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Posted by Troels Emtekær Linnet on October 04, 2016 - 08:14:
Hi Sam.

Please try not to use the tilde.
Use the full path instead.
Sometimes the expansion of tilde can give problems.

The module command looks right.

Then start a new terminal.
Try write: which relax

And also paste in these command: Open the link in a browser.


http://svn.gna.org/viewcvs/*checkout*/relax/trunk/devel_scripts/openmpi_test_install_tcsh.sh?content-type=text%2Fplain

Best Troels

Den tirsdag den 4. oktober 2016 skrev Mahdi, Sam <sam.mahdi.846@xxxxxxxxxxx

:



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 <
tlinnet@xxxxxxxxxxxxx
<javascript:_e(%7B%7D,'cvml','tlinnet@xxxxxxxxxxxxx');>> 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.846@xxxxxxxxxxx
<javascript:_e(%7B%7D,'cvml','sam.mahdi.846@xxxxxxxxxxx');>>:


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 <
tlinnet@xxxxxxxxxxxxx> 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.846@xxxxxxxxxxx>:


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 <
tlinnet@xxxxxxxxxxxxx> 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 <
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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