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batch_compile_screen_networks.py
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batch_compile_screen_networks.py
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# Use this to compile a load of simulations to run on the cluster. Enter the
# parameters desired at the top.
# The files are compiled into [timestamp]/SimName0/MPIFilament
# Output to be placed in [timestamp]/SimNamo0/output/
#
# No need to run anything else before running this file. It does it all.
#
# -- sfs14/akt12 31/05/2019
import os
import sys
import fileinput
import subprocess
import datetime
# Defaults
StepsPerPeriod = 0
RandomMessNumNetworkFilaments = [1]
Nsw = [1]
TimeSteps = 0
Kap_NetworkFilaments = [1]
plot_steps = 0
StepsPerSettlingTime = 0
Bnumber = [1]
Barrier_FS_over_2a = [15*3.14159265358979]
Barrier_distance_cap = 2.0
WeightPerLength = [[0, 0, 0]]
SpermCurvatureDecay = False
SaveExtendedSwimmerData = False
randSeed = [2]
TOL = 1.e-6
# Disabled
NetworkSpringConstantFactor = [0] # k in the spring force k(x-L)
NetworkSpringNaturalLength = 0 # L in the spring force k(x-L)
NetworkSpringConnectionRadius = [0] # Look this far away from end of filament to create a link with another filament end
ProbabilityOfCreatingANetworkSpringLink = 0 # Form a spring link with this probability
EnableSpringLinks = False
ConnectedNodesNumSwimmingFilaments = 0
ConnectedNodesNumNodes = 1
ConnectedNodesConnectionRadius = 0
ConnectedNodesMinNodeSpacing = 0
ConnectedNodesSpacingAwayFromNode = 0
# Set config data here
#NPTS = [[384 * 1, 384 * 1, 384 * 8], [384 * 8, 384 * 1, 384 * 1]] # [NPTS_X, NPTS_Y, NPTS_Z]
#NPTS = [[128,128,256]]
#NPTS = [[384,384,384]]
NPTS = [[288,288,288]]
#NPTS = [[4*1, 8 * 1, 8 * 1]] # [NPTS_X, NPTS_Y, NPTS_Z]
Nworm = 15
ImplEulerSteps = 1
initialFrictionSteps = 0
SedimentationProblem = False
SwimProblem = True
TwoParticleProblem = False
TestInitialisation1 = 'false'
TestInitialisation2 = 'false'
TestInitialisation3 = 'false'
TestInitialisation4 = 'false'
TwoParticleInitialisation = 'false'
# Swimming
if SwimProblem:
SimName0 = 'Swim' # 'ConvCheckBDFb'
GTTallBoxInitialisation = 'false'
RandomMessToSwimThroughInitialisation = 'true'
RandomMessToSwimThroughInitialisationTwoParticle = 'false'
RandomMessToSwimThroughInitialisationAllowOverlap = 'false'
Nworm_swimmer = 15
# Disabled connective stuff
ConnectedNodesInitialisation = False
ConnectedNodesInitialisationAllowOverlap = False
ConnectedNodesNumSwimmingFilaments = 0
ConnectedNodesNumNodes = 1 #
L_worm = Nworm_swimmer*2.2
ConnectedNodesConnectionRadius = 1.2*L_worm
ConnectedNodesMinNodeSpacing = 2.2*ConnectedNodesNumNodes**(-1./3.)*L_worm
ConnectedNodesSpacingAwayFromNode = 0
ConnectedNodesConnectionProbability = 0
EnableSpringLinks = False
NetworkSpringConstant = 0#[0,0.01,0.1] # k in the spring force k*(x-L)
NetworkSpringNaturalLength = 0 # L in the spring force k*(x-L)
# Freeze the swimmer
FrozenSwimmer = 'false'
# WeightPerLength = [[0, 0, -1]] # Comment out for normal use; only for frozen swimmer.
# Work out speed you'd get without collisions, but use gait you get with collisions?
GaitReset = 'false'
initialFrictionSteps = 0 #0 # 1000
StepsPerPeriod = 300
RandomMessNumNetworkFilaments = [200] # [180, 300, 420]
Nsw = [1 + i for i in RandomMessNumNetworkFilaments]
# Nsw = [0 + i for i in RandomMessNumNetworkFilaments]
TimeSteps = 1 * StepsPerPeriod #22 # Total timesteps
Kap_NetworkFilaments = [1000] # [3.6, 36, 3600]
plot_steps = int(StepsPerPeriod / 50) # Save/checkpoint every plot_steps timesteps
SpermCurvatureDecay = True
SaveExtendedSwimmerData = True
#randSeed = [2,3,4,5,6,7,8,9,10,11]
randSeed = [2]
Barrier_FS_over_2a = [15*3.14159265358979] # !!!!!!!!!!!!!!!!!!!!!!!!!!!
TOL = 1.e-6
# Sedimenting
if SedimentationProblem:
SimName0 = 'Sed' # 'ConvCheckBDFb'
GTTallBoxInitialisation = 'true'
RandomMessToSwimThroughInitialisation = 'false'
StepsPerSettlingTime = 300
Nsw = [1]#[800]
TimeSteps = StepsPerSettlingTime/30 # 600 * StepsPerSettlingTime # Total timesteps
Bnumber = [1e3]
plot_steps = int(StepsPerSettlingTime / 100) # Save/checkpoint every plot_steps timesteps
WeightPerLength = [[0, 0, -1]]
#WeightPerLength = [[-1, 0, 0]]
time = datetime.datetime.now().strftime("%y%m%d%H%M")
os.system('mkdir ' + time)
# backup existing config.hpp so that we can restore it later.
if os.path.isfile('config.hpp'):
os.system("cp config.hpp config-backup.hpp")
config_backup = True
else:
config_backup = False
print("Compiling batch of simulations and placing them in /" + time + "/ ...\n")
for i, Nsw_i in enumerate(Nsw):
RandomMessNumNetworkFilaments_i = RandomMessNumNetworkFilaments[i]
for Kap_NetworkFilaments_i in Kap_NetworkFilaments:
for k, Bnumber_i in enumerate(Bnumber):
for j, NPTS_i in enumerate(NPTS):
for randSeed_i in randSeed:
Barrier_FS_over_2a_i = Barrier_FS_over_2a[k]
if SedimentationProblem:
SimName = SimName0 + "-N" + str(Nsw_i) + "-B" + str(Bnumber_i) + "-TallBox" + "-NPTSx" + str(NPTS_i[0]) + "y" + str(NPTS_i[1]) + "z" + str(NPTS_i[2])
if SwimProblem:
SimName = SimName0 + "-Nnetfil" + str(RandomMessNumNetworkFilaments_i) + "-Kap" + str(Kap_NetworkFilaments_i) + "-NPTSx" + str(NPTS_i[0]) + "y" + str(NPTS_i[1]) + "z" + str(NPTS_i[2]) + "-randSeed" + str(randSeed_i)
#SimName = SimName0 + "-Nnetfil" + str(RandomMessNumNetworkFilaments_i) + "-frame0"
SimName = SimName.replace(".", "p")
continue_from_file = ''
#continue_from_file = 'FreeNetwork-Nnetfil420-Kap3p6-NPTS1536'
# continue_from_file = 'FreeNetwork-Nnetfil' + str(RandomMessNumNetworkFilaments_i) + '-frame0' # Leave blank if desired
if len(continue_from_file) > 0:
print("Compiling " + SimName + ", which continues from " + continue_from_file + " ...")
else:
print("Compiling " + SimName + " ...")
NPTS_X_i = NPTS_i[0]
NPTS_Y_i = NPTS_i[1]
NPTS_Z_i = NPTS_i[2]
xxRandomMessBoxSize_x_i = NPTS_X_i / 3.298629
xxRandomMessBoxSize_y_i = NPTS_Y_i / 3.298629
xxRandomMessBoxSize_z_i = NPTS_Z_i / 3.298629
ConnectedNodesBoxSize_x_i = NPTS_X_i / 3.298629
ConnectedNodesBoxSize_y_i = NPTS_Y_i / 3.298629
ConnectedNodesBoxSize_z_i = NPTS_Z_i / 3.298629
xxWeightPerLength_i = WeightPerLength[j]
# change config.hpp
os.system("cp config_template.hpp config.hpp")
with open('config.hpp', 'r') as file:
filedata = file.read()
filedata = filedata.replace('xxSedimentationProblem', ['false', 'true'][int(SedimentationProblem)])
filedata = filedata.replace('xxSwimProblem', ['false', 'true'][int(SwimProblem)])
filedata = filedata.replace('xxTwoParticleProblem', ['false', 'true'][int(TwoParticleProblem)])
filedata = filedata.replace('xxGTTallBoxInitialisation', GTTallBoxInitialisation)
filedata = filedata.replace('xxRandomMessToSwimThroughInitialisationAllowOverlap', RandomMessToSwimThroughInitialisationAllowOverlap)
filedata = filedata.replace('xxRandomMessToSwimThroughInitialisationTwoParticle', RandomMessToSwimThroughInitialisationTwoParticle)
filedata = filedata.replace('xxRandomMessToSwimThroughInitialisation', RandomMessToSwimThroughInitialisation)
filedata = filedata.replace('xxFrozenSwimmer', FrozenSwimmer)
filedata = filedata.replace('xxGaitReset', GaitReset)
filedata = filedata.replace('xxTwoParticleInitialisation', TwoParticleInitialisation)
filedata = filedata.replace('xxConnectedNodesInitialisationAllowOverlap', ['false', 'true'][int(ConnectedNodesInitialisationAllowOverlap)])
filedata = filedata.replace('xxConnectedNodesInitialisation', ['false', 'true'][int(ConnectedNodesInitialisation)])
filedata = filedata.replace('xxTestInitialisation1', TestInitialisation1)
filedata = filedata.replace('xxTestInitialisation2', TestInitialisation2)
filedata = filedata.replace('xxTestInitialisation3', TestInitialisation3)
filedata = filedata.replace('xxTestInitialisation4', TestInitialisation4)
filedata = filedata.replace('xxSimName', SimName)
filedata = filedata.replace('xxNworm', str(Nworm))
filedata = filedata.replace('xxNsw', str(Nsw[i]))
filedata = filedata.replace('xxNPTS_X', str(NPTS_X_i) + "L")
filedata = filedata.replace('xxNPTS_Y', str(NPTS_Y_i) + "L")
filedata = filedata.replace('xxNPTS_Z', str(NPTS_Z_i) + "L")
filedata = filedata.replace('xxTimeSteps', str(TimeSteps))
filedata = filedata.replace('xxplot_steps', str(plot_steps))
filedata = filedata.replace('xxImplEulerSteps', str(ImplEulerSteps))
filedata = filedata.replace('xxinitialFrictionSteps', str(initialFrictionSteps))
filedata = filedata.replace('xxRandomMessBoxSize_x', str(xxRandomMessBoxSize_x_i))
filedata = filedata.replace('xxRandomMessBoxSize_y', str(xxRandomMessBoxSize_y_i))
filedata = filedata.replace('xxRandomMessBoxSize_z', str(xxRandomMessBoxSize_z_i))
filedata = filedata.replace('xxRandomMessNumNetworkFilaments', str(RandomMessNumNetworkFilaments_i))
filedata = filedata.replace('xxRandomMessNumSwimmingFilaments', str(Nsw_i - RandomMessNumNetworkFilaments_i))
filedata = filedata.replace('xxKap_NetworkFilaments', str(Kap_NetworkFilaments_i))
filedata = filedata.replace('xxStepsPerPeriod', str(StepsPerPeriod))
filedata = filedata.replace('xxSpermCurvatureDecay', ['false', 'true'][int(SpermCurvatureDecay)])
filedata = filedata.replace('xxSaveExtendedSwimmerData', ['false', 'true'][int(SaveExtendedSwimmerData)])
filedata = filedata.replace('xxConnectedNodesNumSwimmingFilaments', str(ConnectedNodesNumSwimmingFilaments))
filedata = filedata.replace('xyNworm_swimmer', str(Nworm_swimmer))
filedata = filedata.replace('xxConnectedNodesNumNodes', str(ConnectedNodesNumNodes))
filedata = filedata.replace('xxConnectedNodesBoxSize_x', str(ConnectedNodesBoxSize_x_i))
filedata = filedata.replace('xxConnectedNodesBoxSize_y', str(ConnectedNodesBoxSize_y_i))
filedata = filedata.replace('xxConnectedNodesBoxSize_z', str(ConnectedNodesBoxSize_z_i))
filedata = filedata.replace('xxConnectedNodesConnectionRadius', str(ConnectedNodesConnectionRadius))
filedata = filedata.replace('xxConnectedNodesMinNodeSpacing', str(ConnectedNodesMinNodeSpacing))
filedata = filedata.replace('xxConnectedNodesSpacingAwayFromNode', str(ConnectedNodesSpacingAwayFromNode))
filedata = filedata.replace('xxConnectedNodesConnectionProbability', str(ConnectedNodesConnectionProbability))
filedata = filedata.replace('xxWeightPerLength_x', str(xxWeightPerLength_i[0]))
filedata = filedata.replace('xxWeightPerLength_y', str(xxWeightPerLength_i[1]))
filedata = filedata.replace('xxWeightPerLength_z', str(xxWeightPerLength_i[2]))
filedata = filedata.replace('xxBnumber', str(Bnumber_i))
filedata = filedata.replace('xxBarrier_FS_over_2a', str(Barrier_FS_over_2a_i))
filedata = filedata.replace('xxBarrier_distance_cap', str(Barrier_distance_cap))
filedata = filedata.replace('xxStepsPerSettlingTime', str(StepsPerSettlingTime))
# Network springs
filedata = filedata.replace('xxEnableSpringLinks', ['false', 'true'][int(EnableSpringLinks)])
filedata = filedata.replace('xxNetworkSpringConstant', str(NetworkSpringConstant))
filedata = filedata.replace('xxNetworkSpringNaturalLength', str(NetworkSpringNaturalLength))
filedata = filedata.replace('xxrandSeed', str(randSeed_i))
filedata = filedata.replace('xxTOL', str(TOL))
with open('config.hpp', 'w') as file:
file.write(filedata)
# make
#os.system("export OPENBLAS_NUM_THREADS=1") # sets number of threads openBLAS uses to 1 (no communication overhead between cpus)
#subprocess.call("./make_wrapper_cx2.sh") # Make
#process = subprocess.Popen(["make","MPI_FIL_debug"], stdout=subprocess.PIPE)
process = subprocess.Popen(["make","MPI_FIL"], stdout=subprocess.PIPE)
#print "NOTE DEBUG MODE IS ON"
process.wait()
# make new subdirectory called SimName, copy binary file
os.system('mkdir ' + time + "/" + SimName + ' && cp MPIFilament ' + time + "/" + SimName)
os.chdir(time + "/" + SimName)
os.system('mkdir output')
os.chdir("../..")
os.system("cp config.hpp " + time + "/" + SimName)
if len(continue_from_file) > 0:
os.system("cp ./output/" + continue_from_file + ".par " + time + "/" + SimName + "/output")
os.system("cp ./output/" + continue_from_file + ".dat " + time + "/" + SimName + "/output")
os.system("cp ./output/" + continue_from_file + ".bak " + time + "/" + SimName + "/output")
# Return backup config.hpp
if config_backup:
os.system("cp config-backup.hpp config.hpp")
os.system("rm config-backup.hpp")
print("\nComplete. Simulations have been compiled and placed in /" + time + "/")
#print("\nUse command `python batch_run.py " + time + "" + '` to run.')
print("\nUse command `python batch_run_screen.py " + time + "" + '` to run.')