help increase the
>>> speed of my calculations if I just tell relax to just ignore the spins 
>>> from
>>> the start.
>>>
>>> Sincerely,
>>> Sam
>>>
>>> On Mon, Sep 19, 2016 at 9:12 AM, Troels Emtekær Linnet <
>>> tlin...@nmr-relax.com> wrote:
>>>
 Hi Sam.

 Happy to hear you that you get some progress.

 Protein 1:
 Can you help me to find out, if you are minimizing or running
 Monte-Carlo simulations?
 This COULD be the problem:

 How relax works (at least how it works for relaxation dispersion):
 Step 1: Minimize the error for the target function. Find the
 parameters which best match the target function to the data, by 
 minimizing
 the error.
 Here each individual spin minimization is handed out to a processor
 for calculation.

 Step 2: Determine the error of the minimization by monte carlo
 simulations.
 Create (Standard 500) additional datasets with a copy from the
 original. Modify each datapoint by an error, drawn from a gaussian
 distribution where the width is described by the error of measurements.
 Now hand out each of the datasets to the processor. Each processor
 should now calculate the minimization for all the spins. The 
 minimization
 should be more quick, as the starting position is chosen from Step 1.

 Possible problem: One (or

Re: Using multi-processor for model_free

2016-09-20 Thread Troels Emtekær Linnet

The file:
file #28673:  relax -i data for 4.0,2 a

https://gna.org/bugs/download.php?file_id=28673

Its emtpy?

2016-09-20 20:05 GMT+02:00 Mahdi, Sam :

> Hi Troels,
>
> I am a bit confused what you are talking about. There is no file labeled .?
>
> On Tue, Sep 20, 2016 at 9:15 AM, Troels Emtekær Linnet <
> tlin...@nmr-relax.com> wrote:
>
>> Hi Sam.
>>
>> On
>> https://gna.org/bugs/?25084
>>
>> I cannot open the file.?
>>
>> In the meantime, try to specify the full path to relax. Not just ./relax
>> but /home/user/xxx/relax
>>
>> Best
>> Troels
>>
>> 2016-09-19 23:13 GMT+02:00 Mahdi, Sam :
>>
>>> I just uploaded the 4.0.2 relax -i info. I already have minfx 1.0.12
>>> with 4.0.2. But I can't open relax on multi  processor platform for either
>>> version.
>>>
>>> On Mon, Sep 19, 2016 at 10:47 AM, Troels Emtekær Linnet <
>>> tlin...@nmr-relax.com> wrote:
>>>
 Please upgrade!

 Name   InstalledVersion Current version
 minfx  True 1.0.41.0.12

 relax information:
 Version: 2.2.5 4.0.2


 2016-09-19 19:41 GMT+02:00 Mahdi, Sam :

> Hi Troels,
>
> I have uploaded the bug report for the issue with running relax on
> multiple processors on my fedora 20 computer. I will upload the mpirun
> report bindings on the fedora 24 computer later today (that is not my lab
> so I don't have access to it, and the professor is not in yet). If there 
> is
> any more info that is needed please let me know. Thanks again in advance.
>
> Sincerely,
> Sam
>
> On Mon, Sep 19, 2016 at 10:24 AM, Mahdi, Sam <
> sam.mahdi@my.csun.edu> wrote:
>
>> Hi Troels,
>>
>> Thanks for the quick response!
>>
>> Protein 1: I will attempt to troubleshoot using the advice you gave
>> me. The problem occurs write after it indicates its writing a file for
>> prolate round_3 (so its about to start it). I will run it again and post
>> the output to give you a better idea. I'm pretty sure the output was
>> something like this
>> Over-fit spin deselection:
>> No spins have been deselected.
>> Resetting the minimisation statistics.
>> But I will double check and send you another email with the actual
>> output.
>> Protein 2:
>> I am using the sample script for dAuvergene protocol. So the only
>> thing I've changed since my previous run (the one that worked that you
>> wrote a tutorial for), was the pdb file and the data set I used. The 
>> thing
>> I suspected was causing an issue ,was the pdb file since I slightly
>> modified it, and thats really the only thing different from this run 
>> versus
>> the others.
>>
>> Also side note, if I were to deselect the spins that I don't have
>> data for or I have bad data for, that wouldn't change any of the
>> calculations correct? I never have since I assumed relax would just 
>> ignore
>> all the amino acids I don't have data for, but it may help increase the
>> speed of my calculations if I just tell relax to just ignore the spins 
>> from
>> the start.
>>
>> Sincerely,
>> Sam
>>
>> On Mon, Sep 19, 2016 at 9:12 AM, Troels Emtekær Linnet <
>> tlin...@nmr-relax.com> wrote:
>>
>>> Hi Sam.
>>>
>>> Happy to hear you that you get some progress.
>>>
>>> Protein 1:
>>> Can you help me to find out, if you are minimizing or running
>>> Monte-Carlo simulations?
>>> This COULD be the problem:
>>>
>>> How relax works (at least how it works for relaxation dispersion):
>>> Step 1: Minimize the error for the target function. Find the
>>> parameters which best match the target function to the data, by 
>>> minimizing
>>> the error.
>>> Here each individual spin minimization is handed out to a processor
>>> for calculation.
>>>
>>> Step 2: Determine the error of the minimization by monte carlo
>>> simulations.
>>> Create (Standard 500) additional datasets with a copy from the
>>> original. Modify each datapoint by an error, drawn from a gaussian
>>> distribution where the width is described by the error of measurements.
>>> Now hand out each of the datasets to the processor. Each processor
>>> should now calculate the minimization for all the spins. The 
>>> minimization
>>> should be more quick, as the starting position is chosen from Step 1.
>>>
>>> Possible problem: One (or more) of the spins has really bad data. So
>>> a little change of the data makes the minimization space very different.
>>> Think of a flat table. Where should the "minimization ball" run
>>> into? Maybe you have created a small new bump in the table. This is
>>> typically for "bad" data.

Re: Using multi-processor for model_free

2016-09-20 Thread Mahdi, Sam

Hi Troels,

I am a bit confused what you are talking about. There is no file labeled .?

On Tue, Sep 20, 2016 at 9:15 AM, Troels Emtekær Linnet <
tlin...@nmr-relax.com> wrote:

> Hi Sam.
>
> On
> https://gna.org/bugs/?25084
>
> I cannot open the file.?
>
> In the meantime, try to specify the full path to relax. Not just ./relax
> but /home/user/xxx/relax
>
> Best
> Troels
>
> 2016-09-19 23:13 GMT+02:00 Mahdi, Sam :
>
>> I just uploaded the 4.0.2 relax -i info. I already have minfx 1.0.12 with
>> 4.0.2. But I can't open relax on multi  processor platform for either
>> version.
>>
>> On Mon, Sep 19, 2016 at 10:47 AM, Troels Emtekær Linnet <
>> tlin...@nmr-relax.com> wrote:
>>
>>> Please upgrade!
>>>
>>> Name   InstalledVersion Current version
>>> minfx  True 1.0.41.0.12
>>>
>>> relax information:
>>> Version: 2.2.5 4.0.2
>>>
>>>
>>> 2016-09-19 19:41 GMT+02:00 Mahdi, Sam :
>>>
 Hi Troels,

 I have uploaded the bug report for the issue with running relax on
 multiple processors on my fedora 20 computer. I will upload the mpirun
 report bindings on the fedora 24 computer later today (that is not my lab
 so I don't have access to it, and the professor is not in yet). If there is
 any more info that is needed please let me know. Thanks again in advance.

 Sincerely,
 Sam

 On Mon, Sep 19, 2016 at 10:24 AM, Mahdi, Sam  wrote:

> Hi Troels,
>
> Thanks for the quick response!
>
> Protein 1: I will attempt to troubleshoot using the advice you gave
> me. The problem occurs write after it indicates its writing a file for
> prolate round_3 (so its about to start it). I will run it again and post
> the output to give you a better idea. I'm pretty sure the output was
> something like this
> Over-fit spin deselection:
> No spins have been deselected.
> Resetting the minimisation statistics.
> But I will double check and send you another email with the actual
> output.
> Protein 2:
> I am using the sample script for dAuvergene protocol. So the only
> thing I've changed since my previous run (the one that worked that you
> wrote a tutorial for), was the pdb file and the data set I used. The thing
> I suspected was causing an issue ,was the pdb file since I slightly
> modified it, and thats really the only thing different from this run 
> versus
> the others.
>
> Also side note, if I were to deselect the spins that I don't have data
> for or I have bad data for, that wouldn't change any of the calculations
> correct? I never have since I assumed relax would just ignore all the 
> amino
> acids I don't have data for, but it may help increase the speed of my
> calculations if I just tell relax to just ignore the spins from the start.
>
> Sincerely,
> Sam
>
> On Mon, Sep 19, 2016 at 9:12 AM, Troels Emtekær Linnet <
> tlin...@nmr-relax.com> wrote:
>
>> Hi Sam.
>>
>> Happy to hear you that you get some progress.
>>
>> Protein 1:
>> Can you help me to find out, if you are minimizing or running
>> Monte-Carlo simulations?
>> This COULD be the problem:
>>
>> How relax works (at least how it works for relaxation dispersion):
>> Step 1: Minimize the error for the target function. Find the
>> parameters which best match the target function to the data, by 
>> minimizing
>> the error.
>> Here each individual spin minimization is handed out to a processor
>> for calculation.
>>
>> Step 2: Determine the error of the minimization by monte carlo
>> simulations.
>> Create (Standard 500) additional datasets with a copy from the
>> original. Modify each datapoint by an error, drawn from a gaussian
>> distribution where the width is described by the error of measurements.
>> Now hand out each of the datasets to the processor. Each processor
>> should now calculate the minimization for all the spins. The minimization
>> should be more quick, as the starting position is chosen from Step 1.
>>
>> Possible problem: One (or more) of the spins has really bad data. So
>> a little change of the data makes the minimization space very different.
>> Think of a flat table. Where should the "minimization ball" run into?
>> Maybe you have created a small new bump in the table. This is typically 
>> for
>> "bad" data.
>>
>> This could either be the measurement OR the error estimation. Relax
>> will keep on searching for minimization.
>> If you are "unlucky", some of the created datasets will make relax
>> hang for a very long time.
>>
>> Unfortunately, it is NOT possible to ask a processor about its
>> "current" work, when

Re: Using multi-processor for model_free

2016-09-20 Thread Troels Emtekær Linnet

Hi Sam.

On
https://gna.org/bugs/?25084

I cannot open the file.?

