Location of materials

/ptmp/containers-workshop-october-2021

Create your directory in /ptmp

mkdir -p /ptmp/$USER


OpenMPI - Prime

module load gcc/7.3.0-xegsmw4 openmpi
module load singularity

mpirun -np $SLURM_NTASKS ./prime_mpi

mpirun -np $SLURM_NTASKS singularity exec openmpi_4.0.2.sif ./prime_mpi


Singularity PULL

export SINGULARITY_TMPDIR=$TMPDIR
export SINGULARITY_CACHEDIR=$TMPDIR

singularity pull docker://gcc:8.3.0

Singularity EXEC

which gcc; gcc --version

singularity exec gcc_8.3.0.sif gcc --version

Singularity + MPI

export SINGULARITY_BIND=/ptmp,$TMPDIR
module load gcc/7.3.0-xegsmw4 openmpi

mpirun -np $SLURM_NTASKS singularity exec openmpi_4.0.2.sif ./hello_mpi

DEMO

salloc -N1 -n4 -t30                     # Allocate a regular compute node
salloc -N1 -n4 -pgpu --gres=gpu:1 -t30  # Allocate a GPU node




GCC

singularity exec -B /ptmp gcc 8.3.0 sif gcc hello.c -o hello

TENSORFLOW

singularity exec -B /ptmp tensorflow_2.1.0-gpu.sif python tf-test.py # No GPU

singularity exec --nv -B /ptmp tensorflow_2.1.0-gpu.sif python tf-test.py # With GPU

HISAT2

cp -r /ptmp/containers-workshop-october-2021/hisat2 .
cd hisat2
mkdir HS_out
module load parallel
module load singularity

singularity exec -B /ptmp hisat2_2.2.1.sif hisat2-build Arabidopsis_thaliana.TAIR10.dna.chromosome.1.fa At_chr1

parallel -j 4 "singularity exec -B /ptmp hisat2_2.2.1.sif hisat2 -p 4 -x At_chr1 -1 {1} -2 {2} -S HS_out/{1/.}.sam >& HS_out/{1/.}.log" ::: samples/*_1.* :::+ samples/*_2.*