-- 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
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
] [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, M
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
gt; 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/Open
e, 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
&
blic/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 up
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
st
> 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 did
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
. 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
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 simul
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,
>>
, 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
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.
>
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 runnin
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
ams 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 c
; Can you have a look at:
> http://wiki.nmr-relax.com/OpenMPI
>
> Try the different things like:
> lscpu
> mpirun --report-bindings -np 11 echo "hello world"
> mpirun --report-bindings -np 4 relax --multi='mpi4py'
>
> When we are confident about this, then we will try make
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?
>
> Bes
ntime, 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
>>
8673
>
> 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 Li
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&
sands 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
]>
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
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
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
>
erely,
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 wo
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
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 o
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
[ OK ]
Unit tests
..
[ OK ]
GUI tests
...
[ OK ]
Software verification tests
. [ OK ]
Synopsis
wt 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 proc
;
> 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 <
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,
>
&
na.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.
>>
&g
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 t
, 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=
gt; 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 wel
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
rry 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
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:
> > So
nal.
> 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'
>&g
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
> approp
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
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
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,
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
48 matches
Mail list logo
