<div dir="ltr">Hello,<div><br></div><div> I had segfaults even if I set LD_PRELOAD and used gcc for OpenMPI (dealing with Maker 3 beta though). </div><div> It works fine with MpiCH so I stopped looking into this.</div><div><br></div><div>Ray</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, May 13, 2016 at 6:32 PM, Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">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><br></div><div>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><span class="HOEnZb"><font color="#888888"><div><br></div></font></span><div><span class="HOEnZb"><font color="#888888">—Carson</font></span><div><div class="h5"><br><div><div><br></div><div><br><div><blockquote type="cite"><div>On May 12, 2016, at 3:49 PM, Ray Cui <<a href="mailto:platycerus@gmail.com" target="_blank">platycerus@gmail.com</a>> wrote:</div><br><div><p dir="ltr">Dear Yugui</p><p dir="ltr"> 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">Ray </p>
<div class="gmail_quote">On May 12, 2016 11:32 PM, "Yugui Wang" <<a href="mailto:wangyugui.wei@gmail.com" target="_blank">wangyugui.wei@gmail.com</a>> wrote:<br type="attribution"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi.<br>
<br>
Segmentation fault of MKAER with openmpi on CentOS 7.2.<br>
Both MAKER 2.31.8 and 3.00.0 beta have the same error.<br>
<br>
$ mpirun -mca btl ^openib -n 4 maker<br>
STATUS: Parsing control files...<br>
STATUS: Processing and indexing input FASTA files...<br>
--------------------------------------------------------------------------<br>
mpirun noticed that process rank 2 with PID 39507 on node T620 exited<br>
on signal 11 (Segmentation fault).<br>
--------------------------------------------------------------------------<br>
$ file core.39505<br>
core.39505: ELF 64-bit LSB core file x86-64, version 1 (SYSV),<br>
SVR4-style, from '/usr/bin/perl /bio/hpc-bio/maker-3.00.0/bin/make<br>
$ gdb /usr/bin/perl core.39505<br>
(gdb) where<br>
#0 0x00007f0e4a7d2060 in ?? ()<br>
#1 <signal handler called><br>
#2 0x00007f0e4a7d2060 in ?? ()<br>
#3 <signal handler called><br>
#4 0x00007f0e4bdfba50 in mca_btl_vader_component_progress () from<br>
/usr/lib64/openmpi/lib/openmpi/mca_btl_vader.so<br>
#5 0x00007f0e63ec8eda in opal_progress () from<br>
/usr/lib64/openmpi/lib/libopen-pal.so.13<br>
#6 0x00007f0e4a191ac5 in mca_pml_ob1_probe () from<br>
/usr/lib64/openmpi/lib/openmpi/mca_pml_ob1.so<br>
#7 0x00007f0e65b0dc06 in PMPI_Probe () from /usr/lib64/openmpi/lib/libmpi.so<br>
#8 0x00007f0e59007020 in C_MPI_Recv (buf=buf@entry=0x4146b30,<br>
source=source@entry=-1, tag=tag@entry=1111) at MPI.xs:56<br>
#9 0x00007f0e590071e3 in XS_Parallel__Application__MPI_C_MPI_Recv<br>
(my_perl=<optimized out>, cv=<optimized out>) at MPI.c:391<br>
#10 0x00007f0e657ce39f in Perl_pp_entersub () from<br>
/usr/lib64/perl5/CORE/libperl.so<br>
#11 0x00007f0e657c6b16 in Perl_runops_standard () from<br>
/usr/lib64/perl5/CORE/libperl.so<br>
#12 0x00007f0e65763925 in perl_run () from /usr/lib64/perl5/CORE/libperl.so<br>
#13 0x0000000000400d99 in main ()<br>
$ echo $LD_PRELOAD<br>
/usr/lib64/openmpi/lib/libmpi.so:<br>
$ echo $OMPI_MCA_mpi_warn_on_fork<br>
0<br>
$ rpm -qa openmpi<br>
openmpi-1.10.0-10.el7.x86_64<br>
$ uname -a<br>
Linux T620 3.10.0-327.13.1.el7.x86_64 #1 SMP Thu Mar 31 16:04:38 UTC<br>
2016 x86_64 x86_64 x86_64 GNU/Linux<br>
$ ulimit -a<br>
core file size (blocks, -c) unlimited<br>
data seg size (kbytes, -d) unlimited<br>
scheduling priority (-e) 0<br>
file size (blocks, -f) unlimited<br>
pending signals (-i) 1029973<br>
max locked memory (kbytes, -l) 64<br>
max memory size (kbytes, -m) unlimited<br>
open files (-n) 1024<br>
pipe size (512 bytes, -p) 8<br>
POSIX message queues (bytes, -q) 819200<br>
real-time priority (-r) 0<br>
stack size (kbytes, -s) 102400<br>
cpu time (seconds, -t) unlimited<br>
max user processes (-u) 4096<br>
virtual memory (kbytes, -v) unlimited<br>
file locks (-x) unlimited<br>
$ mpiexec --version<br>
mpiexec (OpenRTE) 1.10.0<br>
<br>
Report bugs to <a href="http://www.open-mpi.org/community/help/" rel="noreferrer" target="_blank">http://www.open-mpi.org/community/help/</a><br>
$<br>
<br>
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