diff --git a/simulation/namd_titan.pbs b/simulation/namd_titan.pbs index 1df6954..5379c86 100644 --- a/simulation/namd_titan.pbs +++ b/simulation/namd_titan.pbs @@ -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' @@ -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 @@ -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 @@ -133,7 +130,7 @@ run 500000 ;# 500ps @EQEOF #Production config file -cat > production.conf <<'@PRODEOF' +cat > production_single.conf <<'@PRODEOF' ############################################################# ## JOB DESCRIPTION ## ############################################################# @@ -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 @@ -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 @@ -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