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_Computing#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_scripts/deploy_scripts/deploy_google_computing_redhat_6_86_x64_upgrade_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_scripts/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
