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some cleanups and small bugfixes to conform better with python conventions

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This commit is contained in:
Axel Kohlmeyer
2019-01-28 17:37:05 -05:00
parent 0cae619320
commit 1465352454
11 changed files with 846 additions and 234 deletions
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63
lib/plumed/Install.py
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@ -1,14 +1,17 @@
#!/usr/bin/env python
# Install.py tool to download, unpack, build, and link to the plumed2 library
# used to automate the steps described in the README file in this dir
"""
Install.py tool to download, unpack, build, and link to the plumed2 library
used to automate the steps described in the README file in this dir
"""
from __future__ import print_function
import sys,os,re,subprocess,hashlib,shutil
sys.path.append('..')
from install_helpers import get_cpus,fullpath,geturl,checkmd5sum
import sys, os, subprocess, shutil
from argparse import ArgumentParser
sys.path.append('..')
from install_helpers import get_cpus, fullpath, geturl, checkmd5sum
parser = ArgumentParser(prog='Install.py',
description="LAMMPS library build wrapper script")
@ -19,7 +22,7 @@ mode = "static"
# help message
help = """
HELP = """
Syntax from src dir: make lib-plumed args="-b"
or: make lib-plumed args="-b -v 2.4.3"
or: make lib-plumed args="-p /usr/local/plumed2 -m shared"
@ -57,13 +60,13 @@ parser.add_argument("-m", "--mode", default=mode, choices=['static', 'shared', '
args = parser.parse_args()
# print help message and exit, if neither build nor path options are given
if args.build == False and not args.path:
if not args.build and not args.path:
parser.print_help()
sys.exit(help)
sys.exit(HELP)
buildflag = args.build
pathflag = args.path != None
plumedpath= args.path
pathflag = args.path is not None
plumedpath = args.path
homepath = fullpath('.')
homedir = "%s/plumed2" % (homepath)
@ -76,31 +79,31 @@ if pathflag:
# download and unpack plumed2 tarball
if buildflag:
url = "https://github.com/plumed/plumed2/releases/download/v%s/plumed-src-%s.tgz" % (version,version)
url = "https://github.com/plumed/plumed2/releases/download/v%s/plumed-src-%s.tgz" % (version, version)
filename = "plumed-src-%s.tar.gz" %version
print("Downloading plumed ...")
geturl(url,filename)
geturl(url, filename)
# verify downloaded archive integrity via md5 checksum, if known.
if version in checksums:
if not checkmd5sum(checksums[version],filename):
if not checkmd5sum(checksums[version], filename):
sys.exit("Checksum for plumed2 library does not match")
print("Unpacking plumed2 source tarball ...")
if os.path.exists("%s/plumed-%s" % (homepath,version)):
shutil.rmtree("%s/plumed-%s" % (homepath,version))
if os.path.exists("%s/plumed-%s" % (homepath, version)):
shutil.rmtree("%s/plumed-%s" % (homepath, version))
if os.path.exists(homedir):
shutil.rmtree(homedir)
cmd = 'cd "%s"; tar -xzvf %s' % (homepath,filename)
subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
os.remove(os.path.join(homepath,filename))
cmd = 'cd "%s"; tar -xzvf %s' % (homepath, filename)
subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True)
os.remove(os.path.join(homepath, filename))
# build plumed
print("Building plumed ...")
n_cpus = get_cpus()
cmd = 'cd %s/plumed-%s; ./configure --prefix=%s --enable-modules=all --enable-static-patch ; make -j%d ; make install' % (homepath,version,homedir,n_cpus)
cmd = 'cd %s/plumed-%s; ./configure --prefix=%s --enable-modules=all --enable-static-patch ; make -j%d ; make install' % (homepath, version, homedir, n_cpus)
try:
txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)
txt = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True)
print(txt.decode('UTF-8'))
except subprocess.CalledProcessError as e:
print("Make failed with:\n %s" % e.output.decode('UTF-8'))
@ -113,20 +116,20 @@ if os.path.isfile("includelink") or os.path.islink("includelink"):
os.remove("includelink")
if os.path.isfile("liblink") or os.path.islink("liblink"):
os.remove("liblink")
os.symlink(os.path.join(homedir,'include'),'includelink')
libpath=os.path.join(homedir,'lib64')
if not os.path.exists(libpath): libpath=os.path.join(homedir,'lib')
os.symlink(libpath,'liblink')
os.symlink(os.path.join(homedir, 'include'), 'includelink')
libpath = os.path.join(homedir, 'lib64')
if not os.path.exists(libpath):
libpath = os.path.join(homedir, 'lib')
os.symlink(libpath, 'liblink')
if os.path.isfile("Makefile.lammps.%s" % mode):
print("Creating Makefile.lammps")
plumedinc = os.path.join('liblink','plumed','src','lib','Plumed.inc.' + mode)
lines1 = open(plumedinc,'r').readlines()
lines2 = open("Makefile.lammps.%s" % mode,'r').readlines()
fp = open("Makefile.lammps",'w')
fp.write(os.path.join("PLUMED_LIBDIR=",homedir,"lib\n"))
plumedinc = os.path.join('liblink', 'plumed', 'src', 'lib', 'Plumed.inc.' + mode)
lines1 = open(plumedinc, 'r').readlines()
lines2 = open("Makefile.lammps.%s" % mode, 'r').readlines()
fp = open("Makefile.lammps", 'w')
fp.write(os.path.join("PLUMED_LIBDIR=", homedir, "lib\n"))
for line in lines1:
fp.write(line)
for line in lines2:
fp.write(line)
fp.close()