In the meantime, try to specify the full path to relax. Not just ./relax
but /home/user/xxx/relax

Best
Troels

2016-09-19 23:13 GMT+02:00 Mahdi, Sam :

> I just uploaded the 4.0.2 relax -i info. I already have minfx 1.0.12 with
> 4.0.2. But I can't open relax on multi  processor platform for either
> version.
>
> On Mon, Sep 19, 2016 at 10:47 AM, Troels Emtekær Linnet <
> tlin...@nmr-relax.com> wrote:
>
>> Please upgrade!
>>
>> Name   InstalledVersion Current version
>> minfx  True 1.0.41.0.12
>>
>> relax information:
>> Version: 2.2.5 4.0.2
>>
>>
>> 2016-09-19 19:41 GMT+02:00 Mahdi, Sam :
>>
>>> Hi Troels,
>>>
>>> I have uploaded the bug report for the issue with running relax on
>>> multiple processors on my fedora 20 computer. I will upload the mpirun
>>> report bindings on the fedora 24 computer later today (that is not my lab
>>> so I don't have access to it, and the professor is not in yet). If there is
>>> any more info that is needed please let me know. Thanks again in advance.
>>>
>>> Sincerely,
>>> Sam
>>>
>>> On Mon, Sep 19, 2016 at 10:24 AM, Mahdi, Sam 
>>> wrote:
>>>
 Hi Troels,

 Thanks for the quick response!

 Protein 1: I will attempt to troubleshoot using the advice you gave me.
 The problem occurs write after it indicates its writing a file for prolate
 round_3 (so its about to start it). I will run it again and post the output
 to give you a better idea. I'm pretty sure the output was something like
 this
 Over-fit spin deselection:
 No spins have been deselected.
 Resetting the minimisation statistics.
 But I will double check and send you another email with the actual
 output.
 Protein 2:
 I am using the sample script for dAuvergene protocol. So the only thing
 I've changed since my previous run (the one that worked that you wrote a
 tutorial for), was the pdb file and the data set I used. The thing I
 suspected was causing an issue ,was the pdb file since I slightly modified
 it, and thats really the only thing different from this run versus the
 others.

 Also side note, if I were to deselect the spins that I don't have data
 for or I have bad data for, that wouldn't change any of the calculations
 correct? I never have since I assumed relax would just ignore all the amino
 acids I don't have data for, but it may help increase the speed of my
 calculations if I just tell relax to just ignore the spins from the start.

 Sincerely,
 Sam

 On Mon, Sep 19, 2016 at 9:12 AM, Troels Emtekær Linnet <
 tlin...@nmr-relax.com> wrote:

> Hi Sam.
>
> Happy to hear you that you get some progress.
>
> Protein 1:
> Can you help me to find out, if you are minimizing or running
> Monte-Carlo simulations?
> This COULD be the problem:
>
> How relax works (at least how it works for relaxation dispersion):
> Step 1: Minimize the error for the target function. Find the
> parameters which best match the target function to the data, by minimizing
> the error.
> Here each individual spin minimization is handed out to a processor
> for calculation.
>
> Step 2: Determine the error of the minimization by monte carlo
> simulations.
> Create (Standard 500) additional datasets with a copy from the
> original. Modify each datapoint by an error, drawn from a gaussian
> distribution where the width is described by the error of measurements.
> Now hand out each of the datasets to the processor. Each processor
> should now calculate the minimization for all the spins. The minimization
> should be more quick, as the starting position is chosen from Step 1.
>
> Possible problem: One (or more) of the spins has really bad data. So a
> little change of the data makes the minimization space very different.
> Think of a flat table. Where should the "minimization ball" run into?
> Maybe you have created a small new bump in the table. This is typically 
> for
> "bad" data.
>
> This could either be the measurement OR the error estimation. Relax
> will keep on searching for minimization.
> If you are "unlucky", some of the created datasets will make relax
> hang for a very long time.
>
> Unfortunately, it is NOT possible to ask a processor about its
> "current" work, when it is doing a minimization for a whole dataset.
> And if it was, it would create an output of 64 spins being minimized
> at the same time, creating a big mess, since the processors are working
> alone. When doing Monte-Carlo simulations, relax are quite silent. Only
> reporting when a whole dataset is done.

Re: Using multi-processor for model_free

2016-09-19 Thread Mahdi, Sam

I just uploaded the 4.0.2 relax -i info. I already have minfx 1.0.12 with
4.0.2. But I can't open relax on multi  processor platform for either
version.

On Mon, Sep 19, 2016 at 10:47 AM, Troels Emtekær Linnet <
tlin...@nmr-relax.com> wrote:

> Please upgrade!
>
> Name   InstalledVersion Current version
> minfx  True 1.0.41.0.12
>
> relax information:
> Version: 2.2.5 4.0.2
>
>
> 2016-09-19 19:41 GMT+02:00 Mahdi, Sam :
>
>> Hi Troels,
>>
>> I have uploaded the bug report for the issue with running relax on
>> multiple processors on my fedora 20 computer. I will upload the mpirun
>> report bindings on the fedora 24 computer later today (that is not my lab
>> so I don't have access to it, and the professor is not in yet). If there is
>> any more info that is needed please let me know. Thanks again in advance.
>>
>> Sincerely,
>> Sam
>>
>> On Mon, Sep 19, 2016 at 10:24 AM, Mahdi, Sam 
>> wrote:
>>
>>> Hi Troels,
>>>
>>> Thanks for the quick response!
>>>
>>> Protein 1: I will attempt to troubleshoot using the advice you gave me.
>>> The problem occurs write after it indicates its writing a file for prolate
>>> round_3 (so its about to start it). I will run it again and post the output
>>> to give you a better idea. I'm pretty sure the output was something like
>>> this
>>> Over-fit spin deselection:
>>> No spins have been deselected.
>>> Resetting the minimisation statistics.
>>> But I will double check and send you another email with the actual
>>> output.
>>> Protein 2:
>>> I am using the sample script for dAuvergene protocol. So the only thing
>>> I've changed since my previous run (the one that worked that you wrote a
>>> tutorial for), was the pdb file and the data set I used. The thing I
>>> suspected was causing an issue ,was the pdb file since I slightly modified
>>> it, and thats really the only thing different from this run versus the
>>> others.
>>>
>>> Also side note, if I were to deselect the spins that I don't have data
>>> for or I have bad data for, that wouldn't change any of the calculations
>>> correct? I never have since I assumed relax would just ignore all the amino
>>> acids I don't have data for, but it may help increase the speed of my
>>> calculations if I just tell relax to just ignore the spins from the start.
>>>
>>> Sincerely,
>>> Sam
>>>
>>> On Mon, Sep 19, 2016 at 9:12 AM, Troels Emtekær Linnet <
>>> tlin...@nmr-relax.com> wrote:
>>>
 Hi Sam.

 Happy to hear you that you get some progress.

 Protein 1:
 Can you help me to find out, if you are minimizing or running
 Monte-Carlo simulations?
 This COULD be the problem:

 How relax works (at least how it works for relaxation dispersion):
 Step 1: Minimize the error for the target function. Find the parameters
 which best match the target function to the data, by minimizing the error.
 Here each individual spin minimization is handed out to a processor for
 calculation.

 Step 2: Determine the error of the minimization by monte carlo
 simulations.
 Create (Standard 500) additional datasets with a copy from the
 original. Modify each datapoint by an error, drawn from a gaussian
 distribution where the width is described by the error of measurements.
 Now hand out each of the datasets to the processor. Each processor
 should now calculate the minimization for all the spins. The minimization
 should be more quick, as the starting position is chosen from Step 1.

 Possible problem: One (or more) of the spins has really bad data. So a
 little change of the data makes the minimization space very different.
 Think of a flat table. Where should the "minimization ball" run into?
 Maybe you have created a small new bump in the table. This is typically for
 "bad" data.

 This could either be the measurement OR the error estimation. Relax
 will keep on searching for minimization.
 If you are "unlucky", some of the created datasets will make relax hang
 for a very long time.

 Unfortunately, it is NOT possible to ask a processor about its
 "current" work, when it is doing a minimization for a whole dataset.
 And if it was, it would create an output of 64 spins being minimized at
 the same time, creating a big mess, since the processors are working alone.
 When doing Monte-Carlo simulations, relax are quite silent. Only reporting
 when a whole dataset is done.

 Is relax stuck in Monte-Carlo simulations?

 Possible solution:
 *) Set Monte-Carlo simulations to 3 (which is minimum), and know that
 you have found the right minimum, but the error estimation of the
 parameters are wrong.
 *) Carefully inspect your data, deselecting all spins which have "bad
 data". Look at their graphs. Consider

Re: Using multi-processor for model_free

2016-09-19 Thread Troels Emtekær Linnet

Please upgrade!

Name   InstalledVersion Current version
minfx  True 1.0.41.0.12

relax information:
Version: 2.2.5 4.0.2


2016-09-19 19:41 GMT+02:00 Mahdi, Sam :

