Hi Karl, As you see from the error message, you seem to be getting this error because the machine is running out of memory. This can in part be caused by a configuration option that might be set in Galaxy's universe_wsgi.ini file (see below).
Did you have any jobs running while trying to download the file? Waiting until those finish might free up some memory.
A thing to try is to connect to the instance, edit Galaxy's universe_wsgi.ini file to se debug = False, restart Galaxy and try again. Are you familiar with that at all?
The basic steps are as follows:
[local]$ ssh -i <path to your AWS private key file> ubuntu@<instance public IP>
[ec2]$ sudo su galaxy
[ec2]$ cd /mnt/galaxyTools/galaxy-central
[ec2]$ vi universe_wsgi.ini -- edit file (around line 226) to set: debug = False
[ec2]$ sh run.sh --stop-daemon
[ec2]$ sh run.sh --daemon
Yet another option is to connect the instance in the same way, look through the data library on the file system and manually copy the file out of the instance. You can use the following command to copy the file to your local instance:
[local]$ scp -i <path to your AWS private key file> ubuntu@<instance public IP>:/mnt/galaxyData/files/000/dataset_<ID>.dat .
Let us know if none of this works,
Enis
On Mon, Mar 28, 2011 at 12:02 PM,
<karlerhard@berkeley.edu> wrote:
Hello,
I'm trying to download the library files I processed on my galaxy cloud
instance, but I'm getting an error. At the top (on the right panel) it
says "Server Error" and then lists the URL where the data should be and
then lists:
Module paste.exceptions.errormiddleware:143 in __call__
<< try:
__traceback_supplement__ = Supplement, self, environ
app_iter = self.application(environ, start_response)
return self.make_catching_iter(app_iter, environ)
except:>> app_iter = self.application(environ, start_response)
Module paste.debug.prints:98 in __call__
<< try:
status, headers, body = wsgilib.intercept_output(
environ, self.app)
if status is None:
# Some error occurred>> environ, self.app)
Module paste.wsgilib:544 in intercept_output
<< try:
for item in app_iter:
output.write(item)
finally:
if hasattr(app_iter, 'close'):>> output.write(item)
MemoryError: out of memory
Is there some easy fix to this? I'd really like to get that data off of
the cloud instance and be able to terminate it.
thanks,
karl
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