Segmentation faults on Bluegene/P
Posted: Thu Nov 22, 2012 1:30 pm
I have been trying to install Neuron 7.3 on a Bluegene/P machine using the two step process that I had earlier used for the compilation of Neuron on a Cray XE6 machine. The specific steps are:
followed by make, make install and
(with and without thread-safe compilers) again followed by make and make install.
Everything works great without the usual configure or build failure hurdles. As I call the nrnivmodl (using absolute paths so as to avoid relative path issues on Bluegene), the mod files are compiled successfully as well. The problem occurs as soon as I submit the jobs using qsub and the associated cobalt-mpirun. The error logs throws the following error:
This generally means that the executable is bigger than the memory available for each process. Given that I have 512 MB/process and my executable is roughly 3 MB, this can not be the true source of my problem. Moreover, if I were to use 2GB/process using a SMP, the segmentation fault still persists (regardless of thread-safe compilers). Makes me believe that there is something uncanny that I have done during the installation's configure step. STDOUT ejects the following segmentation errors:
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./configure --prefix=`pwd` --enable-bluegeneP --with-nmodl-only
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./configure --prefix=`pwd` --enable-bluegeneP --without-nmodl --with-paranrn MPICC=mpixlc MPICXX=mpixlcxx CC=mpixlc CXX=mpixlcxx --host=powerpc64
Everything works great without the usual configure or build failure hurdles. As I call the nrnivmodl (using absolute paths so as to avoid relative path issues on Bluegene), the mod files are compiled successfully as well. The problem occurs as soon as I submit the jobs using qsub and the associated cobalt-mpirun. The error logs throws the following error:
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<Nov 22 17:54:58.054533> BE_MPI (ERROR): The error message in the job record is as follows:
<Nov 22 17:54:58.054584> BE_MPI (ERROR): "killed with signal 6"
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NEURON -- VERSION 7.3 (744:d0b867b1a597) 2012-11-20
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2012
See http://www.neuron.yale.edu/credits.html
Additional mechanisms from files
kv.mod
/test/powerpc64/special: Segmentation violation
5 near line 0