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

[Ray Cui]

Hello,

         I had segfaults even if I set LD_PRELOAD and used gcc for OpenMPI
(dealing with Maker 3 beta though).
         It works fine with MpiCH so I stopped looking into this.

Ray

On Fri, May 13, 2016 at 6:32 PM, Carson Holt <carsonhh at gmail.com> wrote:

> 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> 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/
>> $
>>
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