git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7592 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/Make.py

@@ -0,0 +1,879 @@
+#!/usr/local/bin/python
+# if necessary, edit preceding line to point to your Python
+# or launch as "python Make.py ..."
+
+# Purpose: manage LAMMPS packages, external libraries, and builds
+#          create a version of LAMMPS specific to an input script(s)
+# Syntax: Make.py switch args ...
+# Help: type Make.py or Make.py -h
+
+# -----------------------------------------------------------------------
+# LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+# http://lammps.sandia.gov, Sandia National Laboratories
+# Steve Plimpton, sjplimp@sandia.gov
+#
+# Copyright (2003) Sandia Corporation.  Under the terms of Contract
+# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+# certain rights in this software.  This software is distributed under 
+# the GNU General Public License.
+#
+# See the README file in the top-level LAMMPS directory.
+# -----------------------------------------------------------------------
+
+# hi-level tasks that can be performed:
+
+# install/uninstall packages and build the associated external libs
+#   use -p and -u and -e
+# install packages needed for input script(s)
+#   use -i and -p
+# create new dir with only the source code needed for input script(s)
+#   use -i and -n
+# build LAMMPS, either in src or new dir
+#   use -b
+
+# data structures:
+
+# packstd list = ["COLLOID", "GPU", ...]
+# packuser list = ["USER-SPH", "USER-EWALDN", ...]
+# cfiles,hfiles dicts of LAMMPS *.cpp,*.h files =
+#   {"fix_nve.cpp": "", "angle_diplole.cpp": "USER-MISC", ...}
+# cdep,hdep dicts of files with list of LAMMPS *.h files they include = 
+#   {"fix_nve.cpp": ['fix_nve.h', 'atom.h', 'force.h', ...'], ...}
+# creq,hreq lists of src files needed to build LAMMPS for input scripts =
+#   ["main.cpp", "atom.cpp", ...]
+
+# ISSUES:
+
+# see KLUDGE comments
+# add more general input script parsing, see NOTE comments
+#   including another file
+#   variable substitution could be used to create new command (hard)
+#   single/double quotes could affect args and hide nested commands
+#   hybrid styles can have required sub-styles
+#   if-then-else and run every could nest other commands as args
+# special case: linalg sometimes needed with ATC external lib
+#               could scan atc/Makefile.lammps for it
+# can long makes print incrementally to screen as they progress?
+# add a verbose output option?
+
+# -----------------------------------------------------------------------
+# -----------------------------------------------------------------------
+
+import sys,glob,re,os,commands
+
+# -----------------------------------------------------------------------
+# variables
+
+# support files in lammps/src neeeded for a build
+
+support = ["Makefile","Make.sh","Makefile.package.empty",
+           "Makefile.package.settings.empty"]
+
+# packages that have external libs with their external lib dir
+
+extlibs = {"USER-ATC": "atc", "USER-AWPMD": "awpmd", "USER-CUDA": "cuda",
+           "GPU": "gpu","MEAM": "meam", "POEMS": "poems", "REAX": "reax"}
+
+# help messages
+
+syntax_message = """
+Make.py switch args ...
+Switches: -i file1 file2 ...
+          -p package1 package2 ...
+          -u package1 package2 ...
+          -e package1 arg1 arg2 package2 ...
+          -o dir
+          -b machine
+          -s suffix1 suffix2 ...
+          -l dir
+          -j N
+          -h switch1 switch2 ...
+Help: Make.py or Make.py -h
+"""
+
+ihelp = """
+-i file1 file2 ...
+scan input scripts, make list of needed files and packages
+"""
+
+phelp = """
+-p package1 package2 ...
+specify zero or more packages
+can use "all" or "standard" or "user"
+install packages required by -i input scripts
+also install listed packages
+"""
+
+uhelp = """
+-u package1 package2 ...
+specify zero or more packages
+can specify "all" or "standard" or "user", or package w/out user prefix
+uninstall packages not required by -i input scripts
+also uninstall listed packages
+"""
+
+ehelp = """
+-e package1 arg1 arg2 package2 ...
