script executing-problem ("module: command not found")

jovana.knezevic.83 · 10-13-2009, 08:20 AM

Hello everyone.
I'm trying to execute a script on a cluster (connected via ssh), because I have to load gcc and mpich2 to all the machines before I execute my parallel program on them (it is shared memory), so, to cut the long story short, my script looks like:

#!/bin/bash

module load gcc
module unload mpi.parastation
module load mpi.mpich2/1.0.5

however, on the execution it prints the message:
module: command not found

If I try to execute something "stupid" in the same script, like:
echo "blah blah",
it does print blah blah indeed!

Does anyone have a clue what the problem might be? Some prefixes to module-command? Thanks in advance.

catkin · 10-13-2009, 11:03 AM

Is the module command installed on the remote system? If so then it is not in the directories listed in $PATH and you can either modify $PATH to include the directory containing the module executable or you can give the full path to the module executable instead of its name alone.

DrLove73 · 10-13-2009, 11:04 AM

I think this will help (from https://subtrac.sara.nl/userdoc/wiki/shared/modules):

Quote:

Modules and shells

The module command is shell-independent, but the implementation is shell-dependent:

* bash: module is an exported shell function
* csh/tcsh: module is an alias
* ksh: module is a shell function

Th system-wide initialization scripts take care that the module environment is properly initiated at the start of a job or interactive session, using the method for your login shell. Problems arise when:

* the shell that is used in a job is not the login shell
* a subshell is created to the same shell (only for non-bash shells)
* a subshell is created to another shell

In these cases, it is necessary to define the modules environment :

* bash:
. /usr/share/modules/init/bash
* csh/tcsh:
source /usr/share/modules/init/csh
* ksh:
. /usr/share/modules/init/ksh

We recommend to use bash as login shell and as shell in jobs.

Dobrodosla na linuxquestions.org forume

jovana.knezevic.83 · 10-14-2009, 03:22 AM

Thanks both of you!

@catkin:

The thing is that when I run these "module load" commands from the console, it works, so yes, it should be installed on the machines.
When I type:
whereis -b module, it prints just
module:

Isn't this strange? How can I now the path to the module executable? am I doing something wrong? :)

@DrLove73:

(Hvala, hvala :))
"In these cases, it is necessary to define the modules environment :

* bash:
. /usr/share/modules/init/bash
* csh/tcsh:
source /usr/share/modules/init/csh
* ksh:
. /usr/share/modules/init/ksh"

What does this exactly mean? I'm not very selfconfident at the moment :)

DrLove73 · 10-14-2009, 04:29 AM

I never needed modules so my knowledge is very very limited

I just used intelligent google searching for above.

I also found this tutorial :http://modules.sourceforge.net/docs/...tney_paper.pdf

and http://www-theor.ch.cam.ac.uk/IT/software/modules.html

but this should be more helpful:http://www.uni-koeln.de/rrzk/server/...n/modules.html :

Quote:

Modules in Batch-Scripts
Before loading modules in batch scripts, the module-environment has to be set up by sourcing files that include the module-environment into the shell. These files are:

* /etc/profile.d/modules.sh
for the shells bash and sh and similar ones and
* /etc/profile.d/modules.csh
for csh and tcsh .

For running software available as module, the module has to be loaded in the batch-script. For running software compiled with library-modules in batch scripts, again first load the compiler module that was used on compilation, then load the library.

jovana.knezevic.83 · 10-14-2009, 08:25 AM

Yeap, thanks a lot!!! :)

Sourcing /etc/profile.d/modules.sh in the script solved the problem
"module : command not found"
So it seems to load gcc & mpich on "my" machines.

However, I don't see that I have achieved anything with this, since it gives Segmentation fault immediately and I don't think it was due to my code, but this is another subject. :)

Thanks again!

DrLove73 · 10-14-2009, 12:47 PM

Any time. I have my contact info in my profile, if something get's urgent.