> Hi Troels,
>
> I have uploaded the bug report for the issue with running relax on
> multiple processors on my fedora 20 computer. I will upload the mpirun
> report bindings on the fedora 24 computer later today (that is not my lab
> so I don't have access to it, and the professor is not in yet). If there is
> any more info that is needed please let me know. Thanks again in advance.
>
> Sincerely,
> Sam
>
> On Mon, Sep 19, 2016 at 10:24 AM, Mahdi, Sam 
> wrote:
>
>> Hi Troels,
>>
>> Thanks for the quick response!
>>
>> Protein 1: I will attempt to troubleshoot using the advice you gave me.
>> The problem occurs write after it indicates its writing a file for prolate
>> round_3 (so its about to start it). I will run it again and post the output
>> to give you a better idea. I'm pretty sure the output was something like
>> this
>> Over-fit spin deselection:
>> No spins have been deselected.
>> Resetting the minimisation statistics.
>> But I will double check and send you another email with the actual
>> output.
>> Protein 2:
>> I am using the sample script for dAuvergene protocol. So the only thing
>> I've changed since my previous run (the one that worked that you wrote a
>> tutorial for), was the pdb file and the data set I used. The thing I
>> suspected was causing an issue ,was the pdb file since I slightly modified
>> it, and thats really the only thing different from this run versus the
>> others.
>>
>> Also side note, if I were to deselect the spins that I don't have data
>> for or I have bad data for, that wouldn't change any of the calculations
>> correct? I never have since I assumed relax would just ignore all the amino
>> acids I don't have data for, but it may help increase the speed of my
>> calculations if I just tell relax to just ignore the spins from the start.
>>
>> Sincerely,
>> Sam
>>
>> On Mon, Sep 19, 2016 at 9:12 AM, Troels Emtekær Linnet <
>> tlin...@nmr-relax.com> wrote:
>>
>>> Hi Sam.
>>>
>>> Happy to hear you that you get some progress.
>>>
>>> Protein 1:
>>> Can you help me to find out, if you are minimizing or running
>>> Monte-Carlo simulations?
>>> This COULD be the problem:
>>>
>>> How relax works (at least how it works for relaxation dispersion):
>>> Step 1: Minimize the error for the target function. Find the parameters
>>> which best match the target function to the data, by minimizing the error.
>>> Here each individual spin minimization is handed out to a processor for
>>> calculation.
>>>
>>> Step 2: Determine the error of the minimization by monte carlo
>>> simulations.
>>> Create (Standard 500) additional datasets with a copy from the original.
>>> Modify each datapoint by an error, drawn from a gaussian distribution where
>>> the width is described by the error of measurements.
>>> Now hand out each of the datasets to the processor. Each processor
>>> should now calculate the minimization for all the spins. The minimization
>>> should be more quick, as the starting position is chosen from Step 1.
>>>
>>> Possible problem: One (or more) of the spins has really bad data. So a
>>> little change of the data makes the minimization space very different.
>>> Think of a flat table. Where should the "minimization ball" run into?
>>> Maybe you have created a small new bump in the table. This is typically for
>>> "bad" data.
>>>
>>> This could either be the measurement OR the error estimation. Relax will
>>> keep on searching for minimization.
>>> If you are "unlucky", some of the created datasets will make relax hang
>>> for a very long time.
>>>
>>> Unfortunately, it is NOT possible to ask a processor about its "current"
>>> work, when it is doing a minimization for a whole dataset.
>>> And if it was, it would create an output of 64 spins being minimized at
>>> the same time, creating a big mess, since the processors are working alone.
>>> When doing Monte-Carlo simulations, relax are quite silent. Only reporting
>>> when a whole dataset is done.
>>>
>>> Is relax stuck in Monte-Carlo simulations?
>>>
>>> Possible solution:
>>> *) Set Monte-Carlo simulations to 3 (which is minimum), and know that
>>> you have found the right minimum, but the error estimation of the
>>> parameters are wrong.
>>> *) Carefully inspect your data, deselecting all spins which have "bad
>>> data". Look at their graphs. Consider working with as few spins as
>>> possible, and work your way up! Working this way will greatly increase your
>>> productivity.
>>>
>>> Protein 2:
>>> Are you setting the bonds for the minimization manually?
>>> This looks like the upper/lower bonds are specified wrong. This is not
>>> easy to do. How are you doing it?
>>>
>>> Best
>>> Troels
>>>
>>>
>>>
>>>

Re: Using multi-processor for model_free

2016-09-19 Thread Troels Emtekær Linnet

Hi Sam.

Regarding protein 2.
Try to make a spin_loop after loading the data or use the GUI:
http://wiki.nmr-relax.com/Tutorial_for_model-free_analysis_sam_mahdi#Check_the_spin_containers_via_GUI

Carefully check the spins.
Or deselect all spins, and select 1-2 spins, and run the calculation.
Add more spins, and work your way up.

Maybe the modification to the pdb file make something fishy.

Relax should deselect spins there are not data for. And it should not
influence the calculation time.
It's a lighweight process.

It is quite difficult to write procedures to check for "garbage".

Best
Troels


2016-09-19 19:24 GMT+02:00 Mahdi, Sam :

> Hi Troels,
>
> Thanks for the quick response!
>
> Protein 1: I will attempt to troubleshoot using the advice you gave me.
> The problem occurs write after it indicates its writing a file for prolate
> round_3 (so its about to start it). I will run it again and post the output
> to give you a better idea. I'm pretty sure the output was something like
> this
> Over-fit spin deselection:
> No spins have been deselected.
> Resetting the minimisation statistics.
> But I will double check and send you another email with the actual output.
> Protein 2:
> I am using the sample script for dAuvergene protocol. So the only thing
> I've changed since my previous run (the one that worked that you wrote a
> tutorial for), was the pdb file and the data set I used. The thing I
> suspected was causing an issue ,was the pdb file since I slightly modified
> it, and thats really the only thing different from this run versus the
> others.
>
> Also side note, if I were to deselect the spins that I don't have data for
> or I have bad data for, that wouldn't change any of the calculations
> correct? I never have since I assumed relax would just ignore all the amino
> acids I don't have data for, but it may help increase the speed of my
> calculations if I just tell relax to just ignore the spins from the start.
>
> Sincerely,
> Sam
>
> On Mon, Sep 19, 2016 at 9:12 AM, Troels Emtekær Linnet <
> tlin...@nmr-relax.com> wrote:
>
>> Hi Sam.
>>
>> Happy to hear you that you get some progress.
>>
>> Protein 1:
>> Can you help me to find out, if you are minimizing or running Monte-Carlo
>> simulations?
>> This COULD be the problem:
>>
>> How relax works (at least how it works for relaxation dispersion):
>> Step 1: Minimize the error for the target function. Find the parameters
>> which best match the target function to the data, by minimizing the error.
>> Here each individual spin minimization is handed out to a processor for
>> calculation.
>>
>> Step 2: Determine the error of the minimization by monte carlo
>> simulations.
>> Create (Standard 500) additional datasets with a copy from the original.
>> Modify each datapoint by an error, drawn from a gaussian distribution where
>> the width is described by the error of measurements.
>> Now hand out each of the datasets to the processor. Each processor should
>> now calculate the minimization for all the spins. The minimization should
>> be more quick, as the starting position is chosen from Step 1.
>>
>> Possible problem: One (or more) of the spins has really bad data. So a
>> little change of the data makes the minimization space very different.
>> Think of a flat table. Where should the "minimization ball" run into?
>> Maybe you have created a small new bump in the table. This is typically for
>> "bad" data.
>>
>> This could either be the measurement OR the error estimation. Relax will
>> keep on searching for minimization.
>> If you are "unlucky", some of the created datasets will make relax hang
>> for a very long time.
>>
>> Unfortunately, it is NOT possible to ask a processor about its "current"
>> work, when it is doing a minimization for a whole dataset.
>> And if it was, it would create an output of 64 spins being minimized at
>> the same time, creating a big mess, since the processors are working alone.
>> When doing Monte-Carlo simulations, relax are quite silent. Only reporting
>> when a whole dataset is done.
>>
>> Is relax stuck in Monte-Carlo simulations?
>>
>> Possible solution:
>> *) Set Monte-Carlo simulations to 3 (which is minimum), and know that you
>> have found the right minimum, but the error estimation of the parameters
>> are wrong.
>> *) Carefully inspect your data, deselecting all spins which have "bad
>> data". Look at their graphs. Consider working with as few spins as
>> possible, and work your way up! Working this way will greatly increase your
>> productivity.
>>
>> Protein 2:
>> Are you setting the bonds for the minimization manually?
>> This looks like the upper/lower bonds are specified wrong. This is not
>> easy to do. How are you doing it?
>>
>> Best
>> Troels
>>
>>
>>
>>
>> 2016-09-19 17:11 GMT+02:00 Mahdi, Sam :
>>
>>> Hi Troels,
>>>
>>> I have successfully been able to run the model-free analysis on 64
>>> cores. The issue appears to have been I simply did

Re: Using multi-processor for model_free

2016-09-19 Thread Mahdi, Sam

Hi Troels,

Thanks for the quick response!

Protein 1: I will attempt to troubleshoot using the advice you gave me. The
problem occurs write after it indicates its writing a file for prolate
round_3 (so its about to start it). I will run it again and post the output
to give you a better idea. I'm pretty sure the output was something like
this
Over-fit spin deselection:
No spins have been deselected.
Resetting the minimisation statistics.
But I will double check and send you another email with the actual output.
Protein 2:
I am using the sample script for dAuvergene protocol. So the only thing
I've changed since my previous run (the one that worked that you wrote a
tutorial for), was the pdb file and the data set I used. The thing I
suspected was causing an issue ,was the pdb file since I slightly modified
it, and thats really the only thing different from this run versus the
others.

Also side note, if I were to deselect the spins that I don't have data for
or I have bad data for, that wouldn't change any of the calculations
correct? I never have since I assumed relax would just ignore all the amino
acids I don't have data for, but it may help increase the speed of my
calculations if I just tell relax to just ignore the spins from the start.

Sincerely,
Sam

On Mon, Sep 19, 2016 at 9:12 AM, Troels Emtekær Linnet <
tlin...@nmr-relax.com> wrote:

> Hi Sam.
>
> Happy to hear you that you get some progress.
>
> Protein 1:
> Can you help me to find out, if you are minimizing or running Monte-Carlo
> simulations?
> This COULD be the problem:
>
> How relax works (at least how it works for relaxation dispersion):
> Step 1: Minimize the error for the target function. Find the parameters
> which best match the target function to the data, by minimizing the error.
> Here each individual spin minimization is handed out to a processor for
> calculation.
>
> Step 2: Determine the error of the minimization by monte carlo simulations.
> Create (Standard 500) additional datasets with a copy from the original.
> Modify each datapoint by an error, drawn from a gaussian distribution where
> the width is described by the error of measurements.
> Now hand out each of the datasets to the processor. Each processor should
> now calculate the minimization for all the spins. The minimization should
> be more quick, as the starting position is chosen from Step 1.
>
> Possible problem: One (or more) of the spins has really bad data. So a
> little change of the data makes the minimization space very different.
> Think of a flat table. Where should the "minimization ball" run into?
> Maybe you have created a small new bump in the table. This is typically for
> "bad" data.
>
> This could either be the measurement OR the error estimation. Relax will
> keep on searching for minimization.
> If you are "unlucky", some of the created datasets will make relax hang
> for a very long time.
>
> Unfortunately, it is NOT possible to ask a processor about its "current"
> work, when it is doing a minimization for a whole dataset.
> And if it was, it would create an output of 64 spins being minimized at
> the same time, creating a big mess, since the processors are working alone.
> When doing Monte-Carlo simulations, relax are quite silent. Only reporting
> when a whole dataset is done.
>
> Is relax stuck in Monte-Carlo simulations?
>
> Possible solution:
> *) Set Monte-Carlo simulations to 3 (which is minimum), and know that you
> have found the right minimum, but the error estimation of the parameters
> are wrong.
> *) Carefully inspect your data, deselecting all spins which have "bad
> data". Look at their graphs. Consider working with as few spins as
> possible, and work your way up! Working this way will greatly increase your
> productivity.
>
> Protein 2:
> Are you setting the bonds for the minimization manually?
> This looks like the upper/lower bonds are specified wrong. This is not
> easy to do. How are you doing it?
>
> Best
> Troels
>
>
>
>
> 2016-09-19 17:11 GMT+02:00 Mahdi, Sam :
>
>> Hi Troels,
>>
>> I have successfully been able to run the model-free analysis on 64 cores.
>> The issue appears to have been I simply did not specify the spin number, so
>> after looking at your tutorial and making the proper modifications, it ran
>> with no complications. The results are somewhat reasonable. I decided to
>> try to run 2 other proteins however; and I've come across problems for both
>> again.
>> Protein 1:
>> I set this up just like the tutorial, and it runs with no warnings or
>> errors; however, the run never finishes. At round_3 for the prolate model
>> when it starts to minimize it just stops. I don't mean relax is stopped or
>> closed, I mean it stops doing any calculations. Relax is still open, and if
>> I run the top command, I can still see something is going on with the other
>> cores, but nothing is being calculated. The run with 64 cores is incredibly
>> fast (under 4 hours), so I don't think it's

Re: Using multi-processor for model_free

2016-09-19 Thread Troels Emtekær Linnet

Hi Sam.

