S^2 differences between proteins

[Mahdi, Sam]

Hello everyone,

This isn't as much a problem with relax as it is a general question
regarding S^2 values itself. When comparing different values of S^2 between
proteins, what difference is considered significant. Due to the lower
values I know say an average S^2 value of .1 is a big difference in the
flexibility of one protein to another, but what about say an average
difference of .01, is that still considered a significant change in
considering the relative dynamics of one protein to another? (I.e. if say,
protein A has an average S^2 value of 9, and protein B has an average S^2
value of 8.9, could you make the statement Protein A has significant
dynamic differences, more rigid, when compared to Protein B. Or could you
make the statement due to only a difference of .01, there isn't much of a
overall dynamic difference between the 2 proteins)?

Sincerely,
Sam
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Re: Using Model-free models

[Mahdi, Sam]

Hi Edward,

So there is no point in running model-free unless you have data at 2 field
strengths? I also had a slight side question. I've read your papers on the
diffusion seeded paradigm, and dynamic models 1 and 2. I understand the
importance of the diffusion tensor value, and understand how the d'Auvergne
protocol fixes that. My question is, does the diffusion tensor help the
model selection then? I've run the new protocol on a protein that had data
at 2 different frequencies. I then found out what model it picked for each
residue. Then I ran the model free models with the estimated diffusion
tensor, and selected the model I wanted it to run, to see whether or not I
would obtain a similar value to the d'Auvergne protocol run for those
residues, which it did (i.e. for residues that had S^2 from m4 in
d'Auvergne protocol, the S^2 from my m4 single model free run gave almost
the same values for those residues). From that I assumed, model free models
data would give similar values to the d'Auvergne protocol, if the correct
model was selected; however, I wasn't able to get any model selection which
is why I sent the initial email. That's why my question is, is the
diffusion tensor crucial then for selecting the proper model?

Sincerely,
Sam

On Fri, Nov 11, 2016 at 1:21 AM, Edward d'Auvergne <edw...@nmr-relax.com>
wrote:

> On 10 November 2016 at 23:50, Mahdi, Sam <sam.mahdi@my.csun.edu>
> wrote:
> > Hello everyone,
> >
> > I've been attempting to run model free models (due to only have data at
> one
> > field strength), but I've come across a problem. I have set up both the
> > model free models script and the model free model selection, both models
> > run fine, and I do end up receiving data that does make sense and is
> good;
> > however, the script doesn't seem to actually select any models. I.e. if I
> > put in the m0-m9 in the script, it'll select m9 for every single reside
> and
> > only give me Rex data and no S^2. If I run m0-m4 same thing, it'll run
> > every residue at m4, instead of running through all the models and
> > selecting the data that fits that model. I know it states that the model
> is
> > supposed to loop through every model, then you run the model selection to
> > select what model fits which data set, but I don't know if my script is
> set
> > up incorrectly or what. Here is my script for model-free models:
> > pipes = ['m0','m1','m2','m3','m4']
> > for name in pipes:
> > pipe.create(name,'mf')
> > sequence.read('ssNOE_RGS4Agnes',res_num_col=1)
> > spin.name('N')
> > spin.element(element='N',spin_id='@N')
> > spin.isotope('15N',spin_id='@N')
> > structure.read_pdb('cluster1_12.pdb',read_mol=1)
> > relax_data.read(ri_id='R1_Agnes',ri_type='R1',frq=599.642*1e6,
> > file='R1_RGS4Agnes',res_num_col=1,spin_name_col=2,data_
> col=3,error_col=4)
> > relax_data.read(ri_id='R2_Agnes',ri_type='R2',frq=599.642*1e6,
> > file='R2_RGS4Agnes',res_num_col=1,spin_name_col=2,data_
> col=3,error_col=4)
> > relax_data.read(ri_id='ssNOE_Agnes',ri_type='NOE',frq=599.642*1e6,
> > file='ssNOE_RGS4Agnes',res_num_col=1,spin_name_col=2,
> data_col=3,error_col=4)
> > diffusion_tensor.init(1e-8,fixed=True)
> > sequence.attach_protons()
> > interatom.define(spin_id1='@N',spin_id2='@H',direct_bond=True)
> > interatom.set_dist(spin_id1='@N',spin_id2='@H',ave_dist=1.02*1e-10)
> > structure.get_pos('@N')
> > structure.get_pos('@H')
> > interatom.unit_vectors()
> > value.set(-172*1e-6,'csa',spin_id='@N')
> > model_free.select_model(model=name)
> > minimise.grid_search(inc=11)
> > minimise.execute('newton')
> > results.write(file='results',force=True)
> > state.save('save',force=True)
> >
> > Again I only have it at m0-m4 because I wanted to obtain the m4 data, but
> > even if it is to m9, it'll only run the m9 model (i.e. I will only
> receive
> > Rex data because that's whats attributed to m9).  Here is my model
> > selection script:
> > pipes = ['m0','m1','m2','m3','m4']
> > for name in pipes:
> > print("\n\n#"+name+"#")
> > pipe.create(name,'mf')
> > results.read(file='results.bz2',dir=name)
> > eliminate()
> > model_selection(method='AIC',modsel_pipe='aic')
> > state.save('save',force=True)
> > results.write(file='results',force=True)
> >
> > Again, this is only set up to m4 for the same reasons as before. I don't
> > know whether or not I have something in my script set up, but my final
> > results file just shows the model that was selected for every residue, is
> > the last model I have in my pipes (i.e. if m4 is the last model, it'll
> run
> > model 4, if m9 is the la

Using Model-free models

[Mahdi, Sam]

