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.$A %(mpi4py.__version__, MPI.COMM_WORLD.Get_rank(),MPI.COMM_WORLD.Get_size(), MPI.Get_processor_name()))" Sincerely, Sam On Mon, Oct 3, 2016 at 11:14 PM, Troels Emtekær Linnet < tlin...@nmr-relax.com> wrote: > Hi Sam. > > Please try not to use the tilde. > Use the full path instead. > Sometimes the expansion of tilde can give problems. > > The module command looks right. > > Then start a new terminal. > Try write: which relax > > And also paste in these command: Open the link in a browser. > > > http://svn.gna.org/viewcvs/*checkout*/relax/trunk/devel_ > scripts/openmpi_test_install_tcsh.sh?content-type=text%2Fplain > > Best Troels > > > Den tirsdag den 4. oktober 2016 skrev Mahdi, Sam < > sam.mahdi....@my.csun.edu>: > >> Hi Troels, >> >> So did you want me to simply put something like this? >> alias relax '~/relax-4.0.2/relax' >> >> module load mpi/openmpi-x86_64 >> >> And when you say run the mpirun, did you want me to rerun this script: >> source openmpi_test_install.sh >> >> Sincerely, >> Sam >> >> >> On Mon, Oct 3, 2016 at 10:29 PM, Troels Emtekær Linnet < >> tlin...@nmr-relax.com> wrote: >> >>> Hi Sam. >>> >>> Please modify the file. >>> Remove the old two alias to relax, and make a new alias to the newest >>> version of relax. >>> >>> You could/should also include the module load command here. >>> >>> Then open a new terminal. >>> Try again with mpirun, etc. >>> >>> Den mandag den 3. oktober 2016 skrev Mahdi, Sam < >>> sam.mahdi....@my.csun.edu>: >>> >>>> Hi Troels, >>>> >>>> So it was the tcshrc here was the output >>>> lias rm 'rm -i' >>>> alias cp 'cp -i' >>>> alias mv 'mv -i' >>>> >>>> setenv NMR_CONT CORRECT_ALL >>>> setenv GLOVEDIR ~/glove >>>> >>>> if (-e /usr/local/NMRPipe/com/nmrInit.linux9.com) then >>>> source /usr/local/NMRPipe/com/nmrInit.linux9.com >>>> endif >>>> >>>> set PATH = ($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
