[gridengine users] openmpi jobs in sge and bash+modules

Reuti reuti at staff.uni-marburg.de
Tue Nov 29 00:01:12 UTC 2011


Am 28.11.2011 um 21:00 schrieb Prentice Bisbal:

> On 11/23/2011 10:10 AM, Reuti wrote:
>> Am 23.11.2011 um 16:01 schrieb Prentice Bisbal:
>> 
>>> Schmidt,
>>> 
>>> I've  been having the same problem ever since I upgraded my cluster
>>> nodes to RHEL 6. A few weeks ago.  My SGE installation was not touched
>>> during the upgrade, since it's on an NFS partition, and the head node
>>> was not touched during the upgrade, either. The error seems harmless,
>>> and I haven't tracked it down yet, but the existence of that error
>>> message, harmless or not, is a problem, as users keep reporting it when
>>> they see it.
>> Interesting. Did the version of the bash change with the upgrade?
>> 
>> -- Reuti
>> 
> 
> Sorry for the delayed response. Still behind on my mailing lists since
> going to SC11.
> 
> Yes, the version of bash changed with the upgrade.
> 
> On a 5.7 system:
> 
> $ bash --version
> GNU bash, version 3.2.25(1)-release (x86_64-redhat-linux-gnu)
> Copyright (C) 2005 Free Software Foundation, Inc.
> 
> $ rpm -q bash
> bash-3.2-32.el5

Is this one and the same package. I mean the first looks like 64 bit the latter like 32bit. Or do they use a 32 bit shell on a 64 bit system?


> On a 6.1 system:
> 
> $ bash --version
> 
> GNU bash, version 4.1.2(1)-release (x86_64-unknown-linux-gnu)
> Copyright (C) 2009 Free Software Foundation, Inc.
> License GPLv3+: GNU GPL version 3 or later
> <http://gnu.org/licenses/gpl.html>
> 
> $ rpm -q bash
> bash-4.1.2-8.el6.x86_64

Do you use modules on the headnode of the cluster and forward all variables with -V like the OP? The environment is set by sourcing the created "environment" in the job's spool directory. You can peek into this file and check whether it's there.

The question is for the OP too: do you need -V? Open MPI will use it automatically when going from the master node of the parallel job to the slaves.

-- Reuti


> --
> Prentice
> 
> 
>>> ---
>>> Prentice
>>> 
>>> 
>>> On 11/23/2011 09:07 AM, Schmidt U. wrote:
>>>> Dear all,
>>>> I know, the problem was discusses one or two years before, but I still
>>>> have trouble to eliminate messages in.err file:
>>>> I'm using SGE 6.2u5 and for every allocated node of an openmpi job the
>>>> sge job's error  file has two lines like this:
>>>> //bin/bash: module: line 1: syntax error: unexpected end of file
>>>> /bin/bash: error importing function definition for `module'/
>>>> I defined in global bashrc:
>>>> /MODULEPATH=...
>>>> MODULESHOME=...
>>>> alias module='/usr/bin/modulecmd bash $*'
>>>> module load default_module/
>>>> So far I do not need additional settings in the job script file
>>>> concerning module environment, as well
>>>> /#$ -V/
>>>> is used.
>>>> The both lines/  /bin/bash:.../ in the err file have no effects, but
>>>> even new users are sometimes rattled.
>>>> Is anybody affected as well with this problem and found a solution to
>>>> eliminate these messages ?
>>>> 
>>>> Udo
>>>> 
>>>> 
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>>>> users mailing list
>>>> users at gridengine.org
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