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/*
> checkout*/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
> <javascript:_e(%7B%7D,'cvml','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
>> <javascript:_e(%7B%7D,'cvml','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
>>> <javascript:_e(%7B%7D,'cvml','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
>>>> <javascript:_e(%7B%7D,'cvml','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
>>>>> <javascript:_e(%7B%7D,'cvml','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
>>>>>> <javascript:_e(%7B%7D,'cvml','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
>>>>>>> <javascript:_e(%7B%7D,'cvml','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
>>>>>>>> <javascript:_e(%7B%7D,'cvml','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
>>>>>>>>> <javascript:_e(%7B%7D,'cvml','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
>>>>>>>>>> <javascript:_e(%7B%7D,'cvml','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
>>>>>>>>>>> <javascript:_e(%7B%7D,'cvml','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
>>>>>>>>>>>> <javascript:_e(%7B%7D,'cvml','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
>>>>>>>>>>>>> <javascript:_e(%7B%7D,'cvml','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
>>>>>>>>>>>>>> <javascript:_e(%7B%7D,'cvml','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
>>>>>>>>>>>>>>> <javascript:_e(%7B%7D,'cvml','edw...@nmr-relax.com');>>
>>>>>>>>>>>>>>> wrote:
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>> > On 30 September 2016 at 19:12, Mahdi, Sam <
>>>>>>>>>>>>>>> sam.mahdi....@my.csun.edu
>>>>>>>>>>>>>>> <javascript:_e(%7B%7D,'cvml','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
>>>>>>>>>>>>>>> <javascript:_e(%7B%7D,'cvml','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
>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>
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