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Merge branch 'main' of https://github.com/VirtualPlanetaryLaboratory/…
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@caitlyn-wilhelm
caitlyn-wilhelm committed Jun 1, 2021
2 parents 3f8b309 + 41083b2 commit 24e5090
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3 changes: 3 additions & 0 deletions .gitignore
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Expand Up @@ -140,3 +140,6 @@ dmypy.json

# Pyre type checker
.pyre/

# SCM version
multiplanet/multiplanet_version.py
199 changes: 136 additions & 63 deletions multiplanet/multiplanet.py
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Expand Up @@ -11,107 +11,140 @@
# --------------------------------------------------------------------

## parallel implementation of running vplanet over a directory ##
def parallel_run_planet(input_file, cores, quiet, bigplanet,email):
def parallel_run_planet(input_file, cores, quiet, bigplanet, email):
# gets the folder name with all the sims
folder_name, infiles = GetDir(input_file)
#gets the list of sims
# gets the list of sims
sims = GetSims(folder_name)

#initalizes the checkpoint file
checkpoint_file = os.getcwd() + '/' + '.' + folder_name
# initalizes the checkpoint file
checkpoint_file = os.getcwd() + "/" + "." + folder_name

#checks if the files doesn't exist and if so then it creates it
# checks if the files doesn't exist and if so then it creates it
if os.path.isfile(checkpoint_file) == False:
CreateCP(checkpoint_file,input_file,quiet,sims)
CreateCP(checkpoint_file, input_file, quiet, sims)

#if it does exist, it checks for any 0's (sims that didn't complete) and
#changes them to -1 to be re-ran
# if it does exist, it checks for any 0's (sims that didn't complete) and
# changes them to -1 to be re-ran
else:
ReCreateCP(checkpoint_file,input_file,quiet,sims)
ReCreateCP(checkpoint_file, input_file, quiet, sims)

# Get the SNames (sName and sSystemName) for the simuations
# Save the name of the log file
system_name, body_list = GetSNames(infiles, sims)
logfile = system_name + ".log"


lock = mp.Lock()
workers = []

master_hdf5_file = folder_name + '.bpl'
with h5py.File(master_hdf5_file, 'w') as Master:
master_hdf5_file = folder_name + ".bpl"
with h5py.File(master_hdf5_file, "w") as Master:
for i in range(cores):
workers.append(mp.Process(target=par_worker,
args=(checkpoint_file, system_name, body_list, logfile, infiles, quiet, lock, bigplanet, master_hdf5_file)))
workers.append(
mp.Process(
target=par_worker,
args=(
checkpoint_file,
system_name,
body_list,
logfile,
infiles,
quiet,
lock,
bigplanet,
master_hdf5_file,
),
)
)
for w in workers:
w.start()
for w in workers:
w.join()

if bigplanet == False:
sub.run(['rm', master_hdf5_file])
sub.run(["rm", master_hdf5_file])
if email is not None:
SendMail(email, folder_name)

def SendMail(email,destfolder):

def SendMail(email, destfolder):
Title = "Multi-Planet has finished for " + destfolder
Body = "Please log into your computer to verify the results. This is an auto-generated message."
message = "echo " + Body + " | " + 'mail -s ' + '"'+ Title + '" ' + email
sub.Popen(message , shell=True)
message = "echo " + Body + " | " + "mail -s " + '"' + Title + '" ' + email
sub.Popen(message, shell=True)


def GetDir(input_file):
""" Give it input file and returns name of folder where simulations are located. """
infiles = []
# gets the folder name with all the sims
with open(input_file, 'r') as vpl:
with open(input_file, "r") as vpl:
content = [line.strip().split() for line in vpl.readlines()]
for line in content:
if line:
if line[0] == 'destfolder':
if line[0] == "destfolder":
folder_name = line[1]

if line[0] == 'file':
if line[0] == "file":
infiles.append(line[1])

if folder_name is None:
print("Name of destination folder not provided in file '%s'."
"Use syntax 'destfolder <foldername>'"%inputf)

print(
"Name of destination folder not provided in file '%s'."
"Use syntax 'destfolder <foldername>'" % inputf
)

if os.path.isdir(folder_name) == False:
print("ERROR: Folder", folder_name, "does not exist in the current directory.")
print(
"ERROR: Folder",
folder_name,
"does not exist in the current directory.",
)
exit()

return folder_name, infiles

def CreateCP(checkpoint_file,input_file,quiet,sims):
with open(checkpoint_file,'w') as cp:
cp.write('Vspace File: ' + os.getcwd() + '/' + input_file + '\n')
cp.write('Total Number of Simulations: '+ str(len(sims)) + '\n')

def CreateCP(checkpoint_file, input_file, quiet, sims):
with open(checkpoint_file, "w") as cp:
cp.write("Vspace File: " + os.getcwd() + "/" + input_file + "\n")
cp.write("Total Number of Simulations: " + str(len(sims)) + "\n")
for f in range(len(sims)):
cp.write(sims[f] + " " + "-1 \n")
cp.write('THE END \n')
cp.write("THE END \n")

def ReCreateCP(checkpoint_file,input_file,quiet,sims):

def ReCreateCP(checkpoint_file, input_file, quiet, sims):
if quiet == False:
print('WARNING: multi-planet checkpoint file already exists!')
print('Checking if checkpoint file is corrupt...')
print("WARNING: multi-planet checkpoint file already exists!")
print("Checking if checkpoint file is corrupt...")

datalist = []

with open(checkpoint_file, 'r') as f:
with open(checkpoint_file, "r") as f:
for newline in f:
datalist.append(newline.strip().split())
for l in datalist:
if l[1] == '0':
l[1] = '-1'
if l[1] == "0":
l[1] = "-1"

with open(checkpoint_file, 'w') as f:
with open(checkpoint_file, "w") as f:
for newline in datalist:
f.writelines(' '.join(newline)+'\n')
f.writelines(" ".join(newline) + "\n")


## parallel worker to run vplanet ##
def par_worker(checkpoint_file,system_name, body_list, log_file, in_files, quiet, lock,bigplanet, h5_file):
def par_worker(
checkpoint_file,
system_name,
body_list,
log_file,
in_files,
quiet,
lock,
bigplanet,
h5_file,
):

while True:

Expand All @@ -120,33 +153,39 @@ def par_worker(checkpoint_file,system_name, body_list, log_file, in_files, quiet
if bigplanet == True:
data = {}

with open(checkpoint_file, 'r') as f:
with open(checkpoint_file, "r") as f:
for newline in f:
datalist.append(newline.strip().split())

folder = ''
folder = ""

for l in datalist:
if l[1] == '-1':
if l[1] == "-1":
folder = l[0]
l[1] = '0'
l[1] = "0"
break

if not folder:
lock.release()
return

with open(checkpoint_file, 'w') as f:
with open(checkpoint_file, "w") as f:
for newline in datalist:
f.writelines(' '.join(newline)+'\n')
f.writelines(" ".join(newline) + "\n")

lock.release()

os.chdir(folder)

#runs vplanet on folder and writes the output to the log file
with open('vplanet_log','a+') as vplf:
vplanet = sub.Popen("vplanet vpl.in", shell=True, stdout=sub.PIPE, stderr=sub.PIPE, universal_newlines=True)
# runs vplanet on folder and writes the output to the log file
with open("vplanet_log", "a+") as vplf:
vplanet = sub.Popen(
"vplanet vpl.in",
shell=True,
stdout=sub.PIPE,
stderr=sub.PIPE,
universal_newlines=True,
)
return_code = vplanet.poll()
for line in vplanet.stderr:
vplf.write(line)
Expand All @@ -157,46 +196,77 @@ def par_worker(checkpoint_file,system_name, body_list, log_file, in_files, quiet
lock.acquire()
datalist = []

with open(checkpoint_file, 'r') as f:
with open(checkpoint_file, "r") as f:
for newline in f:
datalist.append(newline.strip().split())

if return_code is None:
for l in datalist:
if l[0] == folder:
l[1] = '1'
l[1] = "1"
break
if quiet == False:
print(folder, "completed")
if bigplanet == True:
with h5py.File(h5_file, 'w') as Master:
group_name = folder.split('/')[-1]
with h5py.File(h5_file, "w") as Master:
group_name = folder.split("/")[-1]
if group_name not in Master:
CreateHDF5Group(data, system_name, body_list, log_file, group_name,in_files, h5_file)
CreateHDF5Group(
data,
system_name,
body_list,
log_file,
group_name,
in_files,
h5_file,
)
else:
for l in datalist:
if l[0] == folder:
l[1] = '-1'
l[1] = "-1"
break
if quiet == False:
print(folder, "failed")

with open(checkpoint_file, 'w') as f:
with open(checkpoint_file, "w") as f:
for newline in datalist:
f.writelines(' '.join(newline)+'\n')

f.writelines(" ".join(newline) + "\n")

lock.release()

os.chdir("../../")


def Arguments():
max_cores = mp.cpu_count()
parser = argparse.ArgumentParser(description="Using multi-processing to run a large number of simulations")
parser.add_argument("-c","--cores", type=int, default=max_cores, help="The total number of processors used")
parser.add_argument("-q","--quiet", action="store_true", help="No command line output for multi-planet")
parser.add_argument("-bp","--bigplanet", action="store_true" ,help="Runs bigplanet and creates the HDF5 files alongside running mutlt-planet")
parser.add_argument("-m","--email",type=str, help="Mails user when multi-planet is completed")
parser = argparse.ArgumentParser(
description="Using multi-processing to run a large number of simulations"
)
parser.add_argument(
"-c",
"--cores",
type=int,
default=max_cores,
help="The total number of processors used",
)
parser.add_argument(
"-q",
"--quiet",
action="store_true",
help="No command line output for multi-planet",
)
parser.add_argument(
"-bp",
"--bigplanet",
action="store_true",
help="Runs bigplanet and creates the HDF5 files alongside running mutlt-planet",
)
parser.add_argument(
"-m",
"--email",
type=str,
help="Mails user when multi-planet is completed",
)
parser.add_argument("InputFile", help="name of the vspace file")
args = parser.parse_args()

Expand All @@ -208,7 +278,10 @@ def Arguments():
except OSError:
raise Exception("Unable to call VPLANET. Is it in your PATH?")

parallel_run_planet(args.InputFile,args.cores,args.quiet,args.bigplanet,args.email)
parallel_run_planet(
args.InputFile, args.cores, args.quiet, args.bigplanet, args.email
)


if __name__ == "__main__":
Arguments()
24 changes: 24 additions & 0 deletions pyproject.toml
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@@ -0,0 +1,24 @@
[build-system]
requires = ["setuptools>=45", "wheel", "setuptools_scm[toml]>=6.0"]
build-backend = "setuptools.build_meta"

[tool.setuptools_scm]
write_to = "multiplanet/multiplanet_version.py"
write_to_template = '__version__ = "{version}"'

[tool.black]
line-length = 79
exclude = '''
/(
\.eggs
| \.git
| \.hg
| \.mypy_cache
| \.tox
| \.venv
| _build
| buck-out
| build
| dist
)/
'''
6 changes: 6 additions & 0 deletions setup.cfg
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@@ -0,0 +1,6 @@
[options]
setup_requires =
setuptools_scm

[metadata]
license_files = LICENSE
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