My unitig consensus jobs are using more memory than requested in the slurm job so the jobs are getting killed. How can I specify a larger mem size to thse cns_canu jobs running utgcns?
The jobs are getting allocated with ~800m-1gb but I think they need 10x that to run properly.
Command line:
canu -d canu2_6FC.loredac_corrected -p canu2_6FC.loredac genomeSize=900m useGrid=true gridOptions="-p batch" minReadLength=750 -corrected -nanopore 6FC.corrected_loredac.fasta.gz
Version: Canu 2.0
Linux, Linux version 3.10.0-957.el7.x86_64 (mockbuild@kbuilder.bsys.centos.org) (gcc version 4.8.5 20150623 (Red Hat 4.8.5-36) (GCC) ) #1 SMP Thu Nov 8 23:39:32 UTC 2018`
CentOS
From logfile in: unitigging/5-consensus
/opt/linux/centos/7.x/x86_64/pkgs/miniconda3/4.3.31/bin/perl
This is perl 5, version 26, subversion 2 (v5.26.2) built for x86_64-linux-thread-multi
Found java:
/opt/linux/centos/7.x/x86_64/pkgs/java/jdk1.8.0_45/bin/java
java version "1.8.0_45"
Found canu:
/bigdata/operations/pkgadmin/opt/linux/centos/7.x/x86_64/pkgs/canu/2.0/Linux-amd64/bin/canu
Canu 2.0
Running job 1 based on SLURM_ARRAY_TASK_ID=1 and offset=0.
-- Using seqFile '../canu2_6FC.loredac.ctgStore/partition.0001'.
-- Opening tigStore '../canu2_6FC.loredac.ctgStore' version 1.
-- Opening output results file './ctgcns/0001.cns.WORKING'.
--
-- Computing consensus for b=0 to e=848692 with errorRate 0.2000 (max 0.4000) and minimum overlap 40
--
Loading corrected-trimmed reads from seqFile '../canu2_6FC.loredac.ctgStore/partition.0001'
/var/spool/slurmd/job1614851/slurm_script: line 103: 37404 Killed $bin/utgcns -R ../canu2_6FC.loredac.${tag}Store/partition
.$jobid -T ../canu2_6FC.loredac.${tag}Store 1 -P $jobid -O ./${tag}cns/$jobid.cns.WORKING -maxcoverage 40 -e 0.2 -pbdagcon -edlib -threads 8
slurmstepd-c26: error: Detected 1 oom-kill event(s) in step 1614851.batch cgroup. Some of your processes may have been killed by the cgroup out-of-memory handler.
My unitig consensus jobs are using more memory than requested in the slurm job so the jobs are getting killed. How can I specify a larger mem size to thse cns_canu jobs running utgcns?
The jobs are getting allocated with ~800m-1gb but I think they need 10x that to run properly.
Command line:
canu -d canu2_6FC.loredac_corrected -p canu2_6FC.loredac genomeSize=900m useGrid=true gridOptions="-p batch" minReadLength=750 -corrected -nanopore 6FC.corrected_loredac.fasta.gzVersion:
Canu 2.0Linux, Linux version 3.10.0-957.el7.x86_64 (mockbuild@kbuilder.bsys.centos.org) (gcc version 4.8.5 20150623 (Red Hat4.8.5-36) (GCC) ) #1 SMP Thu Nov 8 23:39:32 UTC 2018`CentOS
From logfile in:
unitigging/5-consensus