Comments (5)
No ideas from the community?
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Hi @KrisJanssen I am seeing the same error message. Were you able to fix it?
RELION version: 5.0-beta-3-commit-7a062e
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@rahelwoldeyes : unfortunately not, really hoping the devs or other docs with knowledge of cuda and MPI might be able to shed some light…
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I hope so too. It's interesting that the problem started with commit fa8dce3. Commit 90d239e works as expected. Unfortunately, I couldn't determine the root cause
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To further support this issue, the error consistently appears on our cluster regardless of whether Relion is containerized or installed directly.
Describe your problem
Refine3D consistently crashes with a segmentation fault at the beginning of the first iteration, regardless of MPI or GPU use. This occurs for datasets larger than trivially small ones (~500 particles), indicating a potential memory management issue. The dataset appears to be read six times. The problem was introduced in commit fa8dce3, as commit 90d239e works correctly.
Environment:
OS: RHEL 8.6
MPI runtime: mpirun (Open MPI) 4.1.6rc4
RELION version: 5.0-beta-3-commit-d08e4d
Memory: 11264MiB
GPU: NVIDIA GeForce RTX 2080 Ti
GPU Driver: 535.161.07
CUDA: 12.2
Dataset:
Box size: 48 px
Pixel size: 8.53 Å/px #binned 4
Number of particles: 4,000
Job options:
Type of job: Refine3D
Number of MPI processes: 5
Number of threads: 4
Full command:
mpirun --mca btl self,vader,tcp --mca pml ob1 `which relion_refine_mpi` --o Refine3D/job001/run --auto_refine --split_random_halves --ios optimisation_set.star --ref init/intModel.mrc --firstiter_cc --trust_ref_size --ini_high 60 --dont_combine_weights_via_disc --pool 8 --pad 2 --ctf --particle_diameter 340 --flatten_solvent --zero_mask --oversampling 1 --healpix_order 2 --auto_local_healpix_order 4 --offset_range 5 --offset_step 2 --sym C1 --low_resol_join_halves 40 --norm --scale --j 4 --gpu "" --pipeline_control Refine3D/job001/ ```
Error message:
Please cite the full error message as the example below.
WARNING: tomogram S65-TS_002.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S39-TS_001.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S26-TS_004.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S26-TS_002.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S65-TS_002.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S39-TS_001.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S26-TS_006.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S26-TS_004.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S39-TS_005.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S26-TS_002.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S65-TS_002.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S39-TS_001.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S65-TS_002.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S39-TS_001.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S26-TS_006.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S26-TS_004.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S26-TS_004.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S26-TS_002.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S26-TS_003.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S39-TS_005.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S26-TS_002.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S39-TS_002.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S26-TS_006.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S65-TS_001.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S26-TS_006.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S39-TS_006.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S26-TS_001.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S39-TS_005.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S26-TS_003.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S39-TS_005.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S39-TS_002.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S26-TS_005.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S65-TS_001.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S39-TS_006.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S26-TS_003.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S26-TS_001.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S26-TS_003.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S39-TS_002.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S39-TS_002.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S65-TS_001.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S65-TS_001.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S26-TS_005.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S39-TS_006.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S39-TS_006.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S26-TS_001.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S26-TS_001.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S26-TS_005.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S26-TS_005.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S65-TS_002.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S39-TS_001.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S26-TS_004.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S26-TS_002.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S26-TS_006.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S39-TS_005.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S26-TS_003.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S39-TS_002.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S65-TS_001.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S39-TS_006.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S26-TS_001.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S26-TS_005.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S65-TS_002.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S39-TS_001.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S26-TS_004.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S26-TS_002.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S26-TS_006.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S39-TS_005.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S26-TS_003.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S39-TS_002.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S65-TS_001.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S39-TS_006.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S26-TS_001.tomostar has relion-4 definition of projection matrices; converting them now...
WARNING: tomogram S26-TS_005.tomostar has relion-4 definition of projection matrices; converting them now...
[turing023:2658793] *** Process received signal ***
[turing023:2658793] Signal: Segmentation fault (11)
[turing023:2658793] Signal code: Address not mapped (1)
[turing023:2658793] Failing at address: 0x80
[turing023:2658793] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x42520)[0x7efe733c8520]
[turing023:2658793] [ 1] /opt/relion/bin/relion_refine_mpi(+0x4190d0)[0x55c8c15480d0]
[turing023:2658793] [ 2] /opt/relion/bin/relion_refine_mpi(+0x420ca5)[0x55c8c154fca5]
[turing023:2658793] [ 3] /opt/relion/bin/relion_refine_mpi(_ZN15MlOptimiserCuda32doThreadExpectationSomeParticlesEi+0xf6)[0x55c8c1551326]
[turing023:2658793] [ 4] /opt/relion/bin/relion_refine_mpi(_Z36globalThreadExpectationSomeParticlesPvi+0x43)[0x55c8c14d5ed3]
[turing023:2658793] [ 5] /opt/relion/bin/relion_refine_mpi(+0x3a6f5c)[0x55c8c14d5f5c]
[turing023:2658793] [ 6] /lib/x86_64-linux-gnu/libgomp.so.1(GOMP_parallel+0x46)[0x7efe735e2a16]
[turing023:2658793] [ 7] /opt/relion/bin/relion_refine_mpi(_ZN11MlOptimiser24expectationSomeParticlesEll+0xd45)[0x55c8c14b5525]
[turing023:2658793] [ 8] /opt/relion/bin/relion_refine_mpi(_ZN14MlOptimiserMpi11expectationEv+0x1eaa)[0x55c8c1278a2a]
[turing023:2658793] [ 9] /opt/relion/bin/relion_refine_mpi(_ZN14MlOptimiserMpi7iterateEv+0x1d3)[0x55c8c128bd03]
[turing023:2658793] [10] /opt/relion/bin/relion_refine_mpi(main+0x85)[0x55c8c1234565]
[turing023:2658793] [11] /lib/x86_64-linux-gnu/libc.so.6(+0x29d90)[0x7efe733afd90]
[turing023:2658793] [12] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80)[0x7efe733afe40]
[turing023:2658793] [13] /opt/relion/bin/relion_refine_mpi(_start+0x25)[0x55c8c1238005]
[turing023:2658793] *** End of error message ***
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun noticed that process rank 3 with PID 2658663 on node turing023 exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------
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Related Issues (20)
- AreTomo executable was not found HOT 3
- relion_tomo_reconstruct_tomogram_mpi requiring more memory than before and then crashing HOT 2
- Proxy error during build HOT 1
- Refine auto 3D error: Helical reconstruction HOT 1
- Denoise Tomograms with continue Flag HOT 1
- Align tilt-series additional arguments HOT 4
- Import Problem: no such option: -optics-group-name
- Relion 5 fails to reconstruct tomograms by asking for _rlnTomoMicrographNameEven label HOT 10
- BUG in RELION 5: Denoise fails with an assert command HOT 4
- Feature request: Color jobs in the GUI HOT 1
- Improve method finding CUDA libraries HOT 2
- corrupted size vs. prev_size
- Error in running blush regularisation in 3D classification HOT 1
- cannot import data with symbolic links HOT 1
- Import successfull but resulting star file contains only single movie for all tiit angles HOT 3
- Relion tomo segmentation fault in Refine3D
- Relion5 Ctf estimation: BUG: MDin should contain a rlnMicrographPreExposure label HOT 4
- AreTomo alignment and tomogram reconstruction faulty HOT 2
- RELION tomogram reconstruction fails (or produces weird contrast) when carbon is in images HOT 1
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