Hi John, Can you verify that your virtualenv created on the cluster is the one being used by jobs? It should be possible to view using a test job's script file, the path to which is logged at run time.
Thanks, --nate On Mon, Jan 29, 2018 at 1:00 AM, John Letaw <le...@ohsu.edu> wrote: > Hi Nate, > > > > I tried to get this to work, but it is not getting rid of the error. I > was able to symlink the platform dependent lib-dynload libraries to a > recognized directory, which removed the error telling me _hashlib was not > found. Now, I’m just left with: > > > > galaxy.jobs.output_checker DEBUG 2018-01-28 21:50:36,883 Tool produced > standard error failing job - [Could not find platform dependent libraries > <exec_prefix> > > Consider setting $PYTHONHOME to <prefix>[:<exec_prefix>] > > ] > > > > Maybe, as Cao suggested, I should just be installing a common version in > the shared directory between the two filesystems. The job is correctly > being scheduled and completes, metadata is just not written. I’m certainly > open to any additional ideas. > > > > Thanks, > > John > > > > *From: *Nate Coraor <n...@bx.psu.edu> > *Date: *Thursday, January 18, 2018 at 1:12 PM > *To: *Cao Tang <charlietan...@gmail.com> > *Cc: *John Letaw <le...@ohsu.edu>, galaxy-dev <galaxy-dev@lists. > galaxyproject.org> > *Subject: *Re: [galaxy-dev] Cluster Install Path Errors > > > > I think this error most commonly occurs when a virtualenv is used with a > different python than the one it was created with. Is the cluster also > running Ubuntu 14.04? If not, you can create a separate virtualenv for > running tools using the instructions at: > > > > https://docs.galaxyproject.org/en/master/admin/framework_ > dependencies.html#managing-dependencies-manually > > > > Once created, your tools can use it by setting `<param > id="GALAXY_VIRTUAL_ENV">/path/to/venv</param>` on the destination in > job_conf.xml > > > > --nate > > > > On Thu, Jan 18, 2018 at 1:50 PM, Cao Tang <charlietan...@gmail.com> wrote: > > You can try to install: > > https://pypi.python.org/pypi/hashlib > > > > On Thu, Jan 18, 2018 at 1:22 PM, John Letaw <le...@ohsu.edu> wrote: > > Thanks for the response Peter. I currently have this instance installed > on a lustre fs, that is visible on an Ubuntu 14.04 vm. So, there very well > may be mismatches between directories on the VM, and those on the lustre > cluster. This would mean the python installation on the VM needs to > exactly match that which is on the cluster? What else will need to match > to ensure success? > > Thanks, > John > > On 1/18/18, 1:50 AM, "Peter Cock" <p.j.a.c...@googlemail.com> wrote: > > I *think* this is a problem with your copy of Python 2.7 and a > standard library (hashlib) normally present. Do you know how this > Python was installed? If it was compiled from source, then it may have > been missing a few dependencies, and thus you have ended up with > missing a few normally present Python modules. > > Peter > > On Wed, Jan 17, 2018 at 11:15 PM, John Letaw <le...@ohsu.edu> wrote: > > Hi all, > > > > > > > > I have been trying to finish up a production cluster Galaxy > installation, > > and am having trouble with the below error. In the past, when seeing > > something along these lines, I usually can adjust environmental > variables > > either in startup scripts, or by including a script for Galaxy to > source > > before it sends out a job. I have tried all of these different > methods, but > > I can’t seem to get rid of this error message in any tool > invocation. I > > currently have “embed_metadata_in_job” set to False in my > job_conf.xml file. > > This removes a “No module named galaxy_ext.metadata.set_metadata” > error, but > > this hashlib error remains. If I could understand a little more > about the > > steps that are taken when sending out a job, perhaps I could better > diagnose > > this? > > > > > > > > “”” > > > > Could not find platform dependent libraries > > > > Consider setting $PYTHONHOME to [:] > > > > Traceback (most recent call last): > > > > File "~/galaxydev/galaxy/tools/data_source/upload.py", line 14, in > > > > import tempfile > > > > File "/usr/lib64/python2.7/tempfile.py", line 35, in > > > > from random import Random as _Random > > > > File "/usr/lib64/python2.7/random.py", line 49, in > > > > import hashlib as _hashlib > > > > File "/usr/lib64/python2.7/hashlib.py", line 116, in > > > > import _hashlib > > > > ImportError: No module named _hashlib > > > > “”” > > > > > > > > Thanks, > > > > John > > > > > > ___________________________________________________________ > > 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: > > https://lists.galaxyproject.org/ > > > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/ > > > ___________________________________________________________ > 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: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/ > > > > > ___________________________________________________________ > 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: > https://lists.galaxyproject.org/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/ > > >
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