Error messages
From Gerris
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| When I remove the remove droplet command this seems to fix the problem | When I remove the remove droplet command this seems to fix the problem | ||
| + | |||
| + | == Nicholson Canyon viscous serial run == | ||
| + | |||
| + | I got the following error right at the end of a serial run for slide width 2500. It did everything except output the final sim file and print the final time | ||
| + | |||
| + | <pre> | ||
| + | *** Process received signal *** | ||
| + | [NIWA-36410:06681] Signal: Floating point exception (8) | ||
| + | [NIWA-36410:06681] Signal code: Floating point divide-by-zero (3) | ||
| + | [NIWA-36410:06681] Failing at address: 0x7f4b0233b0c9 | ||
| + | [NIWA-36410:06681] [ 0] /lib64/libpthread.so.0(+0xf2d0) [0x7f4b0ad172d0] | ||
| + | [NIWA-36410:06681] [ 1] /usr/lib64/gerris/libtopics3D.so(+0x60c9) [0x7f4b0233b0c9] | ||
| + | [NIWA-36410:06681] [ 2] /usr/lib64/libgfs3D-1.3.so.2(ftt_cell_traverse_condition+0xcc) [0x7f4b0b98318c] | ||
| + | [NIWA-36410:06681] [ 3] /usr/lib64/libgfs3D-1.3.so.2(ftt_cell_traverse_condition+0x126) [0x7f4b0b9831e6] | ||
| + | [NIWA-36410:06681] *** End of error message *** | ||
| + | ./run_nicholson.moab: line 15: 6681 Floating point exceptiongerris3D nicholson_viscous.gfs | ||
| + | </pre> | ||
Revision as of 21:16, 1 December 2011
Contents |
Emily's Favourite Error Messages
This page is a place for storing error messages so I can compare and contrast.
Nicholson Canyon viscous3D parallel runs
I get the same message on both turbine and the new modelling computer and it occurs at the same position:
Modelling computer:
step: 1 t: 0.50000000 dt: 5.000000e-01 cpu: 31.87250000 real: 34.53414900 MAC projection before after rate niter: 7 residual.bias: -7.007e-03 -5.369e-05 residual.first: 7.016e-03 5.373e-05 2 residual.second: 1.461e-02 7.277e-05 2.1 residual.infty: 3.525e-02 7.272e-04 1.7 Approximate projection niter: 3 residual.bias: -1.151e-04 -5.477e-05 residual.first: 1.547e-04 5.481e-05 1.4 residual.second: 5.344e-04 7.187e-05 2 residual.infty: 2.145e-02 7.902e-04 3 [NIWA-36410:06625] *** Process received signal *** [NIWA-36410:06625] Signal: Segmentation fault (11) [NIWA-36410:06625] Signal code: Address not mapped (1) [NIWA-36410:06625] Failing at address: 0x8 [NIWA-36410:06625] [ 0] /lib64/libpthread.so.0(+0xf2d0) [0x7ffb7880b2d0] [NIWA-36410:06625] [ 1] /usr/lib64/libgfs3D-1.3.so.2(+0x4728e) [0x7ffb794a628e] [NIWA-36410:06625] [ 2] /usr/lib64/libgfs3D-1.3.so.2(+0x152a9) [0x7ffb794742a9] [NIWA-36410:06625] *** End of error message *** mpirun noticed that job rank 0 with PID 6619 on node NIWA-36410 exited on signal 15 (Terminated). 7 additional processes aborted (not shown)
Turbine:
step: 1 t: 0.50000000 dt: 5.000000e-01 cpu: 54.26500000 real: 57.84363200 MAC projection before after rate niter: 7 residual.bias: -7.007e-03 -5.369e-05 residual.first: 7.016e-03 5.373e-05 2 residual.second: 1.461e-02 7.277e-05 2.1 residual.infty: 3.525e-02 7.272e-04 1.7 Approximate projection niter: 3 residual.bias: -1.151e-04 -5.477e-05 residual.first: 1.546e-04 5.481e-05 1.4 residual.second: 5.338e-04 7.187e-05 2 residual.infty: 2.141e-02 7.902e-04 3 [rotor03:20387] *** Process received signal *** [rotor03:20387] Signal: Segmentation fault (11) [rotor03:20387] Signal code: Address not mapped (1) [rotor03:20387] Failing at address: 0x8 [rotor03:20387] [ 0] /lib64/libpthread.so.0 [0x7f64b72c0c00] [rotor03:20387] [ 1] /usr/lib64/libgfs3D-1.3.so.2 [0x7f64b8c0944f] [rotor03:20387] [ 2] /usr/lib64/libgfs3D-1.3.so.2 [0x7f64b8bdc609] [rotor03:20387] *** End of error message *** mpirun noticed that job rank 0 with PID 20381 on node rotor03 exited on signal 15 (Terminated). 7 additional processes aborted (not shown)
The same code runs in series, I also tried with 2 and 4 cpus and it failed with the same error message (although at t=1 for 4 nodes and before writing any output for 2 nodes. It seemed to be consistent when it failed.
