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Fix module command #199

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Merged
srmnitc merged 2 commits into from
Dec 12, 2025
Merged

Fix module command #199

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4b3ceb3
remove module altogether
srmnitc Dec 12, 2025
718d768
fix bugs in scheduler
srmnitc Dec 12, 2025
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25 changes: 14 additions & 11 deletions calphy/input.py
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Original file line number Diff line number Diff line change
Expand Up @@ -96,27 +96,27 @@ def _extract_elements_from_pair_coeff(pair_coeff_string):
"""
Extract element symbols from pair_coeff string.
Returns None if pair_coeff doesn't contain element specifications.

Parameters
----------
pair_coeff_string : str
The pair_coeff command string (e.g., "* * potential.eam.fs Cu Zr")

Returns
-------
list or None
List of element symbols in order, or None if no elements found
"""
if pair_coeff_string is None:
return None

pcsplit = pair_coeff_string.strip().split()
elements = []

# Start collecting after we find element symbols
# Elements are typically after the potential filename
started = False

for p in pcsplit:
# Check if this looks like an element symbol
# Element symbols are 1-2 characters, start with uppercase
Expand All @@ -131,7 +131,7 @@ def _extract_elements_from_pair_coeff(pair_coeff_string):
if started:
# We already started collecting elements and hit a non-element
break

return elements if len(elements) > 0 else None


Expand Down Expand Up @@ -208,7 +208,6 @@ class Queue(BaseModel, title="Options for configuring queue"):
memory: Annotated[str, Field(default="3GB")]
commands: Annotated[List, Field(default=[])]
options: Annotated[List, Field(default=[])]
modules: Annotated[List, Field(default=[])]


class Tolerance(BaseModel, title="Tolerance settings for convergence"):
Expand Down Expand Up @@ -356,13 +355,17 @@ def _validate_all(self) -> "Input":
raise ValueError("mass and elements should have same length")

self.n_elements = len(self.element)

# Validate element/mass/pair_coeff ordering consistency
# This is critical for multi-element systems where LAMMPS type numbers
# are assigned based on element order: element[0]=Type1, element[1]=Type2, etc.
if len(self.element) > 1 and self.pair_coeff is not None and len(self.pair_coeff) > 0:
if (
len(self.element) > 1
and self.pair_coeff is not None
and len(self.pair_coeff) > 0
):
extracted_elements = _extract_elements_from_pair_coeff(self.pair_coeff[0])

if extracted_elements is not None:
# pair_coeff specifies elements - check ordering
if set(extracted_elements) != set(self.element):
Expand All @@ -372,7 +375,7 @@ def _validate_all(self) -> "Input":
f" pair_coeff: {extracted_elements}\n"
f"The elements specified must be the same."
)

if list(extracted_elements) != list(self.element):
raise ValueError(
f"Element ordering mismatch detected!\n\n"
Expand Down
205 changes: 100 additions & 105 deletions calphy/scheduler.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,14 +3,14 @@
energy calculations.

Copyright 2021 (c) Sarath Menon^1, Yury Lysogorskiy^2, Ralf Drautz^2
^1: Max Planck Institut für Eisenforschung, Dusseldorf, Germany
^1: Max Planck Institut für Eisenforschung, Dusseldorf, Germany
^2: Ruhr-University Bochum, Bochum, Germany

calphy is published and distributed under the Academic Software License v1.0 (ASL).
calphy is distributed in the hope that it will be useful for non-commercial academic research,
but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
calphy is published and distributed under the Academic Software License v1.0 (ASL).
calphy is distributed in the hope that it will be useful for non-commercial academic research,
but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
calphy API is published and distributed under the BSD 3-Clause "New" or "Revised" License
See the LICENSE FILE for more details.
See the LICENSE FILE for more details.

More information about the program can be found in:
Menon, Sarath, Yury Lysogorskiy, Jutta Rogal, and Ralf Drautz.
Expand All @@ -25,25 +25,26 @@
import os
import stat


class Local:
"""
Local submission script
"""

def __init__(self, options, cores=1, directory=os.getcwd()):
self.queueoptions = {"scheduler": "local",
"jobname": "tis",
"queuename": None,
"memory": None,
"cores": cores,
"hint": None,
"directory": directory,
"options": [],
"commands": [],
"modules": [],
"header": "#!/bin/bash"

}
for (key, val) in options.items():
self.queueoptions = {
"scheduler": "local",
"jobname": "tis",
"queuename": None,
"memory": None,
"cores": cores,
"hint": None,
"directory": directory,
"options": [],
"commands": [],
"header": "#!/bin/bash",
}
for key, val in options.items():
if key in self.queueoptions.keys():
if val is not None:
self.queueoptions[key] = val
Expand All @@ -60,14 +61,10 @@ def write_script(self, outfile):
fout.write(self.queueoptions["header"])
fout.write("\n")

#now write modules
for module in self.queueoptions["modules"]:
fout.write("module load %s\n" %module)

#now finally commands
# now finally commands
for command in self.queueoptions["commands"]:
fout.write("%s\n" %command)
fout.write("%s > %s 2> %s\n" %(self.maincommand, jobout, joberr))
fout.write("%s\n" % command)
fout.write("%s > %s 2> %s\n" % (self.maincommand, jobout, joberr))
self.script = outfile

def submit(self):
Expand All @@ -77,41 +74,42 @@ def submit(self):
st = os.stat(self.script)
os.chmod(self.script, st.st_mode | stat.S_IEXEC)
cmd = [self.script]
proc = sub.Popen(cmd, stdin=sub.PIPE,stdout=sub.PIPE,stderr=sub.PIPE)
proc = sub.Popen(cmd, stdin=sub.PIPE, stdout=sub.PIPE, stderr=sub.PIPE)
return proc


class SLURM:
"""
Slurm class for writing submission script
"""

def __init__(self, options, cores=1, directory=os.getcwd()):
"""
Create class
"""
self.queueoptions = {"scheduler": "slurm",
"jobname": "tis",
"queuename": None,
"walltime": "23:59:00",
"memory": "3GB",
"cores": cores,
"hint": "nomultithread",
"directory": directory,
"options": [],
"commands": [ "uss=$(whoami)",
"find /dev/shm/ -user $uss -type f -mmin +30 -delete",
],
"modules": [],
"header": "#!/bin/bash"

}
for (key, val) in options.items():
self.queueoptions = {
"scheduler": "slurm",
"jobname": "tis",
"queuename": None,
"walltime": "23:59:00",
"memory": "3GB",
"cores": cores,
"hint": "nomultithread",
"directory": directory,
"options": [],
"commands": [
"uss=$(whoami)",
"find /dev/shm/ -user $uss -type f -mmin +30 -delete",
],
"header": "#!/bin/bash",
}
for key, val in options.items():
if key in self.queueoptions.keys():
if val is not None:
if val != "":
self.queueoptions[key] = val
self.maincommand = ""


def write_script(self, outfile):
"""
Write the script file
Expand All @@ -123,69 +121,66 @@ def write_script(self, outfile):
fout.write(self.queueoptions["header"])
fout.write("\n")

#write the main header options
fout.write("#SBATCH --job-name=%s\n" %self.queueoptions["jobname"])
fout.write("#SBATCH --time=%s\n" %self.queueoptions["walltime"])
# write the main header options
fout.write("#SBATCH --job-name=%s\n" % self.queueoptions["jobname"])
fout.write("#SBATCH --time=%s\n" % self.queueoptions["walltime"])
if self.queueoptions["queuename"] is not None:
fout.write("#SBATCH --partition=%s\n"%self.queueoptions["queuename"])
fout.write("#SBATCH --ntasks=%s\n" %str(self.queueoptions["cores"]))
fout.write("#SBATCH --mem-per-cpu=%s\n"%self.queueoptions["memory"])
fout.write("#SBATCH --hint=%s\n" %self.queueoptions["hint"])
fout.write("#SBATCH --chdir=%s\n" %self.queueoptions["directory"])
fout.write("#SBATCH --partition=%s\n" % self.queueoptions["queuename"])
fout.write("#SBATCH --ntasks=%s\n" % str(self.queueoptions["cores"]))
fout.write("#SBATCH --mem-per-cpu=%s\n" % self.queueoptions["memory"])
fout.write("#SBATCH --hint=%s\n" % self.queueoptions["hint"])
fout.write("#SBATCH --chdir=%s\n" % self.queueoptions["directory"])

#now write extra options
# now write extra options
for option in self.queueoptions["options"]:
fout.write("#SBATCH %s\n" %option)
fout.write("#SBATCH %s\n" % option)

