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GARD.bf (Read 3108 times)

tlefebure

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Posts: 36
Cornell University

GARD.bf
Jan 18^th, 2010 at 12:49pm

Hello,

Just installed the new version of Hyphy and noticed that the GARD files have changed. Before I was using LocalGARD.bf that way:

$MPIDIR/mpirun -np $PROCS -machinefile 481-machines $HYPHY /state/partition1/LocalGARD.bf < $ANSW >& 481-output

Now we have:
[tnl7@biosim TemplateBatchFiles]$ ls *GARD*
GARD.bf GARD_GA_CHC.ibf GARDProcessor.bf

I guess I should replace LocalGARD.bf by GARD.bf and also copy GARD_GA_CHC.ibf to each node... Right?

Thanks!

--Tristan

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Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender:	Re: GARD.bf Reply #1 - Jan 19^th, 2010 at 10:14am Hi Tristan, It is probably best to copy the entire TemplateBatchFiles directory because GARD*.bf includes other dependancies, which I can't immediately recall. You definitely need to copy both files you mention. Sergei
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tlefebure

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Posts: 36
Cornell University

Re: GARD.bf
Reply #2 - Jan 19^th, 2010 at 12:28pm

Thanks,

So I copied the directory TemplateBatchFiles to the head node, launched the analysis, it ran for about 2 minutes, and then crashed with that message:
Code:

Could not read command file in ExecuteAFile from: /state/partition1/TemplateBatchFiles/Utility/NJ.bf

Does that mean I have to copy the TemplateBatchFiles to all the nodes?
(that was not the case with the LocalGARD.bf)

Thanks,

--Tristan

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Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender:	Re: GARD.bf Reply #3 - Jan 19^th, 2010 at 12:30pm Hi Tristan, You don't need the entire directory, but some files from it: the error message below is an indication of what files you need. LocalGARD.bf was a monolithic file, but I have since done some re-factoring to share components between analyses (e.g. the neighbor joining routine). Sergei
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tlefebure YaBB Newbies Offline Posts: 36 Cornell University	Re: GARD.bf Reply #4 - Jan 19^th, 2010 at 12:37pm Sergei, sorry if I was not clear, my question is whether the directory should be copied to all the nodes or only the head node. Thnks
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Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender:	Re: GARD.bf Reply #5 - Jan 19^th, 2010 at 12:46pm Hi Tristan, All nodes. Depending on the setup of your cluster, it could be easier to NFS mount (read-only) the directory on the slaves. Cheers, Sergei
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