Hello everyone,

I've been attempting to run model free models (due to only have data at one
field strength), but I've come across a problem. I have set up both the
model free models script and the model free model selection, both models
run fine, and I do end up receiving data that does make sense and is good;
however, the script doesn't seem to actually select any models. I.e. if I
put in the m0-m9 in the script, it'll select m9 for every single reside and
only give me Rex data and no S^2. If I run m0-m4 same thing, it'll run
every residue at m4, instead of running through all the models and
selecting the data that fits that model. I know it states that the model is
supposed to loop through every model, then you run the model selection to
select what model fits which data set, but I don't know if my script is set
up incorrectly or what. Here is my script for model-free models:
pipes = ['m0','m1','m2','m3','m4']
for name in pipes:
pipe.create(name,'mf')
sequence.read('ssNOE_RGS4Agnes',res_num_col=1)
spin.name('N')
spin.element(element='N',spin_id='@N')
spin.isotope('15N',spin_id='@N')
structure.read_pdb('cluster1_12.pdb',read_mol=1)
relax_data.read(ri_id='R1_Agnes',ri_type='R1',frq=599.642*1e6,
file='R1_RGS4Agnes',res_num_col=1,spin_name_col=2,data_col=3,error_col=4)
relax_data.read(ri_id='R2_Agnes',ri_type='R2',frq=599.642*1e6,
file='R2_RGS4Agnes',res_num_col=1,spin_name_col=2,data_col=3,error_col=4)
relax_data.read(ri_id='ssNOE_Agnes',ri_type='NOE',frq=599.642*1e6,
file='ssNOE_RGS4Agnes',res_num_col=1,spin_name_col=2,data_col=3,error_col=4)
diffusion_tensor.init(1e-8,fixed=True)
sequence.attach_protons()
interatom.define(spin_id1='@N',spin_id2='@H',direct_bond=True)
interatom.set_dist(spin_id1='@N',spin_id2='@H',ave_dist=1.02*1e-10)
structure.get_pos('@N')
structure.get_pos('@H')
interatom.unit_vectors()
value.set(-172*1e-6,'csa',spin_id='@N')
model_free.select_model(model=name)
minimise.grid_search(inc=11)
minimise.execute('newton')
results.write(file='results',force=True)
state.save('save',force=True)

Again I only have it at m0-m4 because I wanted to obtain the m4 data, but
even if it is to m9, it'll only run the m9 model (i.e. I will only receive
Rex data because that's whats attributed to m9).  Here is my model
selection script:
pipes = ['m0','m1','m2','m3','m4']
for name in pipes:
print("\n\n#"+name+"#")
pipe.create(name,'mf')
results.read(file='results.bz2',dir=name)
eliminate()
model_selection(method='AIC',modsel_pipe='aic')
state.save('save',force=True)
results.write(file='results',force=True)

Again, this is only set up to m4 for the same reasons as before. I don't
know whether or not I have something in my script set up, but my final
results file just shows the model that was selected for every residue, is
the last model I have in my pipes (i.e. if m4 is the last model, it'll run
model 4, if m9 is the last one, it'll run m9). In this sence it appears to
be a single model scenario even though I've set up to be for multiple
models. Thank you again in advance.

Sincerely,
Sam
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Using modified all models free

[Mahdi, Sam]

Hello everyone,

I had a quick question regarding running the single model free run (m4).
For some proteins we only have data at only one field strength, so I know I
can't use the d'Auvergene protocol (needs a minimum of 4), so I was
thinking I could run the all models free model. The problem is, I know
models m6-m9 are models for another field strength, but since I don't have
data at another field strength, could I just remove them? Or will relax
just not run m6-9 since I've only loaded one field strength?

Sincerely,
Sam
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Re: Using multi-processor for model_free

[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 <sam.mahdi@my.csun.edu>
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 <edw...@nmr-relax.com>
> wrote:
>
>> On Thursday, 6 October 2016, Mahdi, Sam <sam.mahdi@my.csun.edu>
>> 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

[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 <edw...@nmr-relax.com>
wrote:

> On Thursday, 6 October 2016, Mahdi, Sam <sam.mahdi@my.csun.edu> 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

[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 <tlin...@nmr-relax.com
> 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 <sam.mahdi@my.csun.edu
> >:
>
>> 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 <sam.mahdi@my.csun.edu>:
>>>
>>>> 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 <edw...@nmr-relax.com
>>>> > wrote:
>>>>
>>>>> On 5 October 2016 at 22:01, Mahdi, Sam <sam.mahdi@my.csun.edu>
>>>>> 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

Re: Using multi-processor for model_free

[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 <sam.mahdi@my.csun.edu>:
>
>> 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 <edw...@nmr-relax.com>
>> wrote:
>>
>>> On 5 October 2016 at 22:01, Mahdi, Sam <sam.mahdi@my.csun.edu>
>>> 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

[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 <edw...@nmr-relax.com>
wrote:

> On 5 October 2016 at 22:01, Mahdi, Sam <sam.mahdi@my.csun.edu> 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: relax-users Digest, Vol 116, Issue 38

[Mahdi, Sam]

Hi Edward,

Just wanted to update you on the status of my runs. I had 2 potential dimer
structures. I ran Chain A and B for one of them, and Chain B for the other.
All the results were all very similar. There was missing data though
throughout (i.e. I had data for some residues for Chain A that had no data
in Chain B, Or chain A for one pdb file and Chain B for the other pdb file
would have data, but Chain B for the other pdb file wouldn't). The data
that is there for all 3 though does make sense. Thank you so much for your
help

Sincerely,
Sam

On Sat, Oct 1, 2016 at 11:17 AM, Edward d'Auvergne <edw...@nmr-relax.com>
wrote:

> On 1 October 2016 at 20:14, Mahdi, Sam <sam.mahdi@my.csun.edu> wrote:
> > Hi Edward,
> >
> > Oh ok. Thank you for your help, I was able to resolve the problems I had
> > with both proteins, and now they are both running. Since there is
> symmetry
> > within the dimer, both chain A and chain B will give me the same S^2
> results
> > correct?
>
> Hi Sam,
>
> That depends.  If you superimpose A and B and have an RMSD of
> 0.0, then the S2 values will be identical.  But if
> the docking software changed the monomer structures slightly so the
> RMSD is not exactly zero, then the S2 values will be slightly
> different for some residues.  You can use relax to superimpose
> structures and determine the RMSD to very high precision, if you like,
> but I'll leave that to you as a learning exercise ;)
>
> Regards,
>
> Edward
>
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Re: Using multi-processor for model_free

[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 t

Re: Using multi-processor for model_free

[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 <sam.mahdi@my.csun.edu
> >:
>
>> 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 <sam.mahdi@my.csun.edu>:
>>>
>>>> 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

Re: Using multi-processor for model_free

[Mahdi, Sam]

ket 0[core 0[hwt 0-1]]: [BB/..]
> Python 2.7.8
> Python 2.7.8
>
> > mpirun --report-bindings -np 2 /usr/bin/env python --version
> [instance-1:03349] MCW rank 1 bound to socket 0[core 1[hwt 0-1]]: [../BB]
> [instance-1:03349] MCW rank 0 bound to socket 0[core 0[hwt 0-1]]: [BB/..]
> Python 2.7.8
> Python 2.7.8
>
> Testing python, mpi4py and mpirun
> Python 2.7.8
> Python 2.7.8
> 2.0.0
> Mpi4py 2.0.0 process 0 of 2 on instance-1.
> Mpi4py 2.0.0 process 1 of 2 on instance-1.
>
> 
>
> [tlinnet@instance-1 ~]$ mpirun --np 2 relax_4.0.2 --multi='mpi4py'
> --version
> relax 4.0.2
>
>
>
>
>
> 2016-10-03 12:39 GMT+02:00 Troels Emtekær Linnet <tlin...@nmr-relax.com>:
>
>> Hi Sam.
>>
>> The commands reflect the BASH shell and not TCSH.
>> Thats why there i a little difference.
>>
>> Can you display your login script?:
>>
>> One of these should be the right one.
>> cat $HOME/.cshrc
>> cat $HOME/.login,
>> cat $HOME/.tcshrc
>>
>>
>>
>>
>>
>> 2016-10-03 1:50 GMT+02:00 Mahdi, Sam <sam.mahdi@my.csun.edu>:
>>
>>> Hi Troels,
>>>
>>> Here is the output
>>> source openmpi_test_install.sh
>>> http://svn.gna.org/viewcvs/*checkout*/relax/trunk/devel_scri
>>> pts/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_scri
>>> pts/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
>

Re: Using multi-processor for model_free

[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 <tlin...@nmr-relax.com
> 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 <tlin...@nmr-relax.com>:
>
>> Hi Sam.
>>
>> Can you try:
>> mpirun --version
>>
>> Thanks
>>
>> 2016-10-01 0:00 GMT+02:00 Mahdi, Sam <sam.mahdi@my.csun.edu>:
>>
>>> 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 i

Re: relax-users Digest, Vol 116, Issue 38

[Mahdi, Sam]

Hi Edward,

Oh ok. Thank you for your help, I was able to resolve the problems I had
with both proteins, and now they are both running. Since there is symmetry
within the dimer, both chain A and chain B will give me the same S^2
results correct?

Sincerely,
Sam

On Sat, Oct 1, 2016 at 2:21 AM, Edward d'Auvergne <edw...@nmr-relax.com>
wrote:

> On 30 September 2016 at 23:42, Mahdi, Sam <sam.mahdi@my.csun.edu>
> wrote:
> > Hi Edward,
> >
> > So when I ran it as read_mol=0, it gave me the same error. But it worked
> > once I changed it to read_mol=1. I thought mol=0 was for set A and mol=1
> was
> > for set B?
>
> Sorry, I just remembered that the molecule numbering starts from 1.
> So read_mol=1 gives chain ID A and read_mol=2 gives chain ID B.  I
> should add a check for this argument.
>
> Regards,
>
> Edward
>
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Re: relax-users Digest, Vol 116, Issue 38

[Mahdi, Sam]

Hi Edward,

So when I ran it as read_mol=0, it gave me the same error. But it worked
once I changed it to read_mol=1. I thought mol=0 was for set A and mol=1
was for set B?

Sincerely,
Sam

On Fri, Sep 30, 2016 at 2:00 PM, Mahdi, Sam <sam.mahdi@my.csun.edu>
wrote:

> Hi Edward,
>
> The protein itself is a monomer/dimer mix, normally it is a monomer;
> however, the concentrations at which we observe it at (NMR concentrations
> are around 1mM, the protein forms a dimer (primarily). Using titration
> experiments we have found what looks to be an interface (using CSP), and
> have used a docking program to show what the dimer would look like in
> regards to the dimer interface and what is geometrically/energetically
> possible. So we aren't looking for proof of a dimer, but my PI had informed
> me that our S^2 would not be accurate if we used the pdb of the monomer
> (due to slower tumbling effecting our relaxation data, basically having
> data for a dimer, and thus the pdb file must also account for the larger
> size/slower tumbling, basically since the data is for a dimer, the pdb
> file/structure should also be that of a dimer so they correlate). However,
> if the S^2 data doesn't get effected too much whether it is a dimer or
> monomer, then I guess it doesn't matter too much in this case.
>
> Also, could you tell me the exact modification I need to make to my
> script?
> This is what it was before
> structure.read_pdb('cluster1_12.pdb',set_mol_name='hRGS4')
> Is this what I should modify it to?
> structure.read_pdb('cluster1_12.pdb',set_mol_name='hRGS4',read_mol=0)
>
>
>
> Sincerely,
> Sam
>
> On Fri, Sep 30, 2016 at 11:45 AM, Edward d'Auvergne <edw...@nmr-relax.com>
> wrote:
>
>> On 30 September 2016 at 19:45, Mahdi, Sam <sam.mahdi@my.csun.edu>
>> wrote:
>> > Sorry, I just want to make sure I fully understand this so I can
>> explain it
>> > to my PI:
>>
>> No problems, this is by far the most complicated aspect in the field of
>> NMR ;)
>>
>>
>> > So if there is symmetry, I can upload the same pdb file with the dimer
>> (set
>> > A and B) but tell it to read only one set.
>>
>> Load rather than upload, but yes.
>>
>>
>> > Since S^2 isn't effected too much
>> > versus a dimer versus a monomer, the only thing that is important is the
>> > change in co-ordinates of one set of the dimer (i.e. the differnence in
>> > co-ordinates between set A in a monomer, and set A in a dimer
>> co-ordinates,
>> > or set A in a different version of that dimer's co-ordinates).
>>
>> S2 is not affected by the reference frame.  This only matters for
>> comparing diffusion tensors.  Though you will only ever see one
>> tensor, as that is what is in your NMR sample (if you have a
>> monomer-dimer mix, then you're in trouble and will see a lot of
>> artificial Rex and ns motions).
>>
>>
>> > I say this
>> > because I have already run my protein's data with the pdb structure of
>> the
>> > monomer, and I have 2 different pdb files the docking program gave back
>> for
>> > the dimer (2 different ways the dimer could form from one interface).
>>
>> Well, your analysis will always return the same diffusion tensor.  If
>> you want these diffusion tensors to all be in the same frame, use the
>> relax structure.superimpose user function with the method='fit to
>> first' argument.  Then just pick which will be your reference
>> structure and superimpose.  You can superimpose A and B - separately -
>> onto the monomer frame.
>>
>> Let's pick the monomer as the reference frame.  Then:
>>
>> - If you superimpose "dimer 1, struct A" to the monomer, you
>> should find the same tensor.
>> - If you superimpose "dimer 1, struct B" to the monomer, you
>> should find the same tensor.
>> - If you superimpose "dimer 2, struct A" to the monomer, you
>> should find the same tensor.
>> - If you superimpose "dimer 2, struct B" to the monomer, you
>> should find the same tensor.
>>
>> If the docking program did not optimise the internal monomer
>> structure, you will get identical results.  Otherwise you'll see minor
>> internal motion changes.  If your PI was hoping that you would be able
>> to tell him that you have a monomer or one of the 2 dimers in your NMR
>> tube, well then you will need to start to read many, many papers on
>> diffusion tensor prediction.  But know that all prediction methods
>> underestimate the diffusion tensor (e.g. David Case is working 

