def run_install(location):
os.chdir(location)
cwd = os.getcwd()
if cwd.endswith("/"):
cwd = cwd[:-1]
if os.path.exists("packmol"):
print("Packmol folder already exists, so will not re-install")
else:
os.system("git clone https://github.com/mcubeg/packmol")
os.chdir("packmol")
os.system("./configure")
os.system("make")
os.chdir("../")
packmol_mod_file = '''help([[
For detailed instructions, go to:
http://m3g.iqm.unicamp.br/packmol/home.shtml
https://github.com/mcubeg/packmol
]])
whatis("Version: unknown")
whatis("Keywords: Packmol")
whatis("URL: http://m3g.iqm.unicamp.br/packmol/home.shtml")
whatis("Description: Packmol")
prepend_path("PATH", "$CWD/packmol")
'''
while "$CWD" in packmol_mod_file:
packmol_mod_file = packmol_mod_file.replace("$CWD", cwd)
save_module(packmol_mod_file, "packmol")
return cwd + "/packmol/packmol"
def run_install(location, python_path):
NAME = "NLOpt"
FOLDER = "nlopt-2.5.0"
TARFILE = "v2.5.0.tar.gz"
URL = "https://github.com/stevengj/nlopt/archive/v2.5.0.tar.gz"
HASH = "ada08c648bf9b52faf8729412ff6dd6d"
HELPURL = "https://nlopt.readthedocs.io/en/latest/"
VERSION = "2.5.0"
os.chdir(location)
cwd = os.getcwd()
if cwd.endswith("/"):
cwd = cwd[:-1]
if not os.path.exists(FOLDER):
os.system("mkdir %s" % FOLDER)
os.system("mkdir %s/build" % FOLDER)
download_file(cwd, URL, HASH)
os.system("tar -C %s/ -xzf %s" % (FOLDER, TARFILE))
os.system("mv %s/%s %s/src" % (FOLDER, FOLDER, FOLDER))
os.mkdir("%s/src/build" % FOLDER)
os.chdir("%s/src/build" % FOLDER)
# Specific Install Instructions
os.system(
"cmake .. -DCMAKE_INSTALL_PREFIX=%s/nlopt-2.5.0/build -DPYTHON_EXECUTABLE=%s"
% (cwd, python_path))
os.system("make; make install")
###############################
os.chdir("../../../")
else:
print("%s folder already exists, so will not re-install." % NAME)
mod_file = '''help([[
For detailed instructions, go to:
$HELPURL$
]])
whatis("Version: $VERSION$")
whatis("Keywords: $NAME$")
whatis("URL: $HELPURL$")
whatis("Description: $NAME$")
prepend_path("PATH", "$CWD$/$FOLDER$/build/bin")
prepend_path("LD_LIBRARY_PATH", "$CWD$/$FOLDER$/build/lib64")
prepend_path("PYTHONPATH", "$CWD$/$FOLDER$/build/lib/python2.7/site-packages")
'''
rep = {
"$CWD$": cwd,
"$FOLDER$": FOLDER,
"$NAME$": NAME,
"$VERSION$": VERSION,
"$HELPURL$": HELPURL
}
for identifier, word in rep.items():
while identifier in mod_file:
mod_file = mod_file.replace(identifier, str(word))
save_module(mod_file, FOLDER)
def run_install(location):
NAME = "swig"
FOLDER = "swig-3.0.12"
TARFILE = "swig-3.0.12.tar.gz"
URL = "http://prdownloads.sourceforge.net/swig/swig-3.0.12.tar.gz"
HASH = "82133dfa7bba75ff9ad98a7046be687c"
HELPURL = "https://www.swig.org"
VERSION = "3.0.12"
os.chdir(location)
cwd = os.getcwd()
if cwd.endswith("/"):
cwd = cwd[:-1]
if not os.path.exists(FOLDER):
os.system("mkdir %s" % FOLDER)
os.system("mkdir %s/build" % FOLDER)
download_file(cwd, URL, HASH)
# Untar the folder and make it into the build src ideal
os.system("tar -C %s/ -xzf %s" % (FOLDER, TARFILE))
os.system("mv %s/%s %s/src" % (FOLDER, FOLDER, FOLDER))
# Go into the src directory
os.chdir("%s/src" % FOLDER)
# Specific Install Instructions
os.system("./configure --prefix=%s/%s/build" % (cwd, FOLDER))
os.system("make; make install")
###############################
os.chdir("../../")
else:
print("%s folder already exists, so will not re-install." % NAME)
mod_file = '''help([[
For detailed instructions, go to:
$HELPURL$
]])
whatis("Version: $VERSION$")
whatis("Keywords: $NAME$")
whatis("URL: $HELPURL$")
whatis("Description: $NAME$")
prepend_path("PATH", "$CWD$/$FOLDER$/build/bin")
'''
rep = {
"$CWD$": cwd,
"$FOLDER$": FOLDER,
"$NAME$": NAME,
"$VERSION$": VERSION,
"$HELPURL$": HELPURL
}
for identifier, word in rep.items():
while identifier in mod_file:
mod_file = mod_file.replace(identifier, str(word))
save_module(mod_file, FOLDER)
def _squid_setup(anaconda_path, default_modules, lmp_path, packmol_path,
orca_path, orca4_path, vmd_path, ovito_path, queueing_system,
orca_sub_flag, env_vars, orca_env_vars, orca4_env_vars,
lmp_env_vars, mpi_preface, python_path, text_editor_path,
g09_formchk, g09_cubegen, mpirun_path, default_queue,
use_orca4, sandbox_orca, cwd, HOMEDIR, MODULEDIR):
'''
This function will setup the squid sysconst file and module.
