Hi Qiu-Xing Jiang,
I finally ran it with 32 MPI, 16 threads and 2GB per thread. I added the -dont_combine_weights_via_disc command. It again crashed at the particle writing stage but with different errors this time.
Output log:
+ Fitting straight paths for beam-induced movements in all micrographs ...
24/ 24 sec ............................................................~~(,_,">
+ Written out all fitted movements in STAR file: Refine3D5/run_all_ct22_it022_data_shiny.star
+ Calculating per-frame reconstructions ...
4.39/4.39 hrs ............................................................~~(,_,">
+ Calculating per-frame B-factors ...
5/ 5 sec ............................................................~~(,_,">
+ Write out polished particles for all micrographs ...
000/??? sec ~~(,_,"> [oo]write: target and source objects have different size
File: ./src/image.h line: 1257
Error log:
mpiexec has exited due to process rank 20 with PID 51822 on
node cryo-c6 exiting improperly. There are two reasons this could occur:
1. this process did not call "init" before exiting, but others in
the job did. This can cause a job to hang indefinitely while it waits
for all processes to call "init". By rule, if one process calls "init",
then ALL processes must call "init" prior to termination.
2. this process called "init", but exited without calling "finalize".
By rule, all processes that call "init" MUST call "finalize" prior to
exiting or it will be considered an "abnormal termination"
This may have caused other processes in the application to be
terminated by signals sent by mpiexec (as reported here).
I will try the config suggested by Ludo.
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