Re: [HTCondor-users] Docker cmdnotfound

[Todd Tannenbaum <tannenba@xxxxxxxxxxx>]

On 8/2/2016 7:22 AM, Michael Fienen wrote:
> Hi Iain
>
> Well, that’s embarrassing! That’s right, so fixed the typo. Now, if I
> have executable = ./foo.sh, it runs but appears to run outside of docker
> container (e.g. my script foo.py failed in such a way that it would not
> if inside the container).

Are you sure it is running outside the container?  I.e. perhaps it is 
just not finding the proper files in your container due to missing 
environment variables such as PYTHONPATH or whatever.

I'd changing your submit file below to have something like
   executable = /bin/ls
   arguments = -l /etc
just to look around and confirm if you are really inside the docker 
filesystem or not...

Hope this helps
Todd

 I tried “executable=foo.sh” without “./“ and
> get the same error as before.
>
> Getting closer though!
>
> Thanks
> Mike
>
> > On Aug 2, 2016, at 7:15 AM, Iain Bradford Steers <iain.steers@xxxxxxx
> > <mailto:iain.steers@xxxxxxx>> wrote:
> >
> > Hi Mike,
> >
> > I see you're transferring foo.py twice, but calling ./foo.sh?
> >
> > Is that a typo or is foo.sh embedded in the docker image?
> >
> > Cheers, Iain
> > ________________________________________
> > From: HTCondor-users [htcondor-users-bounces@xxxxxxxxxxx
> > <mailto:htcondor-users-bounces@xxxxxxxxxxx>] on behalf of Michael
> > Fienen [mike@xxxxxxxxxxx <mailto:mike@xxxxxxxxxxx>]
> > Sent: 02 August 2016 14:10
> > To: HTCondor-Users Mail List
> > Subject: [HTCondor-users] Docker cmdnotfound
> >
> > Hello HTCondorians!
> >
> > I’m trying a trivial Docker universe job and it’s *almost* working.
> >
> > I’m quite certain that HTCondor was able to make a running container
> > (it took forever the first time, presumably because pulling from
> > docker hub, and subsequent runs are faster but now hanging up).
> >
> > Here’s my simple submit file:
> >
> > universe=docker
> > docker_image=mnfienen/centos6_py35
> > notification=never
> > executable=./foo.sh
> > should_transfer_files=YES
> > output=out_$(Process).out
> > error=err_$(Process).err
> > log = log_$(Process).log
> > transfer_input_files = foo.py, foo.py
> > queue
> >
> > And here’s what I get in the log before it goes to held status:
> > 007 (234.000.000) 08/02 07:00:07 Shadow exception!
> > Error fromslot1_1@xxxxxxx
> > <mailto:slot1_1@xxxxxxx><mailto:slot1_1@xxxxxxx>.xxx.gov
> > <http://xxx.gov/><http://xxx.gov <http://xxx.gov/>>: Error running
> > docker job: cmdnotfound
> > 0  -  Run Bytes Sent By Job
> > 320  -  Run Bytes Received By Job
> > ...
> > 012 (234.000.000) 08/02 07:00:07 Job was held.
> > Error fromslot1_1@xxxxxxx
> > <mailto:slot1_1@xxxxxxx><mailto:slot1_1@xxxxxxx>.xxx.gov
> > <http://xxx.gov/><http://xxx.gov <http://xxx.gov/>>: Error running
> > docker job: cmdnotfound
> > Code 6 Subcode 0
> >
> > I’ve tried a couple things for the executable argument (foo.sh is
> > simply running foo.py which works in the container locally). I tried
> > "executable=foo.sh”, “executable=./foo.sh”, and before that also tried
> > “executable=python foo.py”
> >
> > I’m clearly doing something wrong.
> >
> > Thanks for any help!
> >
> > Cheers,
> > MIke Fienen
> > USGS Wisconsin Water Science Center
> >
> >
> >
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>
>
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--
Todd Tannenbaum <tannenba@xxxxxxxxxxx> University of Wisconsin-Madison
Center for High Throughput Computing   Department of Computer Sciences
HTCondor Technical Lead                1210 W. Dayton St. Rm #4257
Phone: (608) 263-7132                  Madison, WI 53706-1685