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

James jamesresearching at gmail.com
Wed Sep 4 07:58:48 CEST 2013

Dear all,

I'm trying to run Gromacs on a Fujitsu supercomputer but the software is

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.

I then run with

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
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 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
[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.

Thanks in advance,


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