NAMD 2.8 on Cray XE6 segfaulting

From: Tim Robinson (robinson_at_cscs.ch)
Date: Tue Jul 26 2011 - 05:46:01 CDT

Dear Cray XE6 owners/users

I am having trouble getting NAMD 2.8 to run on Cray XE6 (2.7 was no
problem). I have tried with charm-6.3.2 and with charm-6.2.2.

The basic steps are:

./build charm++ mpi-crayxt --no-build-shared --with-production
./config CRAY-XT-g++
make

(I am using gcc/4.5.2 and fftw/2.1.5.2)

The executable crashes very soon after launch:

Charm++> Running on MPI version: 2.2 multi-thread support: 0 (max
supported: -1)
Charm++> Running on 11 unique compute nodes (24-way SMP).
Info: NAMD 2.8 for CRAY-XT-MPI
Info:
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: for updates, documentation, and support information.
Info:
Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
Info: in all publications reporting results obtained with NAMD.
Info:
Info: Based on Charm++/Converse 60202 for mpi-crayxt
Info: Built Tue Jul 26 12:08:28 CEST 2011 by robinson on palu2
[0] Stack Traceback:
  [0:0] [0xb89f10]
[125] Stack Traceback:
  [125:0] [0xb89f10]
  [125:1] [0xb89ebb]
  [125:2] [0xbee6a3]
  [125:3] [0xb15f70]
  [125:4] [0xac55dd]
  [125:5] [0x988153]
<and so on>

The standard error:

------------- Processor 0 Exiting: Caught Signal ------------
Signal: 11
Rank 125 [Tue Jul 26 12:26:57 2011] [c1-0c2s2n3] application called
MPI_Abort(MPI_COMM_WORLD, 1) - process 125
------------- Processor 125 Exiting: Caught Signal ------------
Signal: 6
Rank 124 [Tue Jul 26 12:26:57 2011] [c1-0c2s2n3] application called
MPI_Abort(MPI_COMM_WORLD, 1) - process 124
------------- Processor 124 Exiting: Caught Signal ------------
Signal: 6
Rank 121 [Tue Jul 26 12:26:57 2011] [c1-0c2s2n3] application called
MPI_Abort(MPI_COMM_WORLD, 1) - process 121
------------- Processor 121 Exiting: Caught Signal ------------
<and so on>

Does anyone have a working build of 2.8 on XE6?

Many thanks in advance,

Tim

-- 
Dr Tim Robinson
HPC Application Analyst
Swiss National Supercomputing Centre
Galleria 2, Via Cantonale
6928 Manno

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