Re: Using multi-processor for model_free

[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 <sam.mahdi@my.csun.edu>:
>
>> 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 <sam.mahdi@my.csun.edu>:
>>>
>>>> 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 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: relax-users Digest, Vol 116, Issue 38

[Mahdi, Sam]

Hi Edward,

The protein itself is a monomer/dimer mix, normally it is a monomer;
however, the concentrations at which we observe it at (NMR concentrations
are around 1mM, the protein forms a dimer (primarily). Using titration
experiments we have found what looks to be an interface (using CSP), and
have used a docking program to show what the dimer would look like in
regards to the dimer interface and what is geometrically/energetically
possible. So we aren't looking for proof of a dimer, but my PI had informed
me that our S^2 would not be accurate if we used the pdb of the monomer
(due to slower tumbling effecting our relaxation data, basically having
data for a dimer, and thus the pdb file must also account for the larger
size/slower tumbling, basically since the data is for a dimer, the pdb
file/structure should also be that of a dimer so they correlate). However,
if the S^2 data doesn't get effected too much whether it is a dimer or
monomer, then I guess it doesn't matter too much in this case.

Also, could you tell me the exact modification I need to make to my script?
This is what it was before
structure.read_pdb('cluster1_12.pdb',set_mol_name='hRGS4')
Is this what I should modify it to?
structure.read_pdb('cluster1_12.pdb',set_mol_name='hRGS4',read_mol=0)



Sincerely,
Sam

On Fri, Sep 30, 2016 at 11:45 AM, Edward d'Auvergne <edw...@nmr-relax.com>
wrote:

> On 30 September 2016 at 19:45, Mahdi, Sam <sam.mahdi@my.csun.edu>
> wrote:
> > Sorry, I just want to make sure I fully understand this so I can explain
> it
> > to my PI:
>
> No problems, this is by far the most complicated aspect in the field of
> NMR ;)
>
>
> > So if there is symmetry, I can upload the same pdb file with the dimer
> (set
> > A and B) but tell it to read only one set.
>
> Load rather than upload, but yes.
>
>
> > Since S^2 isn't effected too much
> > versus a dimer versus a monomer, the only thing that is important is the
> > change in co-ordinates of one set of the dimer (i.e. the differnence in
> > co-ordinates between set A in a monomer, and set A in a dimer
> co-ordinates,
> > or set A in a different version of that dimer's co-ordinates).
>
> S2 is not affected by the reference frame.  This only matters for
> comparing diffusion tensors.  Though you will only ever see one
> tensor, as that is what is in your NMR sample (if you have a
> monomer-dimer mix, then you're in trouble and will see a lot of
> artificial Rex and ns motions).
>
>
> > I say this
> > because I have already run my protein's data with the pdb structure of
> the
> > monomer, and I have 2 different pdb files the docking program gave back
> for
> > the dimer (2 different ways the dimer could form from one interface).
>
> Well, your analysis will always return the same diffusion tensor.  If
> you want these diffusion tensors to all be in the same frame, use the
> relax structure.superimpose user function with the method='fit to
> first' argument.  Then just pick which will be your reference
> structure and superimpose.  You can superimpose A and B - separately -
> onto the monomer frame.
>
> Let's pick the monomer as the reference frame.  Then:
>
> - If you superimpose "dimer 1, struct A" to the monomer, you
> should find the same tensor.
> - If you superimpose "dimer 1, struct B" to the monomer, you
> should find the same tensor.
> - If you superimpose "dimer 2, struct A" to the monomer, you
> should find the same tensor.
> - If you superimpose "dimer 2, struct B" to the monomer, you
> should find the same tensor.
>
> If the docking program did not optimise the internal monomer
> structure, you will get identical results.  Otherwise you'll see minor
> internal motion changes.  If your PI was hoping that you would be able
> to tell him that you have a monomer or one of the 2 dimers in your NMR
> tube, well then you will need to start to read many, many papers on
> diffusion tensor prediction.  But know that all prediction methods
> underestimate the diffusion tensor (e.g. David Case is working on this
> exact problem for MD simulations).  In this case, relaxation data is
> not the best NMR method for this.  It would be better to use RDCs from
> a purely steric alignment and to compare that to what PALES prediction
> comes up with (though that itself is still a very rough and imperfect
> method).
>
> Regards,
>
> Edward
>
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Re: relax-users Digest, Vol 116, Issue 38

[Mahdi, Sam]

Sorry, I just want to make sure I fully understand this so I can explain it
to my PI:
So if there is symmetry, I can upload the same pdb file with the dimer (set
A and B) but tell it to read only one set. Since S^2 isn't effected too
much versus a dimer versus a monomer, the only thing that is important is
the change in co-ordinates of one set of the dimer (i.e. the differnence in
co-ordinates between set A in a monomer, and set A in a dimer co-ordinates,
or set A in a different version of that dimer's co-ordinates). I say this
because I have already run my protein's data with the pdb structure of the
monomer, and I have 2 different pdb files the docking program gave back for
the dimer (2 different ways the dimer could form from one interface).

Sincerely,
Sam

On Fri, Sep 30, 2016 at 10:29 AM, Edward d'Auvergne 
wrote:

> Hi Sam,
>
> Please see below:
>
> > I'm a bit confused to that. If the protein is a dimer, and the tumbling
> > decreases, will that not results in altered  relaxation data?
>
> Yes.
>
> > Won't the
> > relaxation data average be higher, since it is relaxing slower due to its
> > increased size (tumbler slower in solution=slower relaxation back to
> > equilibrium)?
>
> No.  R2 will be higher.  R1 could go anywhere.  The NOE may not be
> affected too much, but it may decrease (maybe).  You need to
> understand how the diffusion tensor affects the J(w) spectral density
> curves to understand how R1 and the NOE will be affected.
>
>
> > Also, doesn't S^2 take into account the overall shape of the
> > molecule (as well as tensor type) in it's calculations?
>
> No.  The S2 value is the internal motions of the residue.  It is 100%
> independent of the global tumbling.
>
>
> > So won't a dimer
> > versus a monomer change the results just due to that?
>
> Not at all.  The optimised diffusion tensor should change, and the S2
> value stay the same.
>
>
> > So should I input both, read_mol=0 and read_mol=1?
>
> No, only one.  You can, however, perform a second analysis later with
> read_mol=1 (for comparison).
>
>
> > So
> > structure.read_pdb(file='cluster1_12.pdb', dir=None,
> >  read_mol=None, set_mol_name='hRGS4',
> > read_model=None,set_model_num=0,set_mol_num=1, alt_loc=None,
> verbosity=1,
> > merge=False)
> > So mol_num=0 will be for chain A and mol_num=1 for chain B?
>
> This will have the same IndexError as before - relax will not handle
> two identical molecules in a model-free analysis at the same time.
> Again, this theory simply does not exist.  So I haven't added it to
> relax.  You need to perform the analysis on a single monomer of the
> homodimer.  But please check for symmetry - if you don't have
> symmetry, nobody on the planet can currently analyse non-symmetric
> homodimer data.
>
> Regards,
>
> Edward
>
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Re: Using multi-processor for model_free

