====== Working on binf nodes ======
For availabe bioinformatics nodes, see [[doku:binf_nodes|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