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_ > 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