'''
opls_path = cwd + '/forcefield_parameters/oplsaa.prm'
vars_to_include = [
orca_path, orca4_path, vmd_path, ovito_path, opls_path, packmol_path,
lmp_path, queueing_system, orca_sub_flag, env_vars, orca_env_vars,
orca4_env_vars, lmp_env_vars, mpi_preface, python_path,
text_editor_path, g09_formchk, g09_cubegen, mpirun_path, default_queue
]
s_vars_to_include = [
"orca_path", "orca4_path", "vmd_path", "ovito_path", "opls_path",
"packmol_path", "lmp_path", "queueing_system", "orca_sub_flag",
"env_vars", "orca_env_vars", "orca4_env_vars", "lmp_env_vars",
"mpi_preface", "python_path", "TEXT_EDITOR_PATH", "g09_formchk",
"g09_cubegen", "mpirun_path", "default_queue"
]
exports_and_aliases = """
--------------------------------------------------------------------------
--------- Squid Exports and Aliases v 0.0.1 ---------
--------------------------------------------------------------------------
help([[
For detailed instructions, go to:
https://clancylab.github.io/squid/squid.html
]])
whatis("Version: 1.2")
whatis("Keywords: Squid, Clancy")
whatis("URL: https://clancylab.github.io/squid/squid.html")
whatis("Description: Clancy Lab Codebase")
prepend_path( "PYTHONPATH", "$CWD")
-- Load all dependencies
""" + default_modules
swap_with_this = [("$CWD", cwd), ("$PYTHON_PATH", python_path)]
for k, v in swap_with_this:
while k in exports_and_aliases:
exports_and_aliases = exports_and_aliases.replace(k, v)
for s, v in zip(s_vars_to_include, vars_to_include):
ss = "$" + s.upper()
while ss in exports_and_aliases:
exports_and_aliases = exports_and_aliases.replace(ss, v)
save_module(exports_and_aliases.strip() + "\n", "squid", MODULEDIR)
def _setup_openmpi(orca_path, orca4_path, MODULEDIR):
if isvalid(orca4_path):
# If orca4 is a file, point to folder instead
if os.path.isfile(orca4_path) and orca4_path.endswith("/orca"):
orca4_path = orca4_path[:-5]
if "4.1." in orca4_path:
ompi_v = "3.1.3"
elif "4.0." in orca4_path:
ompi_v = "2.0.2"
run_install_openmpi("./", ompi_v, MODULEDIR)
orca_mod_file = '''help([[
For detailed instructions, go to:
https://orcaforum.cec.mpg.de/
]])
whatis("Version: $VERSION$")
whatis("Keywords: Orca 4")
whatis("URL: https://orcaforum.cec.mpg.de/")
whatis("Description: Orca 4")
load("openmpi/$VERSION$")
prepend_path("PATH", "$ORCA$")
prepend_path("LD_LIBRARY_PATH", "$ORCA$")
'''
swap_with_this = [("$ORCA$", orca4_path), ("$VERSION$", ompi_v)]
for k, v in swap_with_this:
while k in orca_mod_file:
orca_mod_file = orca_mod_file.replace(k, v)
save_module(orca_mod_file, "orca-4", MODULEDIR)
if isvalid(orca_path):
# If orca4 is a file, point to folder instead
if os.path.isfile(orca_path) and orca_path.endswith("/orca"):
orca_path = orca_path[:-5]
run_install_openmpi("./", "1.6.5", MODULEDIR)
orca_mod_file = '''help([[
For detailed instructions, go to:
https://orcaforum.cec.mpg.de/
]])
whatis("Version: $VERSION$")
whatis("Keywords: Orca 3")
whatis("URL: https://orcaforum.cec.mpg.de/")
whatis("Description: Orca 3")
load("openmpi/$VERSION$")
prepend_path("PATH", "$ORCA$")
prepend_path("LD_LIBRARY_PATH", "$ORCA$")
'''
swap_with_this = [("$ORCA$", orca_path), ("$VERSION$", "1.6.5")]
for k, v in swap_with_this:
while k in orca_mod_file:
orca_mod_file = orca_mod_file.replace(k, v)
save_module(orca_mod_file, "orca-3", MODULEDIR)
def run_install(location, MODULEDIR):
os.chdir(location)
cwd = os.getcwd()
if cwd.endswith("/"):
cwd = cwd[:-1]
if os.path.exists("packmol"):
print("Packmol folder already exists, so will not re-install")
else:
