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CL2D upload to appion #4348

Open leginonbot opened 5 months ago

leginonbot commented 5 months ago

Author Name: Reginald McNulty (Reginald McNulty) Original Redmine Issue: 4348, https://emg.nysbc.org/redmine/issues/4348 Original Date: 2016-07-28

I get an MPI error when running CL2D with myami/3.2. When I try with an older myami/trunk, the CL2D run directory has class average stacks but the results have not been uploaded to appion.The same command has been successful with other runs. Is there a way to continue the upload? Errors associated with both runs are below:

MPI Error: he local scratch directory for this session is: /scratch/rmcnulty/1329166.garibaldi01-adm.cluster.net the distributed scratch directory for this session is: /gpfs/work/rmcnulty/1329166.garibaldi01-adm.cluster.net Warning: no access to tty (Bad file descriptor). Thus no job control in this shell. ... Time stamp: 16jul28u07 ... Function name: runXmippCL2D ... Appion directory: /opt/applications/myami/3.2/lib/python2.7/site-packages ... Processing hostname: nodeb0226 ... Using split database Connected to database: 'ap367' ... Committing data to database ... Getting stack data for stackid=388 Old stack info: 'box192bin2'

Traceback (most recent call last): File "/opt/applications/myami/3.2/bin/runXmippCL2D.py", line 659, in cl2d = CL2D() File "/opt/applications/myami/3.2/lib/python2.7/site-packages/appionlib/appionScript.py", line 85, in init self.checkConflicts() File "/opt/applications/myami/3.2/bin/runXmippCL2D.py", line 106, in checkConflicts apDisplay.printError("There is no MPI installed") File "/opt/applications/myami/3.2/lib/python2.7/site-packages/appionlib/apDisplay.py", line 65, in printError raise Exception, colorString("\n FATAL ERROR \n"+text+"\n\a","red") Exception: FATAL ERROR There is no MPI installed

No Results uploaded to Appion error with myami/trunk: ... /gpfs/group/em/appion/rmcnulty/16jun10b/align/cl2d1/alignedStack-4096.hed (4096 kB) ... /gpfs/group/em/appion/rmcnulty/16jun10b/align/cl2d1/alignedStack-8192.hed (4096 kB) ... /gpfs/group/em/appion/rmcnulty/16jun10b/align/cl2d1/alignedStack-12288.hed (4096 kB) ... /gpfs/group/em/appion/rmcnulty/16jun10b/align/cl2d1/alignedStack-16384.hed (4096 kB) ... /gpfs/group/em/appion/rmcnulty/16jun10b/align/cl2d1/alignedStack-20480.hed (4096 kB) ... /gpfs/group/em/appion/rmcnulty/16jun10b/align/cl2d1/alignedStack-24576.hed (4096 kB) ... /gpfs/group/em/appion/rmcnulty/16jun10b/align/cl2d1/alignedStack-28672.hed (4096 kB) ... /gpfs/group/em/appion/rmcnulty/16jun10b/align/cl2d1/alignedStack-32768.hed (4096 kB) ... /gpfs/group/em/appion/rmcnulty/16jun10b/align/cl2d1/alignedStack-36864.hed (4096 kB) ... /gpfs/group/em/appion/rmcnulty/16jun10b/align/cl2d1/alignedStack-40960.hed (4096 kB) ... /gpfs/group/em/appion/rmcnulty/16jun10b/align/cl2d1/alignedStack-45056.hed (4096 kB) ... /gpfs/group/em/appion/rmcnulty/16jun10b/align/cl2d1/alignedStack-49152.hed (4096 kB) ... /gpfs/group/em/appion/rmcnulty/16jun10b/align/cl2d1/alignedStack-53248.hed (4096 kB) ... /gpfs/group/em/appion/rmcnulty/16jun10b/align/cl2d1/alignedStack-54986.hed (1738 kB) ... wrote 54986 particles to file /gpfs/group/em/appion/rmcnulty/16jun10b/align/cl2d1/alignedStack.hed ... size match 53.7 MB vs. 53.7 MB ... finished stack merge of /gpfs/group/em/appion/rmcnulty/16jun10b/align/cl2d1/alignedStack.hed in 2 min 25 sec merged 54986 particles in 21 min 12 sec ... Getting stack data for stackid=388

lines= ['\tlibmpi.so.0 => /opt/applications/openmpi/1.4.3/gnu/lib/libmpi.so.0 (0x00007f74d95a5000)\n', '\tlibmpi_cxx.so.0 => /opt/applications/openmpi/1.4.3/gnu/l ib/libmpi_cxx.so.0 (0x00007f74d938a000)\n', '\tlibopen-rte.so.0 => /opt/applications/openmpi/1.4.3/gnu/lib/libopen-rte.so.0 (0x00007f74d90fd000)\n', '\tlibopen-pa l.so.0 => /opt/applications/openmpi/1.4.3/gnu/lib/libopen-pal.so.0 (0x00007f74d8ea4000)\n'] Wrote 54986 particles to file /gpfs/group/em/appion/rmcnulty/16jun10b/align/cl2d1/alignedStack.hed Traceback (most recent call last): File "/opt/applications/myami/trunk/bin/runXmippCL2D.py", line 660, in cl2d.start() File "/opt/applications/myami/trunk/bin/runXmippCL2D.py", line 632, in start self.apix = apStack.getStackPixelSizeFromStackId(self.runparams['stackid'])*self.runparams['bin'] File "/opt/applications/myami/trunk/lib/python2.6/site-packages/appionlib/apStack.py", line 706, in getStackPixelSizeFromStackId stackdata = getOnlyStackData(stackId, msg=msg) File "/opt/applications/myami/trunk/lib/python2.6/site-packages/appionlib/apStack.py", line 198, in getOnlyStackData stackdata = appiondata.ApStackData.direct_query(stackid) File "/opt/applications/myami/trunk/lib/python2.6/site-packages/sinedon/data.py", line 428, in direct_query result = db.direct_query(cls, dbid, **kwargs) File "/opt/applications/myami/trunk/lib/python2.6/site-packages/sinedon/dbdatakeeper.py", line 59, in direct_query result = self.dbd.multipleQueries(queryinfo, readimages=readimages) File "/opt/applications/myami/trunk/lib/python2.6/site-packages/sinedon/sqldict.py", line 248, in multipleQueries return _multipleQueries(self.db, queryinfo, readimages) File "/opt/applications/myami/trunk/lib/python2.6/site-packages/sinedon/sqldict.py", line 522, in init self.execute() File "/opt/applications/myami/trunk/lib/python2.6/site-packages/sinedon/sqldict.py", line 535, in execute c = self._cursor() File "/opt/applications/myami/trunk/lib/python2.6/site-packages/sinedon/sqldict.py", line 525, in _cursor self.db.ping() _mysql_exceptions.OperationalError: (2006, 'MySQL server has gone away') Exception _mysql_exceptions.OperationalError: (2006, 'MySQL server has gone away') in <bound method CL2D.del of <main.CL2D object at 0x1ca94d0>> ignored

leginonbot commented 5 months ago

Original Redmine Comment Author Name: Anchi Cheng (@anchi2c) Original Date: 2016-07-29T13:45:38Z

No easy way to solve this as the stoping point would be different for each individual case. We currently have a few cases in other classifications, will work on a solution, but won't be ready immediately.