Update: When I run as the Galaxy user, Python does have the right temp directory:
tempfile.gettempdir() '/scratch/galaxy'
So does that mean this upload job isn't running as galaxy, or is skipping the job_environment_setup_file? Or could something else be going on? Any ideas, now I'm really stuck. Thanks, Greg On Wed, Feb 6, 2013 at 3:35 PM, greg <margeemail@gmail.com> wrote:
Ok, when I ran Python in my last two emails I was running as myself, not the galaxy user, and only the galaxy user has write permission to /scratch/galaxy
So that's why Python was ignoring /scratch/galaxy for me. If it doesn't have write access it tries the next temp directory in its list.
I'm going to try debugging as the galaxy user next.
-Greg
On Wed, Feb 6, 2013 at 3:21 PM, greg <margeemail@gmail.com> wrote:
Hi Nate,
I don't see $TMPDIR being set on the cluster, in addition to my previous email I ran:
print os.environ.keys() ['KDE_IS_PRELINKED', 'FACTERLIB', 'LESSOPEN', 'SGE_CELL', 'LOGNAME', 'USER', 'INPUTRC', 'QTDIR', 'PATH', 'PS1', 'LANG', 'KDEDIR', 'TERM', 'SHELL', 'TEMP', 'QTINC', 'G_BROKEN_FILENAMES', 'SGE_EXECD_PORT', 'HISTSIZE', 'KDE_NO_IPV6', 'MANPATH', 'HOME', 'SGE_ROOT', 'QTLIB', 'VIRTUAL_ENV', 'SGE_CLUSTER_NAME', '_', 'SSH_CONNECTION', 'SSH_TTY', 'HOSTNAME', 'SSH_CLIENT', 'SHLVL', 'PWD', 'MAIL', 'LS_COLORS', 'SGE_QMASTER_PORT']
But I think we've narrowed it down to something interfering with Python deciding the temp file location. I just can't figure out what.
On Wed, Feb 6, 2013 at 3:18 PM, Nate Coraor <nate@bx.psu.edu> wrote:
On Feb 6, 2013, at 3:00 PM, greg wrote:
Thanks Nate,
It turns out I already had this as the first line of my job setup file:
export TEMP=/scratch/galaxy
But when I look in that directory, there's plenty of free space, and I also don't see any recent files there. So I'm wondering if the upload jobs aren't seeing that for some reason.
Any ideas on how I could diagnose this more?
Hi Greg,
The first place to look would be in lib/galaxy/datatypes/sniff.py, line 96:
fd, temp_name = tempfile.mkstemp()
If you print temp_name, that will tell you what file the upload tool is writing to. You may also want to take a look at:
http://docs.python.org/2/library/tempfile.html#tempfile.tempdir
Some cluster environments set $TMPDIR, and if that is set, $TEMP will not be used.
--nate
-Greg
Relevant info?
grep env galaxy-dist/universe_wsgi.ini environment_setup_file = /usr/local/galaxy/job_environment_setup_file
cat /usr/local/galaxy/job_environment_setup_file export TEMP=/scratch/galaxy #active Python virtual env just for galaxy source /usr/local/galaxy/galaxy_python/bin/activate ... path setup lines ...
On Wed, Feb 6, 2013 at 2:37 PM, Nate Coraor <nate@bx.psu.edu> wrote:
On Feb 6, 2013, at 2:32 PM, greg wrote:
Hi guys,
When I try to upload a directory of files from a server directory I'm seeing the error below.
It appears to be trying to write to a temp directory somewhere that I'm guessing doesn't have enough space? Is there a way I can direct where it writes to for temporary files like this?
Hi Greg,
There are a few ways. For some parts of Galaxy, you will want to set new_file_path in universe_wsgi.ini to a suitable temp space. However, this is not the case for the upload tool.
Am I understanding right, that these upload jobs are running on our cluster? I think it would be a problem if its trying to use the default temp directory on each cluster node since they aren't provisioned with much space.
This is correct. On the cluster, add something to your user's shell startup files (or see the environment_setup_file option in universe_wsgi.ini) that will set the $TEMP or $TMPDIR environment variable to a suitable temp space.
--nate
Please advise.
Thanks,
Greg
Miscellaneous information:Traceback (most recent call last): File "/misc/local/galaxy/galaxy-dist/tools/data_source/upload.py", line 384, in __main__() File "/misc/local/galaxy/galaxy-dist/tools/data_source/upload.py", line 373, in __main__ add_file( dataset, Job Standard Error
Traceback (most recent call last): File "/misc/local/galaxy/galaxy-dist/tools/data_source/upload.py", line 384, in __main__() File "/misc/local/galaxy/galaxy-dist/tools/data_source/upload.py", line 373, in __main__ add_file( dataset, registry, json_file, output_path ) File "/misc/local/galaxy/galaxy-dist/tools/data_source/upload.py", line 270, in add_file line_count, converted_path = sniff.convert_newlines( dataset.path, in_place=in_place ) File "/misc/local/galaxy/galaxy-dist/lib/galaxy/datatypes/sniff.py", line 99, in convert_newlines fp.write( "%s\n" % line.rstrip( "\r\n" ) ) IOError: [Errno 28] No space left on device ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: