Hi Alan,

The file is first uploaded in /tmp and then copied to your NFS mounted share. I think it might be the last step that's causing trouble.


Regarding NFS4:
Make sure the settings in /etc/idmapd.conf are correct: especially the 'Domain' setting was causing trouble in our case if not set correctly. If it's not working, you can also try to change here the Nobody-user and -group to your galaxy user account, as a temporary fix, and if NFS is only being by Galaxy of course.

See $man idpmapd.conf

Good luck,

Joachim

Joachim Jacob, PhD

Rijvisschestraat 120, 9052 Zwijnaarde
Tel: +32 9 244.66.34
Bioinformatics Training and Services (BITS)
http://www.bits.vib.be
@bitsatvib

On 11/06/2012 08:12 PM, Dave Clements wrote:
Hi Alan,

I'm CC'ing the Galaxy-Dev list on my response to your question.

I talked with Jen Jackson on this. Her suggestion is that the symlink is most likely the problem somehow - this time. When in doubt, getting rid of these good place to start. So recommended starting solution to try - use full paths for everything. Also probably keep all on same partition for the best performance, but that would be hard to defend (there was some debate about this recently).

Many thanks to Jen for her (as always) careful consideration.

Dave C.


On Mon, Nov 5, 2012 at 7:15 AM, Alan V. Cowles <alan.cow...@duke.edu <mailto:alan.cow...@duke.edu>> wrote:

    Hey Dave,

    Thanks for getting back in touch with me.

    We are running our galaxy instance on a vm... with Centos (RHEL)
    6.2, 2 vcpus, and 2gb vram, with a remote postgresql prod server
    as our database instance.

    Our first issue was trying to get it so we could load sequence and
    larger files directly from an nfs mounted directory on the server,
    without uploading via the web (php vs large files problem.) We
    accomplished this via the data libraries interface but it's still
    not very user intuitive.

    Our first demo user attempted to upload 3 large files and actually
    filled up the / partition on the server as galaxy was installed at
    /usr/local.

    After scrapping and rebuilding that, we now have a several hundred
    GB nfs partition, mounted and /usr/local/galaxy is a symlink to a
    folder on this volume.

    The issue we are currently seeing is during an upload, or even
    just linking files it runs for a while before erroring out and
    saying there is no information on the error. The file seems to be
    there and taking up the correct amount of disk space but galaxy
    has a red bar.

    The galaxy server instance is running back grounded in a screen so
    we can always switch over and look at the output it shows to
    standard out as errors happen, and it seems that it has trouble
    changing permissions on the files in the nfs directory, even
    though, root squash is disabled, and the entire directory is 777
    at the top level and everything underneath is owned galaxy:galaxy.

    AC





--
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http://getgalaxy.org/
http://usegalaxy.org/
http://wiki.galaxyproject.org/



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