[gmx-users] jwe1050i + jwe0019i errors = SIGSEGV (Fujitsu)

[Mark Abraham]

On Sep 4, 2013 7:59 AM, "James" <jamesresearching at gmail.com> wrote:
>
> Dear all,
>
> I'm trying to run Gromacs on a Fujitsu supercomputer but the software is
> crashing.
>
> I run grompp:
>
> grompp_mpi_d -f parameters.mdp -c system.pdb -p overthe.top
>
> and it produces the error:
>
> jwe1050i-w The hardware barrier couldn't be used and continues processing
> using the software barrier.
> taken to (standard) corrective action, execution continuing.
> error summary (Fortran)
> error number error level error count
> jwe1050i w 1
> total error count = 1
>
> but still outputs topol.tpr so I can continue.

There's no value in compiling grompp with MPI or in double precision.

> I then run with
>
> export FLIB_FASTOMP=FALSE
> source /home/username/Gromacs463/bin/GMXRC.bash
> mpiexec mdrun_mpi_d -ntomp 16 -v
>
> but it crashes:
>
> starting mdrun 'testrun'
> 50000 steps, 100.0 ps.
> jwe0019i-u The program was terminated abnormally with signal number
SIGSEGV.
> signal identifier = SEGV_MAPERR, address not mapped to object
> error occurs at calc_cell_indices._OMP_1 loc 0000000000233474 offset
> 00000000000003b4
> calc_cell_indices._OMP_1 at loc 00000000002330c0 called from loc
> ffffffff02088fa0 in start_thread
> start_thread at loc ffffffff02088e4c called from loc ffffffff029d19b4 in
> __thread_start
> __thread_start at loc ffffffff029d1988 called from o.s.
> error summary (Fortran)
> error number error level error count
> jwe0019i u 1
> jwe1050i w 1
> total error count = 2
> [ERR.] PLE 0014 plexec The process terminated
>
abnormally.(rank=1)(nid=0x03060006)(exitstatus=240)(CODE=2002,1966080,61440)
> [ERR.] PLE The program that the user specified may be illegal or
> inaccessible on the node.(nid=0x03060006)
>
> Any ideas what could be wrong? It works on my local intel machine.

Looks like it wasn't compiled correctly for the target machine. What was
the cmake command, what does mdrun -version output? Also, if this is the K
computer, probably we can't help, because the compiler docs are officially
unavailable to us. National secret, and all ;-)

Mark

>
> Thanks in advance,
>
> James
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