os.system("git clone https://github.com/mcubeg/packmol")
os.chdir("packmol")
os.system("./configure")
BAD_MARCC_FORTRAN = "FORTRAN=/software/centos7/bin/gfortran"
GOOD_MARCC_FORTRAN = "FORTRAN=/software/apps/compilers/gcc/6.4.0/bin/gfortran"
# On MARCC, if the FORTRAN attempted to use is BAD_MARCC_FOTRAN, then
# switch to GOOD_MARCC_FORTRAN
makefile = open("Makefile", 'r').read()
if BAD_MARCC_FORTRAN in makefile:
makefile = makefile.replace(BAD_MARCC_FORTRAN, GOOD_MARCC_FORTRAN)
fptr = open("Makefile", 'w')
fptr.write(makefile)
fptr.close()
os.system("make")
os.chdir("../")
packmol_mod_file = '''help([[
For detailed instructions, go to:
http://m3g.iqm.unicamp.br/packmol/home.shtml
https://github.com/mcubeg/packmol
]])
whatis("Version: unknown")
whatis("Keywords: Packmol")
whatis("URL: http://m3g.iqm.unicamp.br/packmol/home.shtml")
whatis("Description: Packmol")
prepend_path("PATH", "$CWD/packmol")
'''
while "$CWD" in packmol_mod_file:
packmol_mod_file = packmol_mod_file.replace("$CWD", cwd)
save_module(packmol_mod_file, "packmol", MODULEDIR)
return cwd + "/packmol/packmol"
def run_install(anaconda_path):
homedir = os.path.expanduser("~")
potential_anaconda_install_dirs = [
homedir + "/anaconda",
homedir + "/anaconda2",
"/software/apps/anaconda/5.2/python/2.7"
]
if anaconda_path is not None:
potential_anaconda_install_dirs += [anaconda_path]
for folder in potential_anaconda_install_dirs:
if os.path.exists(folder):
print("Found anaconda at %s" % folder)
anaconda_path = folder
break
if anaconda_path is not None and anaconda_path.strip() not in ["", "None"]:
if anaconda_path.endswith("/"):
anaconda_path = anaconda_path[:-1]
else:
print("Could not find anaconda, so will install it.")
download_file(
homedir,
"https://repo.continuum.io/archive/Anaconda2-5.2.0-Linux-x86_64.sh",
"5c034a4ab36ec9b6ae01fa13d8a04462"
)
os.system('bash ~/Anaconda2-5.2.0-Linux-x86_64.sh -fb')
anaconda_path = homedir + "/anaconda2"
anaconda_module = '''
help([[
For detailed instructions, go to:
http://www.anaconda.com
]])
whatis("Version: Anaconda 5.2.0, Python 2.7")
whatis("Description: Anaconda, Python")
prepend_path("PATH", "$ANACONDA/bin")
prepend_path("LD_LIBRARY_PATH", "$ANACONDA/lib")
'''.replace("$ANACONDA", anaconda_path).replace("$ANACONDA", anaconda_path)
save_module(anaconda_module, "anaconda-2.7")
return anaconda_path
def run_install(location,
VERSION,
SFFX,
name,
extra_lammps_packages=[],
smrff_path=None,
MODULEDIR=None,
compiler="mpicxx"):
LAMMPS_MAKEFILE = '''
# mpi = MPI with its default compiler
SHELL = /bin/sh
# ---------------------------------------------------------------------
# compiler/linker settings
# specify flags and libraries needed for your compiler
CC = $CC$
# Wall and Wextra simply print additional warnings
# m64 compiles for 64 bit memory
# static-libgcc and static-libstdc++ are to make the final binary as
# portable as possible
# g means to compile this with debugging flags
CCFLAGS = -std=c++11 -g -O3 -m64 -static-libgcc -static-libstdc++ -Wall -Wextra
SHFLAGS = -fPIC
DEPFLAGS = -M
LINK = $CC$
LINKFLAGS = -std=c++11 -g -O3 -m64 -static-libgcc -static-libstdc++ -Wall -Wextra
LIB =
SIZE = size
ARCHIVE = ar
ARFLAGS = -rc
SHLIBFLAGS = -shared
# ---------------------------------------------------------------------
# LAMMPS-specific settings, all OPTIONAL
# specify settings for LAMMPS features you will use
# if you change any -D setting, do full re-compile after "make clean"
# LAMMPS ifdef settings
# see possible settings in Section 2.2 (step 4) of manual
LMP_INC = -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64
