<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">With OpenMPI, you must set LD_PRELOAD for libmpi.so and sometimes the ‘-mca btl paramter’. Details can be found in the …/maker/INSTALL file.<div class=""><br class=""></div><div class="">Also we have found a recent issue with maker and intel compiled OpenMPI on CentOS systems. To get around that issue, compile OpenMPI with gcc instead of the intel compiler, or alternatively manually install a separate perl installation without pthread support (i.e. pthreads disabled during the configure step).</div><div class=""><br class=""></div><div class="">—Carson<br class=""><div class=""><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On May 12, 2016, at 3:49 PM, Ray Cui <<a href="mailto:platycerus@gmail.com" class="">platycerus@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><p dir="ltr" class="">Dear Yugui</p><p dir="ltr" class=""> I had the same problem with openmpi. I think it is not compatible with Maker. I now use mpich, which works.</p><p dir="ltr" class="">Ray </p>
<div class="gmail_quote">On May 12, 2016 11:32 PM, "Yugui Wang" <<a href="mailto:wangyugui.wei@gmail.com" class="">wangyugui.wei@gmail.com</a>> wrote:<br type="attribution" class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi.<br class="">
<br class="">
Segmentation fault of MKAER with openmpi on CentOS 7.2.<br class="">
Both MAKER 2.31.8 and 3.00.0 beta have the same error.<br class="">
<br class="">
$ mpirun -mca btl ^openib -n 4 maker<br class="">
STATUS: Parsing control files...<br class="">
STATUS: Processing and indexing input FASTA files...<br class="">
--------------------------------------------------------------------------<br class="">
mpirun noticed that process rank 2 with PID 39507 on node T620 exited<br class="">
on signal 11 (Segmentation fault).<br class="">
--------------------------------------------------------------------------<br class="">
$ file core.39505<br class="">
core.39505: ELF 64-bit LSB core file x86-64, version 1 (SYSV),<br class="">
SVR4-style, from '/usr/bin/perl /bio/hpc-bio/maker-3.00.0/bin/make<br class="">
$ gdb /usr/bin/perl core.39505<br class="">
(gdb) where<br class="">
#0 0x00007f0e4a7d2060 in ?? ()<br class="">
#1 <signal handler called><br class="">
#2 0x00007f0e4a7d2060 in ?? ()<br class="">
#3 <signal handler called><br class="">
#4 0x00007f0e4bdfba50 in mca_btl_vader_component_progress () from<br class="">
/usr/lib64/openmpi/lib/openmpi/mca_btl_vader.so<br class="">
#5 0x00007f0e63ec8eda in opal_progress () from<br class="">
/usr/lib64/openmpi/lib/libopen-pal.so.13<br class="">
#6 0x00007f0e4a191ac5 in mca_pml_ob1_probe () from<br class="">
/usr/lib64/openmpi/lib/openmpi/mca_pml_ob1.so<br class="">
#7 0x00007f0e65b0dc06 in PMPI_Probe () from /usr/lib64/openmpi/lib/libmpi.so<br class="">
#8 0x00007f0e59007020 in C_MPI_Recv (buf=buf@entry=0x4146b30,<br class="">
source=source@entry=-1, tag=tag@entry=1111) at MPI.xs:56<br class="">
#9 0x00007f0e590071e3 in XS_Parallel__Application__MPI_C_MPI_Recv<br class="">
(my_perl=<optimized out>, cv=<optimized out>) at MPI.c:391<br class="">
#10 0x00007f0e657ce39f in Perl_pp_entersub () from<br class="">
/usr/lib64/perl5/CORE/libperl.so<br class="">
#11 0x00007f0e657c6b16 in Perl_runops_standard () from<br class="">
/usr/lib64/perl5/CORE/libperl.so<br class="">
#12 0x00007f0e65763925 in perl_run () from /usr/lib64/perl5/CORE/libperl.so<br class="">
#13 0x0000000000400d99 in main ()<br class="">
$ echo $LD_PRELOAD<br class="">
/usr/lib64/openmpi/lib/libmpi.so:<br class="">
$ echo $OMPI_MCA_mpi_warn_on_fork<br class="">
0<br class="">
$ rpm -qa openmpi<br class="">
openmpi-1.10.0-10.el7.x86_64<br class="">
$ uname -a<br class="">
Linux T620 3.10.0-327.13.1.el7.x86_64 #1 SMP Thu Mar 31 16:04:38 UTC<br class="">
2016 x86_64 x86_64 x86_64 GNU/Linux<br class="">
$ ulimit -a<br class="">
core file size (blocks, -c) unlimited<br class="">
data seg size (kbytes, -d) unlimited<br class="">
scheduling priority (-e) 0<br class="">
file size (blocks, -f) unlimited<br class="">
pending signals (-i) 1029973<br class="">
max locked memory (kbytes, -l) 64<br class="">
max memory size (kbytes, -m) unlimited<br class="">
open files (-n) 1024<br class="">
pipe size (512 bytes, -p) 8<br class="">
POSIX message queues (bytes, -q) 819200<br class="">
real-time priority (-r) 0<br class="">
stack size (kbytes, -s) 102400<br class="">
cpu time (seconds, -t) unlimited<br class="">
max user processes (-u) 4096<br class="">
virtual memory (kbytes, -v) unlimited<br class="">
file locks (-x) unlimited<br class="">
$ mpiexec --version<br class="">
mpiexec (OpenRTE) 1.10.0<br class="">
<br class="">
Report bugs to <a href="http://www.open-mpi.org/community/help/" rel="noreferrer" target="_blank" class="">http://www.open-mpi.org/community/help/</a><br class="">
$<br class="">
<br class="">
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</blockquote></div>
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