hpc-cardio.md

UCS

• https://www.hpc.cam.ac.uk/

• Environment modules

• SLURM usage

• Bright Cluster Management

• VPN (Virtual Private Network)

• https://github.com/jinghuazhao/Computational-Statistics/blob/master/PARALLEL.md

Cardio

• /scratch/public_databases/SOMALOGIC/LatestVersion/
• http://www.internationalgenome.org/faq/what-strand-are-variants-your-vcf-file/
• /scratch/public_databases/phenoscanner/V2

Additional notes

function notes()
{
  #http://portal.hpcwales.co.uk/wordpress/index.php/index/slurm/interactive-use-job-arrays/batch-submission-of-serial-jobs-for-parallel-execution/
  #SBATCH --nodes=3
  #SBATCH --ntasks-per-node=3
  #SBATCH --cpus-per-task=4
  export array=$HOME/SomaLogic/format.subs
  declare -a cohorts=(FHS KORA Malmo QMDiab)
  for s in $(seq 1 ${#cohorts[@]}); do
    export study=${cohorts[$(( $s-1 ))]}
    export joblist=`squeue -u $USER --noheader -o "%i" | sed -n '1h;2,$H;${g;s/\n/:/g;p}'`
    echo $study
    export TMPDIR=/scratch/jhz22/SomaLogic/sumstats/$study
    if [ $s -eq 1 ]
    then
       id=$(sbatch -p long -J $study -a 1-10 -e $study.e -o $study.o -D $PWD --export=ALL $array $study)
    else
  #    sbatch -p long -a 1-10 -e $study.e -o $study.o -D $PWD --export=ALL -d after:$joblist $array
       id=$(sbatch -p long -J $study -a 1-10 -e $study.e -o $study.o -D $PWD --export=ALL -d afterany:$id $array $study)
    fi
  done
}

#!/bin/bash
# 17-12-2018 JHZ

export rt=$HOME/SomaLogic
cd $rt
cat $rt/doc/SomaLogic.list | \
parallel --env rt -j1 -C' ' '
   echo {}; \
   export protein={}; \
   cd $rt/work; \
   if [ ! -d {} ]; then mkdir {}; fi; \
   cd -; \
   R --no-save -q < $rt/QCGWAS.R > $rt/work/{}.log'

function single_protein_as_argument()
{
# mkdir
declare -a prot=(10336-3_3 10337-83_3)
for s in $(seq 1 ${#prot[@]}); do
    export protein=${prot[$(( $s-1 ))]}
    if [ ! -d work/$protein ]; then mkdir $rt/work/$protein; fi
done
# QCGWAS
export protein=$1
R --no-save -q < QCGWAS.R > $rt/work/$protein.log
}