#now write modules
for module in self.queueoptions["modules"]:
fout.write("module load %s\n" %module)

#now finally commands
# now finally commands
for command in self.queueoptions["commands"]:
fout.write("%s\n" %command)
fout.write("%s > %s 2> %s\n" %(self.maincommand, jobout, joberr))
fout.write("%s\n" % command)
fout.write("%s > %s 2> %s\n" % (self.maincommand, jobout, joberr))

self.script = outfile

def submit(self):
"""
Submit the job
"""
cmd = ['sbatch', self.script]
proc = sub.Popen(cmd, stdin=sub.PIPE,stdout=sub.PIPE,stderr=sub.PIPE)
cmd = ["sbatch", self.script]
proc = sub.Popen(cmd, stdin=sub.PIPE, stdout=sub.PIPE, stderr=sub.PIPE)
print(f'submitting {self.queueoptions["jobname"]}')
proc.communicate()
return proc



class SGE:
"""
Slurm class for writing submission script
"""

def __init__(self, options, cores=1, directory=os.getcwd()):
"""
Create class
"""
self.queueoptions = {"scheduler": "sge",
"jobname": "tis",
"walltime": "23:59:00",
"queuename": None,
"memory": "3GB",
"system": "smp",
"commands": [],
"modules": [],
"options": ["-j y",
"-R y",
"-P ams.p",
],
"cores": cores,
"hint": None,
"directory": directory,
"header": "#!/bin/bash"
}
for (key, val) in options.items():
self.queueoptions = {
"scheduler": "sge",
"jobname": "tis",
"walltime": "23:59:00",
"queuename": None,
"memory": "3GB",
"system": "smp",
"commands": [],
"options": [
"-j y",
"-R y",
"-P ams.p",
],
"cores": cores,
"hint": None,
"directory": directory,
"header": "#!/bin/bash",
}
for key, val in options.items():
if key in self.queueoptions.keys():
if val is not None:
self.queueoptions[key] = val
Expand All @@ -195,40 +190,40 @@ def write_script(self, outfile):
"""
Write the script file
"""
jobout = ".".join([outfile, "out"])
joberr = ".".join([outfile, "err"])

with open(outfile, "w") as fout:
fout.write(self.queueoptions["header"])
fout.write("\n")

#write the main header options
fout.write("#$ -N %s\n" %self.queueoptions["jobname"])
fout.write("#$ -l h_rt=%s\n" %self.queueoptions["walltime"])
fout.write("#$ -l qname=%s\n"%self.queueoptions["queuename"])
fout.write("#$ -pe %s %s\n" %( self.queueoptions["system"], str(self.queueoptions["cores"])))
fout.write("#$ -l h_vmem=%s\n"%self.queueoptions["memory"])
fout.write("#$ -cwd %s\n" %self.queueoptions["directory"])

#now write extra options
# write the main header options
fout.write("#$ -N %s\n" % self.queueoptions["jobname"])
fout.write("#$ -l h_rt=%s\n" % self.queueoptions["walltime"])
fout.write("#$ -l qname=%s\n" % self.queueoptions["queuename"])
fout.write(
"#$ -pe %s %s\n"
% (self.queueoptions["system"], str(self.queueoptions["cores"]))
)
fout.write("#$ -l h_vmem=%s\n" % self.queueoptions["memory"])
fout.write("#$ -cwd %s\n" % self.queueoptions["directory"])

# now write extra options
for option in self.queueoptions["options"]:
fout.write("#$ %s\n" %option)

#now write modules
for module in self.queueoptions["modules"]:
fout.write("module load %s\n" %module)
fout.write("#$ %s\n" % option)

#now finally commands
# now finally commands
for command in self.queueoptions["commands"]:
fout.write("%s\n" %command)
fout.write("%s\n" % command)

fout.write("%s > %s 2> %s\n" %(self.maincommand, jobout, joberr))

self.script = outfile
fout.write("%s > %s 2> %s\n" % (self.maincommand, jobout, joberr))

self.script = outfile

def submit(self):
"""
Submit the job
"""
cmd = ['qsub', self.script]
proc = sub.Popen(cmd, stdin=sub.PIPE,stdout=sub.PIPE,stderr=sub.PIPE)
cmd = ["qsub", self.script]
proc = sub.Popen(cmd, stdin=sub.PIPE, stdout=sub.PIPE, stderr=sub.PIPE)
return proc

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