Hi Scott,

I am running SUSE Linux Enterprise Server 11 SP1  (x86_64) - Kernel \r (\l) on both servers.  These are VM's with identical configurations. I know that shutil.move is a python function, but I am not really sure how it works.  I appreciate the assistance.

Iry

From: Scott McManus <scottmcmanus@gatech.edu>
Date: Thursday, August 2, 2012 12:59 PM
To: Iry Witham <iry.witham@jax.org>
Cc: "galaxy-dev@lists.bx.psu.edu" <galaxy-dev@lists.bx.psu.edu>
Subject: Re: [galaxy-dev] Strange "Could not moveŠ." error

Hi Iry-

A call to shutil.move is failing, and this could be because file-copying semantics
are different on your test instance's OS and/or filesystem than they are on your
development instance's OS and/or filesystem. What OS and file system are you
using on each? We can also try writing a small Python script to see if shutil.move
is failing when copying files from a similar source directory to a similar destination
directory. Let me know and I'll be glad to give you a hand.

-Scott

Hi Dev-Team,

I am experiencing a strange error that I cannot replicate on two identical instances of my Galaxy server.  I have a tool that runs fine on my test instance and fails on my development instance.  The servers are identically configured and running the same build.  The handler.log from the successful instance shows the following:

galaxy.jobs DEBUG 2012-08-02 11:31:07,881 (295) Working directory for job is: /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295
galaxy.jobs.handler DEBUG 2012-08-02 11:31:07,881 dispatching job 295 to pbs runner
galaxy.jobs.handler INFO 2012-08-02 11:31:08,083 (295) Job dispatched
galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:08,382 (295) submitting file /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/pbs/295.sh
galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:08,382 (295) command is: perl /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/tools/jax_cnv/cnv-seq.pl         --out-basename cnv_seq_result         --test /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/files/001/dataset_1504.dat             --ref /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/files/001/dataset_1503.dat             --genome-size 2716965481         --p-value 0.001         --bigger-window 1.5             --no-annotate             --log2-threshold 0.6; cd /hpcdata/galaxy-test/galaxy-setup/galaxy-dist; /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/set_metadata.sh ./database/files /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295 . /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/universe_wsgi.ini /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/tmp/tmplTSKeF /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/galaxy.json /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/metadata_in_HistoryDatasetAssociation_689_Oh21hx,/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/metadata_kwds_HistoryDatasetAssociation_689_xgxlZy,/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/metadata_out_HistoryDatasetAssociation_689_H0claK,/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/metadata_results_HistoryDatasetAssociation_689_rdQBs8,,/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/metadata_override_HistoryDatasetAssociation_689_B0U0MV
galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:08,395 (295) queued in default queue as 112605.scyld.localdomain
galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:08,776 (295/112605.scyld.localdomain) PBS job state changed from N to R
galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:27,117 (295/112605.scyld.localdomain) PBS job state changed from R to C
galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:27,118 (295/112605.scyld.localdomain) PBS job has completed successfully
galaxy.jobs DEBUG 2012-08-02 11:31:27,197 finish(): Moved /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/cnv_seq_result.cnv to /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/files/001/dataset_1555.dat as directed by from_work_dir
galaxy.datatypes.metadata DEBUG 2012-08-02 11:31:27,249 loading metadata from file for: HistoryDatasetAssociation 689
galaxy.jobs DEBUG 2012-08-02 11:31:27,382 job 295 ended
galaxy.datatypes.metadata DEBUG 2012-08-02 11:31:27,382 Cleaning up external metadata files

The same log from the failing instance shows the following:

galaxy.jobs DEBUG 2012-08-02 11:54:29,234 (113) Working directory for job is: /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/job_working_directory/000/113
galaxy.jobs.handler DEBUG 2012-08-02 11:54:29,234 dispatching job 113 to pbs runner
galaxy.jobs.handler INFO 2012-08-02 11:54:29,420 (113) Job dispatched
galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:54:29,669 (113) submitting file /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/pbs/113.sh
galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:54:29,669 (113) command is: perl /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/tools/jax_cnv/cnv-seq.pl         --out-basename cnv_seq_result         --test /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/files/000/dataset_131.dat             --ref /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/files/000/dataset_132.dat             --genome-size 2716965481         --p-value 0.001         --bigger-window 1.5             --no-annotate             --log2-threshold 0.6; cd /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist; /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/set_metadata.sh ./database/files /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/job_working_directory/000/113 . /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/universe_wsgi.ini /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/tmp/tmpgTn7ey /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/job_working_directory/000/113/galaxy.json /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/job_working_directory/000/113/metadata_in_HistoryDatasetAssociation_136_VYG968,/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/job_working_directory/000/113/metadata_kwds_HistoryDatasetAssociation_136_yo_4aK,/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/job_working_directory/000/113/metadata_out_HistoryDatasetAssociation_136_D6HwmI,/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/job_working_directory/000/113/metadata_results_HistoryDatasetAssociation_136_zunslF,,/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/job_working_directory/000/113/metadata_override_HistoryDatasetAssociation_136_FDUxso
galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:54:29,680 (113) queued in default queue as 112609.scyld.localdomain
galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:54:30,163 (113/112609.scyld.localdomain) PBS job state changed from N to R
galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:54:33,298 (113/112609.scyld.localdomain) PBS job state changed from R to C
galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:54:33,298 (113/112609.scyld.localdomain) PBS job has completed successfully
galaxy.jobs DEBUG 2012-08-02 11:54:33,354 finish(): Could not move /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/job_working_directory/000/113/cnv_seq_result.cnv to /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/files/000/dataset_140.dat as directed by from_work_dir
galaxy.jobs DEBUG 2012-08-02 11:54:33,467 job 113 ended

Why would one fail and the other succeed? 

Thanks,
Iry

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