Happy to hear you that you get some progress.

Protein 1:
Can you help me to find out, if you are minimizing or running Monte-Carlo
simulations?
This COULD be the problem:

How relax works (at least how it works for relaxation dispersion):
Step 1: Minimize the error for the target function. Find the parameters
which best match the target function to the data, by minimizing the error.
Here each individual spin minimization is handed out to a processor for
calculation.

Step 2: Determine the error of the minimization by monte carlo simulations.
Create (Standard 500) additional datasets with a copy from the original.
Modify each datapoint by an error, drawn from a gaussian distribution where
the width is described by the error of measurements.
Now hand out each of the datasets to the processor. Each processor should
now calculate the minimization for all the spins. The minimization should
be more quick, as the starting position is chosen from Step 1.

Possible problem: One (or more) of the spins has really bad data. So a
little change of the data makes the minimization space very different.
Think of a flat table. Where should the "minimization ball" run into? Maybe
you have created a small new bump in the table. This is typically for "bad"
data.

This could either be the measurement OR the error estimation. Relax will
keep on searching for minimization.
If you are "unlucky", some of the created datasets will make relax hang for
a very long time.

Unfortunately, it is NOT possible to ask a processor about its "current"
work, when it is doing a minimization for a whole dataset.
And if it was, it would create an output of 64 spins being minimized at the
same time, creating a big mess, since the processors are working alone.
When doing Monte-Carlo simulations, relax are quite silent. Only reporting
when a whole dataset is done.

Is relax stuck in Monte-Carlo simulations?

Possible solution:
*) Set Monte-Carlo simulations to 3 (which is minimum), and know that you
have found the right minimum, but the error estimation of the parameters
are wrong.
*) Carefully inspect your data, deselecting all spins which have "bad
data". Look at their graphs. Consider working with as few spins as
possible, and work your way up! Working this way will greatly increase your
productivity.

Protein 2:
Are you setting the bonds for the minimization manually?
This looks like the upper/lower bonds are specified wrong. This is not easy
to do. How are you doing it?

Best
Troels




2016-09-19 17:11 GMT+02:00 Mahdi, Sam :

> Hi Troels,
>
> I have successfully been able to run the model-free analysis on 64 cores.
> The issue appears to have been I simply did not specify the spin number, so
> after looking at your tutorial and making the proper modifications, it ran
> with no complications. The results are somewhat reasonable. I decided to
> try to run 2 other proteins however; and I've come across problems for both
> again.
> Protein 1:
> I set this up just like the tutorial, and it runs with no warnings or
> errors; however, the run never finishes. At round_3 for the prolate model
> when it starts to minimize it just stops. I don't mean relax is stopped or
> closed, I mean it stops doing any calculations. Relax is still open, and if
> I run the top command, I can still see something is going on with the other
> cores, but nothing is being calculated. The run with 64 cores is incredibly
> fast (under 4 hours), so I don't think it's loading calculations or writing
> them, and I've left it there for over 24 hours, and it's still just sorta
> stuck. There are no errors, no outputs, it just says its gonna start to
> minimize and then nothing happens after that.
> Protein2:
> This protein was a little different since the pdb structure was a crystal
> structure. I had to use WhatIf to add the protons onto the pdb file. The
> structure appears to load up fine, all the spins appear to be read, data is
> loaded, vectors and are calculated and define, but when I came to run the
> protocol this error pops up:
>  File "/home/sam2/relax-4.0.2/multi/processor.py", line 494, in run
> self.callback.init_master(self)
>   File "/home/sam2/relax-4.0.2/multi/__init__.py", line 318, in
> default_init_master
> self.master.run()
>   File "/home/sam2/relax-4.0.2/relax.py", line 199, in run
> self.interpreter.run(self.script_file)
>   File "/home/sam2/relax-4.0.2/prompt/interpreter.py", line 279, in run
> return run_script(intro=self.__intro_string, local=locals(),
> script_file=script_file, show_script=self.__show_script,
> raise_relax_error=self.__raise_relax_error)
>   File "/home/sam2/relax-4.0.2/prompt/interpreter.py", line 585, in
> run_script
> return console.interact(intro, local, script_file,
> show_script=show_script, raise_relax_error=raise_relax_error)
>   File "/home/sam2/relax-4.0.2/prompt/interpreter.py", line 484, in
> interact_script
> exec_script(script_file, local)
>   File

Re: Using multi-processor for model_free

2016-09-19 Thread Mahdi, Sam

Hi Troels,

I have successfully been able to run the model-free analysis on 64 cores.
The issue appears to have been I simply did not specify the spin number, so
after looking at your tutorial and making the proper modifications, it ran
with no complications. The results are somewhat reasonable. I decided to
try to run 2 other proteins however; and I've come across problems for both
again.
Protein 1:
I set this up just like the tutorial, and it runs with no warnings or
errors; however, the run never finishes. At round_3 for the prolate model
when it starts to minimize it just stops. I don't mean relax is stopped or
closed, I mean it stops doing any calculations. Relax is still open, and if
I run the top command, I can still see something is going on with the other
cores, but nothing is being calculated. The run with 64 cores is incredibly
fast (under 4 hours), so I don't think it's loading calculations or writing
them, and I've left it there for over 24 hours, and it's still just sorta
stuck. There are no errors, no outputs, it just says its gonna start to
minimize and then nothing happens after that.
Protein2:
This protein was a little different since the pdb structure was a crystal
structure. I had to use WhatIf to add the protons onto the pdb file. The
structure appears to load up fine, all the spins appear to be read, data is
loaded, vectors and are calculated and define, but when I came to run the
protocol this error pops up:
 File "/home/sam2/relax-4.0.2/multi/processor.py", line 494, in run
self.callback.init_master(self)
  File "/home/sam2/relax-4.0.2/multi/__init__.py", line 318, in
default_init_master
self.master.run()
  File "/home/sam2/relax-4.0.2/relax.py", line 199, in run
self.interpreter.run(self.script_file)
  File "/home/sam2/relax-4.0.2/prompt/interpreter.py", line 279, in run
return run_script(intro=self.__intro_string, local=locals(),
script_file=script_file, show_script=self.__show_script,
raise_relax_error=self.__raise_relax_error)
  File "/home/sam2/relax-4.0.2/prompt/interpreter.py", line 585, in
run_script
return console.interact(intro, local, script_file,
show_script=show_script, raise_relax_error=raise_relax_error)
  File "/home/sam2/relax-4.0.2/prompt/interpreter.py", line 484, in
interact_script
exec_script(script_file, local)
  File "/home/sam2/relax-4.0.2/prompt/interpreter.py", line 363, in
exec_script
runpy.run_module(module, globals)
  File "/usr/lib64/python2.7/runpy.py", line 192, in run_module
fname, loader, pkg_name)
  File "/usr/lib64/python2.7/runpy.py", line 72, in _run_code
exec code in run_globals
  File "/home/sam2/relax-4.0.2/HdeA_script.py", line 30, in 
dAuvergne_protocol(pipe_name=name,pipe_bundle=pipe_bundle,
diff_model=DIFF_MODEL,mf_models=MF_MODELS,local_tm_
models=LOCAL_TM_MODELS,grid_inc=GRID_INC,min_algor=MIN_
ALGOR,mc_sim_num=MC_NUM,conv_loop=CONV_LOOP)
  File "/home/sam2/relax-4.0.2/auto_analyses/dauvergne_protocol.py", line
246, in __init__
self.execute()
  File "/home/sam2/relax-4.0.2/auto_analyses/dauvergne_protocol.py", line
600, in execute
self.multi_model(local_tm=True)
  File "/home/sam2/relax-4.0.2/auto_analyses/dauvergne_protocol.py", line
888, in multi_model
self.interpreter.minimise.grid_search(inc=self.grid_inc)
  File "/home/sam2/relax-4.0.2/prompt/uf_objects.py", line 225, in __call__
self._backend(*new_args, **uf_kargs)
  File "/home/sam2/relax-4.0.2/pipe_control/minimise.py", line 172, in
grid_search
model_lower, model_upper, model_inc = grid_setup(lower, upper, inc,
verbosity=verbosity, skip_preset=skip_preset)
  File "/home/sam2/relax-4.0.2/pipe_control/minimise.py", line 341, in
grid_setup
elif values[i] in [None, {}, []]:
IndexError: index 0 is out of bounds for axis 0 with size 0
I should mention this error pops up when it decided to calculate the first
spins upper and lower bounds. So this isn't at the minimization portion of
the calculation (like in the previous bug). Thanks in advance.

Sincerely,
Sam

On Wed, Sep 14, 2016 at 6:34 AM, Troels Emtekær Linnet <
tlin...@nmr-relax.com> wrote:

> Hi Sam.
>
> To tackle this problem, I would advice to create another bug.
> Creation and closing of a bug "leaves trails", which maybe will help
> another person, when googling for the same problem.
>
> To help you, can you do a "relax -i" on both computers?
> That give some indication about package versions and computer setup.
>
> The first thing we need to establish, is that mpirun is working.
> We have to test the installation without relax.
>
> Can you have a look at:
> http://wiki.nmr-relax.com/OpenMPI
>
> Try the different things like:
> lscpu
> mpirun --report-bindings -np 11 echo "hello world"
> mpirun --report-bindings -np 4 relax --multi='mpi4py'
>
> When we are confident about this, then we will try make a small test
> script for relax.
>
> Please try these things at both computers, and provide 2 files with
> commands and output.
>
> Then attach it to the bug

Re: Using multi-processor for model_free

2016-09-14 Thread Troels Emtekær Linnet

Hi Sam.

To tackle this problem, I would advice to create another bug.
Creation and closing of a bug "leaves trails", which maybe will help
another person, when googling for the same problem.

To help you, can you do a "relax -i" on both computers?
That give some indication about package versions and computer setup.

The first thing we need to establish, is that mpirun is working.
We have to test the installation without relax.

Can you have a look at:
http://wiki.nmr-relax.com/OpenMPI

Try the different things like:
lscpu
mpirun --report-bindings -np 11 echo "hello world"
mpirun --report-bindings -np 4 relax --multi='mpi4py'

When we are confident about this, then we will try make a small test script
for relax.

Please try these things at both computers, and provide 2 files with
commands and output.

Then attach it to the bug report.





