Using ramdaq on the NIG Supercomputer System

December 4, 2020 · View on GitHub

NIG Supercomputer System is the supercomputer system hosted by the National Institute of Genetics, Japan. On the NIG Supercomputer System, users can use Singularity(Usage in Japanese) and Univa Grid Engine (UGE) (Usage in Japanese)

In this document, we offer the following instructions:

  1. How to install nextflow on NIG Supercomputer System
  2. How to run ramdaq on NIG Supercomputer System
    1. Run ramdaq on a node
    2. Run ramdaq using Univa Grid Engine (UGE)

1. Install nextflow on NIG Supercomputer System

1. qlogin

qlogin -l s_vmem=20G -l mem_req=20G

2. Type this for Java use

export _JAVA_OPTIONS="-XX:ParallelGCThreads=1 -Xmx1g"

3. Check Java version (OK if version number isZ "1.8.y_z" or "8")

java -version

4. Install nextflow

curl -s https://get.nextflow.io | bash

5. Test nextflow

./nextflow run hello

6. Add the file path of nextflow to $PATH

2-1. Run ramdaq on a node

1. Login to a node by qlogin

qlogin -l s_vmem=20G -l mem_req=20G

2. Type this for Java use

export _JAVA_OPTIONS="-XX:ParallelGCThreads=1 -Xmx1g"

3. Run ramdaq (Below command run ramdaq on the test data)

nextflow run rikenbit/ramdaq -profile test,singularity

2-2. Run ramdaq by Univa Grid Engine (UGE)

1. Prepare a job script (See the example below)

#!/bin/bash
#$ -S /bin/bash
#$ -l s_vmem=20G -l mem_req=20G
#$ -cwd

export _JAVA_OPTIONS="-XX:ParallelGCThreads=1 -Xmx1g"

nextflow run rikenbit/ramdaq -profile test,singularity

2. Submit a job by qsub command

qsub -pe def_slot 4 -l short qsub_test.sh

Note: We empirically recommend to set the number of threads (cores) to be at least max_cpus + 1 when running ramdaq via UGE.

For example, the test config set max_cpus = 2 and we add the option -pe def_slot 3 on qsub.

References

Acknowlegements