 |
 |
Hi Matthew, Previous installations have been from NeuroDebian. I am now moving towards a centrally managed application server and Environment Modules. This scheme will permit users to choose their version, as many do not want to upgrade mid-analysis. The NeuroDebian version relies on FSLPARALLEL and does not use short.q veryshort.q, etc. but rather the default queue. The problem arises when building from source (fslinstaller.py does not support Debian 7.7), the fsl_sub is divergent from that supplied by NeuroDebian in that it still uses SGE_ROOT and the named queues. I suppose a way around this would be to copy from the NeuroDebian-installed /usr/lib/fsl/n.n to my application share. I would much prefer that fsl_sub converged in all distributions. This command: diff bin/fsl_sub /usr/lib/fsl/5.0/fsl_sub shows some fairly substantial differences. Chuck On 01/13/2015 06:58 AM, Matthew Webster wrote: > Hi Chuck > > Do you have SGE_ROOT set correctly? Do you have short.q etc available on your SGE? > > Kind Regards > Matthew > >> Hi Matthew, >> >> Correct, this is not happening. In looking at the fsl_sub installed from the source, I find no reference to the FSLPARALLEL variable. >> >> Best, >> Chuck >> >> >> On 01/13/2015 06:04 AM, Matthew Webster wrote: >>> Hello, >>> fsl_sub should be able to submit to SGE by default - is this not happening for you? >>> >>> Kind Regards >>> Matthew >>> >>>> I have downloaded the source tarball of fsl, but have found that fsl_sub diverges from that available via NeuroDebian, in particular it does not account for FSLPARALLEL. Is there a source download that is grid-enabled? >> >> -- >> Chuck Theobald >> System Administrator >> The Robert and Beverly Lewis Center for Neuroimaging >> University of Oregon >> P: 541-346-0343 >> F: 541-346-0345 -- Chuck Theobald System Administrator The Robert and Beverly Lewis Center for Neuroimaging University of Oregon P: 541-346-0343 F: 541-346-0345