On 13/07/2011 5:35 PM, Luke Goodsell wrote:
Hi,
As the subject suggests, I have a simulation that runs correctly on my
iMac, but fails when I try to run it on a cluster, and I am hoping
someone may be able to suggest which things to try first to resolve
the issue.
Background:
The simulation proceeds perfectly well on the iMac (OS X 10.5) without
error/warning. On the cluster, it begins producing multiple LINCS
warnings at step 14555 (of 7500000) and then segfaults after step
14556 with:
Perhaps your simulation is intrinsically unstable, and you haven't
gotten unlucky enough yet on the iMac. Check out
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
Mark
[node-005:13244] *** Process received signal ***
[node-005:13244] Signal: Segmentation fault (11)
[node-005:13244] Signal code: Address not mapped (1)
[node-005:13244] Failing at address: 0x2aaab1380520
[node-005:13244] [ 0] /lib64/libpthread.so.0 [0x2aaaac402b10]
[node-005:13244] [ 1] mdrun_mpi(nb_kernel410_x86_64_sse+0xa65) [0x947e25]
[node-005:13244] [ 2] mdrun_mpi(do_nonbonded+0x780) [0x8ce890]
[node-005:13244] [ 3] mdrun_mpi(do_force_lowlevel+0x308) [0x6842b8]
[node-005:13244] [ 4] mdrun_mpi(do_force+0xc59) [0x6f7c19]
[node-005:13244] [ 5] mdrun_mpi(do_md+0x5785) [0x626f75]
[node-005:13244] [ 6] mdrun_mpi(mdrunner+0xa07) [0x61e8a7]
[node-005:13244] [ 7] mdrun_mpi(main+0x1363) [0x62c5f3]
[node-005:13244] [ 8] /lib64/libc.so.6(__libc_start_main+0xf4)
[0x2aaaac62d994]
[node-005:13244] [ 9] mdrun_mpi(__gxx_personality_v0+0x479) [0x44b659]
[node-005:13244] *** End of error message ***
Things I have tried:
* Both MPI and non-MPI versions on cluster (same result)
* Harmonising FFTW - configured and compiled fftw3 from same source
using same configuration and ensured correct library was included
during configure step
* Checking the Reproducibility documentation
* Searching the archives - I didn't find anything that described a
similar problem.
Things I think may be involved:
* Different architectures - i686 vs x86_64 - don't know how to test
for this
* Different BLAS/LAPACK libraries - I believe gromacs uses the vecLb
on OS X; maybe I could compile without external BLAS/LAPACK and see if
this makes a difference
* Some other unknown problem
I've currently spent more than 2 weeks trying to diagnose this problem
and don't seem to be making progress. Could anyone suggest what is the
most likely cause of this significant difference in output, and what I
could do to test/fix it?
Any help is greatly appreciated.
Luke
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