Hi,<div><br></div><div>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.</div>
<div><br></div><div>Background:</div><div>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:</div>
<div><br></div><div><div>[node-005:13244] *** Process received signal ***</div><div>[node-005:13244] Signal: Segmentation fault (11)</div><div>[node-005:13244] Signal code: Address not mapped (1)</div><div>[node-005:13244] Failing at address: 0x2aaab1380520</div>
<div>[node-005:13244] [ 0] /lib64/libpthread.so.0 [0x2aaaac402b10]</div><div>[node-005:13244] [ 1] mdrun_mpi(nb_kernel410_x86_64_sse+0xa65) [0x947e25]</div><div>[node-005:13244] [ 2] mdrun_mpi(do_nonbonded+0x780) [0x8ce890]</div>
<div>[node-005:13244] [ 3] mdrun_mpi(do_force_lowlevel+0x308) [0x6842b8]</div><div>[node-005:13244] [ 4] mdrun_mpi(do_force+0xc59) [0x6f7c19]</div><div>[node-005:13244] [ 5] mdrun_mpi(do_md+0x5785) [0x626f75]</div><div>[node-005:13244] [ 6] mdrun_mpi(mdrunner+0xa07) [0x61e8a7]</div>
<div>[node-005:13244] [ 7] mdrun_mpi(main+0x1363) [0x62c5f3]</div><div>[node-005:13244] [ 8] /lib64/libc.so.6(__libc_start_main+0xf4) [0x2aaaac62d994]</div><div>[node-005:13244] [ 9] mdrun_mpi(__gxx_personality_v0+0x479) [0x44b659]</div>
<div>[node-005:13244] *** End of error message ***</div></div><div><br></div><div>Things I have tried:</div><div>* Both MPI and non-MPI versions on cluster (same result)</div><div>* Harmonising FFTW - configured and compiled fftw3 from same source using same configuration and ensured correct library was included during configure step</div>
<div>* Checking the Reproducibility documentation</div><div>* Searching the archives - I didn't find anything that described a similar problem.</div><div><br></div><div>Things I think may be involved:</div><div>* Different architectures - i686 vs x86_64 - don't know how to test for this</div>
<div>* 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</div><div>* Some other unknown problem</div><div><br>
</div><div>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?</div>
<div><br></div><div>Any help is greatly appreciated.</div><div><br></div><div>Luke</div><div><br></div>