2016-09-14 6:40 GMT+02:00 Mahdi, Sam :

> Hi Troels,
>
> So I saw the tutorial you put, and the main problem was I had not
> specified my data was only for the Nitrogen spins. After applying the spin
> column, my data loaded and relax ran model free with no problem. I have a
> script that starts and runs relax and model free all automatic, if you wish
> I can send it via email to you and you can upload it to the tutorial wiki
> page. So I can successfully run model-free in script mode for a
> uni-processor.
> The problem now with the multi-processor is that the script won't load. In
> the bug page I uploaded a screenshot where I had input the 'mpirun -np 4
> ../relax --multi='mpi4py' command, however I had no output. I checked
> processes running in the background, and saw that there was indeed 4
> processess running in the background (1 master and 3 slaves) for relax; but
> there was no output, so I was unable to load any data, or create a pipe or
> anything. This was only on the Fedora 24 computer, not the Fedora 20. On
> the Fedora 20 computer, I was able to successfully open relax on a multi
> processor platform. I can send the screenshots and the relax -i for both
> computers again. I don't know why it doesn't work the fedora 24. Do you
> know what could be causing this?
>
> Thanks again in advance
>
> On Tue, Sep 13, 2016 at 9:32 PM, Troels Emtekær Linnet <
> tlin...@nmr-relax.com> wrote:
>
>> Hi Sam
>>
>> Can you send the mail again and include the maillist?
>>
>> Best Troels
>>
>>
>> Den tirsdag den 13. september 2016 skrev Mahdi, Sam <
>> sam.mahdi@my.csun.edu>:
>>
>>> HI Troels,
>>>
>>> So I saw the tutorial you put, and the main problem was I had not
>>> specified my data was only for the Nitrogen spins. After applying the spin
>>> column, my data loaded and relax ran model free with no problem. I have a
>>> script that starts and runs relax and model free all automatic, if you wish
>>> I can send it via email to you and you can upload it to the tutorial wiki
>>> page. So I can successfully run model-free in script mode for a
>>> uni-processor.
>>> The problem now with the multi-processor is that the script won't load.
>>> In the bug page I uploaded a screenshot where I had input the 'mpirun -np 4
>>> ../relax --multi='mpi4py' command, however I had no output. I checked
>>> processes running in the background, and saw that there was indeed 4
>>> processess running in the background (1 master and 3 slaves) for relax; but
>>> there was no output, so I was unable to load any data, or create a pipe or
>>> anything. This was only on the Fedora 24 computer, not the Fedora 20. On
>>> the Fedora 20 computer, I was able to successfully open relax on a multi
>>> processor platform. I can send the screenshots and the relax -i for both
>>> computers again. I don't know why it doesn't work the fedora 24. Do you
>>> know what could be causing this?
>>>
>>> Thanks again in advance
>>> Sam
>>>
>>> On Tue, Sep 13, 2016 at 1:01 PM, Troels Emtekær Linnet <
>>> tlin...@nmr-relax.com> wrote:
>>>
 Hi Sam.

 I closed the 2 bug reports as invalid.

 The data is not labelled correct.
 But this can be corrected.

 Please see this tutorial I wrote:
 http://wiki.nmr-relax.com/Tutorial_for_model-free_analysis_sam_mahdi

 I hope this give some guidance.

 If you experience any new problems, please feel free to ask!!

 What you experience, will probably be the same for many.
 Your feedback is valuable for the development.

 Please wait with using mpirun and multiple processors, before you are
 absolutely sure
 that it will run on 1 processor.

 Bugfixing when using multiple processors is a nightmare

 Best
 Troels

 2016-09-12 17:36 GMT+02:00 Mahdi, Sam :

> Hi Troels,
>
> I just created another bug report. I simply copy pasted the email, and
> uploaded the script files there.
>
> Sincerely,
> Sam
>
> On Mon, Sep 12, 2016 at 5:14 AM, Troels Emtekær Linnet <
>

Re: Using multi-processor for model_free

2016-09-13 Thread Mahdi, Sam

Hi Troels,

So I saw the tutorial you put, and the main problem was I had not specified
my data was only for the Nitrogen spins. After applying the spin column, my
data loaded and relax ran model free with no problem. I have a script that
starts and runs relax and model free all automatic, if you wish I can send
it via email to you and you can upload it to the tutorial wiki page. So I
can successfully run model-free in script mode for a uni-processor.
The problem now with the multi-processor is that the script won't load. In
the bug page I uploaded a screenshot where I had input the 'mpirun -np 4
../relax --multi='mpi4py' command, however I had no output. I checked
processes running in the background, and saw that there was indeed 4
processess running in the background (1 master and 3 slaves) for relax; but
there was no output, so I was unable to load any data, or create a pipe or
anything. This was only on the Fedora 24 computer, not the Fedora 20. On
the Fedora 20 computer, I was able to successfully open relax on a multi
processor platform. I can send the screenshots and the relax -i for both
computers again. I don't know why it doesn't work the fedora 24. Do you
know what could be causing this?

Thanks again in advance

On Tue, Sep 13, 2016 at 9:32 PM, Troels Emtekær Linnet <
tlin...@nmr-relax.com> wrote:

> Hi Sam
>
> Can you send the mail again and include the maillist?
>
> Best Troels
>
>
> Den tirsdag den 13. september 2016 skrev Mahdi, Sam <
> sam.mahdi@my.csun.edu>:
>
>> HI Troels,
>>
>> So I saw the tutorial you put, and the main problem was I had not
>> specified my data was only for the Nitrogen spins. After applying the spin
>> column, my data loaded and relax ran model free with no problem. I have a
>> script that starts and runs relax and model free all automatic, if you wish
>> I can send it via email to you and you can upload it to the tutorial wiki
>> page. So I can successfully run model-free in script mode for a
>> uni-processor.
>> The problem now with the multi-processor is that the script won't load.
>> In the bug page I uploaded a screenshot where I had input the 'mpirun -np 4
>> ../relax --multi='mpi4py' command, however I had no output. I checked
>> processes running in the background, and saw that there was indeed 4
>> processess running in the background (1 master and 3 slaves) for relax; but
>> there was no output, so I was unable to load any data, or create a pipe or
>> anything. This was only on the Fedora 24 computer, not the Fedora 20. On
>> the Fedora 20 computer, I was able to successfully open relax on a multi
>> processor platform. I can send the screenshots and the relax -i for both
>> computers again. I don't know why it doesn't work the fedora 24. Do you
>> know what could be causing this?
>>
>> Thanks again in advance
>> Sam
>>
>> On Tue, Sep 13, 2016 at 1:01 PM, Troels Emtekær Linnet <
>> tlin...@nmr-relax.com> wrote:
>>
>>> Hi Sam.
>>>
>>> I closed the 2 bug reports as invalid.
>>>
>>> The data is not labelled correct.
>>> But this can be corrected.
>>>
>>> Please see this tutorial I wrote:
>>> http://wiki.nmr-relax.com/Tutorial_for_model-free_analysis_sam_mahdi
>>>
>>> I hope this give some guidance.
>>>
>>> If you experience any new problems, please feel free to ask!!
>>>
>>> What you experience, will probably be the same for many.
>>> Your feedback is valuable for the development.
>>>
>>> Please wait with using mpirun and multiple processors, before you are
>>> absolutely sure
>>> that it will run on 1 processor.
>>>
>>> Bugfixing when using multiple processors is a nightmare
>>>
>>> Best
>>> Troels
>>>
>>> 2016-09-12 17:36 GMT+02:00 Mahdi, Sam :
>>>
 Hi Troels,

 I just created another bug report. I simply copy pasted the email, and
 uploaded the script files there.

 Sincerely,
 Sam

 On Mon, Sep 12, 2016 at 5:14 AM, Troels Emtekær Linnet <
 tlin...@nmr-relax.com> wrote:

> Hi Sam.
>
> Can you produce another bug report.
>
> Please don't attach files to these mails as it will strain  the
> mailinglists.
>
> Cheers
> Troels
>
>
> Den lørdag den 10. september 2016 skrev Mahdi, Sam <
> sam.mahdi@my.csun.edu>:
>
>> Hi Troels,
>>
>> Additional question that I had, if you could also look into this as
>> well on Tuesday please. I have decided to try to write a script to 
>> automate
>> this whole process (since I won't be using the gui to do model free), and
>> I've come across a problem. I can successfully open up relax using 
>> openmpi,
>> and can load the pdb file, and assign all the spins and isotopes; 
>> however,
>> it appears it will only load one data file (the very first one I'll have
>> inputed in the script). I don't know if there is a problem with how I 
>> wrote
>> my script. Not only will it not load the rest of my data sets, it won't
>> actually run

Re: Using multi-processor for model_free

2016-09-12 Thread Troels Emtekær Linnet

Hi Sam.

Can you produce another bug report.

Please don't attach files to these mails as it will strain  the
mailinglists.

Cheers
Troels

Den lørdag den 10. september 2016 skrev Mahdi, Sam <
sam.mahdi@my.csun.edu>:

