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Subject: [OMPI users] mpi error?
From: Matthew MacManes (macmanes_at_[hidden])
Date: 2010-03-11 10:14:27


Can anybody tell me if this is an error associated with openmpi, versus an
issue with the program I am running (MRBAYES,
https://sourceforge.net/projects/mrbayes/)

We are trying to run a large simulated dataset using 1,000,000 bases divided
up into 1000 genes, 5 taxa.. An error is occurring, but we are not sure why.
We are using the MPI version of MRBAYES v3.2-cvs on a linux 16core 24GB RAM
machine. It does not appear as if the program runs out of memory (max memory
usage is 13gb). Maybe this is an OpenMPI problem and not related to
MrBayes...

See snippet of error message below. Can anybody give me any hints about the
source of the problem?

I am using OPENMPI version 1.4.1.

...
Defining charset called gene997
Defining charset called gene998
Defining charset called gene999
Defining charset called gene1000
Defining partition called Genes
[macmanes:02546] *** Process received signal ***
[macmanes:02546] Signal: Segmentation fault (11)
[macmanes:02546] Signal code: Address not mapped (1)
[macmanes:02546] Failing at address: (nil)
[macmanes:02546] [ 0] /lib/libpthread.so.0 [0x7ffd0f322190]
[macmanes:02546] *** End of error message ***
--------------------------------------------------------------------------
mpirun noticed that process rank 13 with PID 2546 on node macmanes exited on
signal 11 (Segmentation fault).
--------------------------------------------------------------------------
macmanes_at_macmanes:~/mrbayes$

Thanks for any help!
Matt

_________________________________
Matthew MacManes
PhD Candidate
University of California- Berkeley
Museum of Vertebrate Zoology
Phone: 510-495-5833
Lab Website: http://ib.berkeley.edu/labs/lacey
Personal Website: http://macmanes.com/