For those here using the modules environment, you also need to add "-v
MODULEPATH".
On 8/5/2012 12:35 PM, Joseph Farran wrote:
Thanks Reuti!
The "-v module" option does the trick.
Best,
Joseph
On 8/5/2012 4:44 AM, Reuti wrote:
Am 05.08.2012 um 05:04 schrieb Joseph Farran:
Howdy.
In reading about GE qrsh, it looks like qrsh set's a minimal path:
$ qrsh echo '$PATH'
/scratch/1125.1.user:/usr/local/bin:/bin:/usr/bin
To add additional paths, one can do:
qrsh -v PATH=/extra:/usr/local/bin:/bin:/usr/bin:/new-path echo '$PATH'
/scratch/1140.1.me:/extra:/usr/local/bin:/bin:/usr/bin:/new-path
And make it permanent via the personal .sge_request file. So all this is
great, but what about sourcing a shell script?
We use the module environment variables and a modules script needs to be
sourced in order for modules to become active.
So when I try loading a module and then running the command, it fails because
it cannot find modules since the modules environment setup has not been read:
$ qrsh "module load pgi/12.6; pgcc simple.c"
bash: module: command not found
bash: pgcc: command not found
If I source my system wide bashrc which also sources modules, then all is good:
$ qrsh ". /data/system-wide-bashrc.sh; module load pgi/12.6; module list"
Currently Loaded Modulefiles:
1) pgi/12.6
So how can I have qrsh automatically source "/data/system-wide-bashrc.sh"?
`module` is a shell function. With recent versions of SGE you can try:
$ qrsh -v module "module load pgi/12.6; module list"
to export it.
I tried adding ". /data/system-wide-bashrc.sh" to my .sge_request file but no
cigar.
These files are only sourced for a queue setup having "shell_start_mode
posix_compliant"
-- Reuti
Joseph
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