Hi, Peter,The script is a bit unique to my configuration (users request ppn,nodes,pcpus for parallel jobs, JSV handles the rest). The script uses these variables to determine memory requirements accordingly (esp. for multi-threaded jobs). We use mem_free as the consumable. The script is attached... hopefully, the list allows it.
-Brian On 08/30/2012 05:48 AM, Peter van Heusden wrote:
I've had exactly the same experience. Java seems to do some kind of calculation based on total system memory, and you need to size h_vmem to much more than the java application's real memory use in order to make the job run. Reuti, have you dealt with this problem? Brian, could you share the memkiller script you use? Thanks, Peter On 08/29/2012 06:09 PM, Brian Smith wrote:We found h_vmem to be highly unpredictable, especially with java-based applications. Stack settings were screwed up, certain applications wouldn't launch (segfaults), and hard limits were hard to determine for things like MPI applications. When your master has to launch 1024 MPI sub-tasks (qrsh), it generally eats up more VMEM than the slave tasks do. It was just hard to get right. -Brian Brian Smith Sr. System Administrator Research Computing, University of South Florida 4202 E. Fowler Ave. SVC4010 Office Phone: +1 813 974-1467 Organization URL: http://rc.usf.edu On 08/29/2012 11:33 AM, Reuti wrote:Am 29.08.2012 um 17:21 schrieb Brian Smith:We use mem_free variable as a consumable. Then, we use a cronjob called memkiller that terminates jobs if they go over their requested (or default) memory allocation andIt would be more straight forward to use directly h_vmem. This is controlled by SGE and the job exceeding the limit will be killed by SGE. If you consume it as a consumable on a exechost level, it could be set to the built in physical memory. Was there any reason to use mem_free? -- Reuti1. Swap space on node is used 2. Swap rate is greater than 100 I/Os per second The user gets emailed with a report if this happens. This has made dealing with the oom killer a thing of the past in our shop. We manage memory on the principle that swap should NEVER be used. If you're hitting oom killer, you're pretty far beyond that in terms of memory utilization; if performance is a consideration, MHO is you should be looking to schedule your memory usage accordingly. Oom killer shouldn't be a factor if memory is handled as a scheduler consideration. -Brian Brian Smith Sr. System Administrator Research Computing, University of South Florida 4202 E. Fowler Ave. SVC4010 Office Phone: +1 813 974-1467 Organization URL: http://rc.usf.edu On 08/29/2012 11:02 AM, Ben De Luca wrote:I was wondering, how people deal with oom conditions on there cluster. We constantly have machines that die because the oom killer takes out critical system services. Has any experiance with the oom_adj proc value, or a patch to grid to support it? /proc/[pid]/oom_adj (since Linux 2.6.11) This file can be used to adjust the score used to select which process should be killed in an out-of-memory (OOM) situation. The kernel uses this value for a bit-shift operation of the process's oom_score value: valid values are in the range -16 to +15, plus the special value -17, which disables OOM-killing altogether for this process. A positive score increases the likelihood of this process being killed by the OOM- killer; a negative score decreases the likelihood. The default value for this file is 0; a new process inherits its parent's oom_adj setting. A process must be privileged (CAP_SYS_RESOURCE) to update this file. _______________________________________________ users mailing list [email protected] https://gridengine.org/mailman/listinfo/users_______________________________________________ users mailing list [email protected] https://gridengine.org/mailman/listinfo/users_______________________________________________ users mailing list [email protected] https://gridengine.org/mailman/listinfo/users_______________________________________________ users mailing list [email protected] https://gridengine.org/mailman/listinfo/users
memkiller.sh
Description: application/shellscript
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