# MPI library
# see discussion in Section 2.2 (step 5) of manual
# MPI wrapper compiler/linker can provide this info
# can point to dummy MPI library in src/STUBS as in Makefile.serial
# use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts
# INC = path for mpi.h, MPI compiler settings
# PATH = path for MPI library
# LIB = name of MPI library
MPI_INC = $MPIINC$ -I$PYTHON_DIR$/include/python3.7m
MPI_PATH = $MPIPATH$ -L$PYTHON_DIR$/lib
MPI_LIB = $MPILIB$ -lpython3.7m
# FFT library
# see discussion in Section 2.2 (step 6) of manual
# can be left blank to use provided KISS FFT library
# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings
# PATH = path for FFT library
# LIB = name of FFT library
FFT_INC =
FFT_PATH =
FFT_LIB =
# JPEG and/or PNG library
# see discussion in Section 2.2 (step 7) of manual
# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC
# INC = path(s) for jpeglib.h and/or png.h
# PATH = path(s) for JPEG library and/or PNG library
# LIB = name(s) of JPEG library and/or PNG library
JPG_INC =
JPG_PATH =
JPG_LIB =
# ---------------------------------------------------------------------
# build rules and dependencies
# do not edit this section
include Makefile.package.settings
include Makefile.package
EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
EXTRA_CPP_DEPENDS = $(PKG_CPP_DEPENDS)
EXTRA_LINK_DEPENDS = $(PKG_LINK_DEPENDS)
# Path to src files
vpath %.cpp ..
vpath %.h ..
# Link target
$(EXE): $(OBJ) $(EXTRA_LINK_DEPENDS)
\t$(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
\t$(SIZE) $(EXE)
# Library targets
lib: $(OBJ) $(EXTRA_LINK_DEPENDS)
\t$(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
shlib: $(OBJ) $(EXTRA_LINK_DEPENDS)
\t$(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
\t\t$(OBJ) $(EXTRA_LIB) $(LIB)
# Compilation rules
%.o:%.cpp
\t$(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
# Individual dependencies
depend : fastdep.exe $(SRC)
\t@./fastdep.exe $(EXTRA_INC) -- $^ > .depend || exit 1
fastdep.exe: ../DEPEND/fastdep.c
\tcc -O -o $@ $<
sinclude .depend
'''
mpi_inc = "-DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1"
mpi_path = ""
mpi_lib = ""
serial_inc = "-I../STUBS"
serial_path = "-L../STUBS"
serial_lib = "-lmpi_stubs"
python_path = sys.executable
PYTHON_DIR = python_path.split("/bin")[0]
while "$PYTHON_DIR$" in LAMMPS_MAKEFILE:
LAMMPS_MAKEFILE = LAMMPS_MAKEFILE.replace("$PYTHON_DIR$", PYTHON_DIR)
while "$CC$" in LAMMPS_MAKEFILE:
LAMMPS_MAKEFILE = LAMMPS_MAKEFILE.replace("$CC$", compiler)
assert SFFX in ["serial", "mpi"],\
"Error - SFFX should be either serial or mpi. It was %s." % SFFX
if SFFX == "mpi":
LAMMPS_MAKEFILE = LAMMPS_MAKEFILE.replace("$MPIINC$", mpi_inc)
LAMMPS_MAKEFILE = LAMMPS_MAKEFILE.replace("$MPIPATH$", mpi_path)
LAMMPS_MAKEFILE = LAMMPS_MAKEFILE.replace("$MPILIB$", mpi_lib)
elif SFFX == "serial":
LAMMPS_MAKEFILE = LAMMPS_MAKEFILE.replace("$MPIINC$", serial_inc)
LAMMPS_MAKEFILE = LAMMPS_MAKEFILE.replace("$MPIPATH$", serial_path)
LAMMPS_MAKEFILE = LAMMPS_MAKEFILE.replace("$MPILIB$", serial_lib)
# Error Handling
VERSION = str(VERSION)
NAME = "LAMMPs"
FOLDER = "lammps/" + name
TARFILE = "lammps-%s.tar.gz" % VERSION
URL = "https://lammps.sandia.gov/tars/lammps-%s.tar.gz" % VERSION
lammps_hashes = {"16Mar18": "8059f1cac17ac74c099ba6c5a5e3a558"}
if VERSION not in lammps_hashes:
lammps_hashes[VERSION] = ""
print(
"For future reference, please store the lammps hash of this .tar.gz file."
