Hi Sam. One thing that bothers me, is that ------- python -c "import mpi4py; print mpi4py.__version__" ------- shows version 1.3.
In the "relax -i" , you uploaded, it says: mpi4py True 2.0.0 /home/crowlab/.local/lib/python2.7/site-packages/mpi4py So, lets check this. Do this in terminal: 3 small lines, and then one big line. ------- python -c "import mpi4py; print mpi4py.__version__" mpirun --np 2 python -c "import sys; print('%s'%sys.version_info)" mpirun --np 2 python -c "import mpi4py; print mpi4py.__version__" mpirun --np 2 python -c "import mpi4py; from mpi4py import MPI; print('Mpi4py %s process %d of %d on %s.' %(mpi4py.__version__, MPI.COMM_WORLD.Get_rank(),MPI.COMM_WORLD.Get_size(), MPI.Get_processor_name()))" ------- And in the end (we have done it before, lets try again): ------- # NOTE: Use the FULL path to relax. Not the alias function. This is important mpirun --np 2 /home/tlinnet/relax-4.0.2/relax --multi='mpi4py' -v mpirun --np 2 /home/tlinnet/relax-4.0.2/relax --multi='mpi4py' -i # If this does not work, please provide relax -v relax -i ------- Best Troels 2016-10-04 21:15 GMT+02:00 Mahdi, Sam <sam.mahdi....@my.csun.edu>: > 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 null use.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: 3900.0000 > CPU min MHz: 1600.0000 > 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.$A %(mpi4py.__version__, > MPI.COMM_WORLD.Get_rank(),MPI.COMM_WORLD.Get_size(), > MPI.Get_processor_name()))" > > > Sincerely, > Sam > > > > On Mon, Oct 3, 2016 at 11:14 PM, Troels Emtekær Linnet < > tlin...@nmr-relax.com> wrote: > >> Hi Sam. >> >> Please try not to use the tilde. >> Use the full path instead. >> Sometimes the expansion of tilde can give problems. >> >> The module command looks right. >> >> Then start a new terminal. >> Try write: which relax >> >> And also paste in these command: Open the link in a browser. >> >> >> http://svn.gna.org/viewcvs/*checkout*/relax/trunk/devel_scri >> pts/openmpi_test_install_tcsh.sh?content-type=text%2Fplain >> >> Best Troels >> >> >> Den tirsdag den 4. oktober 2016 skrev Mahdi, Sam < >> sam.mahdi....@my.csun.edu>: >> >>> Hi Troels, >>> >>> So did you want me to simply put something like this? >>> alias relax '~/relax-4.0.2/relax' >>> >>> module load mpi/openmpi-x86_64 >>> >>> And when you say run the mpirun, did you want me to rerun this script: >>> source openmpi_test_install.sh >>> >>> Sincerely, >>> Sam >>> >>> >>> On Mon, Oct 3, 2016 at 10:29 PM, Troels Emtekær Linnet < >>> tlin...@nmr-relax.com> wrote: >>> >>>> Hi Sam. >>>> >>>> Please modify the file. >>>> Remove the old two alias to relax, and make a new alias to the newest >>>> version of relax. >>>> >>>> You could/should also include the module load command here. >>>> >>>> Then open a new terminal. >>>> Try again with mpirun, etc. >>>> >>>> Den mandag den 3. oktober 2016 skrev Mahdi, Sam < >>>> sam.mahdi....@my.csun.edu>: >>>> >>>>> Hi Troels, >>>>> >>>>> So it was the tcshrc here was the output >>>>> lias rm 'rm -i' >>>>> alias cp 'cp -i' >>>>> alias mv 'mv -i' >>>>> >>>>> setenv NMR_CONT CORRECT_ALL >>>>> setenv GLOVEDIR ~/glove >>>>> >>>>> if (-e /usr/local/NMRPipe/com/nmrInit.linux9.com) then >>>>> source /usr/local/NMRPipe/com/nmrInit.linux9.com >>>>> endif >>>>> >>>>> set PATH = ($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/*checkout*/relax/trunk/devel_scri >>>>> pts/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 get relax to run and work on redhat/centos version 6. >>>>>>>> >>>>>>>> I have updated a deployment script for this: >>>>>>>> http://wiki.nmr-relax.com/Run_relax_at_Google_Cloud_Computin >>>>>>>> g#Install_packages_at_server >>>>>>>> >>>>>>>> Please have a look here: >>>>>>>> http://svn.gna.org/viewcvs/relax/trunk/devel_scripts/deploy_ >>>>>>>> scripts/ >>>>>>>> >>>>>>>> and specific: >>>>>>>> http://svn.gna.org/viewcvs/*checkout*/relax/trunk/devel_scri >>>>>>>> pts/deploy_scripts/deploy_google_computing_redhat_6_86_x64_u >>>>>>>> pgrade_python.sh?content-type=text%2Fplain >>>>>>>> >>>>>>>> This is for centos 6, which should get very close to fedora 20. >>>>>>>> >>>>>>>> For centos 6, the openmpi is version 1.8. And you have 1.7.3 >>>>>>>> >>>>>>>> So, the only difference I can see is the openmpi version. >>>>>>>> Can you upgrade this? >>>>>>>> >>>>>>>> ------ >>>>>>>> [tlinnet@instance-1 ~]$ relax_4.0.2 -i >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> relax 4.0.2 >>>>>>>> >>>>>>>> Molecular dynamics by NMR data >>>>>>>> analysis >>>>>>>> >>>>>>>> Copyright (C) 2001-2006 Edward >>>>>>>> d'Auvergne >>>>>>>> Copyright (C) 2006-2016 the relax >>>>>>>> development team >>>>>>>> >>>>>>>> This is free software which you are welcome to modify and >>>>>>>> redistribute under the conditions of the >>>>>>>> GNU General Public License (GPL). This program, including all >>>>>>>> modules, is licensed under the GPL >>>>>>>> and comes with absolutely no warranty. For details type 'GPL' >>>>>>>> within the relax prompt. >>>>>>>> >>>>>>>> Assistance in using the relax prompt and scripting interface can be >>>>>>>> accessed by typing 'help' within >>>>>>>> the prompt. >>>>>>>> >>>>>>>> Processor fabric: Uni-processor. >>>>>>>> >>>>>>>> >>>>>>>> Hardware information: >>>>>>>> Machine: x86_64 >>>>>>>> Processor: x86_64 >>>>>>>> Processor name: Intel(R) Xeon(R) CPU @ 2.50GHz >>>>>>>> Endianness: little >>>>>>>> Total RAM size: 3426 Mb >>>>>>>> Total swap size: 0 Mb >>>>>>>> >>>>>>>> Operating system information: >>>>>>>> System: Linux >>>>>>>> Release: 2.6.32-642.4.2.el6.x86_64 >>>>>>>> Version: #1 SMP Tue Aug 23 19:58:13 UTC 2016 >>>>>>>> GNU/Linux version: CentOS 6.8 Final >>>>>>>> Distribution: centos 6.8 Final >>>>>>>> Full platform string: Linux-2.6.32-642.4.2.el6.x86_ >>>>>>>> 64-x86_64-with-centos-6.8-Final >>>>>>>> >>>>>>>> Python information: >>>>>>>> Architecture: 64bit ELF >>>>>>>> Python version: 2.7.8 >>>>>>>> Python branch: >>>>>>>> Python build: default, May 15 2016 12:46:09 >>>>>>>> Python compiler: GCC 4.4.7 20120313 (Red Hat 4.4.7-16) >>>>>>>> Libc version: glibc 2.2.5 >>>>>>>> Python implementation: CPython >>>>>>>> Python revision: >>>>>>>> Python executable: /opt/rh/python27/root/usr/bin/python >>>>>>>> Python flags: sys.flags(debug=0, py3k_warning=0, >>>>>>>> division_warning=0, division_new=0, inspect=0, interactive=0, >>>>>>>> optimize=0, >>>>>>>> dont_write_bytecode=0, no_user_site=0, no_site=0, ignore_environment=0, >>>>>>>> tabcheck=0, verbose=0, unicode=0, bytes_warning=0, >>>>>>>> hash_randomization=0) >>>>>>>> Python float info: >>>>>>>> sys.float_info(max=1.7976931348623157e+308, >>>>>>>> max_exp=1024, max_10_exp=308, min=2.2250738585072014e-308, >>>>>>>> min_exp=-1021, >>>>>>>> min_10_exp=-307, dig=15, mant_dig=53, epsilon=2.220446049250313e-16, >>>>>>>> radix=2, rounds=1) >>>>>>>> Python module path: ['/home/tlinnet/relax-4.0.2', >>>>>>>> '/usr/lib64/python2.6/site-packages/openmpi', >>>>>>>> '/usr/lib64/python2.6/site-packages/wx-2.8-gtk2-unicode', >>>>>>>> '/opt/rh/python27/root/usr/lib64/python27.zip', >>>>>>>> '/opt/rh/python27/root/usr/lib64/python2.7', >>>>>>>> '/opt/rh/python27/root/usr/lib64/python2.7/plat-linux2', >>>>>>>> '/opt/rh/python27/root/usr/lib64/python2.7/lib-tk', >>>>>>>> '/opt/rh/python27/root/usr/lib64/python2.7/lib-old', >>>>>>>> '/opt/rh/python27/root/usr/lib64/python2.7/lib-dynload', >>>>>>>> '/opt/rh/python27/root/usr/lib64/python2.7/site-packages', >>>>>>>> '/opt/rh/python27/root/usr/lib/python2.7/site-packages'] >>>>>>>> >>>>>>>> Python packages and modules (most are optional): >>>>>>>> >>>>>>>> Name Installed Version Path >>>>>>>> >>>>>>>> minfx True 1.0.12 >>>>>>>> /home/tlinnet/relax-4.0.2/minfx >>>>>>>> >>>>>>>> bmrblib True 1.0.4 >>>>>>>> /home/tlinnet/relax-4.0.2/bmrblib >>>>>>>> >>>>>>>> numpy True 1.7.1 >>>>>>>> /opt/rh/python27/root/usr/lib64/python2.7/site-packages/numpy >>>>>>>> >>>>>>>> scipy True 0.12.1 >>>>>>>> /opt/rh/python27/root/usr/lib64/python2.7/site-packages/scipy >>>>>>>> >>>>>>>> wxPython True 2.8.12.0 (gtk2-unicode) >>>>>>>> /usr/lib64/python2.6/site-packages/wx-2.8-gtk2-unicode/wx >>>>>>>> >>>>>>>> matplotlib True 1.5.3 >>>>>>>> /opt/rh/python27/root/usr/lib64/python2.7/site-packages/matplotlib >>>>>>>> >>>>>>>> mpi4py True 2.0.0 >>>>>>>> /opt/rh/python27/root/usr/lib64/python2.7/site-packages/mpi4py >>>>>>>> >>>>>>>> epydoc True 3.0.1 >>>>>>>> /opt/rh/python27/root/usr/lib/python2.7/site-packages/epydoc >>>>>>>> >>>>>>>> optparse True 1.5.3 >>>>>>>> /opt/rh/python27/root/usr/lib64/python2.7/optparse.pyc >>>>>>>> >>>>>>>> readline True >>>>>>>> /opt/rh/python27/root/usr/lib64/python2.7/lib-dynload/readline.so >>>>>>>> >>>>>>>> profile True >>>>>>>> /opt/rh/python27/root/usr/lib64/python2.7/profile.pyc >>>>>>>> >>>>>>>> bz2 True >>>>>>>> /opt/rh/python27/root/usr/lib64/python2.7/lib-dynload/bz2.so >>>>>>>> >>>>>>>> gzip True >>>>>>>> /opt/rh/python27/root/usr/lib64/python2.7/gzip.pyc >>>>>>>> >>>>>>>> io True >>>>>>>> /opt/rh/python27/root/usr/lib64/python2.7/io.pyc >>>>>>>> >>>>>>>> xml True 0.8.4 (internal) >>>>>>>> /opt/rh/python27/root/usr/lib64/python2.7/xml/__init__.pyc >>>>>>>> >>>>>>>> xml.dom.minidom True >>>>>>>> /opt/rh/python27/root/usr/lib64/python2.7/xml/dom/minidom.pyc >>>>>>>> >>>>>>>> >>>>>>>> relax information: >>>>>>>> Version: 4.0.2 >>>>>>>> Processor fabric: Uni-processor. >>>>>>>> >>>>>>>> relax C modules: >>>>>>>> >>>>>>>> Module Compiled File type >>>>>>>> Path >>>>>>>> >>>>>>>> target_functions.relax_fit True ELF 64-bit LSB shared >>>>>>>> object, x86-64, version 1 (SYSV), dynamically linked, not stripped >>>>>>>> /home/tlinnet/relax-4.0.2/target_functions/relax_fit.so >>>>>>>> --------- >>>>>>>> >>>>>>>> [tlinnet@instance-1 ~]$ source openmpi_test_install_bash.sh >>>>>>>> http://svn.gna.org/viewcvs/*checkout*/relax/trunk/devel_scri >>>>>>>> pts/openmpi_test_install_bash.sh >>>>>>>> Source the commands with: source openmpi_test_install_bash.sh >>>>>>>> Then do: testopenmpi >>>>>>>> >>>>>>>> [tlinnet@instance-1 ~]$ testopenmpi >>>>>>>> This is functions to test openmpi, python and openmpi. >>>>>>>> >>>>>>>> Shell is: /bin/bash >>>>>>>> >>>>>>>> > which mpirun >>>>>>>> /usr/lib64/openmpi/bin/mpirun >>>>>>>> >>>>>>>> > module avail >>>>>>>> >>>>>>>> -------------------------------------------------------------------------------------- >>>>>>>> /usr/share/Modules/modulefiles ------------------------------ >>>>>>>> -------------------------------------------------------- >>>>>>>> dot module-git module-info modules null use.own >>>>>>>> >>>>>>>> ------------------------------------------------------------ >>>>>>>> --------------------------------- /etc/modulefiles >>>>>>>> ------------------------------------------------------------ >>>>>>>> --------------------------------- >>>>>>>> openmpi-1.8-x86_64 openmpi-x86_64 >>>>>>>> >>>>>>>> > lscpu >>>>>>>> Architecture: x86_64 >>>>>>>> CPU op-mode(s): 32-bit, 64-bit >>>>>>>> Byte Order: Little Endian >>>>>>>> CPU(s): 4 >>>>>>>> On-line CPU(s) list: 0-3 >>>>>>>> Thread(s) per core: 2 >>>>>>>> Core(s) per socket: 2 >>>>>>>> Socket(s): 1 >>>>>>>> NUMA node(s): 1 >>>>>>>> Vendor ID: GenuineIntel >>>>>>>> CPU family: 6 >>>>>>>> Model: 62 >>>>>>>> Model name: Intel(R) Xeon(R) CPU @ 2.50GHz >>>>>>>> Stepping: 4 >>>>>>>> CPU MHz: 2500.000 >>>>>>>> BogoMIPS: 5000.00 >>>>>>>> Hypervisor vendor: KVM >>>>>>>> Virtualization type: full >>>>>>>> L1d cache: 32K >>>>>>>> L1i cache: 32K >>>>>>>> L2 cache: 256K >>>>>>>> L3 cache: 30720K >>>>>>>> NUMA node0 CPU(s): 0-3 >>>>>>>> >>>>>>>> > mpirun --version >>>>>>>> mpirun (Open MPI) 1.8.1 >>>>>>>> >>>>>>>> Report bugs to http://www.open-mpi.org/community/help/ >>>>>>>> >>>>>>>> > mpirun --report-bindings -np 2 echo "hello world" >>>>>>>> hello world >>>>>>>> [instance-1:03337] MCW rank 