Troubleshooting for misalignment correction in RELION-4.0.0

[Jiaxing Tan]

Dear SpIsoNet team members,

Thank you for your efforts on SpIsoNet!

However, I got the error message below when practicing the turotial dataset in RELION-4.0.0

What should I do about this error?

Thanks in advance!

:

Traceback (most recent call last):
  File "/share/home/zhulab/tanjiaxing/software/spisonet/spIsoNet/spIsoNet/bin/relion_wrapper.py", line 20, in <module>
    import mrcfile
ModuleNotFoundError: No module named 'mrcfile'
Traceback (most recent call last):
  File "/share/home/zhulab/tanjiaxing/software/spisonet/spIsoNet/spIsoNet/bin/relion_wrapper.py", line 20, in <module>
    import mrcfile
ModuleNotFoundError: No module named 'mrcfile'
in: /root/build/relion-4.0/src/backprojector.cpp, line 1290
ERROR:
 ERROR: there was something wrong with system call: python /share/home/zhulab/tanjiaxing/software/spisonet/spIsoNet/spIsoNet/bin/relion_wrapper.py Refine3D/job002/run_it001_half1_class001_external_reconstruct.star
in: /root/build/relion-4.0/src/backprojector.cpp, line 1290
ERROR:
 ERROR: there was something wrong with system call: python /share/home/zhulab/tanjiaxing/software/spisonet/spIsoNet/spIsoNet/bin/relion_wrapper.py Refine3D/job002/run_it001_half2_class001_external_reconstruct.star
=== Backtrace  ===
=== Backtrace  ===
/share/apps/software/relion/4.0.0/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x41) [0x4e2561]
/share/apps/software/relion/4.0.0/bin/relion_refine_mpi(_ZN13BackProjector19externalReconstructER13MultidimArrayIdER8FileNameS2_S2_S2_S2_bdi+0x2395) [0x54c725]
/share/apps/software/relion/4.0.0/bin/relion_refine_mpi(_ZN14MlOptimiserMpi12maximizationEv+0x13d4) [0x45ab04]
/share/apps/software/relion/4.0.0/bin/relion_refine_mpi(_ZN14MlOptimiserMpi7iterateEv+0x587) [0x45df37]
/share/apps/software/relion/4.0.0/bin/relion_refine_mpi(_ZN11RelionErrorC1ERKSsS1_l+0x41) [0x4e2561]
/share/apps/software/relion/4.0.0/bin/relion_refine_mpi(_ZN13BackProjector19externalReconstructER13MultidimArrayIdER8FileNameS2_S2_S2_S2_bdi+0x2395) [0x54c725]
/share/apps/software/relion/4.0.0/bin/relion_refine_mpi(_ZN14MlOptimiserMpi12maximizationEv+0x11ce) [0x45a8fe]
/share/apps/software/relion/4.0.0/bin/relion_refine_mpi(_ZN14MlOptimiserMpi7iterateEv+0x587) [0x45df37]
/share/apps/software/relion/4.0.0/bin/relion_refine_mpi(main+0x5f) [0x432edf]
/lib64/libc.so.6(__libc_start_main+0xf5) [0x7effe22853d5]
/share/apps/software/relion/4.0.0/bin/relion_refine_mpi() [0x436adf]
==================
ERROR:
 ERROR: there was something wrong with system call: python /share/home/zhulab/tanjiaxing/software/spisonet/spIsoNet/spIsoNet/bin/relion_wrapper.py Refine3D/job002/run_it001_half1_class001_external_reconstruct.star
/share/apps/software/relion/4.0.0/bin/relion_refine_mpi(main+0x5f) [0x432edf]
/lib64/libc.so.6(__libc_start_main+0xf5) [0x7ff40c7043d5]
/share/apps/software/relion/4.0.0/bin/relion_refine_mpi() [0x436adf]
==================
ERROR:
 ERROR: there was something wrong with system call: python /share/home/zhulab/tanjiaxing/software/spisonet/spIsoNet/spIsoNet/bin/relion_wrapper.py Refine3D/job002/run_it001_half2_class001_external_reconstruct.star
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 2 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
[gpu03:148431] 1 more process has sent help message help-mpi-api.txt / mpi-abort
[warn] Epoll MOD(1) on fd 29 failed.  Old events were 6; read change was 0 (none); write change was 2 (del): Bad file descriptor
[warn] Epoll MOD(4) on fd 29 failed.  Old events were 6; read change was 2 (del); write change was 0 (none): Bad file descriptor

