Re: [OMPI users] Seg fault in opal_progress

Here’s what happens using a debug build: [raijin7:5] ompi_comm_peer_lookup: invalid peer index (2) [raijin7:5:0:5] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x8) /short/z00/bjm900/build/openmpi-mofed4.2/openmpi-3.1.1/build/gcc/debug-1/ompi/mca/pml/

Re: [OMPI users] Seg fault in opal_progress

Hi, Perhaps related — we’re seeing this one with 3.1.1. I’ll see if I can get the application run against our --enable-debug build. Cheers, Ben [raijin7:1943 :0:1943] Caught signal 11 (Segmentation fault: address not mapped to object at address 0x45) /short/z00/bjm900/build/openmpi-mofed4.2/o

Re: [OMPI users] Seg fault in opal_progress

Might be also worth testing a master snapshot and see if that fixes the issue. There are a couple of fixes being backported from master to v3.0.x and v3.1.x now. -Nathan On Jul 11, 2018, at 03:16 PM, Noam Bernstein wrote: On Jul 11, 2018, at 11:29 AM, Jeff Squyres (jsquyres) via users wro

Re: [OMPI users] Seg fault in opal_progress

$ ompi_info | grep -i debug Configure command line: '--prefix=/home/jsquyres/bogus' '--with-usnic' '--with-libfabric=/home/jsquyres/libfabric-current/install' '--enable-mpirun-prefix-by-default' '--enable-debug' '--enable-mem-debug' '--enable-mem-profile' '--disable-mpi-fortran' '--enable-debu

Re: [OMPI users] Seg fault in opal_progress

> On Jul 11, 2018, at 11:29 AM, Jeff Squyres (jsquyres) via users > wrote: >>> >> >> After more extensive testing it’s clear that it still happens with 2.1.3, >> but much less frequently. I’m going to try to get more detailed info with >> version 3.1.1, where it’s easier to reproduce. objdu

Re: [OMPI users] Seg fault in opal_progress

> On Jul 11, 2018, at 11:29 AM, Jeff Squyres (jsquyres) via users > wrote: > > Ok, that would be great -- thanks. > > Recompiling Open MPI with --enable-debug will turn on several > debugging/sanity checks inside Open MPI, and it will also enable debugging > symbols. Hence, If you can get a

Re: [OMPI users] Seg fault in opal_progress

Ok, that would be great -- thanks. Recompiling Open MPI with --enable-debug will turn on several debugging/sanity checks inside Open MPI, and it will also enable debugging symbols. Hence, If you can get a failure when a debug Open MPI build, it might give you a core file that can be used to ge

Re: [OMPI users] Seg fault in opal_progress

> On Jul 11, 2018, at 9:58 AM, Noam Bernstein > wrote: > >> On Jul 10, 2018, at 5:15 PM, Noam Bernstein > > wrote: >> >> >> >> What are useful steps I can do to debug? Recompile with —enable-debug? Are >> there any other versions that are worth trying?

Re: [OMPI users] Seg fault in opal_progress

> On Jul 10, 2018, at 5:15 PM, Noam Bernstein > wrote: > > > > What are useful steps I can do to debug? Recompile with —enable-debug? Are > there any other versions that are worth trying? I don’t recall this error > happening before we switched to 3.1.0. > >

[OMPI users] mpi and gromacs

Hi Although not directly related to ompi, I would like to know if anybody uses gromcas with mpi support? The binary is gmx_mpi and it has some options for threading. However, I am also able to run that by using running mpirun before gmx_mpi. So, it is possible to run gmx_mpi and mpirun -n