---
Gerris Debugging
When running gerris debugging after the fact (i.e. as Stephane suggested doing the following)
% ulimit -c unlimited % <rerun, crash should display "(core dumped)"> % ls core* % gdb gerris3D core gdb> where
I get:
#0 0x00007fd8198c228e in match_periodic_bc () from /usr/lib64/libgfs3D-1.3.so.2 #1 0x00007fd8198902a9 in cell_traverse_boundary_leafs () from /usr/lib64/libgfs3D-1.3.so.2 #2 0x00007fd8198902a9 in cell_traverse_boundary_leafs () from /usr/lib64/libgfs3D-1.3.so.2 #3 0x00007fd8198902a9 in cell_traverse_boundary_leafs () from /usr/lib64/libgfs3D-1.3.so.2 #4 0x00007fd8198902a9 in cell_traverse_boundary_leafs () from /usr/lib64/libgfs3D-1.3.so.2 #5 0x00007fd8198902a9 in cell_traverse_boundary_leafs () from /usr/lib64/libgfs3D-1.3.so.2 #6 0x00007fd8198902a9 in cell_traverse_boundary_leafs () from /usr/lib64/libgfs3D-1.3.so.2 #7 0x00007fd8198c5faf in match_box_bc () from /usr/lib64/libgfs3D-1.3.so.2 #8 0x00007fd8198c8db3 in domain_foreach () from /usr/lib64/libgfs3D-1.3.so.2 #9 0x00007fd8198cde21 in gfs_domain_tag_droplets () from /usr/lib64/libgfs3D-1.3.so.2 #10 0x00007fd8198ce0ae in gfs_domain_remove_droplets () from /usr/lib64/libgfs3D-1.3.so.2 #11 0x00007fd8198d6b59 in gfs_remove_droplets_event () from /usr/lib64/libgfs3D-1.3.so.2 #12 0x00007fd8198d2825 in gfs_event_do () from /usr/lib64/libgfs3D-1.3.so.2 #13 0x00007fd81965fcb7 in slist_container_foreach () from /usr/lib64/libgts-0.7.so.5 #14 0x00007fd8198da97f in simulation_run () from /usr/lib64/libgfs3D-1.3.so.2 #15 0x00007fd8198dc2a8 in gfs_simulation_run () from /usr/lib64/libgfs3D-1.3.so.2 #16 0x0000000000402d3f in main ()
When I remove the remove droplet command this seems to fix the problem
Nicholson Canyon viscous serial run
I got the following error right at the end of a serial run for slide width 2500. It did everything except output the final sim file and print the final time
*** Process received signal *** [NIWA-36410:06681] Signal: Floating point exception (8) [NIWA-36410:06681] Signal code: Floating point divide-by-zero (3) [NIWA-36410:06681] Failing at address: 0x7f4b0233b0c9 [NIWA-36410:06681] [ 0] /lib64/libpthread.so.0(+0xf2d0) [0x7f4b0ad172d0] [NIWA-36410:06681] [ 1] /usr/lib64/gerris/libtopics3D.so(+0x60c9) [0x7f4b0233b0c9] [NIWA-36410:06681] [ 2] /usr/lib64/libgfs3D-1.3.so.2(ftt_cell_traverse_condition+0xcc) [0x7f4b0b98318c] [NIWA-36410:06681] [ 3] /usr/lib64/libgfs3D-1.3.so.2(ftt_cell_traverse_condition+0x126) [0x7f4b0b9831e6] [NIWA-36410:06681] *** End of error message *** ./run_nicholson.moab: line 15: 6681 Floating point exceptiongerris3D nicholson_viscous.gfs
Parallel runs of solid block scenario
I have problems with running the solid block example too. Prior to dying I often (but not always) get the following warning:
Gfs-CRITICAL **: PE 0 (NIWA-36411): gfs_line_center: assertion `a > 0. && a < 1.' failed
The error message when it fails is
