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richelbilderbeek / Cer2016

Community Ecology Research course 2016
GNU General Public License v3.0
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collect_n_taxa needs more memory #95

Closed richelbilderbeek closed 8 years ago

richelbilderbeek commented 8 years ago 
p230198@pg-login:scripts cat collect_n_taxa.log
slurmstepd: Unable to create TMPDIR [/local/7191591]: Permission denied
slurmstepd: Setting TMPDIR to /tmp

The following have been reloaded with a version change:
  1) cURL/7.47.0-foss-2016a => cURL/7.49.1-foss-2016a
  2) expat/2.1.0-foss-2016a => expat/2.2.0-foss-2016a
  3) gettext/0.19.7-foss-2016a => gettext/0.19.6-foss-2016a
  4) libxml2/2.9.3-foss-2016a => libxml2/2.9.4-foss-2016a

/var/spool/slurmd/job7191760/slurm_script: line 10: 101463 Killed                  Rscript collect_n_taxa.R

real    0m55.454s
user    0m48.650s
sys 0m6.431s
slurmstepd: Exceeded step memory limit at some point.
p230198@pg-login:scripts cat collect_n_taxa.sh
#!/bin/bash
#SBATCH --time=1:00:00
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --ntasks=1
#SBATCH --mem=1G
#SBATCH --job-name=collect_n_taxa
#SBATCH --output=collect_n_taxa.log
module load R/3.3.1-foss-2016a
time Rscript collect_n_taxa.R

Change this from 1G to 10G

richelbilderbeek commented 8 years ago 
cat collected_n_taxa.csv | less

resulted in a CSV without NAs, so 10G appeared to be enough.