[GE users] out of memory?

Davide Cittaro davide.cittaro at ifom-ieo-campus.it
Mon Feb 12 14:38:23 GMT 2007

    [ The following text is in the "WINDOWS-1252" character set. ]
    [ Your display is set for the "ISO-8859-10" character set.  ]
    [ Some special characters may be displayed incorrectly. ]

Hi, I'm trying to debug a program I used to run in grid engine. It  
programmatically goes out of memory but, since it runs for days and  
days, it is hard to me to understand what's going on.
BTW, the queue which it is running in has no memory (or other  
resources) limit:

s_rt                  INFINITY
h_rt                  INFINITY
s_cpu                 INFINITY
h_cpu                 INFINITY
s_fsize               INFINITY
h_fsize               INFINITY
s_data                INFINITY
h_data                INFINITY
s_stack               INFINITY
h_stack               INFINITY
s_core                INFINITY
h_core                INFINITY
s_rss                 INFINITY
h_rss                 INFINITY
s_vmem                INFINITY
h_vmem                INFINITY

according to qacct the process doesn't use that much memory:

$ qacct -j 308
account      sge
priority     0
qsub_time    Tue Jan 30 16:28:22 2007
start_time   Tue Jan 30 16:28:26 2007
end_time     Mon Feb 12 04:30:54 2007
granted_pe   NONE
slots        1
failed       0
exit_status  0
ru_wallclock 1080148
ru_utime     1080109
ru_stime     7
ru_maxrss    0
ru_ixrss     0
ru_ismrss    0
ru_idrss     0
ru_isrss     0
ru_minflt    142274
ru_majflt    33
ru_nswap     0
ru_inblock   0
ru_oublock   0
ru_msgsnd    0
ru_msgrcv    0
ru_nsignals  0
ru_nvcsw     572
ru_nivcsw    2438621
cpu          1080117
mem          486778.751
io           0.000
iow          0.000
maxvmem      496.977M

and the machine has 4 Gb RAM + 7.5 Gb swap that never get filled...
The dmesg says

Out of Memory: Killed process 18873 (mfinder).

According to what I wrote, can I exclude that running in grid engine,  
somehow, influenced the memory available to that job? I know it  
sounds weird, but I have to exclude everything before complaining  
with the program author... :-)
Davide Cittaro
HPC and Bioinformatics Systems @ Informatics Core

IFOM - Istituto FIRC di Oncologia Molecolare
via adamello, 16
20139 Milano

tel.: +39(02)574303355
e-mail: davide.cittaro at ifom-ieo-campus.it

More information about the gridengine-users mailing list