Hi - this is an IT question
As you can tell from the subject I am not a sun grid expert. I attempted to install a grid engine to make the most of multiple processors on my i7 imac. I followed the directions from the fsl website. https://www.fmrib.ox.ac.uk/phpwiki/index.php/FslSge with the special instructions by Duncan for a mac. Unfortunately, I think the directions out of date - not everything worked as planned. For example, the link to download sun grid engine no longer works. I could only eventually find a grid engine from Oracle - so now called Oracle Grid Engine, since they bought out Sun a year ago.
After working out that sge-6 on the mac instructions, corresponded to sge on the linux instructions, I proceeded as planned (except having to say no to some java thing they ask about which was not covered and must be part of the new software version). It was quite confusing as to where and how to edit the .bashrc for the mac. Is there a definitive answer for this?
The second patch for the mac for SGE 6.2 failed. Feat returned an error saying that my computer was not a registered server. That is where I gave up. I deleted what bash_profile and bashrc files I remembered that I changed. I deleted the sge and sge-6 folders and the sgeadmin user.
But now when I try to run a Feat it fails. It seems to still be looking for a cluster. Reinstalling fsl does not help.
The error says:
/usr/local/fsl/bin/fsl_sub -T 60 -l logs -N feat3a_flame /usr/local/fsl/bin/feat /Users/DCM/Desktop/analysis_1_human.gfeat/cope1.feat/design.fsf -D /Users/DCM/Desktop/analysis_1_human.gfeat/cope1.feat -I 1 -flame1
/usr/local/fsl/bin/fsl_sub: line 348: exec: qsub: not found
So I guess the questions I have are:
1. How do I fix fsl to its original state?
2. Where is the place to change bashrc on a mac (snow leopard)?
3. Was there any point in using the SGE in the first place, and if so, where does one now download, and is there a correction for the os x patch?
Thanks in advance,
Dan
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