Merge pull request #1228 from invemichele/fix_plumed_install

  else: error()

homepath = fullpath(homepath)

homedir = "%s/plumed2" % (homepath)

if (pathflag):

    if not os.path.isdir(plumedpath): error("Plumed2 path does not exist")

  if os.path.exists("%s/plumed-%s" % (homepath,version)):

    cmd = 'rm -rf "%s/plumed-%s"' % (homepath,version)

    subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)

  if os.path.exists("%s/plumed2" % (homepath)):

    cmd = 'rm -rf "%s/plumed2"' % (homepath)

  if os.path.exists(homedir):

    cmd = 'rm -rf "%s"' % (homedir)

    subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)

  cmd = 'cd "%s"; tar -xzvf %s' % (homepath,filename)

  subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)

  os.remove("%s/%s" % (homepath,filename))

  # build plumed

if buildflag:

  print("Building plumed ...")

   cmd = 'cd %s/plumed-%s; ./configure --prefix=%s/plumed2 --enable-static-patch ; make ; make install' % (homepath,version,homepath)

  try:

    import multiprocessing

    n_cpus = multiprocessing.cpu_count()

  except:

    n_cpus = 1

  cmd = 'cd %s/plumed-%s; ./configure --prefix=%s --enable-static-patch ; make -j%d ; make install' % (homepath,version,homedir,n_cpus)

  txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True)

  print(txt.decode('UTF-8'))

# 

# create 2 links in lib/plumed to plumed2 installation dir

if linkflag: