Re: Using multi-processor for model_free

On 10 October 2016 at 23:12, Mahdi, Sam wrote: > Hi Edward, > > Wanted to update you a prior problem I had. So I ran relax with multiple > processors and single processor with the same data set, and obtained > identical data on my computer. So the previous issue I had

Re: Using multi-processor for model_free

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

Re: Using multi-processor for model_free

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

Re: Using multi-processor for model_free

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,

Re: Using multi-processor for model_free

I think there is nothing more to do here. Call the nearest computer wizard, and give a round of beer. Best Troels Den onsdag den 5. oktober 2016 skrev Mahdi, Sam : > But i already have mpi4py installed from the package list. > > On Wed, Oct 5, 2016 at 2:43 PM, Troels

Re: Using multi-processor for model_free

But i already have mpi4py installed from the package list. On Wed, Oct 5, 2016 at 2:43 PM, Troels Emtekær Linnet wrote: > Hi Sam. > > Akk you PI to run this: > > sudo -- sh -c 'setenv MPICC /usr/lib64/openmpi-1.10/bin/mpicc; pip > install mpi4py' > or > sudo -i > setenv

Re: Using multi-processor for model_free

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

Re: Using multi-processor for model_free

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

Re: Using multi-processor for model_free

Hi Sam. One thing that bothers me, is that --- python -c "import mpi4py; print mpi4py.__version__" --- shows version 1.3. In the "relax -i" , you uploaded, it says: mpi4py True 2.0.0 /home/crowlab/.local/lib/python2.7/site-packages/mpi4py So, lets check this. Do

Re: Using multi-processor for model_free

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 '

Re: Using multi-processor for model_free

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

Re: Using multi-processor for model_free

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

Re: Using multi-processor for model_free

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

Re: Using multi-processor for model_free

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

Re: Using multi-processor for model_free

Hi Sam. I can get relax to run and work on redhat/centos version 6. I have updated a deployment script for this: http://wiki.nmr-relax.com/Run_relax_at_Google_Cloud_Computing#Install_packages_at_server Please have a look here: http://svn.gna.org/viewcvs/relax/trunk/devel_scripts/deploy_scripts/

Re: Using multi-processor for model_free

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,

Re: Using multi-processor for model_free

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

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 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 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. 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: 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

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: 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: 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

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

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 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

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: 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: 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: 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: Using multi-processor for model_free

Also, Congrats to Edward! On Thu, Sep 29, 2016 at 4:11 PM, Mahdi, Sam wrote: > Hi Troels, > > I will upload a bug report with the pdb file, the script I use, and the > data I'm using. > > Sincerely, > Sam > > On Thu, Sep 29, 2016 at 2:25 PM, Troels Emtekær Linnet < >

Re: Using multi-processor for model_free

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

Re: Using multi-processor for model_free

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 =

Re: Using multi-processor for model_free

Hi Sam. Problems with the GUI do not necessary mean a problem. It could be a problem of wxPython. Which version do you have? (relax -i ) To find the specific tests that fails, can you do: > relax --gui-tests --time -t gui_fail.txt Best Troels 2016-09-28 22:44 GMT+02:00 Mahdi, Sam

Re: Using multi-processor for model_free

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

Re: Using multi-processor for model_free

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

Re: Using multi-processor for model_free

To test the speed difference between script and GUI, you could try to run the full test-suite through the terminal or inside the GUI. That should give you a clue about time difference. 2016-09-28 20:32 GMT+02:00 Troels Emtekær Linnet : > If you get different results, for

Re: Using multi-processor for model_free

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

Re: Using multi-processor for model_free

Another possibility for the "slowness" is "the very well known" that, printing to screen makes python slow. Extremely slow... And all the minimization information to screen actually slow downs relax (through python). For even faster calculations, just "log" the relax output with -l, and do not

Re: Using multi-processor for model_free

Hi Sam. Thank you for your valuable feedback! It makes it more fun to help :) Can you check if this is not in your script : http://wiki.nmr-relax.com/Tutorial_for_model-free_analysis_sam_mahdi#Let_us_try_to_execute # Execution. # Change some opt params.# COMMENT THESE OUT FOR REAL

Re: Using multi-processor for model_free

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

Re: Using multi-processor for model_free

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

Re: Using multi-processor for model_free

That looks wrong. NP should be the variable for the number of processors. I suspect the error is not in relax, but somewhere in your system. I think I can't help you more from here. Is there a computer wizard around at your lab? Best Troels Den mandag den 26. september 2016 skrev Mahdi, Sam <

Re: Using multi-processor for model_free

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

Re: Using multi-processor for model_free

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? > >

Re: Using multi-processor for model_free

The file: file #28673: relax -i data for 4.0,2 a https://gna.org/bugs/download.php?file_id=28673 Its emtpy? 2016-09-20 20:05 GMT+02:00 Mahdi, Sam : > Hi Troels, > > I am a bit confused what you are talking about. There is no file labeled .? > > On Tue, Sep 20, 2016

Re: Using multi-processor for model_free

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

Re: Using multi-processor for model_free

Hi Sam. On https://gna.org/bugs/?25084 I cannot open the file.? In the meantime, try to specify the full path to relax. Not just ./relax but /home/user/xxx/relax Best Troels 2016-09-19 23:13 GMT+02:00 Mahdi, Sam : > I just uploaded the 4.0.2 relax -i info. I

Re: Using multi-processor for model_free

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 Installed

Re: Using multi-processor for model_free

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 : >

Re: Using multi-processor for model_free

Hi Sam. Regarding protein 2. Try to make a spin_loop after loading the data or use the GUI: http://wiki.nmr-relax.com/Tutorial_for_model-free_analysis_sam_mahdi#Check_the_spin_containers_via_GUI Carefully check the spins. Or deselect all spins, and select 1-2 spins, and run the calculation. Add

Re: Using multi-processor for model_free

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

Re: Using multi-processor for model_free

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

Re: Using multi-processor for model_free

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

Re: Using multi-processor for model_free

Hi Sam. To tackle this problem, I would advice to create another bug. Creation and closing of a bug "leaves trails", which maybe will help another person, when googling for the same problem. To help you, can you do a "relax -i" on both computers? That give some indication about package versions

Re: Using multi-processor for model_free

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

Re: Using multi-processor for model_free

Hi Sam. Can you produce another bug report. Please don't attach files to these mails as it will strain the mailinglists. Cheers Troels Den lørdag den 10. september 2016 skrev Mahdi, Sam < sam.mahdi@my.csun.edu>: > Hi Troels, > > Additional question that I had, if you could also look into

Re: Using multi-processor for model_free

Hi Troels, Additional question that I had, if you could also look into this as well on Tuesday please. I have decided to try to write a script to automate this whole process (since I won't be using the gui to do model free), and I've come across a problem. I can successfully open up relax using

Re: Using multi-processor for model_free

Hi Troels, Thank you so much. If there is any extra info you need please let me know. Sincerely, Sam On Thu, Sep 8, 2016 at 9:12 AM, Troels Emtekær Linnet wrote: > Hi Sam. > > I will have some time on Tuesday, and then I will look at it. > > Best > Troels > > > Den

Re: Using multi-processor for model_free

Hi Sam. I will have some time on Tuesday, and then I will look at it. Best Troels Den onsdag den 7. september 2016 skrev Mahdi, Sam : > Hello Troels, > > I uploaded all the files, and even added in the entire output that i > recieved using model free in script

Re: Using multi-processor for model_free

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,

Re: Using multi-processor for model_free

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 : >

Re: Using multi-processor for model_free

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