+build external libs for zero or more packages
+can specify package w/out user prefix
+each package can have 1 or 2 optional args
+  arg1 = suffix for lib Makefile
+  arg2 = suffix for lib Makefile.lammps
+example packages with external libs: "gpu", "meam", "user-cuda"
+build external libs for packages required by -i input scripts
+also build external libs for installed packages if none listed
+also build external libs for listed packages
+if arg1 specified, use Makefile.arg1 to build lib, else use Makefile
+if arg2 specified, copy Makefile.lammps.arg2 to Makefile.lammps,
+  else copy Makefile.lammps.arg1 to Makefile.lammps, else do nothing
+"""
+
+ohelp = """
+-o newdir
+create newdir with exactly the needed src files for -i input scripts
+newdir will be at same level as src so LAMMPS build will work
+requires use of -i, cannot use with -p or -u
+newdir will include STUBS and MAKE, but no package dirs
+"""
+
+bhelp = """
+-b machine
+build LAMMPS in src or newdir using Makefile.machine
+assumes external package libs are already built
+if no -o, build in src
+if -o, build in newdir, including STUBS build if needed
+"""
+
+shelp = """
+-s suffix1 suffix2 ...
+specify optimization suffixes to add to style names in -i input scripts
+requires use of -i
+same suffixes as LAMMPS -s command-line switch allows
+example suffixes = "opt", "gpu", "cuda", "omp"
+"""
+
+lhelp = """
+-l dir
+specify LAMMPS home dir
+required if not running Make.py from within lammps/src
+"""
+
+jhelp = """
+-j N
+perform LAMMPS and external lib builds in parallel
+adds "-j N" switch to "make" commands
+N = 0 performs serial make
+default N = 16
+"""
+
+hhelp = """
+Make.py lists all switches
+Make.py -h -i -b ... gives help on each switch
+Make.py -h gives this message
+"""
+
+# -----------------------------------------------------------------------
+# functions
+
+# print syntax message
+
+def syntax():
+  print syntax_message
+  sys.exit()
+
+# help messages
+
+def helptxt(switches):
+  if not switches: switches = ["-h"]
+  for sw in switches:
+    if sw == "-i": print ihelp
+    elif sw == "-p": print phelp
+    elif sw == "-u": print uhelp
+    elif sw == "-e": print ehelp
+    elif sw == "-o": print ohelp
+    elif sw == "-b": print bhelp
+    elif sw == "-s": print shelp
+    elif sw == "-l": print lhelp
+    elif sw == "-j": print jhelp
+    elif sw == "-h": print hhelp
+    else: error("Invalid help switch")
+
+# print error message
+
+def error(str):
+  print "ERROR:",str
+  sys.exit()
+  
+# convert *.cpp file to *.h file
+
+def c2h(file):
+  return file[:-4] + ".h"
+  
+# convert *.h file to *.cpp file
+
+def h2c(file):
+  return file[:-2] + ".cpp"
+  
+# append file to list
+# but only if file is not already in list
+# but only if file is in cfiles or hfiles
+
+def addfile(file,list):
+  if file in list: return
+  if file not in cfiles and file not in hfiles: return
+  list.append(file)
+
+# grab list of LAMMPS package dirs from src/Makefile
+  
+def lammps_packages():
+  txt = open(srcdir + "/Makefile",'r').read()
+  pattern = "PACKAGE = (.*?)\n\n"
+  match = re.search(pattern,txt,re.DOTALL)
+  packstd = match.group(1).replace("\\","").upper().split()
+  pattern = "PACKUSER = (.*?)\n\n"
+  match = re.search(pattern,txt,re.DOTALL)
+  packuser = match.group(1).replace("\\","").upper().split()
+  return packstd,packuser
+
+# uninstall package in LAMMPS src dir
+# package can be upper-case or lower-case
+
+def uninstall_package(package):
+  package = package.lower()
+  cmd = "cd %s; make no-%s" % (srcdir,package)
+  commands.getoutput(cmd)
+  print "  uninstalled",package
+  
+# install package in LAMMPS src dir
+# package can be upper-case or lower-case
+
+def install_package(package):
+  package = package.lower()
+  cmd = "cd %s; make yes-%s" % (srcdir,package)
+  commands.getoutput(cmd)
+  print "  installed",package
+
+# re-parse list of packages input via -e switch
+# one or two flags may be appended to a package
+# convert into dict with value = list of flags
+
+def reparse_packages(packages):
+  dict = {}
+  last = ""
+  for package in packages:
+    upper = package.upper()
+    flag = 0
+    if upper in packstd: flag = 1
+    elif upper in packuser: flag = 1
+    elif "USER-" + upper in packuser: flag = 1
+    if flag:
+      dict[package] = []
+      last = package
+    else:
+      if not last: error("Invalid package in -e list")
+      buildflags = dict[last]
+      if len(buildflags) == 2:
+        error("Too many machine flags appended to package %s" % last)
+      buildflags.append(package)
+  return dict
+
+# detect which packages are installed via "make package-status" command
+# return as list
+
+def detect_installed_packages():
+  cmd = "cd %s; make package-status" % srcdir
+  output = commands.getoutput(cmd)
+  pattern = "Installed\s*(.*): package (.*)"
+  status = re.findall(pattern,output)
+  installed = []
+  for entry in status:
+    if entry[0] == "YES": installed.append(entry[1])
+  return installed
+  
+# create dict of all LAMMPS *.cpp and *.h files with no duplicates
+# key = file
+# value = package dir if file in a package dir
+# value = empty if file is only in lammps/src
+# discard style_*.h files
+
+def lammps_files():
+  files = []
+  for dir in packstd:
+    files += glob.glob(dir + "/*.cpp")
+    files += glob.glob(dir + "/*.h")
+  for dir in packuser:
+    files += glob.glob(dir + "/*.cpp")
+    files += glob.glob(dir + "/*.h")
+  files += glob.glob("*.cpp")
+  files += glob.glob("*.h")
+
+  cfiles = {}
+  hfiles = {}
+  for file in files:
+    dir = os.path.dirname(file)
+    file = os.path.basename(file)
+    if file.find("style_") == 0: continue
+    if file[-2:] == ".h":
+      if file not in hfiles: hfiles[file] = dir
+    else:
+      if file not in cfiles: cfiles[file] = dir
+      
+  return cfiles,hfiles
+
+# parse each cfile,hfile to find list of LAMMPS *.h files it includes
+# create cdep,hdep = dict with key = filename, value = list of *.h files
+# KLUDGE for accelerator_cuda.h to ignore the *.h files it includes
+#        when "cuda" is not explicitly listed as a suffix,
+#        this is b/c it has an ifdef that includes several *cuda*.h files
+
+def dependencies():
+  pattern = re.compile('^#include "(.+?)"',re.MULTILINE)
+
+  cdep = {}
+  for file in cfiles:
+    if cfiles[file]: file = cfiles[file] + "/" + file
+    txt = open(file,'r').read()
+    possible = re.findall(pattern,txt)
+    depends = []
+    for dfile in possible:
+      if dfile in hfiles: depends.append(dfile)
+    cdep[os.path.basename(file)] = depends
+
+  hdep = {}
+  for file in hfiles:
+    if hfiles[file]: file = hfiles[file] + "/" + file
+    txt = open(file,'r').read()
+    possible = re.findall(pattern,txt)
+    depends = []
+    for dfile in possible:
+      if dfile in hfiles: depends.append(dfile)
+    if file == "accelerator_cuda.h" and "cuda" not in suffixes: depends = []
+    hdep[os.path.basename(file)] = depends
+
+  return cdep,hdep
+
+# add style files referenced in input script to lookup list
+# parse input script lines to look for them
+# add suffix for certain styles
+
+def need_from_input_script(file,lookup):
+  lines = open(file,'r').readlines()
+
+  # skip comment and blank lines