[NIWA-36411:10302] *** Process received signal *** [NIWA-36411:10302] Signal: Floating point exception (8) [NIWA-36411:10302] Signal code: Invalid floating point operation (7) [NIWA-36411:10302] Failing at address: 0x7ffbfa528ecd [NIWA-36411:10303] *** Process received signal *** [NIWA-36411:10303] Signal: Floating point exception (8) [NIWA-36411:10303] Signal code: Invalid floating point operation (7) [NIWA-36411:10303] Failing at address: 0x7f855b613ecd [NIWA-36411:10302] [ 0] /lib64/libpthread.so.0(+0xf2d0) [0x7ffbf9ae72d0] [NIWA-36411:10302] [ 1] /usr/lib64/libgts-0.7.so.5(triBoxOverlap+0xfd) [0x7ffbfa528ecd] [NIWA-36411:10302] [ 2] /usr/lib64/libgts-0.7.so.5(gts_bbox_overlaps_triangle+0x122) [0x7ffbfa4f0452] [NIWA-36411:10302] [ 3] /usr/lib64/libgfs3D-1.3.so.2(+0x8e5b2) [0x7ffbfa7c95b2] [NIWA-36411:10302] [ 4] /lib64/libglib-2.0.so.0(g_hash_table_foreach+0x43) [0x7ffbfa21e0d3] [NIWA-36411:10302] [ 5] /usr/lib64/libgts-0.7.so.5(gts_surface_foreach_face+0x35) [0x7ffbfa507215] [NIWA-36411:10302] [ 6] /usr/lib64/libgfs3D-1.3.so.2(+0x9068e) [0x7ffbfa7cb68e] [NIWA-36411:10302] [ 7] /usr/lib64/libgfs3D-1.3.so.2(+0x8f9a7) [0x7ffbfa7ca9a7] [NIWA-36411:10302] [ 8] /usr/lib64/libgfs3D-1.3.so.2(gfs_cell_traverse_cut+0x1f) [0x7ffbfa7cac4f] [NIWA-36411:10302] [ 9] /usr/lib64/libgfs3D-1.3.so.2(+0x4ddb3) [0x7ffbfa788db3] [NIWA-36411:10302] [10] /usr/lib64/libgfs3D-1.3.so.2(gfs_domain_traverse_cut+0x38) [0x7ffbfa789728] [NIWA-36411:10302] [11] /usr/lib64/libgfs3D-1.3.so.2(+0x9cb5b) [0x7ffbfa7d7b5b] [NIWA-36411:10302] [12] /usr/lib64/libgfs3D-1.3.so.2(gfs_simulation_run+0x58) [0x7ffbfa79c2a8] [NIWA-36411:10302] [13] gerris3D(main+0xecf) [0x402d3f] [NIWA-36411:10302] [14] /lib64/libc.so.6(__libc_start_main+0xfd) [0x7ffbf9789bfd] [NIWA-36411:10302] [15] gerris3D() [0x401d99] [NIWA-36411:10302] *** End of error message *** [NIWA-36411:10303] [ 0] /lib64/libpthread.so.0(+0xf2d0) [0x7f855abd22d0] [NIWA-36411:10303] [ 1] /usr/lib64/libgts-0.7.so.5(triBoxOverlap+0xfd) [0x7f855b613ecd] [NIWA-36411:10303] [ 2] /usr/lib64/libgts-0.7.so.5(gts_bbox_overlaps_triangle+0x122) [0x7f855b5db452] [NIWA-36411:10303] [ 3] /usr/lib64/libgfs3D-1.3.so.2(+0x8e5b2) [0x7f855b8b45b2] [NIWA-36411:10303] [ 4] /lib64/libglib-2.0.so.0(g_hash_table_foreach+0x43) [0x7f855b3090d3] [NIWA-36411:10303] [ 5] /usr/lib64/libgts-0.7.so.5(gts_surface_foreach_face+0x35) [0x7f855b5f2215] [NIWA-36411:10303] [ 6] /usr/lib64/libgfs3D-1.3.so.2(+0x9068e) [0x7f855b8b668e] [NIWA-36411:10303] [ 7] /usr/lib64/libgfs3D-1.3.so.2(+0x8f9a7) [0x7f855b8b59a7] [NIWA-36411:10303] [ 8] /usr/lib64/libgfs3D-1.3.so.2(gfs_cell_traverse_cut+0x1f) [0x7f855b8b5c4f] [NIWA-36411:10303] [ 9] /usr/lib64/libgfs3D-1.3.so.2(+0x4ddb3) [0x7f855b873db3] [NIWA-36411:10303] [10] /usr/lib64/libgfs3D-1.3.so.2(gfs_domain_traverse_cut+0x38) [0x7f855b874728] [NIWA-36411:10303] [11] /usr/lib64/libgfs3D-1.3.so.2(+0x9cb5b) [0x7f855b8c2b5b] [NIWA-36411:10303] [12] /usr/lib64/libgfs3D-1.3.so.2(gfs_simulation_run+0x58) [0x7f855b8872a8] [NIWA-36411:10303] [13] gerris3D(main+0xecf) [0x402d3f] [NIWA-36411:10303] [14] /lib64/libc.so.6(__libc_start_main+0xfd) [0x7f855a874bfd] [NIWA-36411:10303] [15] gerris3D() [0x401d99] [NIWA-36411:10303] *** End of error message *** mpirun noticed that job rank 0 with PID 10302 on node NIWA-36411 exited on signal 8 (Floating point exception). 