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Commit ffd8667c authored by Kurt A. O'Hearn's avatar Kurt A. O'Hearn
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Testing: add script for submitting short jobs.

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test_harness/zno_6912_control → test_harness/control_zno_6912_mpi
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View file @ ffd8667c
File moved
test_harness/silica_300000_mpi_not_gpu_control deleted 100644 → 0
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simulation_name silica.300000_mpi_not_gpu ! output files will carry this name + their specific ext.
ensemble_type 1 ! 0: NVE 1: Berendsen NVT 2: Nose-Hoover NVT(under testing) 3: semi-isotropic NPT 4: isotropic NPT 5: anisotropic NPT (under development)
nsteps 100 ! number of simulation steps
dt 0.10 ! time step in fs
proc_by_dim 2 2 2 ! distribution of processors by dimensions
geo_format 0 ! 0: custom 1: pdb (only if natoms < 100000) 2: ASCII restart 3: binary restart
tabulate_long_range 0 ! number of sampling points for cubic spline interpolation, 0 no interpolation
energy_update_freq 10
remove_CoM_vel 500 ! remove the transrot vel of CoM every 'this many' steps
reposition_atoms 1 ! 1:center of mass to center of box
reneighbor 1
vlist_buffer 0
nbrhood_cutoff 4.5 ! bond cutoff in A
hbond_cutoff 0 ! hbond cutoff in A
thb_cutoff 0.001 ! cutoff value for three body interactions
qeq_freq 1 ! frequency to update charges with QEq
q_err 1e-6 ! norm of the relative residual in QEq solve
temp_init 0.01 ! initial temperature of the system
temp_final 300.0 ! final temperature of the system
t_mass 500.0 ! 0.16666 for nhNVT ! 500.0 for bNVT, iNPT, sNPT ! in fs, thermal inertia
t_rate 5.0 ! in K
t_freq 1.0 ! in ps
t_mode 2 ! 2: constant slope
pressure 0.000101325 0.000101325 0.000101325 ! desired pressure of the simulated system in GPa, 1atm = 0.000101325 GPa
p_mass 10000.00 10000.00 10000.00 ! in fs, pressure inertia parameter
write_freq 0 ! write trajectory after so many steps
traj_method 1 ! 0: simple parallel I/O, 1: MPI I/O
traj_title micelle ! (no white spaces)
atom_info 1 ! 0: no atom info, 1: print basic atom info in the trajectory file
atom_forces 0 ! 0: basic atom format, 1: print force on each atom in the trajectory file
atom_velocities 1 ! 0: basic atom format, 1: print the velocity of each atom in the trajectory file
bond_info 1 ! 0: do not print bonds, 1: print bonds in the trajectory file
angle_info 1 ! 0: do not print angles, 1: print angles in the trajectory file
restart_format 1 ! 0: restarts in ASCII 1: restarts in binary
restart_freq 10000 ! 0: do not output any restart files. >0: output a restart file at every 'this many' steps
bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs
test_harness/submit_short_jobs.bash 0 → 100755
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View file @ ffd8667c
#!/bin/bash
function submit_job_serial
{
SIM_NAME="spuremd-${4}"
qsub -l "walltime=${JOB_TIME},nodes=${JOB_NODES}:ppn=${JOB_PPN},feature=${JOB_FEATURE},mem=${JOB_MEM}" \
-o "${SIM_NAME}" -j oe << EOF
#!/bin/bash
module purge
module load GNU/6.2 MKL/11.2
cd "\${PBS_O_WORKDIR}"
../sPuReMD/bin/spuremd "${1}" "${2}" "${3}"
EOF
}
function submit_job_mpi
{
SIM_NAME="puremd-${4}"
qsub -l "walltime=${JOB_TIME},nodes=${JOB_NODES}:ppn=${JOB_PPN},feature=${JOB_FEATURE},mem=${JOB_MEM}" \
-o "${SIM_NAME}" -j oe << EOF
#!/bin/bash
module purge
module load GNU/6.2 MKL/11.2 OpenMPI/2.0.2
cd "\${PBS_O_WORKDIR}"
mpirun -np "${JOB_PPN}" "../PuReMD/bin/puremd "${1}" "${2}" "${3}"
EOF
}
function submit_job_mpi_gpu
{
SIM_NAME="pg-puremd-${4}"
qsub -l "walltime=${JOB_TIME},nodes=${JOB_NODES}:ppn=${JOB_PPN},feature=${JOB_FEATURE},mem=${JOB_MEM}" \
-o "${SIM_NAME}" -j oe << EOF
#!/bin/bash
module purge
module load GNU/6.2 MKL/11.2 OpenMPI/2.0.2 CUDA/9.0
cd "\${PBS_O_WORKDIR}"
mpirun -np "${JOB_PPN}" "../PG-PuReMD/bin/pg-puremd "${1}" "${2}" "${3}"
EOF
}
############
# Serial Runs #
############
JOB_TIME="03:59:00"
JOB_NODES="1"
JOB_PPN="1"
JOB_FEATURE="lac"
JOB_MEM="120gb"
sub_job_serial "../data/benchmarks/water/water_6540.pdb" \
"../data/benchmarks/water/ffield.water" \
"control_water_6540_serial" \
"water_6540_serial"
sub_job_serial "../data/benchmarks/silica/silica_6000.pdb" \
"../data/benchmarks/silica/ffield-bio" \
"control_silica_6000_serial" \
"silica_6000_serial"
sub_job_serial "../data/benchmarks/metal/zno_6912.pdb" \
"../data/benchmarks/metal/ffield.zno" \
"control_zno_6912_serial" \
"zno_6912_serial"
############
# MPI Runs #
############
JOB_TIME="03:59:00"
JOB_NODES="1"
JOB_PPN="2"
JOB_FEATURE="lac"
JOB_MEM="120gb"
sub_job_mpi "../data/benchmarks/water/water_6540.pdb" \
"../data/benchmarks/water/ffield.water" \
"control_water_6540_mpi" \
"water_6540_mpi"
sub_job_mpi "../data/benchmarks/silica/silica_6000.pdb" \
"../data/benchmarks/silica/ffield-bio" \
"control_silica_6000_mpi" \
"silica_6000_mpi"
sub_job_mpi "../data/benchmarks/metal/zno_6912.pdb"
"../data/benchmarks/metal/ffield.zno" \
"control_zno_6912_mpi" \
"zno_6912_mpi"
################
# MPI-GPU Runs #
################
JOB_TIME="03:59:00"
JOB_NODES="2"
JOB_PPN="1"
JOB_FEATURE="lac"
JOB_MEM="120gb"
sub_job_mpi_gpu "../data/benchmarks/water/water_6540.pdb" \
"../data/benchmarks/water/ffield.water" \
"control_water_6540_mpi_gpu" \
"water_6540_mpi_gpu"
sub_job_mpi_gpu "../data/benchmarks/silica/silica_6000.pdb" \
"../data/benchmarks/silica/ffield-bio" \
"control_silica_6000_mpi_gpu" \
"silica_6000_mpi_gpu"
sub_job_mpi_gpu "../data/benchmarks/metal/zno_6912.pdb" \
"../data/benchmarks/metal/ffield.zno"
"control_zno_6912_mpi_gpu" \
"zno_6912_mpi_gpu"
test_harness/water_327000_mpi_not_gpu_control deleted 100644 → 0
+ 0
− 44
View file @ 218cbf83
simulation_name water.327000_mpi_not_gpu ! output files will carry this name + their specific ext.
ensemble_type 1 ! 0: NVE 1: Berendsen NVT 2: Nose-Hoover NVT(under testing) 3: semi-isotropic NPT 4: isotropic NPT 5: anisotropic NPT (under development)
nsteps 100 ! number of simulation steps
dt 0.10 ! time step in fs
proc_by_dim 2 2 2 ! distribution of processors by dimensions
geo_format 0 ! 0: custom 1: pdb (only if natoms < 100000) 2: ASCII restart 3: binary restart
tabulate_long_range 0 ! number of sampling points for cubic spline interpolation, 0 no interpolation
energy_update_freq 10
remove_CoM_vel 500 ! remove the transrot vel of CoM every 'this many' steps
reposition_atoms 1 ! 1:center of mass to center of box
reneighbor 1
vlist_buffer 0
nbrhood_cutoff 4.5 ! bond cutoff in A
hbond_cutoff 7.5 ! hbond cutoff in A
thb_cutoff 0.001 ! cutoff value for three body interactions
qeq_freq 1 ! frequency to update charges with QEq
q_err 1e-6 ! norm of the relative residual in QEq solve
temp_init 0.01 ! initial temperature of the system
temp_final 300.0 ! final temperature of the system
t_mass 500.0 ! 0.16666 for nhNVT ! 500.0 for bNVT, iNPT, sNPT ! in fs, thermal inertia
t_rate 5.0 ! in K
t_freq 1.0 ! in ps
t_mode 2 ! 2: constant slope
pressure 0.000101325 0.000101325 0.000101325 ! desired pressure of the simulated system in GPa, 1atm = 0.000101325 GPa
p_mass 10000.00 10000.00 10000.00 ! in fs, pressure inertia parameter
write_freq 0 ! write trajectory after so many steps
traj_method 1 ! 0: simple parallel I/O, 1: MPI I/O
traj_title micelle ! (no white spaces)
atom_info 1 ! 0: no atom info, 1: print basic atom info in the trajectory file
atom_forces 0 ! 0: basic atom format, 1: print force on each atom in the trajectory file
atom_velocities 1 ! 0: basic atom format, 1: print the velocity of each atom in the trajectory file
bond_info 1 ! 0: do not print bonds, 1: print bonds in the trajectory file
angle_info 1 ! 0: do not print angles, 1: print angles in the trajectory file
restart_format 1 ! 0: restarts in ASCII 1: restarts in binary
restart_freq 10000 ! 0: do not output any restart files. >0: output a restart file at every 'this many' steps
bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs
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