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 > <javascript:_e(%7B%7D,'cvml','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 >> <javascript:_e(%7B%7D,'cvml','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/*ch >>> eckout*/relax/trunk/devel_scripts/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
