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Reconstructing tomograms, which worked fine in a previous version (RELION-5.0-beta-3-commit-63311fe) now seems to be broken. The first issue I see is that it now requires more RAM. Something that I could run before with 128 GB easily (perhaps more than enough) now I have to increase to 400 GB to manage, otherwise it runs into OOM errors.
Once enough memory is available, it runs into this error:
TomoBackprojectProgram::getCtfCorrectedSNR BUG: invalid access of newSNR array...
Please see full error message below. I'm trying to re-run something that worked fine in a previous version. I saw there were changes to reconstruct_tomogram.cpp (c3edb97) and wanted to compare the results before and after.
Error message:
UPDATE: I edited the error message below to reflect the actual job corresponding to the binned tomogram dimensions above. The error is the same though.
in: /scicore/projects/scicore-p-structsoft/ubuntu/software/RELION/ver5.0/src/jaz/tomography/programs/reconstruct_tomogram.cpp, line 310
ERROR:
TomoBackprojectProgram::getCtfCorrectedSNR BUG: invalid access of newSNR array...
terminate called after throwing an instance of 'RelionError'
[scb05:972747] *** Process received signal ***
[scb05:972747] Signal: Aborted (6)
[scb05:972747] Signal code: (-6)
[scb05:972747] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x42520)[0x14cdd210a520]
[scb05:972747] [ 1] /lib/x86_64-linux-gnu/libc.so.6(pthread_kill+0x12c)[0x14cdd215e9fc]
[scb05:972747] [ 2] /lib/x86_64-linux-gnu/libc.so.6(raise+0x16)[0x14cdd210a476]
[scb05:972747] [ 3] /lib/x86_64-linux-gnu/libc.so.6(abort+0xd3)[0x14cdd20f07f3]
[scb05:972747] [ 4] /scicore/soft/easybuild/apps/GCCcore/12.3.0/lib64/libstdc++.so.6(+0xa9a49)[0x14cdd2481a49]
[scb05:972747] [ 5] /scicore/soft/easybuild/apps/GCCcore/12.3.0/lib64/libstdc++.so.6(+0xb4e6a)[0x14cdd248ce6a]
[scb05:972747] [ 6] /scicore/soft/easybuild/apps/GCCcore/12.3.0/lib64/libstdc++.so.6(+0xb3ed9)[0x14cdd248bed9]
[scb05:972747] [ 7] /scicore/soft/easybuild/apps/GCCcore/12.3.0/lib64/libstdc++.so.6(__gxx_personality_v0+0x86)[0x14cdd248c5f6]
[scb05:972747] [ 8] /scicore/soft/easybuild/apps/GCCcore/12.3.0/lib64/libgcc_s.so.1(+0x17864)[0x14cde3945864]
[scb05:972747] [ 9] /scicore/soft/easybuild/apps/GCCcore/12.3.0/lib64/libgcc_s.so.1(_Unwind_Resume+0x12d)[0x14cde39462bd]
[scb05:972747] [10] /scicore/projects/scicore-p-structsoft/ubuntu/software/RELION/ver5.0/build_amdfftw/bin/relion_tomo_reconstruct_tomogram_mpi[0x44b974]
[scb05:972747] [11] /scicore/projects/scicore-p-structsoft/ubuntu/software/RELION/ver5.0/build_amdfftw/bin/relion_tomo_reconstruct_tomogram_mpi[0x4feef6]
[scb05:972747] [12] /scicore/soft/easybuild/apps/GCCcore/12.3.0/lib64/libgomp.so.1(+0x1e45e)[0x14cdd8a3145e]
[scb05:972747] [13] /lib/x86_64-linux-gnu/libc.so.6(+0x94ac3)[0x14cdd215cac3]
[scb05:972747] [14] /lib/x86_64-linux-gnu/libc.so.6(+0x126850)[0x14cdd21ee850]
[scb05:972747] *** End of error message ***
Command terminated by signal 6
133.84user 42.36system 0:45.40elapsed 388%CPU (0avgtext+0avgdata 41107392maxresident)k
srun: error: scb05: task 4: Exited with exit code 134
16848inputs+0outputs (2716major+40074934minor)pagefaults 0swaps
srun: Job step aborted: Waiting up to 32 seconds for job step to finish.
slurmstepd: error: *** JOB 442534 ON scb04 CANCELLED AT 2024-06-21T19:05:10 DUE TO TIME LIMIT ***
slurmstepd: error: *** STEP 442534.0 ON scb04 CANCELLED AT 2024-06-21T19:05:10 DUE TO TIME LIMIT ***
srun: got SIGCONT
srun: forcing job termination
The text was updated successfully, but these errors were encountered:
Describe your problem
Reconstructing tomograms, which worked fine in a previous version (RELION-5.0-beta-3-commit-63311fe) now seems to be broken. The first issue I see is that it now requires more RAM. Something that I could run before with 128 GB easily (perhaps more than enough) now I have to increase to 400 GB to manage, otherwise it runs into OOM errors.
Once enough memory is available, it runs into this error:
Please see full error message below. I'm trying to re-run something that worked fine in a previous version. I saw there were changes to
reconstruct_tomogram.cpp
(c3edb97) and wanted to compare the results before and after.Environment:
Dataset:
Job options:
Error message:
UPDATE: I edited the error message below to reflect the actual job corresponding to the binned tomogram dimensions above. The error is the same though.
The text was updated successfully, but these errors were encountered: