def get_interface_timings(npart, domain, box, mixing, np, nn, ts, diff,
accuracy):
diff = diff
mixing = mixing
grids = get_grid_sizes(npart, domain, box)
timings = []
for (cutoff_idx, P_idx, grid_idx,
ewald_error) in get_interface_points(npart, domain, box):
# extract parameters
cutoff = Config.cutoff_values[cutoff_idx]
P = Config.order_values[P_idx]
grid = grids[grid_idx]
ewald = ewald_error[0][0]
# load data
output_dir = Config.get_test_timings_dir(Config.test)
fp = os.path.join(
output_dir, "Output-%s-%s-%.2f-%.2f-%d-%dx%dx%d" %
(diff, mixing, ewald, cutoff, P, grid[0], grid[1], grid[2]))
#t = extract_timings_from_log_full( fp ) # tuple (total, real, kspace)
t = extract_timings_from_log(fp) # tuple (total, real, kspace)
# store
timings.append((t, (cutoff_idx, P_idx, grid_idx, ewald_error)))
#print timings[-1]
return timings
def run_interface_timings(npart, domain, box, mixing, np, nn, ts, diffmode,
accuracy):
grids = get_grid_sizes(npart, domain, box)
nprocs = np
#Config.create_dir( timings_dir )
timings_dir = Config.get_test_timings_dir(Config.test)
Config.create_dir(timings_dir)
# LSF Job submission
lsf_config = JobScript.LSF_Config()
lsf_config.group = "aices"
lsf_config.jobname = "PPPM-Timings"
#lsf_config.time = "%d:00" % (min(120, 2.5*np))
lsf_config.time = "2:00"
lsf_config.memory = "1000"
lsf_config.nthreads = np
lsf_config.parallelism_type = "openmpi"
lsf_config.arch_string = "Harpertown"
# Command
lsf_config.command = []
# Lammps Config
lmp_config = PPPMUtilities.LammpsPPPMConfig()
lmp_config.npart = npart
lmp_config.timesteps = ts
lmp_config.mixing = mixing
lmp_config.diff = diffmode
for (cutoff_idx, P_idx, grid_idx,
ewald_error) in get_interface_points(npart, domain, box):
lmp_config.ewald = ewald_error[0][0]
lmp_config.cutoff = Config.cutoff_values[cutoff_idx]
lmp_config.order = Config.order_values[P_idx]
lmp_config.grid = grids[grid_idx]
print lmp_config.ewald
print lmp_config.cutoff, "(", cutoff_idx, ")"
print lmp_config.order, "(", P_idx, ")"
print lmp_config.grid, "(", grid_idx, ")"
lmp_infile = os.path.join(
timings_dir, "Lammps-%s-%s-%.2f-%.2f-%d-%dx%dx%d" %
(lmp_config.diff, lmp_config.mixing, lmp_config.ewald,
lmp_config.cutoff, lmp_config.order, lmp_config.grid[0],
lmp_config.grid[1], lmp_config.grid[2]))
lmp_config.write_config_file(lmp_infile)
# LSF
outputfile = os.path.join(
timings_dir, "Output-%s-%s-%.2f-%.2f-%d-%dx%dx%d" %
(lmp_config.diff, lmp_config.mixing, lmp_config.ewald,
lmp_config.cutoff, lmp_config.order, lmp_config.grid[0],
lmp_config.grid[1], lmp_config.grid[2]))
lsf_config.command.append(
textwrap.dedent("""
export OMP_NUM_THREADS=1
mpirun -np %d $HOME/MD-libs/lammps-22Jan14/src/lmp_openmpi -l /dev/null < %s > %s
""" % (np, lmp_infile, outputfile)))
# Script
lsf_config.command = "\n".join(lsf_config.command)
jobscript = os.path.join(timings_dir, "Jobscript-Interface")
lsf_config.write_jobscript(jobscript)
print "Submitting job (Interface timing)... ",
subprocess.check_call("bsub < %s" % jobscript, shell=True)
print "Done"