Appion

When prepping a Frelaign run, it start on guppy and then the last lines of the file
[see : name: frealign_recon2.appionsub.job
user: bcarr
appion path: /ami/data00/appion/10may20c/recon/frealign_recon2
submit time: 2010-12-14 20:24:47
status: Done ]

are:

... Time stamp: 10dec14u24
... Function name: prepFrealign
... Appion directory: /usr/lib64/python2.4/site-packages
... Load average is high 4.24
!!! WARNING: Using split database
Connected to database: 'ap6'
... Committing data to database
... Getting stack data for stackid=1496
Old stack info: 'no ctf'
... Stack 1496 pixel size: 0.83
... Looking up symmetry for input: D7
... Selected symmetry group: D7 -- D7 (z)
... Selected symmetry d7 with id 19
... Run directory: /ami/data00/appion/10may20c/recon/frealign_recon2
!!! WARNING: directory '/ami/data00/appion/10may20c/recon/frealign_recon2'
already exists.
... Writing function log to: prepFrealign.log
... Found 8 processors on this machine
... Running Appion version 'r15117'
... IBLOW set to 1, requiring 8.3 GB memory
... Getting stack data for stackid=1496
Old stack info: 'no ctf'
... requesting 8.3 GB of memory
... Current symmetry: 7-fold symmetry along the z axis, 2-fold rotational axis 90 degrees from z
EMAN: proc3d /ami/data17/appion/09nov02c/models/accepted/09nov02p03/groel-initmodel.mrc
/am ... =320,320,320 scale=1.9639
EMAN 1.9 Cluster ($Date: 2009/02/18 05:12:22 $).
Run 'proc3d help' for detailed help.
Original image : 192x192x192 Mean=0.0659 Sigma=0.248 Min=-1.32e-05 Max=1.68
Sampling : 1.63 A/pixel Origin = 0,0,0
Final image : 320x320x320 Mean=0.108 Sigma=0.309
Sampling : 0.829981 A/pixel Origin = 23.683,23.683,23.683
... Creating parameter file: /ami/data00/appion/10may20c/recon/frealign_recon2/params.iter000.par
... querying stack particles from stackid=1496 at Tue Dec 14 20:25:18 2010
... sorting particles
... received 4800 stack particles in 2.11 sec
... Writing out particle parameters
... particle 200 -- 46.68 sec remain
... particle 400 -- 44.54 sec remain
... particle 600 -- 42.28 sec remain
... particle 800 -- 40.15 sec remain
... particle 1000 -- 38.16 sec remain
... particle 1200 -- 36.18 sec remain
... particle 1400 -- 34.19 sec remain
... particle 1600 -- 32.2 sec remain
... particle 1800 -- 30.2 sec remain
... particle 2000 -- 28.2 sec remain
... particle 2200 -- 26.2 sec remain
... particle 2400 -- 24.19 sec remain
... particle 2600 -- 22.18 sec remain
... particle 2800 -- 20.17 sec remain
... particle 3000 -- 18.16 sec remain
... particle 3200 -- 16.14 sec remain
... particle 3400 -- 14.13 sec remain
... particle 3600 -- 12.12 sec remain
... particle 3800 -- 10.1 sec remain
... particle 4000 -- 8.09 sec remain
... particle 4200 -- 6.06 sec remain
... particle 4400 -- 4.04 sec remain
... particle 4600 -- 2.02 sec remain
... particle 4800 -- 0.0 nsec remain
Initial files:
Stack: start.hed
Volume: initmodel.hed
Params: params.iter000.par

... Multi node run, iteration 1
... Multi node run, iteration 2
... Multi node run, iteration 3
... Multi node run, iteration 4
... Multi node run, iteration 5
... Multi node run, iteration 6
... Multi node run, iteration 7
... Multi node run, iteration 8
... Multi node run, iteration 9
... Multi node run, iteration 10
tar --exclude=*.tar -cf frealign_recon2.tar *
Traceback (most recent call last):
File "/opt/appion/bin/prepFrealign.py", line 830, in ?
frealign.start()
File "/opt/appion/bin/prepFrealign.py", line 824, in start
self.prepareForCluster()
File "/opt/appion/bin/prepFrealign.py", line 776, in prepareForCluster
frealignq['refineIter'] = appiondata.ApRefineIterData.direct_query(self.params['reconiterid'])
File "/usr/lib64/python2.4/site-packages/sinedon/data.py", line 403, in direct_query
result = db.direct_query(cls, dbid, **kwargs)
File "/usr/lib64/python2.4/site-packages/sinedon/dbdatakeeper.py", line 66, in direct_query
raise RuntimeError('direct_query should only return a single result')
RuntimeError: direct_query should only return a single result