Segfault with distance selection
Hello,
I'm trying to compute the distances between pairs of residues using distance. I'm not sure how/ if this issue is meaningfully different than #3762 (closed).
I'm very new to GROMACS and it's likely I'm formatting my .ndx incorrectly; the command runs perfectly when I use the default selection "System" instead of my custom selection "Contacts", which I built with a non-GROMACS tool. But either way, it's generating a segfault.
I've attached my .xtc and .ndx:
Attached is the command and result:
Executable: /home/whitford/BIN/nd/gmx-5.1.4_gnu6_openmpi3.1.2_redwood/bin/gmx_mpi
Data prefix: /home/whitford/BIN/nd/gmx-5.1.4_gnu6_openmpi3.1.2_redwood
Command line:
gmx_mpi distance -f CA_11.xtc -n /path/to/ndx_CA_full.ndx -select 'group "Contacts"' -oall CA_11_dists.xvg -oh CA_11_hist.xvg
Reading frame 0 time 0.000 [c3005:17547] *** Process received signal ***
[c3005:17547] Signal: Segmentation fault (11)
[c3005:17547] Signal code: Address not mapped (1)
[c3005:17547] Failing at address: 0x3c0000003b
[c3005:17547] [ 0] /lib64/libpthread.so.0(+0xf630)[0x2b261f4cc630]
[c3005:17547] [ 1] /home/whitford/BIN/nd/gmx-5.1.4_gnu6_openmpi3.1.2_redwood/bin/../lib64/libgromacs_mpi.so.1(_ZN3gmx17SelectionCompiler7compileEPNS_19SelectionCollectionE+0xb56)[0x2b261d39c5d6]
[c3005:17547] [ 2] /home/whitford/BIN/nd/gmx-5.1.4_gnu6_openmpi3.1.2_redwood/bin/../lib64/libgromacs_mpi.so.1(_ZN3gmx19SelectionCollection7compileEv+0x61)[0x2b261d3cff91]
[c3005:17547] [ 3] /home/whitford/BIN/nd/gmx-5.1.4_gnu6_openmpi3.1.2_redwood/bin/../lib64/libgromacs_mpi.so.1(_ZN3gmx35TrajectoryAnalysisCommandLineRunner4Impl12parseOptionsEPNS_26TrajectoryAnalysisSettingsEPNS_30TrajectoryAnalysisRunnerCommonEPNS_19SelectionCollectionEPiPPc+0x1cd)[0x2b261d3f110d]
[c3005:17547] [ 4] /home/whitford/BIN/nd/gmx-5.1.4_gnu6_openmpi3.1.2_redwood/bin/../lib64/libgromacs_mpi.so.1(_ZN3gmx35TrajectoryAnalysisCommandLineRunner3runEiPPc+0x7f)[0x2b261d3f125f]
[c3005:17547] [ 5] /home/whitford/BIN/nd/gmx-5.1.4_gnu6_openmpi3.1.2_redwood/bin/../lib64/libgromacs_mpi.so.1(_ZN3gmx35TrajectoryAnalysisCommandLineRunner4Impl23RunnerCommandLineModule3runEiPPc+0x37)[0x2b261d3f15f7]
[c3005:17547] [ 6] /home/whitford/BIN/nd/gmx-5.1.4_gnu6_openmpi3.1.2_redwood/bin/../lib64/libgromacs_mpi.so.1(_ZN3gmx24CommandLineModuleManager3runEiPPc+0x2ec)[0x2b261cf3747c]
[c3005:17547] [ 7] /home/whitford/BIN/nd/gmx-5.1.4_gnu6_openmpi3.1.2_redwood/bin/gmx_mpi(main+0x7c)[0x40cfcc]
[c3005:17547] [ 8] /lib64/libc.so.6(__libc_start_main+0xf5)[0x2b26201c1555]
[c3005:17547] [ 9] /home/whitford/BIN/nd/gmx-5.1.4_gnu6_openmpi3.1.2_redwood/bin/gmx_mpi[0x40d0fe]
[c3005:17547] *** End of error message ***
Segmentation fault