- Dataset: 6n4o
- Software: NAMD2.cuda (namd-multicore/2.14-iimklc-2020a-avx2)
- Resource: 1 tasks, 24 cores, nodes, 3 GPUs, with NVLink
- CPU: Xeon Silver 4216 (Cascade Lake), 2.1 GHz
- GPU: Tesla-V100-SXM2-32GB, 8 cores/GPU
- Simulation speed: 8.09934 ns/day
- Efficiency: 60.0 %
- Site: Cedar
- Date: Jan. 30, 2022, 9:14 p.m.
- Submission script:
#!/bin/bash
#SBATCH -c24--gpus=v100l:3
#SBATCH --mem-per-cpu=2000 --time=1:0:0
# Usage: sbatch $0 number_of_steps
INPFILE=namd.in
STEPS=$1
TMPFILE=tf_${SLURM_JOBID}
RUN_IN=run_${SLURM_JOBID}.in
cp ${INPFILE} ${RUN_IN}
echo numsteps $1 >> run_${SLURM_JOBID}.in
module load StdEnv/2020 intel/2020.1.217 cuda/11.0 namd-multicore/2.14
echo ${SLURM_NODELIST} running on ${SLURM_CPUS_PER_TASK} cores
cat /proc/cpuinfo | grep "model name" | uniq
namd2 +p${SLURM_CPUS_PER_TASK} +idlepoll ${RUN_IN} > ${TMPFILE}
- Notes:
#!/bin/bash
echo "Usage: sh cal_speed.sh output_filename nsteps"
grep CPUTime $1 | cut -f5 -d " " | awk -v steps=$2 '{ print 3.6*2.4*steps*0.01/$1}'
- Simulation input file:
# Amber/(t,s,x)leap generated parm and crd file
parmfile prmtop.parm7
ambercoor inpcrd.rst7
# Input
bincoordinates equilibration.coor
binvelocities equilibration.vel
extendedsystem equilibration.xsc
# Output
restartfreq 10000
dcdfreq 10000
outputEnergies 10000
outputPressure 10000
outputname equilibration
# Number of steps
# numsteps 10000
# AMBER Force Field settings
amber on
rigidBonds all
useSettle on
rigidTolerance 1.0e-8
cutoff 9.0
pairlistdist 11.0
switching off
exclude scaled1-4
readexclusions yes
1-4scaling 0.83333333
scnb 2.0
zeromomentum on
ljcorrection on
# Integrator Parameters
timestep 1.0
nonbondedFreq 1
fullElectFrequency 1
stepspercycle 10
wrapAll on
# Temperature control
langevin on
langevinTemp 300
langevinDamping 1.0
# Pressure control
useGroupPressure yes
LangevinPiston on
LangevinPistonTarget 1.0
LangevinPistonPeriod 200
LangevinPistonDecay 100
LangevinPistonTemp 300
# PME settings
PME on
PMEGridSizeX 144
PMEGridSizeY 144
PMEGridSizeZ 144