Hi Matei, Oh my old friend Œh_vmem¹. Do your jobs actually run at all or does SGE kill them straight away? I long time ago I had problems with h_vmem and multi-threaded jobs that I gave up on it. As a test I¹d run a job without h_vmem set and then monitor the actual vmem usage with qstat -j. If the vmem is genuinely around ~20G or below then it¹s an h_vmem problem otherwise it may be a problem with samtools. Cheers,
Chris On 16/01/2015 17:35, "Matei David" <ma...@cs.toronto.edu> wrote: >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 The University of Dundee is a registered Scottish Charity, No: SC015096 ------------------------------------------------------------------------------ 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
