Hi Weili,
I've never seen this before. Are you sure another MPI program runs fine on
your cluster? Also, does the program work with only a very few and small
images using the same script?
HTH,
S
> 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
>
>
>
--
Sjors Scheres
MRC Laboratory of Molecular Biology
Francis Crick Avenue, Cambridge Biomedical Campus
Cambridge CB2 0QH, U.K.
tel: +44 (0)1223 267061
http://www2.mrc-lmb.cam.ac.uk/groups/scheres
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