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SBP bug (Read 626 times)
Matt
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SBP bug
Aug 5th, 2010 at 2:50pm
 
I am encountering an error when trying to run SBP analysis on my local machine. this happens when running both ./HYPHYMP (manually inputting options) and ./HYPHYMPI (using batchfile). This is using rev914, checked out today.

It is related to using the Model Option: Global w/variation+HM. The error (below) does not happen when not using this option.

batchfile:
Code:
inputOptions = {};
inputOptions ["00"] = "Codon";
inputOptions ["01"] = DIRECTORY_SEPARATOR + "home" + DIRECTORY_SEPARATOR + "macmanes" + DIRECTORY_SEPARATOR + "PAML" + DIRECTORY_SEPARATOR + "codeml" + DIRECTORY_SEPARATOR + "dqa_genus" + DIRECTORY_SEPARATOR + "seq" + DIRECTORY_SEPARATOR + "dqa_genus78.phy";
inputOptions ["02"] = "Universal";
inputOptions ["03"] = "Run 1";
inputOptions ["04"] = "1000";
inputOptions ["05"] = "GY94W9";
inputOptions ["06"] = "Global w/variation+HM";
inputOptions ["07"] = "Gamma+Inv";
inputOptions ["08"] = "6";
inputOptions ["09"] = DIRECTORY_SEPARATOR + "home" + DIRECTORY_SEPARATOR + "macmanes" + DIRECTORY_SEPARATOR + "Desktop" + "results_SBP.txt";
ExecuteAFile (DIRECTORY_SEPARATOR + "home" + DIRECTORY_SEPARATOR + "macmanes" + DIRECTORY_SEPARATOR + "hyphy" + DIRECTORY_SEPARATOR + "HYPHY" + DIRECTORY_SEPARATOR + "TemplateBatchFiles" + DIRECTORY_SEPARATOR + "SingleBreakpointRecomb.bf", inputOptions); 



the error:

Code:
macmanes@macmanes:~/hyphy/HYPHY$ /home/macmanes/apps/openmpi-1.4.2/bin/mpirun -np 16 ./HYPHYMPI /home/macmanes/Desktop/matt_dqagenus.bf
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------

There are 63 potential breakpoints.
How many KH samples should be drawn per breakpoint ?
How many rate classes should we have?
Master node received an error:
While attempting to construct category variable c: HMM is not a valid HMM-component model (square matrix of dimension 7) identifier in call to 'category'
Call stack
3 : Category variable: {c,resp+1,catFreqMatrix,MEAN,(1-P)*GammaDist(_x_,alpha,alpha)*(_x_>0),(1-P)*CGammaDist(_x_,alpha,alpha)*(_x_>0)+P,0,1e25,(1-P)*CGammaDist(_x_,alpha+1,alpha)*(_x_>0),HMM}
2 : Select Template Model for {filteredData}
1 : ExecuteAFile from file DIRECTORY_SEPARATOR+"home"+DIRECTORY_SEPARATOR+"macmanes"+DIRECTORY_SEPARATOR+"hyphy"+DIRECTORY_SEPARATOR+"HYPHY"+DIRECTORY_SEPARATOR+"TemplateBatchFiles"+DIRECTORY_SEPARATOR+"SingleBreakpointRecomb.bf" using basepath /home/macmanes/Desktop/. reading input from inputOptions

[macmanes:03600] *** Process received signal ***
[macmanes:03600] Signal: Segmentation fault (11)
[macmanes:03600] Signal code: Address not mapped (1)
[macmanes:03600] Failing at address: 0x31
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 3600 on node macmanes exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
macmanes@macmanes:~/hyphy/HYPHY$ 



seems like a bug to me...
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Sergei
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Posts: 1658
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Re: SBP bug
Reply #1 - Aug 5th, 2010 at 2:52pm
 
Hi Matt,

Yeah - it is a bug (in the way how Global w/variation + HM is defined in the model file).
I have not updated these model definitions in a long time and haven't used them myself.

I bet ANY analysis that uses Global w/variation + HM codon model will die.

I'll add this to my 'to-fix' list, thanks for the report.

Sergei
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