Re: Using multi-processor for model_free

On 30 September 2016 at 01:35, Mahdi, Sam wrote: > Also, Congrats to Edward! Thanks :) ___ relax (http://www.nmr-relax.com) This is the relax-users mailing list relax-users@gna.org To unsubscribe from this list, get a

Re: relax-users Digest, Vol 116, Issue 33

Hi Sam if you log to file, tail -f of the log file gives a good overview of the output and minimisation without the overhead regards gary -- --- Dr Gary Thompson[Leeds Biological NMR Facility] Astbury

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

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? regards gary -- --- Dr Gary Thompson[Leeds Biological NMR Facility] Astbury

Re: Using multi-processor for model_free

On 28 September 2016 at 22:44, Mahdi, Sam wrote: > Hey Troels, > > I ran the relax -x and recieve this error at the GUI tests > = > = GUI tests = > = > > ** > Gtk:ERROR:gtkfilesystemmodel.c:746:gtk_file_system_model_sort:

Re: Using multi-processor for model_free

On 28 September 2016 at 20:32, Troels Emtekær Linnet wrote: > If you get different results, for the same setup, this is not good. > Not at all ! Hi, Sorry for not being more involved, I've been in what could be called paternity leave. This point is very, very important.

Re: Issue in ModelFree Calculation

On 26 August 2016 at 18:25, wrote: > Hi Edward, > Thank you for your suggestions. Extremely sorry for my late reply. I already > tried what Troel had told me. As I didn't install the SciPy package (not > required for ModelFree analysis), I am unable to perform the full

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

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

Re: Using multi-processor for model_free

On 30 September 2016 at 19:03, Mahdi, Sam wrote: > Hi Edward, > > So the GUI problems came from relax 2.2.5 The actual output is big, so I > will only post where the errors started > relax> monte_carlo.error_analysis() > > relax> results.write(file='devnull',

Re: Using multi-processor for model_free

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

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

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

Re: Using multi-processor for model_free

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

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

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

Re: Using multi-processor for model_free

On 30 September 2016 at 17:37, Mahdi, Sam wrote: > Hi Edward, > > I also wanted to add, for running a multi-processor platform problem. I > installed openmpi from the fedora package list, not from the site itself. I > installed both openmpi, mpi4py, and the openmpi

Re: Using multi-processor for model_free

On 30 September 2016 at 19:47, Mahdi, Sam wrote: > I get the same results with the full path mpirun -np 5 ~/relax-4.0.2/relax > --multi="mpi4py" -v > Still no output. The reason is because either OpenMPI or mpi4py are not working. If you compiled OpenMPI, then you'll

Re: Using multi-processor for model_free

Hi Edward, So the GUI problems came from relax 2.2.5 The actual output is big, so I will only post where the errors started relax> monte_carlo.error_analysis() relax> results.write(file='devnull', dir='pipe_name', compress_type=1, force=True) Opening the null device file for writing. Traceback

Re: Using multi-processor for model_free

On 30 September 2016 at 19:12, Mahdi, Sam wrote: > Hi Edward, > > So I ran the the mpirun commands you suggested. The echo world works fine. I > get the same results you did. For the relax one, this is the output I > recieved > [~/relax-4.0.2]> mpirun -np 5 ./relax

Re: Using multi-processor for model_free

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 : >

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

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

Re: Using multi-processor for model_free

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

Re: Using multi-processor for model_free

Hi Sam. I am trying to setup myself on Google Cloud Platform. Here I setting up for a Redhat 6 distro, in hope it gets close to Fedora 20. I am currently making a deployment script. The process is written here:

Re: Using multi-processor for model_free

Hi Sam. Hm. Alright. But to rule it out in my head, can you try this: mpirun -np 5 /home/users/software/relax-4.0.2/relax --multi="mpi4py" -v Or similar destination path. But please try the full path. Best Troels 2016-09-30 19:47 GMT+02:00 Mahdi, Sam : > I get the

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

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 wrote: > Hi Edward, > > The protein

Re: Using multi-processor for model_free

Hi Sam. Can you try: mpirun --version Thanks 2016-10-01 0:00 GMT+02:00 Mahdi, Sam : > Hi Troels, > > Here is a list of the packages I got off of the fedora package list > Openmpi: > openmpi-1.7.3-1.fc.20(64-bit) > openmpi-devel-1.7.3-1.fc20(64bit) >

Re: Using multi-processor for model_free

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

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

On 30 September 2016 at 19:45, Mahdi, Sam 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

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

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