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: [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
configure-cluster.log
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configure-imac.log
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