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spider reference based alignement not working anymore in appion #2333

Closed leginonbot closed 7 months ago

leginonbot commented 7 months ago

Author Name: Melody Campbell (Melody Campbell) Original Redmine Issue: 2333, https://emg.nysbc.org/redmine/issues/2333 Original Date: 2013-04-19

it was working fine yesterday, now get appion error saying "no error code set by the system" don't work on cronus3 or longboard

command generated: /opt/myamisnap/bin/appion runJob.py /opt/myamisnap/bin/appion refBasedAlignment2.py --projectid=368 --template-list=239,238,237,236,235,234,233,232,231,230,229,228,227,226,225,224,223,222,221,220,219 --runname=refbased-21hp-bin4 --stack=72 --last-ring=19 --first-ring=2 --rundir=/ami/data15/appion/13mar09f/align/refbased-21hp-bin4 --description="try with correct binning 19-2-3" --lowpass=15 --highpass=2000 --xy-search=3 --xy-step=1 --num-iter=3 --num-part=30855 --bin=4 --csym=1 --commit --expid=11349 --jobtype=partalign --ppn=1 --nodes=1 --walltime=240 --jobid=879

won't work if posted into a terminal, also won't work if runJob.py parts taken out.

leginonbot commented 7 months ago

Original Redmine Comment Author Name: Melody Campbell (Melody Campbell) Original Date: 2013-04-19T17:47:01Z

actually imagic msa won't work either with the same error. "Error: Job submission to guppy.scripps.edu failed. No error code has been set by the system."

this was on longboard/beta

here isthe command: /opt/myamisnap/bin/appion runJob.py /opt/myamisnap/bin/appion imagicMSA.py --projectid=368 --alignid=81 --lpfilt=10 --hpfilt=600 --mask_radius=.95 --mask_dropoff=0.1 --bin=1 --numiters=50 --MSAdistance=modulation --overcorrection=0.8 --description="i'm so annoyed" --nproc=16 --commit --rundir=/ami/data15/appion/13jan26d/align/imagicmsa-21hp --runname=imagicmsa-21hp --expid=11031 --jobtype=alignanalysis --ppn=4 --nodes=4 --walltime=240 --jobid=881

leginonbot commented 7 months ago

Original Redmine Comment Author Name: Melody Campbell (Melody Campbell) Original Date: 2013-04-19T17:50:33Z

in fact, kerden feature analysis and make stack won't work either... maybe everything is broken?

/opt/myamisnap/bin/appion runJob.py /opt/myamisnap/bin/appion makestack2.py --single=start.hed --selectionid=29 --no-invert --normalized --xmipp-normalize=4.5 --boxsize=160 --bin=20 --description="test" --projectid=368 --preset=en --session=13jan26d --runname=stack13 --rundir=/ami/data15/appion/13jan26d/stacks/stack13 --no-rejects --no-wait --commit --limit=10 --continue --expid=11031 --jobtype=makestack2 --ppn=1 --nodes=1 --walltime=240 --jobid=883

Warning: The output directory (/ami/data15/appion/13jan26d/stacks/stack13) may not have been created on guppy.scripps.edu. Error: Job submission to guppy.scripps.edu failed. No error code has been set by the system.

leginonbot commented 7 months ago

Original Redmine Comment Author Name: Amber Herold (Amber Herold) Original Date: 2013-04-19T18:01:31Z

Anchi, Sargis, have either of you made any changes in the last day that could cause this? Kids have a half day today, so I wont be in again till Monday to troubleshoot.

leginonbot commented 7 months ago

Original Redmine Comment Author Name: Melody Campbell (Melody Campbell) Original Date: 2013-04-19T22:28:58Z

We think scipy is broken:

Python 2.6.6 (r266:84292, Sep 11 2012, 08:34:23) [GCC 4.4.6 20120305 (Red Hat 4.4.6-4)] on linux2 Type "help", "copyright", "credits" or "license" for more information.

from scipy import stats Traceback (most recent call last): File "", line 1, in File "/usr/lib64/python2.6/site-packages/scipy/stats/init.py", line 7, in from stats import File "/usr/lib64/python2.6/site-packages/scipy/stats/stats.py", line 199, in import scipy.linalg as linalg File "/usr/lib64/python2.6/site-packages/scipy/linalg/init.py", line 8, in from basic import File "/usr/lib64/python2.6/site-packages/scipy/linalg/basic.py", line 17, in from lapack import get_lapack_funcs File "/usr/lib64/python2.6/site-packages/scipy/linalg/lapack.py", line 18, in from scipy.linalg import clapack ImportError: /usr/lib64/python2.6/site-packages/scipy/linalg/clapack.so: undefined symbol: clapack_sgesv

Thanks so much Sargis!!

leginonbot commented 7 months ago

Original Redmine Comment Author Name: Sargis Dallakyan (@dallakyan) Original Date: 2013-04-20T00:27:53Z

Uninstalled lapack that was causing from scipy import stats to fail. I've installed lapapck today for em_hole_finder (http://emg.nysbc.org/redmine/issues/2319). Will need to check em_hole_finder again on Monday to see if it still work.

Melody, please test and close this bug if it works.

Thank you all.

leginonbot commented 7 months ago

Original Redmine Comment Author Name: Melody Campbell (Melody Campbell) Original Date: 2013-04-20T16:19:06Z

awesome, works perfectly, thanks sargis!!