> Hi Troels,
>
> Additional question that I had, if you could also look into this as well
> on Tuesday please. I have decided to try to write a script to automate this
> whole process (since I won't be using the gui to do model free), and I've
> come across a problem. I can successfully open up relax using openmpi, and
> can load the pdb file, and assign all the spins and isotopes; however, it
> appears it will only load one data file (the very first one I'll have
> inputed in the script). I don't know if there is a problem with how I wrote
> my script. Not only will it not load the rest of my data sets, it won't
> actually run dAuvergne's protocol either, it'll just load the data set and
> exit out of the program. Attached is the script I wrote for relax.
>
> This is the output once relax has loaded
>
> script = 'model_free_sample_script.py'
> 
> 
> from time import asctime, localtime
> from auto_analyses.dauvergne_protocol import dAuvergne_protocol
> DIFF_MODEL=['local_tm','sphere','prolate','oblate','ellipsoid','final']
> MF_MODELS=['m0','m1','m2','m3','m4','m5','m6','m7','m8','m9']
> LOCAL_TM_MODELS=['tm0','tm1','tm2','tm3','tm4','tm5','tm6','
> tm7','tm7','tm8','tm9']
> GRID_INC=11
> MIN_ALGOR='newton'
> MC_NUM=500
> CONV_LOOP=True
> pipe_bundle="mf(%s)"%asctime(localtime())
> name="origin-"+pipe_bundle
> pipe.create(name,'mf',bundle=pipe_bundle)
> structure.read_pdb('2d9j.pdb',set_mol_name='hRGS7')
> structure.load_spins('@N',ave_pos=True)
> structure.load_spins('@NE1',ave_pos=True)
> structure.load_spins('@H',ave_pos=True)
> structure.load_spins('@HE1',ave_pos=True)
> spin.isotope('15N',spin_id='@N*')
> spin.isotope('1H',spin_id='@H*')
> relax_data.read(ri_id='R1_Agnes',ri_type='R1',frq=599.642*1e6,
> file='R1_Agnes',res_num_col=1,data_col=2,error_col=3)
> relax_data.read(ri_id='R2_Agnes',ri_type='R2',frq=599.642*1e6,
> file='R2_Agnes',res_num_col=1,data_col=2,error_col=3)
> relax_data.read(ri_id='ssNOE_Agnes',ri_type='NOE',frq=599.642*1e6,
> file='ssNOE_Agnes',res_num_col=1,data_col=2,error_col=3)
> relax_data.read(ri_id='R1_NMRFAM',ri_type='R1',frq=799.642*1e6,
> file='R1_NMRFAM',res_num_col=1,data_col=2,error_col=3)
> relax_data.read(ri_id='R2_NMRFAM',ri_type='R2',frq=799.642*1e6,
> file='R2_NMRFAM',res_num_col=1,data_col=2,error_col=3)
> relax_data.read(ri_id='ssNOE_NMRFAM',ri_type='NOE',frq=799.642*1e6,
> file='ssNOE_NMRFAM',res_num_col=1,data_col=2,error_col=3)
> interatom.define(spin_id1='@N',spin_id2='@H', direct_bond=True)
> interatom.define(spin_id1='@NE1',spin_id2='@HE1', direct_bond=True)
> interatom.set_dist(spin_id1='@N*',spin_id2='@H*',ave_dist=1.02*1e-10)
> interatom.unit_vectors()
> value.set(-172*1e-6,'csa',spin_id='@N*')
> dAuvergne_protocol(pipe_name=name,pipe_bundle=pipe_bundle,
> diff_model=DIFF_MODEL,mf_models=MF_MODELS,local_tm_
> models=LOCAL_TM_MODELS,grid_inc=GRID_INC,min_algor=MIN_
> ALGOR,mc_sim_num=MC_NUM,conv_loop=CONV_LOOP)
>
> So it indicates that my script has loaded. However, after it loads the
> spins from the pdb file, this is what happens after my first data set has
> been loaded:
>
> relax> relax_data.read(ri_id='R1_Agnes', ri_type='R1', frq=599642000.0,
> file='R1_Agnes', dir=None, spin_id_col=None, mol_name_col=None,
> res_num_col=1, res_name_col=None, spin_num_col=None, spin_name_col=None,
> data_col=2, error_col=3, sep=None, spin_id=None)
> Opening the file 'R1_Agnes' for reading.
> RelaxWarning: The sequence data in the line ['Residue', 'R1', 'Error'] is
> invalid, the residue number data 'Residue' is invalid.
> RelaxWarning: The sequence data in the line ['1'] is invalid, the data is
> missing.
> RelaxWarning: The sequence data in the line ['2'] is invalid, the data is
> missing.
> RelaxWarning: The sequence data in the line ['3'] is invalid, the data is
> missing.
> RelaxWarning: The sequence data in the line ['4'] is invalid, the data is
> missing.
> RelaxWarning: The sequence data in the line ['5'] is invalid, the data is
> missing.
> RelaxWarning: The sequence data in the line ['6'] is invalid, the data is
> missing.
> RelaxWarning: The sequence data in the line ['7'] is invalid, the data is
> missing.
> RelaxWarning: The sequence data in the line ['8'] is invalid, the data is
> missing.
> RelaxWarning: The sequence data in the line ['9'] is invalid, the data is
> missing.
> RelaxWarning: The sequence data in the line ['10'] is invalid, the data is
> missing.
> RelaxWarning: The sequence data in the line ['11'] is invalid, the data is
> missing.
> RelaxWarning: The sequence data in the line ['16'] is invalid, the data is
> missing.
> RelaxWarning: The sequence data in the line ['17'] is invalid, the data is
> missing.
> RelaxWarning:

Re: Using multi-processor for model_free

2016-09-09 Thread Mahdi, Sam

Hi Troels,

Additional question that I had, if you could also look into this as well on
Tuesday please. I have decided to try to write a script to automate this
whole process (since I won't be using the gui to do model free), and I've
come across a problem. I can successfully open up relax using openmpi, and
can load the pdb file, and assign all the spins and isotopes; however, it
appears it will only load one data file (the very first one I'll have
inputed in the script). I don't know if there is a problem with how I wrote
my script. Not only will it not load the rest of my data sets, it won't
actually run dAuvergne's protocol either, it'll just load the data set and
exit out of the program. Attached is the script I wrote for relax.

This is the output once relax has loaded

script = 'model_free_sample_script.py'

from time import asctime, localtime
from auto_analyses.dauvergne_protocol import dAuvergne_protocol
DIFF_MODEL=['local_tm','sphere','prolate','oblate','ellipsoid','final']
MF_MODELS=['m0','m1','m2','m3','m4','m5','m6','m7','m8','m9']
LOCAL_TM_MODELS=['tm0','tm1','tm2','tm3','tm4','tm5','tm6','tm7','tm7','tm8','tm9']
GRID_INC=11
MIN_ALGOR='newton'
MC_NUM=500
CONV_LOOP=True
pipe_bundle="mf(%s)"%asctime(localtime())
name="origin-"+pipe_bundle
pipe.create(name,'mf',bundle=pipe_bundle)
structure.read_pdb('2d9j.pdb',set_mol_name='hRGS7')
structure.load_spins('@N',ave_pos=True)
structure.load_spins('@NE1',ave_pos=True)
structure.load_spins('@H',ave_pos=True)
structure.load_spins('@HE1',ave_pos=True)
spin.isotope('15N',spin_id='@N*')
spin.isotope('1H',spin_id='@H*')
relax_data.read(ri_id='R1_Agnes',ri_type='R1',frq=599.642*1e6,
file='R1_Agnes',res_num_col=1,data_col=2,error_col=3)
relax_data.read(ri_id='R2_Agnes',ri_type='R2',frq=599.642*1e6,
file='R2_Agnes',res_num_col=1,data_col=2,error_col=3)
relax_data.read(ri_id='ssNOE_Agnes',ri_type='NOE',frq=599.642*1e6,
file='ssNOE_Agnes',res_num_col=1,data_col=2,error_col=3)
relax_data.read(ri_id='R1_NMRFAM',ri_type='R1',frq=799.642*1e6,
file='R1_NMRFAM',res_num_col=1,data_col=2,error_col=3)
relax_data.read(ri_id='R2_NMRFAM',ri_type='R2',frq=799.642*1e6,
file='R2_NMRFAM',res_num_col=1,data_col=2,error_col=3)
relax_data.read(ri_id='ssNOE_NMRFAM',ri_type='NOE',frq=799.642*1e6,
file='ssNOE_NMRFAM',res_num_col=1,data_col=2,error_col=3)
interatom.define(spin_id1='@N',spin_id2='@H', direct_bond=True)
interatom.define(spin_id1='@NE1',spin_id2='@HE1', direct_bond=True)
interatom.set_dist(spin_id1='@N*',spin_id2='@H*',ave_dist=1.02*1e-10)
interatom.unit_vectors()
value.set(-172*1e-6,'csa',spin_id='@N*')
dAuvergne_protocol(pipe_name=name,pipe_bundle=pipe_bundle,diff_model=DIFF_MODEL,mf_models=MF_MODELS,local_tm_models=LOCAL_TM_MODELS,grid_inc=GRID_INC,min_algor=MIN_ALGOR,mc_sim_num=MC_NUM,conv_loop=CONV_LOOP)

So it indicates that my script has loaded. However, after it loads the
spins from the pdb file, this is what happens after my first data set has
been loaded:

relax> relax_data.read(ri_id='R1_Agnes', ri_type='R1', frq=599642000.0,
file='R1_Agnes', dir=None, spin_id_col=None, mol_name_col=None,
res_num_col=1, res_name_col=None, spin_num_col=None, spin_name_col=None,
data_col=2, error_col=3, sep=None, spin_id=None)
Opening the file 'R1_Agnes' for reading.
RelaxWarning: The sequence data in the line ['Residue', 'R1', 'Error'] is
invalid, the residue number data 'Residue' is invalid.
RelaxWarning: The sequence data in the line ['1'] is invalid, the data is
missing.
RelaxWarning: The sequence data in the line ['2'] is invalid, the data is
missing.
RelaxWarning: The sequence data in the line ['3'] is invalid, the data is
missing.
RelaxWarning: The sequence data in the line ['4'] is invalid, the data is
missing.
RelaxWarning: The sequence data in the line ['5'] is invalid, the data is
missing.
RelaxWarning: The sequence data in the line ['6'] is invalid, the data is
missing.
RelaxWarning: The sequence data in the line ['7'] is invalid, the data is
missing.
RelaxWarning: The sequence data in the line ['8'] is invalid, the data is
missing.
RelaxWarning: The sequence data in the line ['9'] is invalid, the data is
missing.
RelaxWarning: The sequence data in the line ['10'] is invalid, the data is
missing.
RelaxWarning: The sequence data in the line ['11'] is invalid, the data is
missing.
RelaxWarning: The sequence data in the line ['16'] is invalid, the data is
missing.
RelaxWarning: The sequence data in the line ['17'] is invalid, the data is
missing.
RelaxWarning: The sequence data in the line ['18'] is invalid, the data is
missing.
RelaxWarning: The sequence data in the line ['21'] is invalid, the data is
missing.
RelaxWarning: The sequence data in the line ['22'] is invalid, the data is
missing.
RelaxWarning: The sequence data in the line ['23'] is invalid, the data is
missing.
RelaxWarning: The sequence data in the line ['26'] is invalid, the data is
missing.

Re: Using multi-processor for model_free

2016-09-08 Thread Mahdi, Sam

Hi Troels,

Thank you so much. If there is any extra info you need please let me know.

Sincerely,
Sam

On Thu, Sep 8, 2016 at 9:12 AM, Troels Emtekær Linnet  wrote:

> Hi Sam.
>
> I will have some time on Tuesday, and then I will look at it.
>
> Best
> Troels
>
>
> Den onsdag den 7. september 2016 skrev Mahdi, Sam <
> sam.mahdi@my.csun.edu>:
>
>> Hello Troels,
>>
>> I  uploaded all the files, and even added in the entire output that i
>> recieved using model free in script mode. I didn't know if all the files
>> uploaded need to have that link, so only the initial files that were
>> uploaded it, have it.
>> Thank you in advance for your help!
>> Sincerely,
>> Sam
>>
>> On Wed, Sep 7, 2016 at 12:41 AM, Troels Emtekær Linnet <
>> tlin...@nmr-relax.com> wrote:
>>
>>> Hi Sam.
>>>
>>> You should be able to upload more files after the initial upload.
>>> In the comment thread, please also make a link to this discussion.
>>>
>>> https://mail.gna.org/public/relax-users/2016-09/threads.html#1
>>>
>>> Best
>>> Troels
>>>
>>>
>>>
>>> 2016-09-06 19:10 GMT+02:00 Mahdi, Sam :
>>>
 Thank you for your reply. When I come to upload my data though, I see
 there are only 4 available slots I can upload my data. I have a total of 6
 data files however, that need to be uploaded (3 of each frequency). I also
 need to upload the relax -i of 2 different computers, and the script file
 I've been using for a total of 9 files that need to be uploaded. Is there a
 way to increase the amount I can upload, or can I upload more after the
 initial submission?