)
HASH = lammps_hashes[VERSION]
HELPURL = "https://lammps.sandia.gov"
os.chdir(location)
cwd = os.getcwd()
if cwd.endswith("/"):
cwd = cwd[:-1]
MODULE_LOADERS = ""
if not os.path.exists(FOLDER):
os.system("mkdir -p %s" % FOLDER)
download_file(cwd, URL, HASH)
# Untar the file to the folder openmpi/openmpi-VERSION
os.system("tar -xzf %s -C %s" % (TARFILE, FOLDER))
# Now we have lammps/version/lammps-version/src
# So, we mv it back
os.system("mv %s/lammps-%s %s/.." % (FOLDER, VERSION, FOLDER))
os.system("rm -rf %s" % FOLDER)
os.system("mv lammps/lammps-%s %s" % (VERSION, FOLDER))
# Change into src, configure, and make
os.chdir("%s/src" % FOLDER)
if smrff_path is not None and os.path.exists(smrff_path):
print("Will install smrff into this lammps install.")
if VERSION != "16Mar18":
print(
"WARNING! SMRFF is only guaranteed to work for lammps version 16Mar18. Will compile anyways, but good luck."
)
os.system("cp -rf %s/lammps/lammps-16Mar18/src/* ." % smrff_path)
fptr = open("MAKE/Makefile.%s" % SFFX, 'w')
fptr.write(LAMMPS_MAKEFILE)
fptr.close()
for pkg in extra_lammps_packages:
os.system("make yes-%s" % pkg)
# Setup stubs if serial
if SFFX == "serial":
os.chdir("STUBS")
os.system("make")
os.chdir("../")
# Bug fix before compiling
fname = "python_impl.cpp"
possibly_buggy_file = open(fname, 'r').read().strip()
bad_line = " char *pystr = PY_STRING_AS_STRING(pValue);"
good_line = " const char *pystr = PY_STRING_AS_STRING(pValue);"
if bad_line in possibly_buggy_file:
fptr = open(fname, 'w')
fptr.write(possibly_buggy_file.replace(bad_line, good_line))
fptr.close()
os.system("make %s -j 4" % SFFX)
os.system("make %s -j 4 mode=shlib" % SFFX)
###############################
os.chdir("../../../")
print("CURRENT DIR = %s" % os.getcwd())
else:
print("%s folder already exists, so will not re-install." % NAME)
mod_file = '''help([[
For detailed instructions, go to:
$HELPURL$
This version of LAMMPS was compiled with the following packages:
''' + "\n ".join(extra_lammps_packages) + '''
''' + (" SMRFF" if smrff_path is not None else "") + '''
]])
whatis("Version: $VERSION$")
whatis("Keywords: $NAME$")
whatis("URL: $HELPURL$")
whatis("Description: $NAME$")
prepend_path("PATH", "$CWD$/$FOLDER$/src")
prepend_path("PYTHONPATH", "$CWD$/$FOLDER$/python")
prepend_path("LD_LIBRARY_PATH", "$CWD$/$FOLDER$/src")
$MODULE_LOADERS$
'''
rep = {
"$CWD$": cwd,
"$FOLDER$": FOLDER,
"$NAME$": NAME,
"$VERSION$": VERSION,
"$HELPURL$": HELPURL,
"$MODULE_LOADERS$": MODULE_LOADERS,
}
for identifier, word in rep.items():
while identifier in mod_file:
mod_file = mod_file.replace(identifier, str(word))
HOMEDIR = os.path.expanduser("~")
if MODULEDIR is None:
MODULEDIR = HOMEDIR + "/.modules"
if not os.path.exists("%s/lammps" % MODULEDIR):
os.makedirs("%s/lammps" % MODULEDIR, exist_ok=True)
save_module(mod_file, FOLDER, MODULEDIR)
return cwd + "/" + FOLDER + "/src/lmp_" + SFFX
def _squid_setup(anaconda_path,
default_modules,
lmp_path,
packmol_path,
orca_path, orca4_path,
vmd_path, ovito_path,
queueing_system,
orca_sub_flag,
env_vars, orca_env_vars, orca4_env_vars,
lmp_env_vars, mpi_preface, python_path,
text_editor_path, g09_formchk, g09_cubegen,
mpirun_path, default_queue,
use_orca4, sandbox_orca,
cwd, HOMEDIR):
'''
This function will setup the squid sysconst file and module.
