Appion

would you mind taking a look at the rmaxlike uploading? It looks the processing for this session finished , but was not able to find the inherited parameters (e.g. -p for project id) from basicScript. What is weird is that this only happens for some sessions, and not others. I was able to upload the run info manually by copy/pasting the final uploadRelion2DMaxlikeAlign.py line from the command line. Thanks,

I did a test with the same session but only ~5000 particles and got the results below. It looks like the upload script can't find the -p parameter it inherited from basicScript? This doesn't happen every time, results were uploaded as expected when I tried a run with a different session.

Maximization ...
000/??? sec ~~(,_,">                                                          [oo]^M   0/   0 sec ............................................................~~(,_,">
 ... completed in 18 min 21 sec
 ... Alignment time: 18 min 21 sec
 ... writing stack to disk from memory: part16jul07l40_average.hed
 ... wrote 9 particles to header file
 ... finished in 13.93 msec
 ... writing MRC: average.mrc size:(28, 28) dtype:float32
 ... Time stamp: 16jul07l59
 ... Function name: uploadRelion2DMaxlikeAlign
Usage: uploadRelion2DMaxlikeAlign.py --jobid=ID [ --commit ]

uploadRelion2DMaxlikeAlign.py: error: no such option: -p
 ... Closing out function log: relionMaxlikeAlignment.log
 ... Ended at Thu, 07 Jul 2016 11:59:40
^[[1;33m!!! DEBUG: Memory increase during run: 43.539 MB^[[0m
^[[32mTotal run time:   18 min 46 sec^[[0m
 ... Run directory:
 /gpfs/appion/cnegro/16jun19a/align/rmaxlike10

lines= ['\tlibmpi_cxx.so.1 => /cm/shared/apps/openmpi/gcc/64/1.8.5/lib64/libmpi_cxx.so.1 (0x00002aaaac072000)\n', '\tlibmpi.so.1 => /cm/shared/apps/openmpi/gcc/64/1.8.5/lib64/libmpi.so.1 (0x00002aaaac28c000)\n', '\tlibopen-rte.so.7 => /cm/shared/apps/openmpi/gcc/64/1.8.5/lib64/libopen-rte.so.7 (0x00002aaaad778000)\n', '\tlibopen-pal.so.6 => /cm/shared/apps/openmpi/gcc/64/1.8.5/lib64/libopen-pal.so.6 (0x00002aaaad9ef000)\n']
self.params['maxlikejobid'] 12
Wrote 5219 particles to file
mpinodes is equal to 1
mpiprocs = 15
mpinodes = 1
reading class averages from file part16jul07l40_it010_classes.mrcs
uploadRelion2DMaxlikeAlign.py  -p 207  -j 12  -R /gpfs/appion/cnegro/16jun19a/align/rmaxlike10  -n rmaxlike10

I ran a Relion 2D averaging run on one of Giovana’s datasets. It looks like the job finished up fine, see: /gpfs/appion/bcarr/16jun19a/align/rmaxlike9 but never got upload to the database. Can you please check this out. Maybe this is a permissions problem or maybe a real issue. I am sending this via email for now rather than using the redmine site as I suspect it is the former.