Hello Nate
Is it galaxy or samtools consuming the memory when this happens?
I believe it's samtools. I asked our sysadmin to add 1GB swap :-)
Is debug = False set in universe_wsgi.ini?
No. If I set it to false, I get the same error as Michael described in
http://gmod.827538.n3.nabble.com/Possible-Bug-tt969896.html#a969896
regards,,
Isabelle
--
Isabelle Phan, DPhil
Seattle Biomedical Research Institute
+1(206)256 7113
________________________________________
From: Nate Coraor [nate(a)bx.psu.edu]
Sent: Monday, August 30, 2010 10:47 AM
To: Isabelle Phan
Cc: 'galaxy-dev(a)lists.bx.psu.edu'
Subject: Re: [galaxy-dev] swap issue
Isabelle Phan wrote:
Hello,
I am running galaxy, using a postgres backend.
The galaxy server systematically gets killed whenever I try uploading a bam file. The
samtools process is still running.
This is the end of the log:
2010-08-26 18:08:11,371 INFO sqlalchemy.engine.threadlocal.TLEngine.0x...4610
{'param_1': 8}
sqlalchemy.engine.threadlocal.TLEngine.0x...4610 INFO 2010-08-26 18:08:11,371
{'param_1': 8}
2010-08-26 18:08:11,378 INFO sqlalchemy.pool.QueuePool.0x...4ed0 Connection
<connection object at 0x567bf30; dsn: 'dbname=galaxy host=/var
closed: 0> being returned to pool
sqlalchemy.pool.QueuePool.0x...4ed0 INFO 2010-08-26 18:08:11,378 Connection
<connection object at 0x567bf30; dsn: 'dbname=galaxy host=/var
closed: 0> being returned to pool
10.1.20.44 - - [26/Aug/2010:18:08:06 -0700] "POST /root/history_item_updates
HTTP/1.1" 200 - "http://galaxy:8080/history" "Mozilla/5.0 (X1
(x86_64); en-US; rv:1.9.2.8) Gecko/20100722 Firefox/3.6.8"
Killed
I have the following options set in universe_wsgi.ini:
database_engine_option_server_side_cursors = True
database_engine_option_strategy = threadlocal
It seems to be running out of swap. I monitored memory usage with 'top' and
galaxy died when available swap hit 0k free.
I am not superuser on the machine where galaxy is running and I have no other server
available. Is there something I could do to prevent galaxy from dying?
Hi Isabelle,
Is it galaxy or samtools consuming the memory when this happens?
Is debug = False set in universe_wsgi.ini?
Thanks,
--nate
Thanks,
Isabelle
--
Isabelle Phan, DPhil
Seattle Biomedical Research Institute
+1(206)256 7113
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