The additional argument:

--external_reconstruct --keep_lowres --solvent_correct_fsc

Version of RELION: Relion-4.0.0

[Jiaxing Tan]

The command is:

 ++++ Executing new job on Sun Apr 28 00:43:38 2024
 ++++ with the following command(s):
`which relion_refine_mpi` --o Refine3D/job002/run --auto_refine --split_random_halves --i ../tutorial/job025_tutorial.star --ref ../tutorial/HA_reference.mrc --ini_high 10 --dont_combine_weights_via_disc --scratch_dir /ssd --pool 30 --pad 2  --ctf --particle_diameter 170 --flatten_solvent --zero_mask --solvent_mask ../tutorial/mask.mrc --oversampling 1 --healpix_order 2 --auto_local_healpix_order 4 --offset_range 5 --offset_step 4 --sym C3 --low_resol_join_halves 40 --norm --scale  --j 4 --gpu "0:1:2:3:4:5:6:7" --external_reconstruct --keep_lowres --solvent_correct_fsc --pipeline_control Refine3D/job002/
 ++++ 

[Jiaxing Tan]

Here is the contents of run.out

RELION version: 4.0.0
Precision: BASE=double

 === RELION MPI setup ===
 + Number of MPI processes             = 9
 + Number of threads per MPI process   = 4
 + Total number of threads therefore   = 36
 + Leader  (0) runs on host            = gpu03
 + Follower     1 runs on host            = gpu03
 =================
 + Follower     2 runs on host            = gpu03
 + Follower     3 runs on host            = gpu03
 + Follower     4 runs on host            = gpu03
 + Follower     5 runs on host            = gpu03
 + Follower     6 runs on host            = gpu03
 + Follower     7 runs on host            = gpu03
 + Follower     8 runs on host            = gpu03
 uniqueHost gpu03 has 8 ranks.
 Follower 1 will distribute threads over devices  0
 Thread 0 on follower 1 mapped to device 0
 Thread 1 on follower 1 mapped to device 0
 Thread 2 on follower 1 mapped to device 0
 Thread 3 on follower 1 mapped to device 0
 Follower 2 will distribute threads over devices  1
 Thread 0 on follower 2 mapped to device 1
 Thread 1 on follower 2 mapped to device 1
 Thread 2 on follower 2 mapped to device 1
 Thread 3 on follower 2 mapped to device 1
 Follower 3 will distribute threads over devices  2
 Thread 0 on follower 3 mapped to device 2
 Thread 1 on follower 3 mapped to device 2
 Thread 2 on follower 3 mapped to device 2
 Thread 3 on follower 3 mapped to device 2
 Follower 4 will distribute threads over devices  3
 Thread 0 on follower 4 mapped to device 3
 Thread 1 on follower 4 mapped to device 3
 Thread 2 on follower 4 mapped to device 3
 Thread 3 on follower 4 mapped to device 3
 Follower 5 will distribute threads over devices  4
 Thread 0 on follower 5 mapped to device 4
 Thread 1 on follower 5 mapped to device 4
 Thread 2 on follower 5 mapped to device 4
 Thread 3 on follower 5 mapped to device 4
 Follower 6 will distribute threads over devices  5
 Thread 0 on follower 6 mapped to device 5
 Thread 1 on follower 6 mapped to device 5
 Thread 2 on follower 6 mapped to device 5
 Thread 3 on follower 6 mapped to device 5
 Follower 7 will distribute threads over devices  6
 Thread 0 on follower 7 mapped to device 6
 Thread 1 on follower 7 mapped to device 6
 Thread 2 on follower 7 mapped to device 6
 Thread 3 on follower 7 mapped to device 6
 Follower 8 will distribute threads over devices  7
 Thread 0 on follower 8 mapped to device 7
 Thread 1 on follower 8 mapped to device 7
 Thread 2 on follower 8 mapped to device 7
 Thread 3 on follower 8 mapped to device 7
 Running CPU instructions in double precision.
 + On host gpu03: free scratch space = 9.76267 Gb.
 Copying particles to scratch directory: /ssd/relion_volatile/
   0/   0 sec ............................................................~~(,_,">
 For optics_group 1, there are 0 particles on the scratch disk.
 Estimating initial noise spectra from 1000 particles
   6/   6 sec ............................................................~~(,_,">
 Auto-refine: Iteration= 1
 Auto-refine: Resolution= 9.86353 (no gain for 0 iter)
 Auto-refine: Changes in angles= 999 degrees; and in offsets= 999 Angstroms (no gain for 0 iter)
 Estimating accuracies in the orientational assignment ...
   1/   1 sec ............................................................~~(,_,">
 Auto-refine: Estimated accuracy angles= 1.988 degrees; offsets= 0.782069 Angstroms
 CurrentResolution= 9.86353 Angstroms, which requires orientationSampling of at least 6.54545 degrees for a particle of diameter 170 Angstroms
 Oversampling= 0 NrHiddenVariableSamplingPoints= 7200
 OrientationalSampling= 15 NrOrientations= 1440
 TranslationalSampling= 5.24 NrTranslations= 5
=============================
 Oversampling= 1 NrHiddenVariableSamplingPoints= 230400
 OrientationalSampling= 7.5 NrOrientations= 11520
 TranslationalSampling= 2.62 NrTranslations= 20
=============================
 Expectation iteration 1
8.67/8.67 min ............................................................~~(,_,">
 Averaging half-reconstructions up to 40 Angstrom resolution to prevent diverging orientations ...
 Note that only for higher resolutions the FSC-values are according to the gold-standard!
 Calculating solvent-corrected gold-standard FSC ...
  + randomize phases beyond:       16.768 Angstroms
 Maximization ...
000/??? sec ~~(,_,">                                                          [oo]
 + Making system call for external reconstruction: python /share/home/zhulab/tanjiaxing/software/spisonet/spIsoNet/spIsoNet/bin/relion_wrapper.py Refine3D/job002/run_it001_half1_class001_external_reconstruct.star

 RELION version: 4.0.0

 RELION version: 4.0.0
 exiting with an error ...
 exiting with an error ...

[YUNTAO LIU]

Hi Jiaxing,

I noticed that there is a error about missing  mrcfile module:

  File "/share/home/zhulab/tanjiaxing/software/spisonet/spIsoNet/spIsoNet/bin/relion_wrapper.py", line 20, in <module>

    import mrcfile
ModuleNotFoundError: No module named 'mrcfile'

It seems that the conda or python environment is not correctly installed or activated. I wonder if you can successfully execute "spisonet.py reconstruct". 

--
You received this message because you are subscribed to the Google Groups "spIsoNet" group.
To unsubscribe from this group and stop receiving emails from it, send an email to spisonet+u...@googlegroups.com.
To view this discussion on the web, visit https://groups.google.com/d/msgid/spisonet/69c78a9f-fb57-4422-b7df-d565285f955fn%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

--

Best Regards,

Yuntao Liu,  Postdoc.

California NanoSystem Institute

University of California Los Angeles

[Bryce Brownfield]

Hi all,

I am having a similar issue. I was able to run spisonet.py reconstruct, but relion throws the "ModuleNotFoundError: No module named 'mrcfile'" error. Any thoughts on how to troubleshoot? I tried installing the mrcfile module with pip, but it says the module is there.

[Julian Storm]

Hi all, 

I am having the same issue. Has anyone found a solution yet?

Best,

Julian