1 bound to socket 0[core 1[hwt 0-1]]: >>>>>>>> [../BB] >>>>>>>> [instance-1:03337] MCW rank 0 bound to socket 0[core 0[hwt 0-1]]: >>>>>>>> [BB/..] >>>>>>>> hello world >>>>>>>> >>>>>>>> > mpirun --report-bindings -np 2 python -c 'print " Hello " ' >>>>>>>> [instance-1:03341] MCW rank 1 bound to socket 0[core 1[hwt 0-1]]: >>>>>>>> [../BB] >>>>>>>> [instance-1:03341] MCW rank 0 bound to socket 0[core 0[hwt 0-1]]: >>>>>>>> [BB/..] >>>>>>>> Hello >>>>>>>> Hello >>>>>>>> >>>>>>>> > mpirun --report-bindings -np 2 python --version >>>>>>>> [instance-1:03345] MCW rank 1 bound to socket 0[core 1[hwt 0-1]]: >>>>>>>> [../BB] >>>>>>>> [instance-1:03345] MCW rank 0 bound to socket 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 null >>>>>>>>>> use.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: 3900.0000 >>>>>>>>>> CPU min MHz: 1600.0000 >>>>>>>>>> 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 null >>>>>>>>>> use.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: 3900.0000 >>>>>>>>>> CPU min MHz: 1600.0000 >>>>>>>>>> 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 is extra and pointless. I only use >>>>>>>>>>>>> the openmpi when I load my modules. I have not compiled or >>>>>>>>>>>>> configured >>>>>>>>>>>>> anything with these packages. I just installed them directly from >>>>>>>>>>>>> the >>>>>>>>>>>>> package list. If you need any more info on what is installed on >>>>>>>>>>>>> these >>>>>>>>>>>>> computers let me know! >>>>>>>>>>>>> >>>>>>>>>>>>> Sincerely, >>>>>>>>>>>>> Sam >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> On Fri, Sep 30, 2016 at 2:23 PM, Troels Emtekær Linnet < >>>>>>>>>>>>> tlin...@nmr-relax.com> wrote: >>>>>>>>>>>>> >>>>>>>>>>>>>> Hi Sam. >>>>>>>>>>>>>> >>>>>>>>>>>>>> I am trying to setup myself on Google Cloud Platform. >>>>>>>>>>>>>> >>>>>>>>>>>>>> Here I setting up for a Redhat 6 distro, in hope it gets >>>>>>>>>>>>>> close to Fedora 20. >>>>>>>>>>>>>> >>>>>>>>>>>>>> I am currently making a deployment script. >>>>>>>>>>>>>> >>>>>>>>>>>>>> The process is written here: >>>>>>>>>>>>>> http://wiki.nmr-relax.com/Run_relax_at_Google_Cloud_Computin >>>>>>>>>>>>>> g#Install_packages_at_server >>>>>>>>>>>>>> >>>>>>>>>>>>>> But that is a little old, since the configurations has >>>>>>>>>>>>>> changed a little since 2015. >>>>>>>>>>>>>> And the last deployment script is for Ubuntu. >>>>>>>>>>>>>> >>>>>>>>>>>>>> Getting the packages right is a pain.... ;) >>>>>>>>>>>>>> >>>>>>>>>>>>>> Let me return when I know some more. >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> 2016-09-30 23:03 GMT+02:00 Mahdi, Sam < >>>>>>>>>>>>>> sam.mahdi....@my.csun.edu>: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> 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 >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>> >>>>>>> >>>>>> >>>>> >>> > _______________________________________________ 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