[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 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: relax-users Digest, Vol 116, Issue 38

[Mahdi, Sam]

Hi Edward,

I'm a bit confused to that. If the protein is a dimer, and the tumbling
decreases, will that not results in altered  relaxation data? Won't the
relaxation data average be higher, since it is relaxing slower due to its
increased size (tumbler slower in solution=slower relaxation back to
equilibrium)? Also, doesn't S^2 take into account the overall shape of the
molecule (as well as tensor type) in it's calculations? So won't a dimer
versus a monomer change the results just due to that?
So should I input both, read_mol=0 and read_mol=1? So
structure.read_pdb(file='cluster1_12.pdb', dir=None,
 read_mol=None, set_mol_name='hRGS4',
read_model=None,set_model_num=0,set_mol_num=1, alt_loc=None, verbosity=1,
merge=False)
So mol_num=0 will be for chain A and mol_num=1 for chain B?

Sincerely,
Sam

On Fri, Sep 30, 2016 at 9:17 AM, Edward d'Auvergne <edw...@nmr-relax.com>
wrote:

> On 30 September 2016 at 17:31, Mahdi, Sam <sam.mahdi@my.csun.edu>
> wrote:
> > Hi Gary,
> >
> > There is only a monomer version of it on pdb, so if you mean it in that
> > sense, yes. I obtained results from it; however the S^2 were very high,
> but
> > I attributed this to having data for a dimer, but using a monomer pdb
> file.
>
> Hi Sam,
>
> This cannot be the case.  The S2 values are often very similar in a
> monomer and homodimer case.  Or a trimer, tetramer, etc.  The only
> difference is that the global tumbling - the diffusion tensor - is
> slower in the dimer/trimer/tetramer/etc. (and the tensor type and
> shape will be different due to the different hydrodynamic+water shell
> shape).
>
>
> > If you mean have I tried to just delete set B from the pdb file I
> uploaded,
> > I have not attempted that.
>
> With relax, you should never modify the PDB files - relax can do that
> for you much better and to the PDB standard via the PDB user
> functions.
>
>
> > So I am a bit confused here, so if I add read_mol=1 instead of my
> > read_mol=0, it'll only read set A?
>
> Sorry, I meant "read_mol=0" for PDB chain ID A.  The argument
> read_mol=1 will pull out chain ID B.
>
>
> > Assuming symmetry, relax will
> > automatically calculate and determine set B?
>
> Assuming symmetry, you will get the identical results for read_mol=0
> and read_mol=1.  There might be slight differences in bond orientation
> if the symmetry is not perfect.
>
> If there is no symmetry, the relaxation data for monomer A and monomer
> B will be different, but it will be averaged to a single value.  If
> this is the case, as I said before there is no theory on the planet
> for properly handling such averaged data, and you cannot perform any
> model-free, reduced spectral density mapping (J(w) mapping), or other
> analysis on it.
>
> I hope this clarifies the situation a little better.
>
> Regards,
>
> Edward
>
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Re: Using multi-processor for model_free

[Mahdi, Sam]

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.


--
Ran 1253 tests in 10.734s

FAILED (errors=4)


That was for relax 2.2.5

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

Ran 83 tests in 296.397s

OK


===
= Software verification tests =
===

..
--
Ran 2 tests in 0.184s

OK


===
= Summary of the relax test suite =
===



Optional packages/modules
=

Tests skipped due to missing optional packages/modules/software:


Module/package/software  System test count  Unit test
count   GUI test count Verification test count

Art Palmer's Modelfree4 software 2
000
Dasha model-free software1
000





Synopsis


System/functional tests
. [ OK ]
Unit tests
..
[ OK ]
GUI tests
...
[ OK ]
Software verification tests
. [ OK ]
Synopsis

[ OK ]



crowlab: [~/relax-4.0.2]>





On Fri, Sep 30, 2016 at 9:26 AM, Edward d'Auvergne <edw...@nmr-relax.com>
wrote:

> On 30 September 2016 at 17:37, Mahdi, Sam <sam.mahdi@my.csun.edu>
> 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: relax-users Digest, Vol 116, Issue 38

[Mahdi, Sam]

Hi Gary,

There is only a monomer version of it on pdb, so if you mean it in that
sense, yes. I obtained results from it; however the S^2 were very high, but
I attributed this to having data for a dimer, but using a monomer pdb file.
If you mean have I tried to just delete set B from the pdb file I uploaded,
I have not attempted that.
So I am a bit confused here, so if I add read_mol=1 instead of my
read_mol=0, it'll only read set A? Assuming symmetry, relax will
automatically calculate and determine set B?

Sincerely,
Sam

On Fri, Sep 30, 2016 at 1:26 AM, Edward d'Auvergne 
wrote:

> On 30 September 2016 at 10:16, Edward d'Auvergne 
> wrote:
> > On 29 September 2016 at 09:55, Gary Thompson 
> wrote:
> >> Hi Sam
> >>
> >> have you tried with only one set of coordinates (i presume these are
> both homo dimers with some form of symetry plane or axis?
> >
> > Looking at the file attached to https://gna.org/bugs/?25133, the
> > problem is at the start of the script:
> >
> > """
> > relax> structure.read_pdb(file='cluster1_12.pdb', dir=None,
> > read_mol=None, set_mol_name='hRGS4', read_model=None,
> > set_model_num=None, alt_loc=None, verbosity=1, merge=False)
> >
> > Internal relax PDB parser.
> > Opening the file 'cluster1_12.pdb' for reading.
> > Adding molecule 'hRGS4' (from the original molecule number 1).
> > Merging with molecule 'hRGS4' (from the original molecule number 2).
> > """
> >
> > Note the text "Merging".  This is because you are setting all
> > molecules in the PDB file to the single molecule name "hRGS4".  What
> > you need to do is read a single molecule (via the 'read_mol'
> > argument).  Note Gary's text about symmetry.  If you have a homo dimer
> > without symmetry, there is absolutely no theory on the planet
> > currently developed to handle relaxation data in this situation.
>
> Running the RGS4_modelfree_sample_script.py script with the
> "read_mol=1" argument for the structure.read_pdb user function causes
> the IndexError to go away.  Unfortunately I don't have the time to
> investigate and turn this into a self-explanatory check and RelaxError
> yet.
>
> Cheers,
>
> Edward
>
> ___
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Re: Using multi-processor for model_free

[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 <sam.mahdi@my.csun.edu>
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 <edw...@nmr-relax.com>
> wrote:
>
>> On 29 September 2016 at 00:23, Mahdi, Sam <sam.mahdi@my.csun.edu>
>> 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
>> > m

Re: Using multi-processor for model_free

[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 <edw...@nmr-relax.com>
wrote:

> On 29 September 2016 at 00:23, Mahdi, Sam <sam.mahdi@my.csun.edu>
> 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 t

Re: Using multi-processor for model_free

[Mahdi, Sam]

Also, Congrats to Edward!