 On Mon, Sep 5, 2016 at 2:46 AM, Troels Emtekær Linnet <
 tlin...@nmr-relax.com> wrote:

> Hi Sam.
>
> To solve this problem, it would be easier to have access to some of
> your data.
> Can you upload to: https://gna.org/bugs/?group=relax
>
> Take each of your data files, and delete all data, except 2 spins.
> Also provide your script file, or a description of which button you
> press in the GUI.
>
> Please also provide information about your system with:
> relax -i
>
> Then I will make a tutorial for you. To be added here:
> http://wiki.nmr-relax.com/Category:Tutorials
>
> If there is a problem in relax, I will write a systemtest which will
> solve the problem.
> And the problem will never return.
>
> If this a user error, the tutorial should help to prevent this, and
> would be the first step before
> adding/modifying the manual.
>
> Regarding using mpirun.
> Have a look at this page. Maybe it helps.
> http://wiki.nmr-relax.com/OpenMPI
>
>
> Cheers.
>
>
> 2016-09-03 4:13 GMT+02:00 Mahdi, Sam :
>
>> Hello everyone,
>>
>> So I was able to set up and run the dauvergne_protocol successfully by
>> using the script in the wiki. The problem I have come across now is
>> the
>> program doesn't seem to read my data. Using the gui interface I was
>> able to
>> successfully load my data and run it. When I upload my data using the
>> script command:
>> relax_data.read(ri_id='R1_Agnes',ri_type='R1',frq=599.642*1e6,
>> file='R1_Agnes',res_num_col=1,data_col=2,error_col=3)
>>
>> The output file simply gives errors for amino acids I don't have data
>> for:
>> RelaxWarning: The sequence data in the line ['1'] is invalid, the
>> data is
>> missing.
>>
>> This is fine as relax just ignores these values and continues its
>> calculations. I only receive this warning for values I don't have
>> data for.
>> This is the same thing I got when using the gui interface (the gui
>> however
>> showed my values that I have data for and the residue it corresponds
>> to,
>> using the script I don't receive such an output, I don't know whether
>> this
>> is normal or not). However, since I don't get this warning for every
>> amino
>> acid, I assume this means it has read the values for the other amino
>> acids.
>> All of my data is the same, relax warnings only pop up for amino
>> acids that
>> I don't have data for. The problem is, when I enter the dAuvergne
>> protocol,
>> I get the protocol working, it starts running local_tm however it
>> appears
>> none of my data has been uploaded:
>> RelaxWarning: The spin '#hRGS7:2@N' has been deselected because of
>> missing
>> relaxation data
>> RelaxWarning: The spin '#hRGS7:3@N' has been deselected because of
>> missing
>> relaxation data
>>
>> And I get that warning for every single amino acid. From the output,
>> it
>> appears to have read the file since it knows exactly which amino
>> acids I
>> don't have data for, but I don't know why when it comes to running the
>> protocol, it tells me I havn't

Re: Using multi-processor for model_free

2016-09-08 Thread Troels Emtekær Linnet

Hi Sam.

I will have some time on Tuesday, and then I will look at it.

Best
Troels

Den onsdag den 7. september 2016 skrev Mahdi, Sam :

> Hello Troels,
>
> I  uploaded all the files, and even added in the entire output that i
> recieved using model free in script mode. I didn't know if all the files
> uploaded need to have that link, so only the initial files that were
> uploaded it, have it.
> Thank you in advance for your help!
> Sincerely,
> Sam
>
> On Wed, Sep 7, 2016 at 12:41 AM, Troels Emtekær Linnet <
> tlin...@nmr-relax.com
> > wrote:
>
>> Hi Sam.
>>
>> You should be able to upload more files after the initial upload.
>> In the comment thread, please also make a link to this discussion.
>>
>> https://mail.gna.org/public/relax-users/2016-09/threads.html#1
>>
>> Best
>> Troels
>>
>>
>>
>> 2016-09-06 19:10 GMT+02:00 Mahdi, Sam > >:
>>
>>> Thank you for your reply. When I come to upload my data though, I see
>>> there are only 4 available slots I can upload my data. I have a total of 6
>>> data files however, that need to be uploaded (3 of each frequency). I also
>>> need to upload the relax -i of 2 different computers, and the script file
>>> I've been using for a total of 9 files that need to be uploaded. Is there a
>>> way to increase the amount I can upload, or can I upload more after the
>>> initial submission?
>>>
>>> On Mon, Sep 5, 2016 at 2:46 AM, Troels Emtekær Linnet <
>>> tlin...@nmr-relax.com
>>> > wrote:
>>>
 Hi Sam.

 To solve this problem, it would be easier to have access to some of
 your data.
 Can you upload to: https://gna.org/bugs/?group=relax

 Take each of your data files, and delete all data, except 2 spins.
 Also provide your script file, or a description of which button you
 press in the GUI.

 Please also provide information about your system with:
 relax -i

 Then I will make a tutorial for you. To be added here:
 http://wiki.nmr-relax.com/Category:Tutorials

 If there is a problem in relax, I will write a systemtest which will
 solve the problem.
 And the problem will never return.

 If this a user error, the tutorial should help to prevent this, and
 would be the first step before
 adding/modifying the manual.

 Regarding using mpirun.
 Have a look at this page. Maybe it helps.
 http://wiki.nmr-relax.com/OpenMPI


 Cheers.


 2016-09-03 4:13 GMT+02:00 Mahdi, Sam >:

> Hello everyone,
>
> So I was able to set up and run the dauvergne_protocol successfully by
> using the script in the wiki. The problem I have come across now is the
> program doesn't seem to read my data. Using the gui interface I was
> able to
> successfully load my data and run it. When I upload my data using the
> script command:
> relax_data.read(ri_id='R1_Agnes',ri_type='R1',frq=599.642*1e6,
> file='R1_Agnes',res_num_col=1,data_col=2,error_col=3)
>
> The output file simply gives errors for amino acids I don't have data
> for:
> RelaxWarning: The sequence data in the line ['1'] is invalid, the data
> is
> missing.
>
> This is fine as relax just ignores these values and continues its
> calculations. I only receive this warning for values I don't have data
> for.
> This is the same thing I got when using the gui interface (the gui
> however
> showed my values that I have data for and the residue it corresponds
> to,
> using the script I don't receive such an output, I don't know whether
> this
> is normal or not). However, since I don't get this warning for every
> amino
> acid, I assume this means it has read the values for the other amino
> acids.
> All of my data is the same, relax warnings only pop up for amino acids
> that
> I don't have data for. The problem is, when I enter the dAuvergne
> protocol,
> I get the protocol working, it starts running local_tm however it
> appears
> none of my data has been uploaded:
> RelaxWarning: The spin '#hRGS7:2@N' has been deselected because of
> missing
> relaxation data
> RelaxWarning: The spin '#hRGS7:3@N' has been deselected because of
> missing
> relaxation data
>
> And I get that warning for every single amino acid. From the output, it
> appears to have read the file since it knows exactly which amino acids
> I
> don't have data for, but I don't know why when it comes to running the
> protocol, it tells me I havn't inputed any data. I have typed
> everything
> directly according to the script from the wiki.

Re: Using multi-processor for model_free

2016-09-07 Thread Mahdi, Sam

Hello Troels,

I  uploaded all the files, and even added in the entire output that i
recieved using model free in script mode. I didn't know if all the files
uploaded need to have that link, so only the initial files that were
uploaded it, have it.
Thank you in advance for your help!
Sincerely,
Sam

On Wed, Sep 7, 2016 at 12:41 AM, Troels Emtekær Linnet <
tlin...@nmr-relax.com> wrote:

> Hi Sam.
>
> You should be able to upload more files after the initial upload.
> In the comment thread, please also make a link to this discussion.
>
> https://mail.gna.org/public/relax-users/2016-09/threads.html#1
>
> Best
> Troels
>
>
>
> 2016-09-06 19:10 GMT+02:00 Mahdi, Sam :
>
>> Thank you for your reply. When I come to upload my data though, I see
>> there are only 4 available slots I can upload my data. I have a total of 6
>> data files however, that need to be uploaded (3 of each frequency). I also
>> need to upload the relax -i of 2 different computers, and the script file
>> I've been using for a total of 9 files that need to be uploaded. Is there a
>> way to increase the amount I can upload, or can I upload more after the
>> initial submission?
>>
>> On Mon, Sep 5, 2016 at 2:46 AM, Troels Emtekær Linnet <
>> tlin...@nmr-relax.com> wrote:
>>
>>> Hi Sam.
>>>
>>> To solve this problem, it would be easier to have access to some of your
>>> data.
>>> Can you upload to: https://gna.org/bugs/?group=relax
>>>
>>> Take each of your data files, and delete all data, except 2 spins.
>>> Also provide your script file, or a description of which button you
>>> press in the GUI.
>>>
>>> Please also provide information about your system with:
>>> relax -i
>>>
>>> Then I will make a tutorial for you. To be added here:
>>> http://wiki.nmr-relax.com/Category:Tutorials
>>>
>>> If there is a problem in relax, I will write a systemtest which will
>>> solve the problem.
>>> And the problem will never return.
>>>
>>> If this a user error, the tutorial should help to prevent this, and
>>> would be the first step before
>>> adding/modifying the manual.
>>>
>>> Regarding using mpirun.
>>> Have a look at this page. Maybe it helps.
>>> http://wiki.nmr-relax.com/OpenMPI
>>>
>>>
>>> Cheers.
>>>
>>>
>>> 2016-09-03 4:13 GMT+02:00 Mahdi, Sam :
>>>
 Hello everyone,

 So I was able to set up and run the dauvergne_protocol successfully by
 using the script in the wiki. The problem I have come across now is the
 program doesn't seem to read my data. Using the gui interface I was
 able to
 successfully load my data and run it. When I upload my data using the
 script command:
 relax_data.read(ri_id='R1_Agnes',ri_type='R1',frq=599.642*1e6,
 file='R1_Agnes',res_num_col=1,data_col=2,error_col=3)

 The output file simply gives errors for amino acids I don't have data
 for:
 RelaxWarning: The sequence data in the line ['1'] is invalid, the data
 is
 missing.

 This is fine as relax just ignores these values and continues its
 calculations. I only receive this warning for values I don't have data
 for.
 This is the same thing I got when using the gui interface (the gui
 however
 showed my values that I have data for and the residue it corresponds to,
 using the script I don't receive such an output, I don't know whether
 this
 is normal or not). However, since I don't get this warning for every
 amino
 acid, I assume this means it has read the values for the other amino
 acids.
 All of my data is the same, relax warnings only pop up for amino acids
 that
 I don't have data for. The problem is, when I enter the dAuvergne
 protocol,
 I get the protocol working, it starts running local_tm however it
 appears
 none of my data has been uploaded:
 RelaxWarning: The spin '#hRGS7:2@N' has been deselected because of
 missing
 relaxation data
 RelaxWarning: The spin '#hRGS7:3@N' has been deselected because of
 missing
 relaxation data

 And I get that warning for every single amino acid. From the output, it
 appears to have read the file since it knows exactly which amino acids I
 don't have data for, but I don't know why when it comes to running the
 protocol, it tells me I havn't inputed any data. I have typed everything
 directly according to the script from the wiki. From running the
 protoco,
 it appears everything has properly been uploaded, structure data,
 magnetic
 dipole interactions, csa, the data pipe, the analysis variables, the
 python
 module imports, and setting up the spins from the pdb file. It appears
 the
 only error is from loading the actual relaxation data.

 On a completely unrelated side note, I have been attempting to run
 relax on
 multiple processors. I have tried 2 different computers, both fedora
 linux.
 I have mpi4py and openmpi

Re: Using multi-processor for model_free

2016-09-07 Thread Troels Emtekær Linnet

Hi Sam.

You should be able to upload more files after the initial upload.
In the comment thread, please also make a link to this discussion.

https://mail.gna.org/public/relax-users/2016-09/threads.html#1

Best
Troels



2016-09-06 19:10 GMT+02:00 Mahdi, Sam :

> Thank you for your reply. When I come to upload my data though, I see
> there are only 4 available slots I can upload my data. I have a total of 6
> data files however, that need to be uploaded (3 of each frequency). I also
> need to upload the relax -i of 2 different computers, and the script file
> I've been using for a total of 9 files that need to be uploaded. Is there a
> way to increase the amount I can upload, or can I upload more after the
> initial submission?
>
> On Mon, Sep 5, 2016 at 2:46 AM, Troels Emtekær Linnet <
> tlin...@nmr-relax.com> wrote:
>
>> Hi Sam.
>>
>> To solve this problem, it would be easier to have access to some of your
>> data.
>> Can you upload to: https://gna.org/bugs/?group=relax
>>
>> Take each of your data files, and delete all data, except 2 spins.
>> Also provide your script file, or a description of which button you press
>> in the GUI.
>>
>> Please also provide information about your system with:
>> relax -i
>>
>> Then I will make a tutorial for you. To be added here:
>> http://wiki.nmr-relax.com/Category:Tutorials
>>
>> If there is a problem in relax, I will write a systemtest which will
>> solve the problem.
>> And the problem will never return.
>>
>> If this a user error, the tutorial should help to prevent this, and would
>> be the first step before
>> adding/modifying the manual.
>>
>> Regarding using mpirun.
>> Have a look at this page. Maybe it helps.
>> http://wiki.nmr-relax.com/OpenMPI
>>
>>
>> Cheers.
>>
>>
>> 2016-09-03 4:13 GMT+02:00 Mahdi, Sam :
>>
>>> Hello everyone,
>>>
>>> So I was able to set up and run the dauvergne_protocol successfully by
>>> using the script in the wiki. The problem I have come across now is the
>>> program doesn't seem to read my data. Using the gui interface I was able
>>> to
>>> successfully load my data and run it. When I upload my data using the
>>> script command:
>>> relax_data.read(ri_id='R1_Agnes',ri_type='R1',frq=599.642*1e6,
>>> file='R1_Agnes',res_num_col=1,data_col=2,error_col=3)
>>>
>>> The output file simply gives errors for amino acids I don't have data
>>> for:
>>> RelaxWarning: The sequence data in the line ['1'] is invalid, the data is
>>> missing.
>>>
>>> This is fine as relax just ignores these values and continues its
>>> calculations. I only receive this warning for values I don't have data
>>> for.
>>> This is the same thing I got when using the gui interface (the gui
>>> however
>>> showed my values that I have data for and the residue it corresponds to,
>>> using the script I don't receive such an output, I don't know whether
>>> this
>>> is normal or not). However, since I don't get this warning for every
>>> amino
>>> acid, I assume this means it has read the values for the other amino
>>> acids.
>>> All of my data is the same, relax warnings only pop up for amino acids
>>> that
>>> I don't have data for. The problem is, when I enter the dAuvergne
>>> protocol,
>>> I get the protocol working, it starts running local_tm however it appears
>>> none of my data has been uploaded:
>>> RelaxWarning: The spin '#hRGS7:2@N' has been deselected because of
>>> missing
>>> relaxation data
>>> RelaxWarning: The spin '#hRGS7:3@N' has been deselected because of
>>> missing
>>> relaxation data
>>>
>>> And I get that warning for every single amino acid. From the output, it
>>> appears to have read the file since it knows exactly which amino acids I
>>> don't have data for, but I don't know why when it comes to running the
>>> protocol, it tells me I havn't inputed any data. I have typed everything
>>> directly according to the script from the wiki. From running the protoco,
>>> it appears everything has properly been uploaded, structure data,
>>> magnetic
>>> dipole interactions, csa, the data pipe, the analysis variables, the
>>> python
>>> module imports, and setting up the spins from the pdb file. It appears
>>> the
>>> only error is from loading the actual relaxation data.
>>>
>>> On a completely unrelated side note, I have been attempting to run relax
>>> on
>>> multiple processors. I have tried 2 different computers, both fedora
>>> linux.
>>> I have mpi4py and openmpi downloaded on both. On one, I can get relax on
>>> multiple cores working (havn't been able to successfully run it due to
>>> being unable to upload any data properly). On the other however, I type
>>> in
>>> the mpirun -np --multi='mpi4py' script, but I get no output. I can see
>>> that
>>> it's running in the background (top command), but nothing pops up, no
>>> text
>>> command, nothing. I typed the same mpirun with the --gui, but that opened
>>> up nothing. On a uni-processor (typing in the exact same command without
>>>

Re: Using multi-processor for model_free

2016-09-06 Thread Mahdi, Sam

Thank you for your reply. When I come to upload my data though, I see there
are only 4 available slots I can upload my data. I have a total of 6 data
files however, that need to be uploaded (3 of each frequency). I also need
to upload the relax -i of 2 different computers, and the script file I've
been using for a total of 9 files that need to be uploaded. Is there a way
to increase the amount I can upload, or can I upload more after the initial
submission?

On Mon, Sep 5, 2016 at 2:46 AM, Troels Emtekær Linnet  wrote:

> Hi Sam.
>
> To solve this problem, it would be easier to have access to some of your
> data.
> Can you upload to: https://gna.org/bugs/?group=relax
>
> Take each of your data files, and delete all data, except 2 spins.
> Also provide your script file, or a description of which button you press
> in the GUI.
>
> Please also provide information about your system with:
> relax -i
>
> Then I will make a tutorial for you. To be added here:
> http://wiki.nmr-relax.com/Category:Tutorials
>
> If there is a problem in relax, I will write a systemtest which will solve
> the problem.
> And the problem will never return.
>
> If this a user error, the tutorial should help to prevent this, and would
> be the first step before
> adding/modifying the manual.
>
> Regarding using mpirun.
> Have a look at this page. Maybe it helps.
> http://wiki.nmr-relax.com/OpenMPI
>
>
> Cheers.
>
>
> 2016-09-03 4:13 GMT+02:00 Mahdi, Sam :
>
>> Hello everyone,
>>
>> So I was able to set up and run the dauvergne_protocol successfully by
>> using the script in the wiki. The problem I have come across now is the
>> program doesn't seem to read my data. Using the gui interface I was able
>> to
>> successfully load my data and run it. When I upload my data using the
>> script command:
>> relax_data.read(ri_id='R1_Agnes',ri_type='R1',frq=599.642*1e6,
>> file='R1_Agnes',res_num_col=1,data_col=2,error_col=3)
>>
>> The output file simply gives errors for amino acids I don't have data for:
>> RelaxWarning: The sequence data in the line ['1'] is invalid, the data is
>> missing.
>>
>> This is fine as relax just ignores these values and continues its
>> calculations. I only receive this warning for values I don't have data
>> for.
>> This is the same thing I got when using the gui interface (the gui however
>> showed my values that I have data for and the residue it corresponds to,
>> using the script I don't receive such an output, I don't know whether this
>> is normal or not). However, since I don't get this warning for every amino
>> acid, I assume this means it has read the values for the other amino
>> acids.
>> All of my data is the same, relax warnings only pop up for amino acids
>> that
>> I don't have data for. The problem is, when I enter the dAuvergne
>> protocol,
>> I get the protocol working, it starts running local_tm however it appears
>> none of my data has been uploaded:
>> RelaxWarning: The spin '#hRGS7:2@N' has been deselected because of
>> missing
>> relaxation data
>> RelaxWarning: The spin '#hRGS7:3@N' has been deselected because of
>> missing
>> relaxation data
>>
>> And I get that warning for every single amino acid. From the output, it
>> appears to have read the file since it knows exactly which amino acids I
>> don't have data for, but I don't know why when it comes to running the
>> protocol, it tells me I havn't inputed any data. I have typed everything
>> directly according to the script from the wiki. From running the protoco,
>> it appears everything has properly been uploaded, structure data, magnetic
>> dipole interactions, csa, the data pipe, the analysis variables, the
>> python
>> module imports, and setting up the spins from the pdb file. It appears the
>> only error is from loading the actual relaxation data.
>>
>> On a completely unrelated side note, I have been attempting to run relax
>> on
>> multiple processors. I have tried 2 different computers, both fedora
>> linux.
>> I have mpi4py and openmpi downloaded on both. On one, I can get relax on
>> multiple cores working (havn't been able to successfully run it due to
>> being unable to upload any data properly). On the other however, I type in
>> the mpirun -np --multi='mpi4py' script, but I get no output. I can see
>> that
>> it's running in the background (top command), but nothing pops up, no text
>> command, nothing. I typed the same mpirun with the --gui, but that opened
>> up nothing. On a uni-processor (typing in the exact same command without
>> indicating how many cores i.e. no -np --multi='mpi4py') it works just
>> fine,
>> so I don't think its my openmpi that's an issue. I don't know whether this
>> is an issue with my mpi4py or a personal computer issue (since on the
>> other
>> computer relax runs just fine on multiple cores).
>>
>> Sincerely,
>> Sam
>>
>> P.S. when I do enter the top command to see what's running. My master
>> shows
>> mpirun, and the 3 slaves display python

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