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Sat, May 11, 22:04

Install.py
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#!/usr/bin/env python
# install.py tool to download, compile, and setup the kim-api library
# used to automate the steps described in the README file in this dir
from __future__ import print_function
import sys,os,re,subprocess
# help message
help = """
Syntax from src dir: make lib-kim args="-b -v version -a kim-name"
or: make lib-kim args="-b -a everything"
or: make lib-kim args="-n -a kim-name"
or: make lib-kim args="-p /usr/local/open-kim -a kim-name"
Syntax from lib dir: python Install.py -b -v version -a kim-name
or: python Install.py -b -a everything
or: python Install.py -n -a kim-name
or: python Install.py -p /usr/local/open-kim -a kim-name
specify one or more options, order does not matter
-v = version of KIM API library to use
default = kim-api-v1.8.2 (current as of June 2017)
-b = download and build base KIM API library with example Models
this will delete any previous installation in the current folder
-n = do NOT download and build base KIM API library.
Use an existing installation
-p = specify location of KIM API installation (implies -n)
-a = add single KIM model or model driver with kim-name
to existing KIM API lib (see example below).
If kim-name = everything, then rebuild KIM API library with
*all* available OpenKIM Models (make take a long time).
-vv = be more verbose about what is happening while the script runs
Examples:
make lib-kim args="-b" # install KIM API lib with only example models
make lib-kim args="-a Glue_Ercolessi_Adams_Al__MO_324507536345_001" # Ditto plus one model
make lib-kim args="-b -a everything" # install KIM API lib with all models
make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # only add one model or model driver
See the list of KIM model drivers here:
https://openkim.org/kim-items/model-drivers/alphabetical
See the list of all KIM models here:
https://openkim.org/kim-items/models/by-model-drivers
See the list of example KIM models included by default here:
https://openkim.org/kim-api
in the "What is in the KIM API source package?" section
"""
def error(str=None):
if not str: print(help)
else: print("ERROR",str)
sys.exit()
# expand to full path name
# process leading '~' or relative path
def fullpath(path):
return os.path.abspath(os.path.expanduser(path))
def which(program):
def is_exe(fpath):
return os.path.isfile(fpath) and os.access(fpath, os.X_OK)
fpath, fname = os.path.split(program)
if fpath:
if is_exe(program):
return program
else:
for path in os.environ["PATH"].split(os.pathsep):
path = path.strip('"')
exe_file = os.path.join(path, program)
if is_exe(exe_file):
return exe_file
return None
def geturl(url,fname):
success = False
if which('curl') != None:
cmd = 'curl -L -o "%s" %s' % (fname,url)
try:
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
success = True
except subprocess.CalledProcessError as e:
print("Calling curl failed with: %s" % e.output.decode('UTF-8'))
if not success and which('wget') != None:
cmd = 'wget -O "%s" %s' % (fname,url)
try:
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
success = True
except subprocess.CalledProcessError as e:
print("Calling wget failed with: %s" % e.output.decode('UTF-8'))
if not success:
error("Failed to download source code with 'curl' or 'wget'")
return
# parse args
args = sys.argv[1:]
nargs = len(args)
if nargs == 0: error()
thisdir = os.environ['PWD']
version = "kim-api-v1.8.2"
buildflag = False
everythingflag = False
addflag = False
verboseflag = False
pathflag = False
iarg = 0
while iarg < len(args):
if args[iarg] == "-v":
if iarg+2 > len(args): error()
version = args[iarg+1]
iarg += 2
elif args[iarg] == "-b":
buildflag = True
iarg += 1
elif args[iarg] == "-n":
buildflag = False
iarg += 1
elif args[iarg] == "-p":
if iarg+2 > len(args): error()
kimdir = fullpath(args[iarg+1])
pathflag = True
buildflag = False
iarg += 2
elif args[iarg] == "-a":
addflag = True
if iarg+2 > len(args): error()
addmodelname = args[iarg+1]
if addmodelname == "everything":
buildflag = True
everythingflag = True
addflag = False
iarg += 2
elif args[iarg] == "-vv":
verboseflag = True
iarg += 1
else: error()
thisdir = os.path.abspath(thisdir)
url = "https://s3.openkim.org/kim-api/%s.tgz" % version
# set KIM API directory
if pathflag:
if not os.path.isdir(kimdir):
print("\nkim-api is not installed at %s" % kimdir)
error()
# configure LAMMPS to use existing kim-api installation
with open("%s/Makefile.KIM_DIR" % thisdir, 'w') as mkfile:
mkfile.write("KIM_INSTALL_DIR=%s\n\n" % kimdir)
mkfile.write(".DUMMY: print_dir\n\n")
mkfile.write("print_dir:\n")
mkfile.write(" @printf $(KIM_INSTALL_DIR)\n")
with open("%s/Makefile.KIM_Config" % thisdir, 'w') as cfgfile:
cfgfile.write("include %s/lib/kim-api/Makefile.KIM_Config" % kimdir)
print("Created %s/Makefile.KIM_DIR\n using %s" % (thisdir,kimdir))
else:
kimdir = os.path.join(os.path.abspath(thisdir), "installed-" + version)
# download KIM tarball, unpack, build KIM
if buildflag:
# check to see if an installed kim-api already exists and wipe it out.
if os.path.isdir(kimdir):
print("kim-api is already installed at %s.\nRemoving it for re-install" % kimdir)
cmd = 'rm -rf "%s"' % kimdir
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
# configure LAMMPS to use kim-api to be installed
with open("%s/Makefile.KIM_DIR" % thisdir, 'w') as mkfile:
mkfile.write("KIM_INSTALL_DIR=%s\n\n" % kimdir)
mkfile.write(".DUMMY: print_dir\n\n")
mkfile.write("print_dir:\n")
mkfile.write(" @printf $(KIM_INSTALL_DIR)\n")
with open("%s/Makefile.KIM_Config" % thisdir, 'w') as cfgfile:
cfgfile.write("include %s/lib/kim-api/Makefile.KIM_Config" % kimdir)
print("Created %s/Makefile.KIM_DIR\n using %s" % (thisdir,kimdir))
# download entire kim-api tarball
print("Downloading kim-api tarball ...")
geturl(url,"%s/%s.tgz" % (thisdir,version))
print("Unpacking kim-api tarball ...")
cmd = 'cd "%s"; rm -rf "%s"; tar -xzvf %s.tgz' % (thisdir,version,version)
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
# configure kim-api
print("Configuring kim-api ...")
cmd = 'cd "%s/%s"; ./configure --prefix="%s"' % (thisdir,version,kimdir)
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
# build kim-api
print("Configuring example Models")
cmd = 'cd "%s/%s"; make add-examples' % (thisdir,version)
txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
if verboseflag: print (txt.decode("UTF-8"))
if everythingflag:
print("Configuring all OpenKIM models, this will take a while ...")
cmd = 'cd "%s/%s"; make add-OpenKIM' % (thisdir,version)
txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
if verboseflag: print(txt.decode("UTF-8"))
print("Building kim-api ...")
cmd = 'cd "%s/%s"; make' % (thisdir,version)
txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
if verboseflag: print(txt.decode("UTF-8"))
# install kim-api
print("Installing kim-api ...")
cmd = 'cd "%s/%s"; make install' % (thisdir,version)
txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
if verboseflag: print(txt.decode("UTF-8"))
cmd = 'cd "%s/%s"; make install-set-default-to-v1' %(thisdir,version)
txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
if verboseflag: print(txt.decode("UTF-8"))
# remove source files
print("Removing kim-api source and build files ...")
cmd = 'cd "%s"; rm -rf %s; rm -rf %s.tgz' % (thisdir,version,version)
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
# add a single model (and possibly its driver) to existing KIM installation
if addflag:
if not os.path.isdir(kimdir):
print("\nkim-api is not installed")
error()
# download single model
print("Downloading tarball for %s..." % addmodelname)
url = "https://openkim.org/download/%s.tgz" % addmodelname
geturl(url,"%s/%s.tgz" % (thisdir,addmodelname))
print("Unpacking item tarball ...")
cmd = 'cd "%s"; tar -xzvf %s.tgz' % (thisdir,addmodelname)
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
print("Building item ...")
cmd = 'cd "%s/%s"; make; make install' %(thisdir,addmodelname)
try:
txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
except subprocess.CalledProcessError as e:
# Error: but first, check to see if it needs a driver
firstRunOutput = e.output.decode("UTF-8")
cmd = 'cd "%s/%s"; make kim-item-type' % (thisdir,addmodelname)
txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
txt = txt.decode("UTF-8")
if txt == "ParameterizedModel":
# Get and install driver
cmd = 'cd "%s/%s"; make model-driver-name' % (thisdir,addmodelname)
txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
adddrivername = txt.decode("UTF-8").strip()
print("First installing model driver: %s..." % adddrivername)
cmd = 'cd "%s"; python Install.py -n -a %s' % (thisdir,adddrivername)
try:
txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
except subprocess.CalledProcessError as e:
print(e.output)
sys.exit()
if verboseflag: print(txt.decode("UTF-8"))
# now install the model that needed the driver
print("Now installing model : %s" % addmodelname)
cmd = 'cd "%s"; python Install.py -n -a %s' % (thisdir,addmodelname)
try:
txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
except subprocess.CalledProcessError as e:
print(e.output)
sys.exit()
print(txt.decode("UTF-8"))
sys.exit()
else:
print(firstRunOutput)
print("Error, unable to build and install OpenKIM item: %s" \
% addmodelname)
sys.exit()
# success the first time
if verboseflag: print(txt.decode("UTF-8"))
print("Removing kim item source and build files ...")
cmd = 'cd "%s"; rm -rf %s; rm -rf %s.tgz' %(thisdir,addmodelname,addmodelname)
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)

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