Hi Nate,
Thanks for the reply. In syslog I'm getting;
Jul 16 20:36:41 galaxy kernel: [ 117.123921] Out of memory: Kill process 1390 (python) score 986 or sacrifice child
Jul 16 20:36:41 galaxy kernel: [ 117.124087] Killed process 1390 (python) total-vm:43496348kB, anon-rss:32611892kB, file-rss:1800kB
(END)
It's a 32GB VM. I could increase it but I wouldn't expect 32GB to be too little. I've attached the full syslog.
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1
Hi All,
I have a weird issue that's just cropped up. After a new install of
galaxy (checked out on Monday from github) on a ubuntu vm, using
postgres rather than sqlite as well as a few other production
recommendations, I started playing around with the Data Libraries
functionality. I linked a bunch of fastq.gz files into galaxy (around
150 in total) and everything was working fine. I went home and the
next day, it was down.
I tried to start it up as usual (using an init.d script), it worked
for less than a minute and then disappeared again. So I tried running
it as the galaxy user using ./run.sh and I get a seg fault;
Starting server in PID 23173.
serving on http://144.124.110.39:8080
Segmentation fault
Tried again with strace
Starting server in PID 23552.
serving on http://144.124.110.39:8080
[{WIFSIGNALED(s) && WTERMSIG(s) == SIGKILL}], 0, NULL) = 23552
- --- SIGCHLD {si_signo=SIGCHLD, si_code=CLD_KILLED, si_pid=23552,
si_status=SIGKILL, si_utime=1590, si_stime=1930} ---
rt_sigreturn() = 23552
write(2, "Killed\n", 7Killed
) = 7
read(10, "", 8192) = 0
exit_group(137) = ?
+++ exited with 137 +++
I can't see anything odd in the log file and I've turned debugging on
in galaxy.ini. I'm at a bit of a loss. Does anyone know what might be
causing it?
Cheers,
- --
Dr. Martin Vickers
Data Manager/HPC Systems Administrator
Institute of Biological, Environmental and Rural Sciences
IBERS New Building
Aberystwyth University
w: http://www.martin-vickers.co.uk/
e: mjv08@aber.ac.uk
t: 01970 62 2807
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