> From: Michael Stauffer <[email protected]> > Date: Tuesday, 24 February 2015 17:04 > To: "[email protected]" <[email protected]> > Subject: Re: [gridengine users] Memory errors even after setting >h_vmem (Simon Andrews)
> You might also check how much vmem vs. res. mem the jobs/applications >are requesting. I found that some > applications (Matlab, I'm looking at you!!!) request MUCH for vmem than >actual res. mem they use. We use > CentOS 6. So my h_vmem defaults and limits are a lot higher than what's actually used. The main offender > seems to be the java engine matlab and some other apps use, it allocs >way too much vmdm. We've also seen problems with jvms setting up large numbers of threads and consuming too much memory when run on nodes with a lot of resources, in our case we've worked round this by changing the memory settings on launch (specifically setting -XX:+UseG1GC -XX:ParallelGCThreads=2") helped a lot. The applications which are triggering the problems this time around are R and a C program (bowtie), and in both cases it's the allocation of a large array (~2GB which causes the issue, even when we're giving it hundreds of gigs of h_vmem). Simon. The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT Registered Charity No. 1053902. The information transmitted in this email is directed only to the addressee. If you received this in error, please contact the sender and delete this email from your system. The contents of this e-mail are the views of the sender and do not necessarily represent the views of the Babraham Institute. Full conditions at: www.babraham.ac.uk<http://www.babraham.ac.uk/terms> _______________________________________________ users mailing list [email protected] https://gridengine.org/mailman/listinfo/users
