Re: [wgs-assembler-users] Configuration SGE

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@Ludovic. virtual_free and h_vmem are mandatory to work in our cluster. 
Thanks for the answer.

@Brian. I increased these values because my batch of fastq files has 
around 40Gb so I thought I had to use (following the ovlHashBits table 
from here <http://wgs-assembler.sourceforge.net/wiki/index.php/RunCA>, 
if I want to use 2 threads on sge):

ovlHashBits         = 27
ovlHashBlockLength = 260000000
ovlRefBlockSize     = 7630000
ovlThreads          = 2
sge = -pe thread 2 -l h_vmem=50G

Instead this, it works better if I decrease the ovlHasBits & 
ovlHashBlockLength values and increase the ovlRefBlockSize & ovlThreads 
values?:

ovlHashBits         = 25
ovlHashBlockLength = 240000000
ovlRefBlockSize     = 18000000
ovlThreads          = 6
sge = -pe thread 2 -l h_vmem=50G

Thanks for your help,

Miquel

On 2015?01?20? 00:29, Brian Walenz wrote:
> I've never seen large overlap jobs perform better than small jobs.  
> Target an 8gb job with ~4 CPUs each.  My default configuration is:
>
> ovlHashBits         = 22
> ovlHashBlockLength  = 200000000
> ovlRefBlockSize     = 18000000
> ovlThreads          = 6
>
> The two 'hash' sizes control how big the job is.  The 'ref block size' 
> controls how many reads are processed by each job, i.e., how long the 
> job runs.
>
> b
>
>
> On Mon, Jan 19, 2015 at 5:10 AM, Ludovic Mallet 
> <lud...@un... 
> <mailto:lud...@un...>> wrote:
>
>     Hi,
>     Not the best expert, but to me, virtual_free allow the job to swap,
>     which you should try to avoid.
>     and I think h_vmem is the hard limit, so the job would be killed
>     whenever the line is crossed.
>
>     from http://gridengine.eu/grid-engine-internals
>     "hard limitation: All processes of the job combined are limited
>     from the
>     Linux kernel that they are able to use only the requested amount of
>     memory. Further malloc() calls will fail."
>
>     whether h_vmem is hard by default if GE has to be checked again,
>     but I'd
>     rather use mem_free instead
>
>     Best,
>     ludovic
>
>     On 19/01/15 02:22, Miguel Grau wrote:
>     > Dear all,
>     >
>     > I am having some troubles to config wgs 8.2 assembler with SGE
>     options.
>     > I always get a malloc memory error and I am not sure why. I am
>     working
>     > with 3 paired fastq files (6 files in total) with 100b length
>     reads (15
>     > million reads in each fastq file). My config file:
>     >
>     > useGrid          = 1
>     > scriptOnGrid     = 1
>     >
>     > sge                   = -A assembly
>     > sgeMerTrim            = -l h_vmem=150G -l virtual_free=150G
>     > sgeScript             = -l h_vmem=50G -l virtual_free=50G
>     > sgeOverlap            =  -l h_vmem=100G -l virtual_free=100G
>     > sgeMerOverlapSeed     = -l h_vmem=100G -l virtual_free=100G
>     > sgeMerOverlapExtend   = -l h_vmem=100G -l virtual_free=100G
>     > sgeConsensus          = -l h_vmem=100G -l virtual_free=100G
>     > sgeFragmentCorrection = -l h_vmem=100G -l virtual_free=100G
>     > sgeOverlapCorrection  = -l h_vmem=100G -l virtual_free=100G
>     >
>     > overlapper     = ovl #Best for illumina
>     > unitigger        = bogart  #Best for illumina
>     >
>     > #For 50GB...
>     > ovlHashBits        = 28
>     > ovlHashBlockLength = 480000000
>     > #100Gb for overlap
>     > ovlStoreMemory=102400
>     >
>     > ovlThreads     = 2
>     > ovlRefBlockSize  = 7630000
>     > frgCorrBatchSize = 1000000
>     > frgCorrThreads   = 8
>     >
>     > The error that I have now is:
>     >
>     >
>     ------------------------------------------------------------------------------
>     > bucketizing /reads/a6/0-overlaptrim-overlap/001/000278.ovb.gz
>     > bucketizing /reads/a6/0-overlaptrim-overlap/001/000276.ovb.gz
>     > bucketizing /reads/a6/0-overlaptrim-overlap/001/000275.ovb.gz
>     > bucketizing /reads/a6/0-overlaptrim-overlap/001/000280.ovb.gz
>     > bucketizing DONE!
>     > overlaps skipped:
>     >         1211882406 OBT - low quality
>     >                  0 DUP - non-duplicate overlap
>     >                  0 DUP - different library
>     >                  0 DUP - dedup not requested
>     > terminate called after throwing an instance of 'std::bad_alloc'
>     >     what():  std::bad_alloc
>     >
>     > Failed with 'Aborted'
>     >
>     > Backtrace (mangled):
>     >
>     >
>     /miquel/wgs-8.2/Linux-amd64/bin/overlapStoreBuild(_Z17AS_UTL_catchCrashiP7siginfoPv+0x27)[0x40a697]
>     > /lib64/libpthread.so.0[0x3ff1c0f710]
>     > /lib64/libc.so.6(gsignal+0x35)[0x3ff1432925]
>     > /lib64/libc.so.6(abort+0x175)[0x3ff1434105]
>     > ....
>     >
>     ----------------------------------------------------------------------------------
>     >
>     > Some idea for the best config?
>     >
>     > Thank you,
>     >
>     >
>     > Miguel
>     >
>     >
>     >
>     >
>     >
>     >
>     >
>     ------------------------------------------------------------------------------
>     > 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
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>
>
>     ------------------------------------------------------------------------------
>     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
>     _______________________________________________
>     wgs-assembler-users mailing list
>     wgs...@li...
>     <mailto:wgs...@li...>
>     https://lists.sourceforge.net/lists/listinfo/wgs-assembler-users
>
>
>
>
> ------------------------------------------------------------------------------
> 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
>
>
> _______________________________________________
> wgs-assembler-users mailing list
> wgs...@li...
> https://lists.sourceforge.net/lists/listinfo/wgs-assembler-users