Hi Troels, Here is the output source openmpi_test_install.sh http://svn.gna.org/viewcvs/*checkout*/relax/trunk/devel_scripts/openmpi_test_install.sh Source the commands with: source openmpi_test_install.sh Then do: testopenmpi
function: Command not found. This is functions to test openmpi, 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_scripts/openmpi_test_install.sh Source the commands with: source openmpi_test_install.sh Then do: testopenmpi function: Command not found. This is functions to test openmpi, 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
