NAMD crashes with OpenMPI/OpenMX

From: Thomas Albers (
Date: Mon Jun 13 2011 - 11:50:35 CDT


We have a collection of four computers (Phenom X4, Phenom II X6) that we
would like to run NAMD on. Since the pre-built binaries scale very
poorly across several computers we built NAMD to use OpenMPI/Open-MX,
however the ApoA1 benchmark will segfault repoducibly (although never in
the same place).

See below what a typical run looks like. Where should I go look for the


ta_at_porsche ~/apoa1 $ mpirun --prefix /usr/local -H
/usr/local/Linux-x86_64-g++/namd2 apoa1.namd > /tmp/apoa1.log
------------- Processor 7 Exiting: Caught Signal ------------
Signal: 11
MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
mpirun has exited due to process rank 1 with PID 3698 on
node ferrari exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
[porsche:05893] 3 more processes have sent help message help-mpi-api.txt
/ mpi-abort
[porsche:05893] Set MCA parameter "orte_base_help_aggregate" to 0 to see
all help / error messages

ta_at_porsche ~/apoa1 $ cat /tmp/apoa1.log
Charm++> Running on MPI version: 2.1 multi-thread support:
Charm++> Running on 4 unique compute nodes (4-way SMP).
Charm++> cpu topology info is gathered in 0.001 seconds.
Info: Based on Charm++/Converse 60303 for mpi-linux-x86_64
Info: Built Fri Jun 10 14:07:31 EDT 2011 by root on porsche
Info: 1 NAMD 2.8 Linux-x86_64-MPI 8 ferrari ta
Info: Running on 8 processors, 8 nodes, 4 physical nodes.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.00325823
..TIMING: 380 CPU: 122.606, 0.305961/step Wall: 122.606,
0.305961/step, 0.0101987 hours remaining, 283.066406 MB
of memory in use.
[7] Stack Traceback:
  [7:0] +0x324d0 [0x7fe2a453f4d0]
  [7:1] [0xb71985]

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