Troubleshooting for spisonet run

[Rajiv Ranjan Singh]

I was trying to run misalignment correction run in relion 4.01 on our different workstation 

This started.  with following errors in cli:

+ WARNING: will ignore (but maintain) values for the unknown label: rlnPipeLineNodeTypeLabelDepth

WARNING: cannot find do_blush in the defined joboptions. Ignoring it ...

WARNING: cannot find do_blush in the defined joboptions. Ignoring it ...

WARNING: cannot find trust_ref_size in the defined joboptions. Ignoring it ...

WARNING: cannot find do_blush in the defined joboptions. Ignoring it ...

WARNING: cannot find dendrogram_minclass in the defined joboptions. Ignoring it ...

WARNING: cannot find dendrogram_threshold in the defined joboptions. Ignoring it ...

WARNING: cannot find do_filaments in the defined joboptions. Ignoring it ...

WARNING: cannot find do_blush in the defined joboptions. Ignoring it ...

WARNING: cannot find trust_ref_size in the defined joboptions. Ignoring it ...

WARNING: cannot find do_blush in the defined joboptions. Ignoring it ...

WARNING: cannot find trust_ref_size in the defined joboptions. Ignoring it ...

WARNING: cannot find do_blush in the defined joboptions. Ignoring it ...

WARNING: cannot find trust_ref_size in the defined joboptions. Ignoring it ...

output of run.out

It looks like orte_init failed for some reason; your parallel process is

likely to abort.  There are many reasons that a parallel process can

fail during orte_init; some of which are due to configuration or

environment problems.  This failure appears to be an internal failure;

here's some additional information (which may only be relevant to an

Open MPI developer):

 

  orte_session_dir failed

  --> Returned value Error (-1) instead of ORTE_SUCCESS

 

 

output of run.err

[spgpu:25326] opal_os_dirpath_create: Error: Unable to create the sub-directory (/tmp/openmpi-sessions-spuser@spgpu_0/29059) of (/tmp/openmpi-sessions-spuser@spgpu_0/29059/0/0), mkdir failed [1]

[spgpu:25326] [[29059,0],0] ORTE_ERROR_LOG: Error in file util/session_dir.c at line 107

[spgpu:25326] [[29059,0],0] ORTE_ERROR_LOG: Error in file util/session_dir.c at line 402

[spgpu:25326] [[29059,0],0] ORTE_ERROR_LOG: Error in file ess_hnp_module.c at line 638

 

Please advise.

Best,

Rajiv

Rajiv Ranjan Singh

[YUNTAO LIU]

Hi Rajiv,

It seems that the RELION fails from the start. Whether there are some files generated in the output folder? Did you try to run relion without external_reconstruct and whether that works? 

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Best Regards,

Yuntao Liu,  Postdoc.

California NanoSystem Institute

University of California Los Angeles

[Rajiv Ranjan Singh]

I was running from the folder Relion-project directory all run done through Relion5 and then trying to run Relion 4 with spisonet. This was giver error I have reported earlier. 

Am I missing something?

Best,

Rajiv

[Rajiv Ranjan Singh]

I tried without external reconstruct as well. Its reflecting same errors.

However, when I am running relion5 it progress with or without external reconstruction.

The caveat is spisonet not compatible with relion 5 and it does not have output shown on tutorials only giving following output after each iterations

Maximization...

000/??? sec ~~(,_,">                                                          [oo]

 + Making system call for external reconstruction: relion_external_reconstruct Refine3D/job146/run_it001_half1_class001_external_reconstruct.star

 + External reconstruction finished successfully, reading result back in ... 

1.02/1.02 min ............................................................~~(,_,">

 Auto-refine: Iteration= 2

Please advise!

Rajiv Ranjan Singh

[yun...@g.ucla.edu]

Hi Rajiv,

We currently do not have chance to thoroughly test how spIsoNet interact with RELION5, or in run spIsoNet in a RELION5 project directory. I do not know whether people in this group have any experiences.  For the time being,  you may need to start a RELION4 project and import particles to that.