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/*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
