Hi, I'm using samtools 1.0, and I'm seeing a process started with "samtools sort -@ 4 -m 5G ..." reach VSZ 30441316 (and get killed by SGE or the kernel because of reaching ulimit). 4 threads x 5G should be 20G at most, right?
The samtools sort documentation mentions that "-m" is "approximately" max mem per thread. I'm not sure what to make of that, is there a range we could expect? In my case, the approximation seems to be quite far off: 30/4 = 7.5, which is 150% of what I specified as max. If that might matter, the reads I'm dealing with are quite big (>4Kbp average length), could that be causing problems with RAM usage estimation? What h_vmem would should I ask for to safely sort with "-@ 4 -m 5G"? Thanks, Matei ------------------------------------------------------------------------------ New Year. New Location. New Benefits. New Data Center in Ashburn, VA. GigeNET is offering a free month of service with a new server in Ashburn. Choose from 2 high performing configs, both with 100TB of bandwidth. Higher redundancy.Lower latency.Increased capacity.Completely compliant. http://p.sf.net/sfu/gigenet _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