+  # NOTE: need to treat concatenated lines
+  # NOTE: need to handle quoted args when split into words
+  # NOTE: need to treat if and run every and print, which nest commands
+
+  cmds = {}
+  for line in lines:
+    if line.find("#") >= 0: line = line[:line.find("#")]
+    line = line.strip()
+    if len(line) == 0: continue
+    words = line.split()
+    cmds[words[0]] = words[1:]
+
+  # for commands with styles, generate file associated with style name
+  # suffixes induce multiple file variants
+  # final else handles command styles if "CommandStyle" found in *.h file
+    
+  for cmd in cmds:
+    args = cmds[cmd]
+    files = []
+    if cmd == "atom_style":
+      files.append("atom_vec_" + args[0])
+      for suffix in suffixes: files.append("atom_vec_" + args[0] + "/" + suffix)
+    elif cmd == "pair_style":
+      files.append("pair_" + args[0])
+      for suffix in suffixes: files.append("pair_" + args[0] + "/" + suffix)
+    elif cmd == "bond_style":
+      files.append("bond_" + args[0])
+      for suffix in suffixes: files.append("bond_" + args[0] + "/" + suffix)
+    elif cmd == "angle_style":
+      files.append("angle_" + args[0])
+      for suffix in suffixes: files.append("angle_" + args[0] + "/" + suffix)
+    elif cmd == "dihedral_style":
+      files.append("dihedral_" + args[0])
+      for suffix in suffixes: files.append("dihedral_" + args[0] + "/" + suffix)
+    elif cmd == "improper_style":
+      files.append("improper_" + args[0])
+      for suffix in suffixes: files.append("improper_" + args[0] + "/" + suffix)
+    elif cmd == "kspace_style":
+      files.append(args[0])
+      for suffix in suffixes: files.append(args[0] + "/" + suffix)
+    elif cmd == "run_style":
+      files.append(args[0])
+      for suffix in suffixes: files.append(args[0] + "/" + suffix)
+    elif cmd == "min_style":
+      files.append("min_" + args[0])
+    elif cmd == "compute":
+      files.append("compute_" + args[2])
+      for suffix in suffixes: files.append("compute_" + args[2] + "/" + suffix)
+    elif cmd == "dump":
+      files.append("dump_" + args[2])
+    elif cmd == "fix":
+      files.append("fix_" + args[2])
+      for suffix in suffixes: files.append("fix_" + args[2] + "/" + suffix)
+    elif cmd == "region":
+      files.append("region_" + args[1])
+    else:
+      tmpfile = cmd + ".cpp"
+      if tmpfile not in cfiles: continue
+      if cfiles[tmpfile]: tmpfile = cfiles[tmpfile] + "/" + tmpfile
+      txt = open(c2h(tmpfile)).read()
+      if not "CommandStyle" in txt: continue
+      files.append(cmd)
+
+    for file in files:
+      file = file.replace("/","_") + ".cpp"
+      addfile(file,lookup)
+
+# add additional CPP files required to build LAMMPS to lookup list
+# always add main.cpp
+# always add atom_vec_atomic,
+#   since Atom class creates it directly
+# always add compute_temp, compute_pe, compute_pressure,
+#   since Output class creates these computes directly
+# always add verlet and min_cg,
+#   since Update class creates them directly
+# always add src/neigh_*.cpp since are part of Neighbor class,
+#   but only neighbor.cpp is inferred by neighbor.h
+# KLUDGE:
+#   likewise add USER-OMP/neigh_*.cpp if any USER-OMP files are in lookup
+#   likewise add USER-CUDA/neigh_*.cpp if any USER-CUDA files are in lookup
+      
+def need_additional(lookup):
+  addfile("main.cpp",lookup)
+  addfile("atom_vec_atomic.cpp",lookup)
+  addfile("compute_temp.cpp",lookup)
+  addfile("compute_pe.cpp",lookup)
+  addfile("compute_pressure.cpp",lookup)
+  addfile("verlet.cpp",lookup)
+  addfile("min_cg.cpp",lookup)
+