'''
opls_path = cwd + '/forcefield_parameters/oplsaa.prm'
vars_to_include = [
orca_path, orca4_path, vmd_path, ovito_path, opls_path, packmol_path,
lmp_path, queueing_system, orca_sub_flag, env_vars,
orca_env_vars, orca4_env_vars, lmp_env_vars, mpi_preface, python_path,
text_editor_path, g09_formchk, g09_cubegen, mpirun_path, default_queue]
s_vars_to_include = [
"orca_path", "orca4_path", "vmd_path", "ovito_path", "opls_path",
"packmol_path", "lmp_path", "queueing_system",
"orca_sub_flag", "env_vars", "orca_env_vars", "orca4_env_vars",
"lmp_env_vars", "mpi_preface", "python_path", "TEXT_EDITOR_PATH",
"g09_formchk", "g09_cubegen", "mpirun_path", "default_queue"]
sysconst_file_string = """# System Constants. This includes paths to where things are installed
orca_path = "$ORCA_PATH"
orca4_path = "$ORCA4_PATH"
use_orca4 = """ + str(use_orca4) + """
sandbox_orca = """ + str(sandbox_orca) + """
g09_formchk = "$G09_FORMCHK"
g09_cubegen = "$G09_CUBEGEN"
vmd_path = "$VMD_PATH"
ovito_path = "$OVITO_PATH"
opls_path = "$OPLS_PATH"
packmol_path = "$PACKMOL_PATH"
lmp_path = "$LMP_PATH"
python_path = "$PYTHON_PATH"
mpirun_path = "$MPIRUN_PATH"
queueing_system = "$QUEUEING_SYSTEM" # nbs, pbs, slurm
default_queue = "$DEFAULT_QUEUE"
slurm_default_allocation = None
nbs_ssh = None
nbs_bin_path = ""
# Default modules to load in pysub submission.
default_pysub_modules = ["squid"]
# Submission flags for queueing system
orca_sub_flag = "$ORCA_SUB_FLAG"
# A list of all paths/environment variables needed for queue submission
env_vars = '''$ENV_VARS'''
orca_env_vars = '''$ORCA_ENV_VARS'''
orca4_env_vars = '''$ORCA4_ENV_VARS'''
lmp_env_vars = '''$LMP_ENV_VARS'''
# Mpi preface for job submission
mpi_preface = "$MPI_PREFACE"
"""
for s, v in zip(s_vars_to_include, vars_to_include):
ss = "$" + s.upper()
while ss in sysconst_file_string:
sysconst_file_string = sysconst_file_string.replace(
"$%s" % s.upper(), str(v)
)
fptr_sysconst = open("squid/sysconst.py", 'w')
fptr_sysconst.write(sysconst_file_string)
fptr_sysconst.close()
exports_and_aliases = """
--------------------------------------------------------------------------
--------- Squid Exports and Aliases v 0.0.1 ---------
--------------------------------------------------------------------------
help([[
For detailed instructions, go to:
https://clancylab.github.io/squid/squid.html
]])
whatis("Version: 1.2")
whatis("Keywords: Squid, Clancy")
whatis("URL: https://clancylab.github.io/squid/squid.html")
whatis("Description: Clancy Lab Codebase")
prepend_path( "PYTHONPATH", "$CWD")
-- Aliases
set_alias('chkDFT','python $CWD/console_scripts/chkDFT.py')
set_alias('scanDFT','python $CWD/console_scripts/scanDFT.py')
set_alias('chko','function _chko() { chkDFT $1 -dft orca $@ ; } ; _chko')
set_alias('viewo','function _viewo() { chkDFT $1 -dft orca -v $@ ; } ; _viewo')
set_alias('otail','function _otail() { tail orca/$1/$1.out $2 $3 ; } ; _otail')
set_alias('tailo','otail')
set_alias('otxt','function _otxt() { orca/$1/$1.out & ; } ; _otxt')
set_alias('txto','otxt')
set_alias('get_ext_list','$PYTHON_PATH $CWD/console_scripts/get_ext_list.py')
set_alias('pysub','$CWD/console_scripts/pysub.py $PWD/')
set_alias('procrustes','$CWD/console_scripts/procrustes.py $PWD/')
set_alias('view_lmp','function _view_lmp() { $PYTHON_PATH $CWD/console_scripts/view_lmp.py $1 $@ ; } ; _view_lmp')