On Thu, Sep 29, 2016 at 4:11 PM, Mahdi, Sam <sam.mahdi@my.csun.edu>
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 <sam.mahdi@my.csun.edu>:
>>
>>> 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.inter

Re: Using multi-processor for model_free

[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 <sam.mahdi@my.csun.edu>:
>
>> 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,
>

Re: Using multi-processor for model_free

[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 <sam.mahdi@my.csun.edu>
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 <tlin...@nmr-relax.com>:
>>
>>> 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 <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

Re: Using multi-processor for model_free

[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 <tlin...@nmr-relax.com>:
>
>> 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 <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 <sam.mahdi@my.csun.edu>
>>> wrote:
>>>
>>>> Hi Troels,
>>>>
>>>>
>>>> I have attempted the fix for

Re: Using multi-processor for model_free

[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 <sam.mahdi@my.csun.edu>
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=$NPROC+8|bc in multi-processor mode
>
> And any command I type in after that gets no response.
>
> I've also checked the spins via script. For 2 scenarios. Scenario 1- All
> hydrogens are kept as HN and Scenario 2- I change all the HN spins to H.
> The output from Scenario one is, it read all the Nitrogen spins
> accordingly :
> Objects:
>   element: 'N'
>   isotope: '15N'
>   name: 'N'
>   num: 1304
>   pos: array([ 13.196,  15.218,   3.192
> ])
>   select: True
>  hRGS4 178 THR #hRGS4:178@1304
> Class containing all the spin system specific data.
>
>
> Objects:
>   element: 'N'
>   isotope: '15N'
>   name: 'N'
>   num: 2617
>   pos: array([ 22.6960002,  10.683,  -4.15
> ])
>   select: True
>  hRGS4 178 THR #hRGS4:178@2617
>
> But no hydrogens.
>
> Scenario 2-  I still recieve the same error.
> RelaxError: Multiple alternate location indicators are present in the PDB
> file, but the desired coordinate set has not been specified.
>
> Sincerely,
> Sam
>
> On Mon, Sep 26, 2016 at 2:19 PM, Mahdi, Sam <sam.mahdi@my.csun.edu>
> wrote:
>
>> Hi Troels,
>>
>> I have attempted the fix for running on a multi-processor platform by
>> creating the script you told me too, and I still got the same result. I
>> have uploaded a screenshot that shows again, relax is running in the
>> background, but there is no output for relax, nor can I input any commands.
>> The only output I recieve is this:
>> Running relax with NP=$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
>>>
>>> 

Re: Using multi-processor for model_free

[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 <sam.mahdi@my.csun.edu>
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 <sam.mahdi@my.csun.edu>:
>>
>>> 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.
&g

Re: Using multi-processor for model_free

[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 <sam.mahdi@my.csun.edu>
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 <sam.mahdi@my.csun.edu>
> 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 <sam.mahdi@my.csun.edu>:
>>>
>>>> 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 <sam.mahdi@my.csun.edu>:
>>>>>
>>>>>> 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 1.0.4    1.0.12
>>>>>>>
>>>>>>> relax information:
>>>>>>> Version: 2.2.5 4.0.2
>>>>>>>
>>>>>>>
>>>>>>> 2016-09-19 19:41 GMT+02:00 Mahdi, Sam <sam.mahdi@my.csun.edu>:
>>>>>>>
>>>>>>>> Hi Troels,
>>>>>>>>
>>>>>>>> I have uploaded the bug report for the issue with running relax on
>>>&g

Re: Using multi-processor for model_free

[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 <sam.mahdi@my.csun.edu>:
>
>> 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 <sam.mahdi@my.csun.edu>:
>>>
>>>> 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 <sam.mahdi@my.csun.edu>:
>>>>>
>>>>>> 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 
>>>>>>> fr

Re: Using multi-processor for model_free

[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 <sam.mahdi@my.csun.edu>:
>
>> 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 1.0.4    1.0.12
>>>
>>> relax information:
>>> Version: 2.2.5 4.0.2
>>>
>>>
>>> 2016-09-19 19:41 GMT+02:00 Mahdi, Sam <sam.mahdi@my.csun.edu>:
>>>
>>>> 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.
>>>>>>
&

Re: Using multi-processor for model_free

[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 <sam.mahdi@my.csun.edu>:
>
>> 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.
>>>>
>>>> This could either be the measurement OR the error estimation. Relax
>>>> will keep on searching for minimization.
>>>> If you are "unlucky&quo

Re: Using multi-processor for model_free

[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 <sam.mahdi@my.csun.edu>:
>
>> 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

Re: Using multi-processor for model_free

[Mahdi, Sam]

-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 <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
>>
>> 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.
>&

Re: Using multi-processor for model_free

[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 <sam.mahdi@my.csun.edu>:
>>>
>>>> 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 

