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Refs #36 gpu namd for Titan
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@VickieLynch
VickieLynch committed Jan 2, 2014
1 parent 866ff16 commit 7939c7e
Showing 1 changed file with 30 additions and 57 deletions.
87 changes: 30 additions & 57 deletions simulation/namd_titan.pbs
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Original file line number Diff line number Diff line change
Expand Up @@ -2,13 +2,10 @@
#PBS -A MAT049
#PBS -N namdTest
#PBS -j oe
#PBS -l walltime=6:00:00,nodes=126
#PBS -l walltime=2:00:00,nodes=3
#PBS -l gres=widow2%widow3

MPIRUN="aprun -n 504"
NAMD=/sw/xk6/namd/2.8/cle4.0_gnu4.5.3/CRAY-XT-g++/namd2

cd /tmp/work/vel/camm
cd $PBS_O_WORKDIR

#Eq config file
cat > equilibrate.conf <<'@EQEOF'
Expand All @@ -23,7 +20,7 @@ cat > equilibrate.conf <<'@EQEOF'
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
set temperature 290 ;# initial temperature, in Kelvin
set temperature TEMP ;# initial temperature, in Kelvin
set charge 42 ;# hydrogen charge
set pressure 1.01325 ;# in bar -> 1 atm
set inputname init ;# prefix for input files
Expand Down Expand Up @@ -88,7 +85,7 @@ langevinDamping 1.0 ;# damping coefficient (gamma) of 1/ps
langevinHydrogen off ;# don't couple langevin bath to hydrogens
# Control parameters for annealing
#reassignFreq 3000 ;# number of timesteps between temperature reassignment
#reassignTemp 290 ;# new temperature when reassignment happens
#reassignTemp TEMP ;# new temperature when reassignment happens
#reassignIncr -1.0 ;# temperature increment when reassignment happens
#reassignHold 10.0 ;# target or limit temperature
Expand Down Expand Up @@ -133,7 +130,7 @@ run 500000 ;# 500ps
@EQEOF

#Production config file
cat > production.conf <<'@PRODEOF'
cat > production_single.conf <<'@PRODEOF'
#############################################################
## JOB DESCRIPTION ##
#############################################################
Expand All @@ -145,7 +142,7 @@ cat > production.conf <<'@PRODEOF'
#############################################################
## ADJUSTABLE PARAMETERS ##
#############################################################
set temperature 290 ;# initial temperature, in Kelvin
set temperature TEMP ;# initial temperature, in Kelvin
set charge 42 ;# hydrogen charge
set pressure 1.01325 ;# in bar -> 1 atm
set inputname production00 ;# prefix for input files
Expand Down Expand Up @@ -210,7 +207,7 @@ langevinDamping 1.0 ;# damping coefficient (gamma) of 1/ps
langevinHydrogen off ;# don't couple langevin bath to hydrogens
# Control parameters for annealing
#reassignFreq 3000 ;# number of timesteps between temperature reassignment
#reassignTemp 290 ;# new temperature when reassignment happens
#reassignTemp TEMP ;# new temperature when reassignment happens
#reassignIncr -1.0 ;# temperature increment when reassignment happens
#reassignHold 10.0 ;# target or limit temperature
Expand Down Expand Up @@ -251,58 +248,34 @@ outputTiming 1000
#minimize 1000 ;# perform 1000 minimization steps
firsttimestep 0 ;# reset frame counter
run 4000000 ;# 4ns
run 3000000 ;# 4ns
@PRODEOF
mkdir -p center/toppar
mkdir -p backward/toppar
mkdir -p forward/toppar
mv Q42_*b.psf backward/toppar/Q42.psf
mv Q42_*f.psf forward/toppar/Q42.psf
mv Q42_*.psf center/toppar/Q42.psf
cd center
#equilibrium run
cp /tmp/work/vel/camm/toppar/crd.md18_vmd_autopsf.pdb toppar
cp /tmp/work/vel/camm/toppar/par_all27_prot_lipid.inp toppar
cp /tmp/work/vel/camm/init.xsc .
cp ../equilibrate.conf .
cp ../production.conf .
$MPIRUN $NAMD equilibrate.conf > equilibrate.log &
cd ../backward
sed -i -e 's/TEMP/'"$TEMP"'/g' equilibrate.conf
sed -i -e 's/TEMP/'"$TEMP"'/g' production_single.conf
mkdir -p toppar
mv Q42_*.psf toppar/Q42.psf
#equilibrium run
cp /tmp/work/vel/camm/toppar/crd.md18_vmd_autopsf.pdb toppar
cp /tmp/work/vel/camm/toppar/par_all27_prot_lipid.inp toppar
cp /tmp/work/vel/camm/init.xsc .
cp ../equilibrate.conf .
cp ../production.conf .
$MPIRUN $NAMD equilibrate.conf > equilibrate.log &
cd ../forward
#equilibrium run
cp /tmp/work/vel/camm/toppar/crd.md18_vmd_autopsf.pdb toppar
cp /tmp/work/vel/camm/toppar/par_all27_prot_lipid.inp toppar
cp /tmp/work/vel/camm/init.xsc .
cp ../equilibrate.conf .
cp ../production.conf .
$MPIRUN $NAMD equilibrate.conf > equilibrate.log &
cp /tmp/work/vel/camm/crd.md18_vmd_autopsf.pdb toppar
cp /tmp/work/vel/camm/par_all27_prot_lipid.inp toppar
cp /tmp/work/vel/camm/equilibrate/init.xsc .
source /opt/modules/3.2.6.6/init/tcsh
module swap PrgEnv-pgi PrgEnv-gnu
module load craype-hugepages8M
module list

wait
setenv HUGETLB_DEFAULT_PAGE_SIZE 8M
setenv HUGETLB_MORECORE no

echo PBS opts: walltime=02:00:00,nodes=3
echo aprun opts: -n 3 -N 1 -d 8 -r 1
echo NAMD opts: +ppn 7 +pemap 2-14:2 +commap 0
echo conf file: production_single.conf
echo log file: production_single.log

aprun -n 3 -N 1 -d 8 -r 1 /lustre/atlas1/bio024/world-shared/NAMD_binaries/titan/NAMD_build_2013-Sep-27-64875/NAMD_2.9_CRAY-XT-ugni-smp-Titan-CUDA/namd2 +ppn 7 +pemap 2-14:2 +commap 0 equilibrate.conf >& equilibrate.log

cd ../center
#production run
mv equilibrate.restart.coor production00.restart.coor
mv equilibrate.restart.vel production00.restart.vel
mv equilibrate.restart.xsc production00.restart.xsc
$MPIRUN $NAMD production.conf > production.log &
cd ../backward
#production run
mv equilibrate.restart.coor production00.restart.coor
mv equilibrate.restart.vel production00.restart.vel
mv equilibrate.restart.xsc production00.restart.xsc
$MPIRUN $NAMD production.conf > production.log &
cd ../forward
#production run
mv equilibrate.restart.coor production00.restart.coor
mv equilibrate.restart.vel production00.restart.vel
mv equilibrate.restart.xsc production00.restart.xsc
$MPIRUN $NAMD production.conf > production.log &

wait
aprun -n 3 -N 1 -d 8 -r 1 /lustre/atlas1/bio024/world-shared/NAMD_binaries/titan/NAMD_build_2013-Sep-27-64875/NAMD_2.9_CRAY-XT-ugni-smp-Titan-CUDA/namd2 +ppn 7 +pemap 2-14:2 +commap 0 production_single.conf >& production_single.log

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