[maker-devel] Segmentation fault of MKAER with openmpi on CentOS 7.2

[Carson Holt]

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.

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).

—Carson


> On May 12, 2016, at 3:49 PM, Ray Cui <platycerus at gmail.com> wrote:
> 
> Dear Yugui
> 
>     I had the same problem with openmpi. I think it is not compatible with Maker. I now use mpich, which works.
> 
> Ray
> 
> On May 12, 2016 11:32 PM, "Yugui Wang" <wangyugui.wei at gmail.com <mailto:wangyugui.wei at gmail.com>> wrote:
> Hi.
> 
> Segmentation fault of MKAER with openmpi on CentOS 7.2.
> Both MAKER 2.31.8 and 3.00.0 beta have the same error.
> 
> $ mpirun -mca btl ^openib -n 4 maker
> STATUS: Parsing control files...
> STATUS: Processing and indexing input FASTA files...
> --------------------------------------------------------------------------
> mpirun noticed that process rank 2 with PID 39507 on node T620 exited
> on signal 11 (Segmentation fault).
> --------------------------------------------------------------------------
> $ file core.39505
> core.39505: ELF 64-bit LSB core file x86-64, version 1 (SYSV),
> SVR4-style, from '/usr/bin/perl /bio/hpc-bio/maker-3.00.0/bin/make
> $ gdb /usr/bin/perl core.39505
> (gdb) where
> #0  0x00007f0e4a7d2060 in ?? ()
> #1  <signal handler called>
> #2  0x00007f0e4a7d2060 in ?? ()
> #3  <signal handler called>
> #4  0x00007f0e4bdfba50 in mca_btl_vader_component_progress () from
> /usr/lib64/openmpi/lib/openmpi/mca_btl_vader.so
> #5  0x00007f0e63ec8eda in opal_progress () from
> /usr/lib64/openmpi/lib/libopen-pal.so.13
> #6  0x00007f0e4a191ac5 in mca_pml_ob1_probe () from
> /usr/lib64/openmpi/lib/openmpi/mca_pml_ob1.so
> #7  0x00007f0e65b0dc06 in PMPI_Probe () from /usr/lib64/openmpi/lib/libmpi.so
> #8  0x00007f0e59007020 in C_MPI_Recv (buf=buf at entry=0x4146b30,
> source=source at entry=-1, tag=tag at entry=1111) at MPI.xs:56
> #9  0x00007f0e590071e3 in XS_Parallel__Application__MPI_C_MPI_Recv
> (my_perl=<optimized out>, cv=<optimized out>) at MPI.c:391
> #10 0x00007f0e657ce39f in Perl_pp_entersub () from
> /usr/lib64/perl5/CORE/libperl.so
> #11 0x00007f0e657c6b16 in Perl_runops_standard () from
> /usr/lib64/perl5/CORE/libperl.so
> #12 0x00007f0e65763925 in perl_run () from /usr/lib64/perl5/CORE/libperl.so
> #13 0x0000000000400d99 in main ()
> $ echo $LD_PRELOAD
> /usr/lib64/openmpi/lib/libmpi.so:
> $ echo $OMPI_MCA_mpi_warn_on_fork
> 0
> $ rpm -qa openmpi
> openmpi-1.10.0-10.el7.x86_64
> $ uname -a
> Linux T620 3.10.0-327.13.1.el7.x86_64 #1 SMP Thu Mar 31 16:04:38 UTC
> 2016 x86_64 x86_64 x86_64 GNU/Linux
> $ ulimit -a
> core file size          (blocks, -c) unlimited
> data seg size           (kbytes, -d) unlimited
> scheduling priority             (-e) 0
> file size               (blocks, -f) unlimited
> pending signals                 (-i) 1029973
> max locked memory       (kbytes, -l) 64
> max memory size         (kbytes, -m) unlimited
> open files                      (-n) 1024
> pipe size            (512 bytes, -p) 8
> POSIX message queues     (bytes, -q) 819200
> real-time priority              (-r) 0
> stack size              (kbytes, -s) 102400
> cpu time               (seconds, -t) unlimited
> max user processes              (-u) 4096
> virtual memory          (kbytes, -v) unlimited
> file locks                      (-x) unlimited
> $ mpiexec --version
> mpiexec (OpenRTE) 1.10.0
> 
> Report bugs to http://www.open-mpi.org/community/help/ <http://www.open-mpi.org/community/help/>
> $
> 
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