set_alias('vmd_lmp','function _vmd_lmp() { $PYTHON_PATH $CWD/console_scripts/vmd_lmp.py $1 $@ ; } ; _vmd_lmp')
-- Load all dependencies
""" + default_modules
swap_with_this = [
("$CWD", cwd),
("$PYTHON_PATH", python_path)
]
for k, v in swap_with_this:
while k in exports_and_aliases:
exports_and_aliases = exports_and_aliases.replace(k, v)
for s, v in zip(s_vars_to_include, vars_to_include):
ss = "$" + s.upper()
while ss in exports_and_aliases:
exports_and_aliases = exports_and_aliases.replace(ss, v)
save_module(exports_and_aliases.strip() + "\n", "squid")
def run_install(location, version, MODULEDIR):
# Error Handling
version = str(version)
assert version.count(".") == 2, VERSION_ERROR
MAIN_VERSION = ".".join(version.split(".")[:-1])
VERSION = str(version)
NAME = "OpenMPI"
FOLDER = "openmpi/" + str(version)
TARFILE = "openmpi-" + VERSION + ".tar.gz"
URL = "https://download.open-mpi.org/release/open-mpi/v" +\
MAIN_VERSION +\
"/openmpi-" + VERSION +\
".tar.gz"
HASH = {
"3.1.4": "ee6d8b66c967a38aa74e3d52a9f52ec0",
"3.1.3": "121bab028a16ba50e27ab0952bf99e11",
"2.1.5": "6918dc76ca4f0ba0f41fe44dfd5a976b",
"2.0.2": "886698becc5bea8c151c0af2074b8392",
"1.6.5": "d7e98ac8ae1a27a0e37a68b6588c3d97",
}
HELPURL = "https://www.open-mpi.org"
os.chdir(location)
cwd = os.getcwd()
if cwd.endswith("/"):
cwd = cwd[:-1]
if not os.path.exists(FOLDER):
os.system("mkdir -p %s/build" % FOLDER)
download_file(cwd, URL, HASH)
# Untar the file to the folder openmpi/openmpi-VERSION
os.system("tar -xzf %s -C %s" % (TARFILE, FOLDER))
# Move that new folder to be named src
os.system("mv %s/openmpi-%s %s/src" % (FOLDER, VERSION, FOLDER))
# Change into src, configure, and make
os.chdir("%s/src" % FOLDER)
os.system("./configure --prefix=%s/%s/build" % (cwd, FOLDER))
os.system("make -j 4")
os.system("make install")
###############################
os.chdir("../../../")
else:
print("%s folder already exists, so will not re-install." % NAME)
mod_file = '''help([[
For detailed instructions, go to:
$HELPURL$
]])
whatis("Version: $VERSION$")
whatis("Keywords: $NAME$")
whatis("URL: $HELPURL$")
whatis("Description: $NAME$")
prepend_path("PATH", "$CWD$/$FOLDER$/build/bin")
prepend_path("LD_LIBRARY_PATH", "$CWD$/$FOLDER$/build/lib")
'''
rep = {
"$CWD$": cwd,
"$FOLDER$": FOLDER,
"$NAME$": NAME,
"$VERSION$": VERSION,
"$HELPURL$": HELPURL
}
for identifier, word in rep.items():
while identifier in mod_file:
mod_file = mod_file.replace(identifier, str(word))
HOMEDIR = os.path.expanduser("~")
if MODULEDIR is None:
MODULEDIR = HOMEDIR + "/.modules"
if not os.path.exists("%s/openmpi" % MODULEDIR):
os.makedirs("%s/openmpi" % MODULEDIR, exist_ok=True)
save_module(mod_file, FOLDER, MODULEDIR)
def run_install(location, version):
# Error Handling
version = str(version)
assert version.count(".") == 2, VERSION_ERROR
MAIN_VERSION = ".".join(version.split(".")[:-1])
VERSION = str(version)
NAME = "OpenMPI"
FOLDER = "openmpi/" + str(version)
TARFILE = "openmpi-" + VERSION + ".tar.gz"
URL = "https://download.open-mpi.org/release/open-mpi/v" +\
MAIN_VERSION +\
"/openmpi-" + VERSION +\
".tar.gz"
HASH = {
"2.1.5": "X",
"2.0.2": "X",
"1.6.5": "X",
}
HELPURL = "https://www.open-mpi.org"
os.chdir(location)
cwd = os.getcwd()
if cwd.endswith("/"):
cwd = cwd[:-1]
if not os.path.exists(FOLDER):
os.system("mkdir -p %s/build" % FOLDER)