Re: Using multi-processor for model_free

[Mahdi, Sam]

s
missing.
RelaxWarning: The sequence data in the line ['27'] is invalid, the data is
missing.
RelaxWarning: The sequence data in the line ['28'] is invalid, the data is
missing.
RelaxWarning: The sequence data in the line ['31'] is invalid, the data is
missing.
RelaxWarning: The sequence data in the line ['40'] is invalid, the data is
missing.
RelaxWarning: The sequence data in the line ['46'] is invalid, the data is
missing.
RelaxWarning: The sequence data in the line ['58'] is invalid, the data is
missing.
RelaxWarning: The sequence data in the line ['61'] is invalid, the data is
missing.
RelaxWarning: The sequence data in the line ['62'] is invalid, the data is
missing.
RelaxWarning: The sequence data in the line ['63'] is invalid, the data is
missing.
RelaxWarning: The sequence data in the line ['73'] is invalid, the data is
missing.
RelaxWarning: The sequence data in the line ['76'] is invalid, the data is
missing.
RelaxWarning: The sequence data in the line ['79'] is invalid, the data is
missing.
RelaxWarning: The sequence data in the line ['81'] is invalid, the data is
missing.
RelaxWarning: The sequence data in the line ['82'] is invalid, the data is
missing.
RelaxWarning: The sequence data in the line ['85'] is invalid, the data is
missing.
RelaxWarning: The sequence data in the line ['94'] is invalid, the data is
missing.
RelaxWarning: The sequence data in the line ['97'] is invalid, the data is
missing.
RelaxWarning: The sequence data in the line ['99'] is invalid, the data is
missing.
RelaxWarning: The sequence data in the line ['106'] is invalid, the data is
missing.
RelaxWarning: The sequence data in the line ['115'] is invalid, the data is
missing.
RelaxWarning: The sequence data in the line ['121'] is invalid, the data is
missing.
RelaxWarning: The sequence data in the line ['126'] is invalid, the data is
missing.
RelaxWarning: The sequence data in the line ['127'] is invalid, the data is
missing.
RelaxWarning: The sequence data in the line ['134'] is invalid, the data is
missing.
RelaxWarning: The sequence data in the line ['135'] is invalid, the data is
missing.
RelaxWarning: The sequence data in the line ['136'] is invalid, the data is
missing.
RelaxWarning: The sequence data in the line ['137'] is invalid, the data is
missing.
RelaxWarning: The sequence data in the line ['139'] is invalid, the data is
missing.

RelaxError: The spin ID '#hRGS7:12' corresponds to multiple spins,
including '#hRGS7:12@N' and '#hRGS7:12@H'.
crowlab: [~/relax-4.0.2]>

As you can see, I have all 6 data sets set to load, but only the very first
one appears to do so, and after it loads, it just exits out of relax.
Again, I don't know if this is a problem with how I wrote the script. The
Relax_script1 is the one that I load up to run the whole thing. The model
free script.py is just the script it reads once relax has opened up.
Again, I can see all the spins are properly loaded, and the isotopes are
set. It just everything after the first data set that doesn't load. Thanks
again in advance.

Sincerely,
Sam

On Thu, Sep 8, 2016 at 10:15 AM, Mahdi, Sam <sam.mahdi@my.csun.edu>
wrote:

> 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 <
> tlin...@nmr-relax.com> 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 <sam.mahdi@my.csun.edu>:
>>>>
>>>>> 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 

Re: Using multi-processor for model_free

[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 <tlin...@nmr-relax.com
> 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 <sam.mahdi@my.csun.edu>:
>>>
>>>> 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 <sam.mahdi@my.csun.edu>:
>>>>>
>>>>>> 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
>>>>

Re: Using multi-processor for model_free

[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 <sam.mahdi@my.csun.edu>:
>
>> 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 <sam.mahdi@my.csun.edu>:
>>>
>>>> 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
>>>

Re: Using multi-processor for model_free

[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 <sam.mahdi@my.csun.edu>:
>
>> 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

Using multi-processor for model_free

[Mahdi, Sam]

Hello everyone,

I am attempting to run relax on a multi-processor mode. I have been able to
successfully set-up relax to operate in a multi-processor mode by using the
mpirun -np #ofprocessors /location/of/relax --multi='mpi4py'

The problem I encounter is when using the --tee log dauvergne_protocol.py
command. I receive this error
RelaxError: the script file 'dauvergne_protocol.py' does not exist

I located the script file and tried to direct to it's path
mpirun /usr/local/Relax/relax-2.2.5/relax --multi='mpi4py' --tee log
/usr/local/Relax/relax-2.2.5/auto-analyses/dauvergne_protocol.py

But i received this error
RelaxError: the script file
'/usr/local/Relax/relax-2.2.5/auto-analyses/dauvergne_protocol.py' does not
exist.

Even though I have the script, it doesn't seem to be able to locate it.

On a side note, in the manual, one dash doesn't actually run the command.
I.e. in the manual it displays -multi='mpi4py' . What it should be is
--multi='mpi4py' . The same goes for -tee. It should be --tee.

Sincerely,
Sam
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Re: Using multi-processor for nmr relax

[Mahdi, Sam]

So I have downloaded both mpi4py and open mpi. When I attempt to run the
command: mpirun -np 2 /home/student/relax-4.0.2/relax -multi='mpi4py' -tee
log dauvergne_protocol.py

I receive this error

Usage: relax [options] [script_file]

RelaxError: incorrect number of arguments
Usage: relax [options] [script_file]

RelaxError: incorrect number of arguments

I am using a fedora linux computer. This is for attempting to use
multiprocessors for model-free anlysis.


On Tue, Aug 30, 2016 at 10:05 AM, Edward d'Auvergne <edw...@nmr-relax.com>
wrote:

> On 30 August 2016 at 17:08, Mahdi, Sam <sam.mahdi@my.csun.edu> wrote:
> > Hi Edward,
> >
> > Thanks for the quick reply. In the "Further Details" section that shows
> the
> > email archive. When Dr. Thompson is setting up the code to run relax in a
> > multi-processor mode he uses the commands "lamboot" and "lamhalt". From
> what
> > I could find, these are commands from the lam/mpi program and not open
> mpi.
> > I know in the manual in "usage of the multi-processor" page, it shows the
> > open mpi command "mpirun", but that is the only indication I've seen of
> > using open mpi to start relax in multi-processor mode.
>
> I think the old mpi4py can handle these older MPI implementations as
> well.  Anyway, you only need that "mpirun" command.
>
> Regards,
>
> Edward
>
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Re: Using multi-processor for nmr relax

[Mahdi, Sam]

Hi Edward,

Thanks for the quick reply. In the "Further Details" section that shows the
email archive. When Dr. Thompson is setting up the code to run relax in a
multi-processor mode he uses the commands "lamboot" and "lamhalt". From
what I could find, these are commands from the lam/mpi program and not open
mpi. I know in the manual in "usage of the multi-processor" page, it shows
the open mpi command "mpirun", but that is the only indication I've seen of
using open mpi to start relax in multi-processor mode.

Thanks in advance.
Sam

On Tue, Aug 30, 2016 at 6:59 AM, Edward d'Auvergne <edw...@nmr-relax.com>
wrote:

> On 30 August 2016 at 02:57, Mahdi, Sam <sam.mahdi@my.csun.edu> wrote:
> > Hello everyone,
> >
> > I was looking to attempt to run relax on a multi-processor platform. I
> was
> > looking at Gary Thompsons overview, and I realized it uses lam/mpi format
> > which is no longer provided. I've decided to use it's replacement, open
> > mpi. Is there any updated overview that uses open mpi? One that shows a
> > step by step guide for how to setup relax to run on multi-processors
> (with
> > commands and outputs showed).
>
> Hi Sam,
>
> Gary Thompson's multi-processor system is based on OpenMPI.  Please see:
>
> http://www.nmr-relax.com/manual/The_multi_processor_framework.html
>
> Which instructions are you referring to?
>
> Regards,
>
> Edward
>
>
>
> >
> > Thank you
> > Sam
> > ___
> > relax (http://www.nmr-relax.com)
> >
> > This is the relax-users mailing list
> > relax-users@gna.org
> >
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> > reminder, or change your subscription options,
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>
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Using multi-processor for nmr relax

[Mahdi, Sam]

Hello everyone,

I was looking to attempt to run relax on a multi-processor platform. I was
looking at Gary Thompsons overview, and I realized it uses lam/mpi format
which is no longer provided. I've decided to use it's replacement, open
mpi. Is there any updated overview that uses open mpi? One that shows a
step by step guide for how to setup relax to run on multi-processors (with
commands and outputs showed).

Thank you
Sam
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Troubleshooting model-free analysis

[Mahdi, Sam]

Hi, I had some general questions regarding model-free analysis that came up
as I was running it. About 2 months ago, I ran model-free on a 126 residue
protein. The pdb file I used for the protein had an extra 7 residue
modifier at one of the terminals, which made it 133 residues; thus, my data
did not match the pdf file. That run took a little over a week, with the
sphere model running about 2 models, along with every other model being
about 2. The data for this run I obtained was unusable (values as small as
5x10^-30 for S^2). I attributed this to the fact that my pdf files sequence
did not align with my data.

I adjusted my relax data (simply added 7 residues with no values), and ran
it again (all settings the same as before, everything automatic). This time
it has taken almost a month, with the sphere model on its 20th run. I saw
in a previous email that the max is 30 iterations. Is it normal to hit the
max? Does this mean my data is bad if it requires the max 30 iterations?
Also, why is it running up to 20 now? The 7 residues I added didn't have
data, so it doesn't run models for them. I assumed there would be a
difference in time since the data is now attributed to different spins, but
not this much of a difference.

Thank you in advance!
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Fwd: Troubleshooting model-free analysis

[Mahdi, Sam]

-- Forwarded message --
From: Mahdi, Sam <sam.mahdi@my.csun.edu>
Date: Fri, Jul 1, 2016 at 4:56 PM
Subject: Troubleshooting model-free analysis
To: relax-users@gna.org


I had 2 questions regarding the relax model-free analysis.
1: When uploading a pdb file for the spin system, is there a certain way to
have some residues spins ignored? i.e. give it a certain range. E.g. The
structural data for the pdb file I want uses an extra linker at the
C-terminus of my protein that is about 7 residues long. The relaxation data
I have however is for the protein without those 7 extra residues (thus
residue 7 for the pdb file is residue 1 for my relaxation data). Is there a
way I can get the relax program to ignore the first 7 residues? I tried
typing in the range I wanted (residue 8 to residue 133 inputed as [8-133])
in the molecule number to read option, but when I did that, it gave me this
error RelaxError: No PDB file has been loaded. When I removed the range, it
uploaded the file but with all the residues, including the linker I didn't
want.

2: The relaxation data I have is for the backbone (NH), thus the values I
have for the backbone are for that bond. The pdb file I uploaded has both
of their spins. The relaxation data I have is one value for each residue
(for the NH bond). So I assumed that value is the same for both the
Nitrogen and Hydrogen spin of that residue. E.g. If residue 3 has a R1
value of 1.03, I assume the nitrogen spin and hydrogen spin both have an R1
value of 1.03. When I upload the relaxation data with the Nitrogen @N spin
id string it works fine, each residue has the proper value. However, the
value for the hydrogen is 0 for each residue.  I tried to create a new data
set, this time with the spin id string for Hydrogen using the same R1 file
I had used for the nitrogen, but when I did this I was given this error:
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 ['0', '0'] is invalid, the
error data is missing.
RelaxWarning: The sequence data in the line ['0', '0'] is invalid, the
error data is missing.
RelaxWarning: The sequence data in the line ['0', '0'] is invalid, the
error data is missing.
RelaxWarning: The sequence data in the line ['0', '0'] is invalid, the
error data is missing.
RelaxWarning: The sequence data in the line ['0', '0'] is invalid, the
error data is missing.
Traceback (most recent call last):
  File "/usr/local/Relax/relax-2.2.5/gui/wizard.py", line 163, in _apply
self.exec_status = self.on_execute()
  File "/usr/local/Relax/relax-2.2.5/gui/uf_objects.py", line 867, in
on_execute
return_status = self.execute(self.name, **kargs)
  File "/usr/local/Relax/relax-2.2.5/gui/uf_objects.py", line 797, in
execute
return_status = interpreter.apply(uf, *args, **kwds)
  File "/usr/local/Relax/relax-2.2.5/gui/interpreter.py", line 112, in apply
apply(fn, args, kwds)
  File "/usr/local/Relax/relax-2.2.5/generic_fns/relax_data.py", line 1033,
in read
pack_data(ri_id, ri_type, frq, values, errors, mol_names=mol_names,
res_nums=res_nums, res_names=res_names, spin_nums=spin_nums,
spin_names=spin_names, spin_id=spin_id)
  File "/usr/local/Relax/relax-2.2.5/generic_fns/relax_data.py", line 870,
in pack_data
new_id = new_ids[0]
IndexError: list index out of range

I don't know why it states the sequence data in the ling [0,0] is invalid
with missing error data. It is the same file I used for the nitrogen and
that worked fine. If I do not upload a hydrogen file, naturally when relax
is run, I will recieve an error stating that every single hydrogen spin has
been deselected due to the absence of data, and then it'll stop the
simulations.
Extra info:
 this is how the script looks when I upload it with the NItrogen Id string
elax> relax_data.display(ri_id='R1_NMRFAM')
# mol_nameres_numres_namespin_numspin_name
value   error
hRGS7 1  GLY 1
N   0   0
hRGS7 2  SER 8
N   0   0
hRGS7 2  SER 14  H
NoneNone
hRGS7 3  SER 19
N   0   0
hRGS7 3  SER 25  H
NoneNone
hRGS7 4  GLY 30
N   0   0
hRGS7 4  GLY 34  H
NoneNone
hRGS7 5  SER 37
N1.150.03
hRGS7 5  SER 43  H
NoneNone
hRGS7 6  SER 48
N   0.832   0.011
hRGS7 6