Dear Dr. Scheres,
We were running Relion 1.3 Particle Sorting to group my particles for 2D classification. However, we kept receiving the same error messages. Please refer to the run log below. Our HPC computing staff advised me contacting you to see how best we can resolve this problem.
=== RELION MPI setup ===
+ Number of MPI processes = 6
+ Master (0) runs on host = compute-0-42.local
+ Slave 1 runs on host = compute-0-44.local
+ Slave 2 runs on host = compute-0-45.local
+ Slave 3 runs on host = compute-0-46.local
+ Slave 4 runs on host = compute-0-48.local
+ Slave 5 runs on host = compute-0-49.local
=================
[compute-0-44:32404] *** Process received signal ***
[compute-0-44:32404] Signal: Segmentation fault (11)
[compute-0-44:32404] Signal code: Invalid permissions (2)
[compute-0-44:32404] Failing at address: 0x2b90d14ca210
[compute-0-45:07652] *** Process received signal ***
[compute-0-45:07652] Signal: Segmentation fault (11)
[compute-0-45:07652] Signal code: Invalid permissions (2)
[compute-0-45:07652] Failing at address: 0x2ab68d296210
[compute-0-42:32274] *** Process received signal ***
[compute-0-42:32274] Signal: Segmentation fault (11)
[compute-0-42:32274] Signal code: Invalid permissions (2)
[compute-0-42:32274] Failing at address: 0x2b18956b9210
[compute-0-42:32274] [ 0] /lib64/libpthread.so.0 [0x38cc80eb10]
[compute-0-42:32274] [ 1] /apps1/relion/1.3/openmpi/intel/lib/librelion-1.3.so.1(_ZN9Projector26computeFourierTransformMapER13MultidimArrayIdES2_iib+0x49c) [0x2b189443e75c]
[compute-0-42:32274] [ 2] /apps1/relion/1.3/openmpi/intel/lib/librelion-1.3.so.1(_ZN14ParticleSorter10initialiseEv+0x126f) [0x2b189442240f]
[compute-0-42:32274] [ 3] /apps1/relion/1.3/openmpi/intel/bin/relion_particle_sort_mpi(main+0x200) [0x4020d0]
[compute-0-42:32274] [ 4] /lib64/libc.so.6(__libc_start_main+0xf4) [0x38cbc1d994]
[compute-0-42:32274] [ 5] /apps1/relion/1.3/openmpi/intel/bin/relion_particle_sort_mpi(__gxx_personality_v0+0xa9) [0x401e19]
[compute-0-42:32274] *** End of error message ***
[compute-0-44:32404] [ 0] /lib64/libpthread.so.0 [0x33a240eb10]
[compute-0-44:32404] [ 1] /apps1/relion/1.3/openmpi/intel/lib/librelion-1.3.so.1(_ZN9Projector26computeFourierTransformMapER13MultidimArrayIdES2_iib+0x49c) [0x2b90d003c75c]
[compute-0-44:32404] [ 2] /apps1/relion/1.3/openmpi/intel/lib/librelion-1.3.so.1(_ZN14ParticleSorter10initialiseEv+0x126f) [0x2b90d002040f]
[compute-0-44:32404] [ 3] /apps1/relion/1.3/openmpi/intel/bin/relion_particle_sort_mpi(main+0x200) [0x4020d0]
[compute-0-44:32404] [ 4] /lib64/libc.so.6(__libc_start_main+0xf4) [0x33a181d994]
[compute-0-44:32404] [ 5] /apps1/relion/1.3/openmpi/intel/bin/relion_particle_sort_mpi(__gxx_personality_v0+0xa9) [0x401e19]
[compute-0-44:32404] *** End of error message ***
[compute-0-45:07652] [ 0] /lib64/libpthread.so.0 [0x3a55e0eb10]
[compute-0-45:07652] [ 1] /apps1/relion/1.3/openmpi/intel/lib/librelion-1.3.so.1(_ZN9Projector26computeFourierTransformMapER13MultidimArrayIdES2_iib+0x49c) [0x2ab68c01b75c]
[compute-0-45:07652] [ 2] /apps1/relion/1.3/openmpi/intel/lib/librelion-1.3.so.1(_ZN14ParticleSorter10initialiseEv+0x126f) [0x2ab68bfff40f]
[compute-0-45:07652] [ 3] /apps1/relion/1.3/openmpi/intel/bin/relion_particle_sort_mpi(main+0x200) [0x4020d0]
[compute-0-45:07652] [ 4] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3a5521d994]
[compute-0-45:07652] [ 5] /apps1/relion/1.3/openmpi/intel/bin/relion_particle_sort_mpi(__gxx_personality_v0+0xa9) [0x401e19]
[compute-0-45:07652] *** End of error message ***
--------------------------------------------------------------------------
mpiexec noticed that process rank 0 with PID 32274 on node compute-0-42 exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
I would appreciate your kind help if you could guide me through this step.
Thank you.
Best,
Weili
Wei-Li Liu, PhD
Assistant Professor
Department of Anatomy & Structural Biology
Gruss-Lipper Biophotonics Center
Albert Einstein College of Medicine
1300 Morris Park Avenue
Forchheimer 628D
Bronx, NY 10461
Email: [log in to unmask]
Phone: 718-430-2876
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