1 additional process aborted (not shown) core
The following was generated using the debugging suggestion above. This was running on a 8 core modelling computer. Looking at the core dump using gdb I get:
#0 0x00007f330388fecd in triBoxOverlap () from /usr/lib64/libgts-0.7.so.5 #1 0x00007f3303857452 in gts_bbox_overlaps_triangle () from /usr/lib64/libgts-0.7.so.5 #2 0x00007f3303b305b2 in face_overlaps_box () from /usr/lib64/libgfs3D-1.3.so.2 #3 0x00007f33035850d3 in g_hash_table_foreach () from /lib64/libglib-2.0.so.0 #4 0x00007f330386e215 in gts_surface_foreach_face () from /usr/lib64/libgts-0.7.so.5 #5 0x00007f3303b3268e in cell_is_cut () from /usr/lib64/libgfs3D-1.3.so.2 #6 0x00007f3303b319a7 in cell_traverse_cut () from /usr/lib64/libgfs3D-1.3.so.2 #7 0x00007f3303b31c4f in gfs_cell_traverse_cut () from /usr/lib64/libgfs3D-1.3.so.2 #8 0x00007f3303aefdb3 in domain_foreach () from /usr/lib64/libgfs3D-1.3.so.2 #9 0x00007f3303af0728 in gfs_domain_traverse_cut () from /usr/lib64/libgfs3D-1.3.so.2 #10 0x00007f3303b3eb5b in simulation_moving_run () from /usr/lib64/libgfs3D-1.3.so.2 #11 0x00007f3303b032a8 in gfs_simulation_run () from /usr/lib64/libgfs3D-1.3.so.2 #12 0x0000000000402d3f in main ()
Actually If I do a serial run of the simple version I get the following error message and debug info
#0 0x00007fe13609c0c9 in print_interface () from /usr/lib64/gerris/libtopics3D.so #1 0x00007fe13dac518c in ftt_cell_traverse_condition () from /usr/lib64/libgfs3D-1.3.so.2 #2 0x00007fe13dac51e6 in ftt_cell_traverse_condition () from /usr/lib64/libgfs3D-1.3.so.2 #3 0x00007fe13dac51e6 in ftt_cell_traverse_condition () from /usr/lib64/libgfs3D-1.3.so.2 #4 0x00007fe13dac51e6 in ftt_cell_traverse_condition () from /usr/lib64/libgfs3D-1.3.so.2 #5 0x00007fe13daf56d7 in box_traverse_condition () from /usr/lib64/libgfs3D-1.3.so.2 #6 0x00007fe13dafadb3 in domain_foreach () from /usr/lib64/libgfs3D-1.3.so.2 #7 0x00007fe13dafb5fc in gfs_domain_cell_traverse_condition () from /usr/lib64/libgfs3D-1.3.so.2 #8 0x00007fe13609b9fd in gfs_output_interface_grid_event () from /usr/lib64/gerris/libtopics3D.so #9 0x00007fe13db04825 in gfs_event_do () from /usr/lib64/libgfs3D-1.3.so.2 #10 0x00007fe13d891cb7 in slist_container_foreach () from /usr/lib64/libgts-0.7.so.5 #11 0x00007fe13db4999b in simulation_moving_run () from /usr/lib64/libgfs3D-1.3.so.2 #12 0x00007fe13db0e2a8 in gfs_simulation_run () from /usr/lib64/libgfs3D-1.3.so.2 #13 0x0000000000402d3f in main ()
