Segmentation Fault relion_refine_mpi #1154
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No ideas from the community? |
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Hi @KrisJanssen I am seeing the same error message. Were you able to fix it? |
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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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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: Dataset: Job options: Error message: Please cite the full error message as the example below. |
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I am also seeing this problem, it is still open I see. |
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Yes, this is still an issue for me. It is good to know the problem is related to 2D extraction in Warp Linux #1181 . |
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interesting, your particles are also coming from Warp Linux then? Is there any workaround? I tried older versions of RELION but I can only go back so far because only the latest versions work on our latest debian system. p.s. I recognize your name from GRC, we chatted briefly! Cool to see familiar names popping up after that :) |
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@rahelwoldeyes and @DrJesseHansen : not sure about the warp Linux thing: I can trigger the issue with any generic data processed in a generic Ubuntu docker container … |
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@DrJesseHansen My particles are from Warp Linux. I haven't found a workaround yet. I'm unsure if downgrading to an older RELION-5 version is advisable, given the bug fixes and improvements in newer versions. @KrisJanssen Thanks for pointing out that this isn't a Warp Linux-specific problem.
@DrJesseHansen I remember! It's nice to see you here. The GRS/GRC is a great way to connect with people. |
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I figured out how to somewhat get around this issue. It turns out there were somehow some bad particles in the dataset. I’m guessing this is a WARP issue, since I extracted the exact same particles in the RELION pipeline and had no issue. Anyway, I split my particles into 10 subsets and refined each: 3 failed with this same error, 7 ran okay. Sub-splitting can help you reduce "waste" when throwing out the bad particles. I have no idea what is wrong with those problematic particles causing the crash. Now when I run the jobs I am getting a different error! haha. This one is about "corrupted size vs previous size". issue #794 p.s. I am running relion 5 commit 6331fe. |
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Hmm, could someone try the following: line 1534 of src/ml_optimiser.cpp in the new version is this: if (do_write_data && (mymodel.data_dim == 3 || mydata.is_tomo) ) And might need to be changed to this: if (do_write_data && !optimisationSet.isEmpty() && (mymodel.data_dim == 3 || mydata.is_tomo) ) Please recompile the code and test again. Not sure how this is related to particles from Warp, but let's give it a go... |
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@scheres Thanks for the suggestion, but it didn't fix the problem for me. I get the same error message. How did it go for you @KrisJanssen @DrJesseHansen? |
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Could you then carefully compare the star files you get from warp with those you get when extracting particles in relion? |
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hi, comparing the star files is interesting. Optics tables are identical except Warp has AC at 0.07 and Relion at 0.1. The data tables though have some differences (see image below):
I should mention too that if I generate 3D subvols in Warp then use relion_reconstruct I actually do get a reasonable looking reconstruction, however when I do the same with 2D images and relion_tomo_reconstruct (see command below) it outputs merged.mrc as an empty volume. relion_tomo_reconstruct_particle --i reextracted_bin8_2D_optimisation_set.star --theme classic --o Reconstruct/job001/ --b 40 --bin 8 --j 1 --j_out 1 --j_in 1 --sym C1
Jesse |
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There was an issue with Euler angle conversion in WarpTools. It has been fixed with 2.0.0dev26 and I at leaset now get the same angles with RELION5 and WarpTools (warpem/warp#227) |
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I still get the error though, with the right euler angles. Anyone have any ideas about a smart way to check which tomogram the offending particle is from (I have >350 tomograms, and I don't want to run too many tests) |
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@rahelwoldeyes @DrJesseHansen @KrisJanssen I ran a script removing all particles that are found on only 0 or 1 tilts, and afterwards it worked for me. See also: warpem/warp#243 |
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WOW This worked! Thank you! Amazing.... can I ask, how did you figure this out? |
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I think _rlnTomoVisibleFrames means in which of your tilts is the particle seen. How I figured it out was a bit of a coincidence... I was just looking through the star file and saw that I had a particle (luckily in the second tomogram from the top) that had all zeroes in the _rlnTomoVisibleFrames list, whereas most particles had all ones, and thought this might be the issue. It worked for my first star file, but not for the second. So there I decided to also remove the particles only seen on one tilt, and that seems to do the trick. |
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Wow, thank you @rkjensen and everyone! It works!! |
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hi all, just want to update here. This does seem to allow the job to run, but the result is still suboptimal and I can't figure out why. When I extract 3D volumes rather than 2D I get the following outcome: I can do a relion_reconstruct and it gives a very reasonable looking volume, suggesting the data are fine. When I try to refine these 3D subvolumes I get an error I have not seen in 5 years #582. Instead if I try extracting with 2D images I get the following outcome: relion_reconstruct_particle gives an empty volume, already not a good sign. When I do a 3D refine I see my map getting progressively worse, the reference turns more faint with each iteration then after it 5 it's an empty volume. any thoughts? best Jesse |
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update: I figured it out. When I run the 2D particles with a refine job it always gives the weird result where the density eventually disappears, but if I run a 3D classification with 1 class then it works. Not sure why this happens, but it did the trick. Now I can use the output particles and volume from 3D classification to continue with subsequent steps. |
Describe your problem
I created a docker image to benchmark running relion 4.0.1-commit-ex417f on multiple hosts in our organization.
For the benchmark, I use a standard dataset: ftp://ftp.mrc-lmb.cam.ac.uk/pub/scheres/relion_benchmark.tar.gz
The dockerfile is here: https://gist.github.com/KrisJanssen/7ff75ad91926e46daa767d71c48f7ced
So far, the resulting container ran fine on any system I threw it at, wheter on-premises or on some of our Azure VMs.
Today, I wanted to test the same image and job on a new on-premise system, ultimately resulting in a segmentation fault.
Environment:
Dataset:
Job options:
Error message:
Please cite the full error message as the example below.
Starting the job:
Then finally, it all goes pear-shaped:
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