[maker-devel] openmpi instantly chokes on maker

[Justin Peyton]

I am working on getting maker running on a system running ubuntu 14.04. I
have installed maker and it runs great on a small but real data set. When I
try it with openmpi with the exact same inputs, however, I get the below
error almost instantly.

STATUS: Parsing control files...
STATUS: Processing and indexing input FASTA files...
[molybdenum:23241] *** Process received signal ***
[molybdenum:23241] Signal: Segmentation fault (11)
[molybdenum:23241] Signal code: Address not mapped (1)
[molybdenum:23241] Failing at address: 0x50c
[molybdenum:23241] [ 0]
/lib/x86_64-linux-gnu/libc.so.6(+0x36c30)[0x7f99bd0e8c30]
[molybdenum:23241] [ 1]
/usr/lib/libperl.so.5.18(Perl_csighandler+0x22)[0x7f99bd5155a2]
[molybdenum:23241] [ 2]
/lib/x86_64-linux-gnu/libc.so.6(+0x36c30)[0x7f99bd0e8c30]
[molybdenum:23241] [ 3]
/lib/x86_64-linux-gnu/libc.so.6(__poll+0x2d)[0x7f99bd19fbad]
[molybdenum:23241] [ 4]
/usr/local/openmpi/lib/libopen-pal.so.6(+0x72156)[0x7f99bcbcc156]
[molybdenum:23241] [ 5]
/usr/local/openmpi/lib/libopen-pal.so.6(opal_libevent2021_event_base_loop+0x13b)[0x7f99bcbc34bb]
[molybdenum:23241] [ 6]
/usr/local/openmpi/lib/libopen-rte.so.7(+0x3897e)[0x7f99bce6e97e]
[molybdenum:23241] [ 7]
/lib/x86_64-linux-gnu/libpthread.so.0(+0x8182)[0x7f99bc944182]
[molybdenum:23241] [ 8]
/lib/x86_64-linux-gnu/libc.so.6(clone+0x6d)[0x7f99bd1acefd]
[molybdenum:23241] *** End of error message ***
SIGTERM received
SIGTERM received
SIGTERM received
SIGTERM received
SIGTERM received
[molybdenum:23252] *** Process received signal ***
[molybdenum:23252] Signal: Segmentation fault (11)
[molybdenum:23252] Signal code: Address not mapped (1)
[molybdenum:23252] Failing at address: 0x50c
[molybdenum:23252] [ 0]
/lib/x86_64-linux-gnu/libc.so.6(+0x36c30)[0x7fb191b31c30]
[molybdenum:23252] [ 1]
/usr/lib/libperl.so.5.18(Perl_csighandler+0x22)[0x7fb191f5e5a2]
[molybdenum:23252] [ 2]
/lib/x86_64-linux-gnu/libc.so.6(+0x36c30)[0x7fb191b31c30]
[molybdenum:23252] [ 3]
/lib/x86_64-linux-gnu/libc.so.6(__poll+0x2d)[0x7fb191be8bad]
[molybdenum:23252] [ 4]
/usr/local/openmpi/lib/libopen-pal.so.6(+0x72156)[0x7fb191615156]
[molybdenum:23252] [ 5]
/usr/local/openmpi/lib/libopen-pal.so.6(opal_libevent2021_event_base_loop+0x13b)[0x7fb19160c4bb]
[molybdenum:23252] [ 6]
/usr/local/openmpi/lib/libopen-rte.so.7(+0x3897e)[0x7fb1918b797e]
[molybdenum:23252] [ 7]
/lib/x86_64-linux-gnu/libpthread.so.0(+0x8182)[0x7fb19138d182]
[molybdenum:23252] [ 8]
/lib/x86_64-linux-gnu/libc.so.6(clone+0x6d)[0x7fb191bf5efd]
[molybdenum:23252] *** End of error message ***
SIGTERM received
--------------------------------------------------------------------------
mpiexec noticed that process rank 2 with PID 23241 on node molybdenum
exited on signal 11 (Segmentation fault).


I have tried reinstalling both maker and openmpi. I have tried two
different versions of both maker and openmpi. I am curenlty working with
maker 2.31.6 and openmpi 1.8.3 because I have had those work together on
another system. I have triple checked that LD_PRELOAD is properly set. I
have a feeling that I am pissing something small. I appreciate all the help.

Justin Peyton
The Ohio State University
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