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GARD Processor (Read 3682 times)

hannah

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GARD Processor
Dec 7^th, 2008 at 9:07am

Dear all,

I have run the processor successfully on 7 data files, but my 8th file is giving me trouble. It gets down to KH test and then I get an error and segmentation fault:

KH Testing partition 2
Tree 1 base LRT = 22.2011. p-value = 0.9543
Tree 3 base LRT = 22.2011. p-value = Error:MPI Node:0
Operation MAccess is not defined for 0
Current BL Command:jvec[1][k]=vec2[k]
Signal:11 info.si_errno:0(Success) si_code:1(SEGV_MAPERR)
Failing at addr:0x31
/opt/gridengine/default/spool/compute-4-11/job_scripts/51182: line 46: 6009 Segmentation fault (core dumped)

Since I have run the other datasets exactly the same way, with no problems, I guess it is something specific to this dataset?

any insight would be appreciated!
Hannah

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Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender:	Re: GARD Processor Reply #1 - Dec 7^th, 2008 at 6:04pm Dear Hannah, Can you send me (spond at ucsd dot edu) the offending files (both the alignment and the GARD splits file) - I would like you try to recreate the error. Also, you don't need to run the processor in an MPI environment. Cheers, Sergei
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hannah YaBB Newbies Offline Feed your monkey! Posts: 5	Re: GARD Processor Reply #2 - Dec 7^th, 2008 at 8:20pm Sergei, Thanks for the quick reply. I have just sent the files. I get the error running in either an MPI environment (linux, using only one processor) or non-MPI (gui on mac). Thanks again, Hannah
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Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender:	Re: GARD Processor Reply #3 - Dec 8^th, 2008 at 11:23am Dear Hannah, There indeed was a bug in the processor module. Please download the attached file and drop it (replacing the original) into TemplateBatchFiles of your HyPhy distribution. Best, Sergei
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hannah YaBB Newbies Offline Feed your monkey! Posts: 5	Re: GARD Processor Reply #4 - Dec 8^th, 2008 at 12:36pm Thanks! It worked. It's refreshing to have responsive and knowledgeable developers; you are enabling the rest of us to do our science. I will spread the good word about HyPhy and GARD. -Hannah
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Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender:	Re: GARD Processor Reply #5 - Dec 8^th, 2008 at 4:25pm Dear Hannah, Thanks for the best feedback a developer can hope for. You made my day:) Cheers, Sergei
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