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 <
tlinnet@xxxxxxxxxxxxx>:
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.846@xxxxxxxxxxx>:
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 <
tlinnet@xxxxxxxxxxxxx> 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 <
tlinnet@xxxxxxxxxxxxx>:
Hi Sam.
Can you try:
mpirun --version
Thanks
2016-10-01 0:00 GMT+02:00 Mahdi, Sam <sam.mahdi.846@xxxxxxxxxxx>:
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 <
tlinnet@xxxxxxxxxxxxx> 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.846@xxxxxxxxxxx
:
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 <
tlinnet@xxxxxxxxxxxxx> 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.846@xxxxxxxxxxx>:
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 <
tlinnet@xxxxxxxxxxxxx> 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.846@xxxxxxxxxxx>:
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 <
edward@xxxxxxxxxxxxx>
wrote:
On 30 September 2016 at 19:12, Mahdi, Sam <
sam.mahdi.846@xxxxxxxxxxx>
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
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