download_file(cwd, URL, HASH)
# Untar the file to the folder openmpi/openmpi-VERSION
os.system("tar -xzf %s -C %s" % (TARFILE, FOLDER))
# Move that new folder to be named src
os.system("mv %s/openmpi-%s %s/src" % (FOLDER, VERSION, FOLDER))
# Change into src, configure, and make
os.chdir("%s/src" % FOLDER)
os.system("./configure --prefix=%s/%s/build" % (cwd, FOLDER))
os.system("make -j 4")
os.system("make install")
###############################
os.chdir("../../../")
else:
print("%s folder already exists, so will not re-install." % NAME)
mod_file = '''help([[
For detailed instructions, go to:
$HELPURL$
]])
whatis("Version: $VERSION$")
whatis("Keywords: $NAME$")
whatis("URL: $HELPURL$")
whatis("Description: $NAME$")
prepend_path("PATH", "$CWD$/$FOLDER$/build/bin")
prepend_path("LD_LIBRARY_PATH", "$CWD$/$FOLDER$/build/lib")
'''
rep = {
"$CWD$": cwd,
"$FOLDER$": FOLDER,
"$NAME$": NAME,
"$VERSION$": VERSION,
"$HELPURL$": HELPURL
}
for identifier, word in rep.items():
while identifier in mod_file:
mod_file = mod_file.replace(identifier, str(word))
HOMEDIR = os.path.expanduser("~")
if not os.path.exists("%s/.modules" % HOMEDIR):
os.mkdir("%s/.modules" % HOMEDIR)
if not os.path.exists("%s/.modules/openmpi" % HOMEDIR):
os.mkdir("%s/.modules/openmpi" % HOMEDIR)
save_module(mod_file, FOLDER)
def run_install(location, VERSION, MODULEDIR):
NAME = "NLOpt"
FOLDER = "nlopt/%s" % VERSION
TARFILE = "v%s.tar.gz" % VERSION
URL = "https://github.com/stevengj/nlopt/archive/v%s.tar.gz" % VERSION
HASH = {
"2.5.0": "ada08c648bf9b52faf8729412ff6dd6d",
"2.6.1": "108eeca31ec184f955b3c26d016fe3fa",
}[VERSION]
HELPURL = "https://nlopt.readthedocs.io/en/latest/"
python_path = sys.executable
os.chdir(location)
cwd = os.getcwd()
if cwd.endswith("/"):
cwd = cwd[:-1]
if not os.path.exists(FOLDER):
os.makedirs("%s/build" % FOLDER, exist_ok=True)
download_file(cwd, URL, HASH)
os.system("tar -C %s/ -xzf %s" % (FOLDER, TARFILE))
os.system("mv %s/nlopt-%s %s/src" % (FOLDER, VERSION, FOLDER))
os.makedirs("%s/src/build" % FOLDER, exist_ok=True)
os.chdir("%s/src/build" % FOLDER)
# Specific Install Instructions
os.system(
"cmake .. -DCMAKE_INSTALL_PREFIX=%s/%s/build -DPYTHON_EXECUTABLE=%s"
% (cwd, FOLDER, python_path))
os.system("make; make install")
###############################
os.chdir("../../../")
else:
print("%s folder already exists, so will not re-install." % NAME)
mod_file = '''help([[
For detailed instructions, go to:
$HELPURL$
This version of nlopt was compiled with python 3.7.
]])
whatis("Version: $VERSION$")
whatis("Keywords: $NAME$")
whatis("URL: $HELPURL$")
whatis("Description: $NAME$")
prepend_path("PATH", "$CWD$/$FOLDER$/build/bin")
prepend_path("LD_LIBRARY_PATH", "$CWD$/$FOLDER$/build/lib")
prepend_path("LD_LIBRARY_PATH", "$CWD$/$FOLDER$/build/lib64")
prepend_path("PYTHONPATH", "$CWD$/$FOLDER$/build/lib/python3.7/site-packages")
'''
rep = {
"$CWD$": cwd,
"$FOLDER$": FOLDER,
"$NAME$": NAME,
"$VERSION$": VERSION,
"$HELPURL$": HELPURL
}
for identifier, word in rep.items():
while identifier in mod_file:
mod_file = mod_file.replace(identifier, str(word))
HOMEDIR = os.path.expanduser("~")
if MODULEDIR is None:
MODULEDIR = HOMEDIR + "/.modules"
if not os.path.exists("%s/nlopt" % MODULEDIR):
os.makedirs("%s/nlopt" % MODULEDIR, exist_ok=True)
save_module(mod_file, FOLDER, MODULEDIR)