Hello,
On 27/01/14 16:50, Reuti wrote:
> Hi,
>
> Am 27.01.2014 um 17:26 schrieb Txema Heredia:
>
>> I have been trying to use modulefiles from my compute nodes with no avail.
>>
>> When a job starts, the modulecmd command is in the path, but the module
>> function is nowhere to be found. I have tried to add calls to
>> /etc/profile.d/modules.sh in both /etc/bashrc and ~/.bashrc, and even
>> setting the queue shell to "/bin/bash -l" with no luck (it is not a valid
>> shell). The only mens to have access to the "module" function is either to
>> add ". /etc/profile.d/modules.sh"
>
> This could also be done in a "starter_method" of the queue which calls the
> real script:
>
> #!/bin/bash
> . /etc/profile.d/modules.sh
> exec "${@}"
We use Modules a lot - including in cluster jobs.
I don't actually have a starter_method like that set in the queue - although
that seems like a good idea (thanks Reuti!). So it's possible without that.
>> at the beginning of my job script, or either log into the compute node in an
>> interactive session and there softstop and restart the sge_execd daemon.
>>
>> What am I missing? How can I have the module function available in my jobs?
>
> Any of the profiles are only sourced in case of "shell_start_mode
> posix_compliant" in the queue definition and listing bash in `qconf -mconf`
> "login_shells".
>
> The module command is a function, which needs to be defined. For serial jobs
> it should work to define the function in the submitting session, export the
> function and use `qsub -v module ...`.
Yes; do have the shell set to posix_compliant. Not sure you really need it
though.
What we tend to do is source /etc/profile.d/modules.sh in the job script - a
simple example would be this:
#!/bin/sh
#$ -S /bin/sh
OUTFILE="$HOME/moduletest_$(date "+%Y%m%d_%H:%M:%S")_$HOSTNAME_$JOB_ID.out"
echo "Job $JOB_NAME (job ID $JOB_ID) started by $USER, executed on $HOSTNAME"
>> $OUTFILE
echo "PATH: $PATH" >> $OUTFILE
echo "ENVIRONMENT: $ENVIRONMENT" >> $OUTFILE
echo "SHELL: $SHELL" >> $OUTFILE
. /etc/profile.d/modules.sh
module load fast_ep/1175
echo "$(which fast_ep)" >> $OUTFILE
echo "PATH: $PATH" >> $OUTFILE
(I use this to test the nodes have the correct /etc/profile.d/modules.sh - so
at least for us, this works :) $HOME - i.e. my home directory - is a globally
mounted NFS share, which is why I output there).
Tina
>
> -- Reuti
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>
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Tina Friedrich, Computer Systems Administrator, Diamond Light Source Ltd
Diamond House, Harwell Science and Innovation Campus - 01235 77 8442
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