zip upload fails

[Miklos Espak]

Hi,

I get an error when I try to upload a file set (~2GB) to our XNAT server, saying that there is no sufficient disk space.

On the root fs there is less space, that's true, but the data directories are on a different fs which has almost 2TB space.

In xdat.log I see this:

2014-11-20 11:18:16,491 [http-80-2] ERROR org.nrg.xnat.turbine.utils.ImageUploadHelper - unable to open temporary directory for unpacking: mkdir failed

But it does not tell where it wanted to create the directory.

That's with XNAT 1.6.1.

Does XNAT use the root fs for zip uploads?

Is there a way to tell not to?

Is it an apache httpd / tomcat setting, eventually?

Thanks,

Miklos

[Herrick, Rick]

Yes, the location of that work folder is dependent on the Tomcat configuration. There’s an environment variable, I think CATALINA_TMPDIR, that’s used by the startup configuration to determine where to write incoming data before passing it onto the application. I believe if you set that to a folder somewhere you have available space and restart Tomcat you should be good.

 

Rick Herrick

Sr. Programmer/Analyst

Neuroinformatics Research Group

Washington University School of Medicine

(314) 827-4250

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[Miklos Espak]

Thank you, Rick.

I just set it and we'll test it tomorrow, but it should be all right.

Cheers,

Miklos

[Noman Ghafoor]

Thanks, Rick. It was helpful for me. 

I was having this error with compressed uploads > 1 GB;

unable to open temporary directory for unpacking: mkdir failed

Solution;

1. Open the setenv.sh file located in the ${XNAT_HOME}/bin directory.

2. Add the following line at the end of the file to set the CATALINA_TMPDIR environment variable to the desired folder location: export CATALINA_TMPDIR=/path/to/temp/folder by default, it was taking value from /usr/share/tomcat9/temp

3. I changed the path to where excessive space is available, in my case, /data/CATALINA_TMPDIR Thanks