User Tools

Site Tools


doku:bioinf_nodes

Working on binf nodes

For availabe bioinformatics nodes, see High performance parallel storage + large memory nodes

Interactive mode

1. VSC-3 >  salloc -N 1 -p binf --qos normal_binf -C binf -L intel@vsc
            (... add   --nodelist binf-13   to request a specific node) 

2. VSC-3 >  squeue -u $USER

3. VSC-3 >  srun -n 4 hostname   (... while still on the login node !)

4. VSC-3 >  ssh binf-11  (... or whatever else node had been assigned)

5. VSC-3 >  module purge

6. VSC-3 >  module load intel/17 
            cd examples/09_special_hardware/binf
            icc -xHost -qopenmp sample.c
            export OMP_NUM_THREADS=8
            ./a.out

Working on binf nodes cont.

SLURM submission slrm.sbmt.scrpt

#!/bin/bash
#
#  usage: sbatch ./slrm.sbmt.scrpt          
#
#SBATCH -J gmxbinfs    
#SBATCH -N 2
#SBATCH --partition binf        
#SBATCH --qos normal_binf         
#SBATCH -C binf        
#SBATCH --ntasks-per-node 24
#SBATCH --ntasks-per-core 1
 
module purge
module load intel/17  intel-mkl/2017  intel-mpi/2017  gromacs/5.1.4_binf
 
export I_MPI_PIN=1
export I_MPI_PIN_PROCESSOR_LIST=0-23
export I_MPI_FABRICS=shm:tmi          
export I_MPI_TMI_PROVIDER=psm2        
export OMP_NUM_THREADS=1      
export MDRUN_ARGS=" -dd 0 0 0 -rdd 0 -rcon 0 -dlb yes -dds 0.8  -tunepme -v -nsteps 10000 " 
 
mpirun -np $SLURM_NTASKS gmx_mpi mdrun ${MDRUN_ARGS}  -s hSERT_5HT_PROD.0.tpr  -deffnm hSERT_5HT_PROD.0  -px hSERT_5HT_PROD.0_px.xvg  -pf hSERT_5HT_PROD.0_pf.xvg  -swap hSERT_5HT_PROD.0.xvg
doku/bioinf_nodes.txt · Last modified: 2021/05/14 18:40 by goldenberg