+  user_cuda = user_omp = 0
+  for file in lookup:
+    if file[-2:] == ".h":
+      if hfiles[file] == "USER-CUDA": user_cuda = 1
+      if hfiles[file] == "USER-OMP": user_omp = 1
+    else:
+      if cfiles[file] == "USER-CUDA": user_cuda = 1
+      if cfiles[file] == "USER-OMP": user_omp = 1
+    
+  for file in cfiles:
+    if file.find("neigh_") == 0:
+      if cfiles[file] == "": addfile(file,lookup)
+      if cfiles[file] == "USER-CUDA" and user_cuda: addfile(file,lookup)
+      if cfiles[file] == "USER-OMP" and user_omp: addfile(file,lookup)
+
+# creq,hreq = list of all CPP and H files needed to build LAMMPS
+# inferred from lookup list and each file's dependencies in cdep,hdep
+# when an H file is added, also add corresponding CPP file to lookup
+# addfile insures no duplicates in creq,hreq
+
+def resolve_dependencies(lookup):
+  creq = []
+  hreq = []
+
+  i = 0
+  while i < len(lookup):
+    file = lookup[i]
+    if file[-2:] == ".h":
+      hreq.append(file)
+      dfiles = hdep[file]
+      addfile(h2c(file),lookup)
+    else:
+      creq.append(file)
+      dfiles = cdep[file]
+    for dfile in dfiles: addfile(dfile,lookup)
+    i += 1
+    
+  return creq,hreq
+
+# -----------------------------------------------------------------------
+# main program
+
+# defaults
+
+infiles = []
+packflag = 0
+packages = []
+unpackflag = 0
+unpackages = []
+extflag = 0
+extpackages = []
+newdir = ""
+build = ""
+suffixes = []
+lammpsdir = ""
+jmake = 16
+helpflag = 0
+help = []
+
+# parse command-line args
+
+args = sys.argv
+narg = len(args)
+
+if narg == 1: syntax()
+
+iarg = 1
+while iarg < narg:
+  if args[iarg] == "-i":
+    if iarg+2 > narg: syntax()
+    iarg += 1
+    while iarg < narg and args[iarg][0] != '-':
+      infiles.append(args[iarg])
+      iarg += 1
+  elif args[iarg] == "-p":
+    packflag = 1
+    iarg += 1
+    while iarg < narg and args[iarg][0] != '-':
+      packages.append(args[iarg])
+      iarg += 1
+  elif args[iarg] == "-u":
+    unpackflag = 1
+    iarg += 1
+    while iarg < narg and args[iarg][0] != '-':
+      unpackages.append(args[iarg])
+      iarg += 1
+  elif args[iarg] == "-e":
+    extflag = 1
+    iarg += 1
+    while iarg < narg and args[iarg][0] != '-':
+      extpackages.append(args[iarg])
+      iarg += 1
+  elif args[iarg] == "-o":
+    if iarg+2 > narg: syntax()
+    newdir = args[iarg+1]
+    iarg += 2
+  elif args[iarg] == "-b":
+    if iarg+2 > narg: syntax()
+    build = args[iarg+1]
+    iarg += 2
+  elif args[iarg] == "-s":
+    if iarg+2 > narg: syntax()
+    iarg += 1
+    while iarg < narg and args[iarg][0] != '-':
+      suffixes.append(args[iarg])
+      iarg += 1
+  elif args[iarg] == "-l":
+    if iarg+2 > narg: syntax()
+    lammpsdir = args[iarg+1]
+    iarg += 2
+  elif args[iarg] == "-j":
+    if iarg+2 > narg: syntax()
+    jmake = int(args[iarg+1])
+    iarg += 1
+  elif args[iarg] == "-h":
+    helpflag = 1
+    iarg += 1
+    while iarg < narg and args[iarg][0] == '-':
+      help.append(args[iarg])
+      iarg += 1
+  else: syntax()
+
+# help
+
+if helpflag: helptxt(help)
+  
+# error check
+
+if newdir:
+  if not infiles: error("Cannot use -o without -i")
+  if packflag: error("Cannot use -o with -p")
+  if unpackages: error("Cannot use -o with -u")
+
+if suffixes:
+  if not infiles: error("Cannot use -s without -i")
+
+# setup strings
+# srcdir = LAMMPS src dir
+# check that srcdir is valid via 2 "empty" files and version.h
+# libdir = LAMMPS lib dir
+# newdir = new src dir
+# makestr = -j N for parallel make
+  
+if lammpsdir: srcdir = lammpsdir + "/src"
+else: srcdir = "."
+
+if not os.path.isfile(srcdir + "/Makefile.package.empty") \
+      or not os.path.isfile(srcdir + "/Makefile.package.settings.empty") \
+      or not os.path.isfile(srcdir + "/version.h"):
+  error("Not running in LAMMPS src dir, use -l switch")
+
+if srcdir == ".": libdir = "../lib"
+else: libdir = srcdir[:-3] + "lib"
+
+if newdir:
+  if srcdir == ".": newdir = "../" + newdir
+  else: newdir = srcdir[:-3] + newdir
+
+if jmake == 0: makestr = ""
+else: makestr = "-j %d" % jmake
+  
+# packstd,packuser = list of package dirs in lammps/src
+
+packstd,packuser = lammps_packages()
+
+# -i switch
+# cfiles,hfiles = all LAMMPS src files
+# cdep,hdep = src files with list of *.h files each depends on
+# lookup = needed *.cpp files = default + input script styles
+# creq,hreq = files needed to build LAMMPS = lookup + dependencies
+# packneed = needed packages
+
+if infiles:
+  print "Scanning input scripts ..."
+  cfiles,hfiles = lammps_files()
+  cdep,hdep = dependencies()
+  lookup = []
+  for file in infiles: need_from_input_script(file,lookup)
+  need_additional(lookup)
+  creq,hreq = resolve_dependencies(lookup)
+  
+  packneed = []
+  for file in creq:
+    if cfiles[file] and cfiles[file] not in packneed:
+      packneed.append(cfiles[file])
+  for file in hreq:
+    if hfiles[file] and hfiles[file] not in packneed:
+      packneed.append(hfiles[file])
+
+  print "  scripts require %d LAMMPS *.cpp files" % len(creq)
+  print "  scripts require %d LAMMPS *.h files" % len(hreq)
+  print "  scripts require %d packages:" % len(packneed),
+  print packneed
+
+# -u switch
+# if -i, add unneeded packages to list
+# add explicitly named packages to list
+# uninstall packages in list only if installed
+
+if unpackflag:
+  print "Uninstalling packages ..."
+  
+  list = []
+  if infiles:
+    for package in packstd:
+      if package not in packneed: list.append(package)
+    for package in packuser:
+      if package not in packneed: list.append(package)
+  for entry in unpackages:
+    entry = entry.upper()
+    if entry == "ALL":
+      for package in packstd:
+        if package not in list: list.append(package)
+      for package in packuser:
+        if package not in list: list.append(package)
+    elif entry == "STANDARD":
+      for package in packstd:
+        if package not in list: list.append(package)
+    elif entry == "USER":
+      for package in packuser:
+        if package not in list: list.append(package)
+    elif entry in packstd:
+      if entry not in list: list.append(entry)
+    elif entry in packuser:
+      if entry not in list: list.append(entry)
+    elif "USER-" + entry in packuser:
+      if "USER-" + entry not in list: list.append("USER-" + entry)
+    else: error("Invalid package %s to uninstall" % entry.lower())
+
+  installed_packages = detect_installed_packages()
+  for package in list:
+    if package in installed_packages: uninstall_package(package)
+    
+# -p switch
+# if -i, add needed packages to list
+# add explicitly named packages to list
+# install packages in list only if uninstalled
+
+if packflag:
+  print "Installing packages ..."
+  
+  list = []
+  if infiles:
+    for package in packneed: list.append(package)
+  for entry in packages:
+    entry = entry.upper()
+    if entry == "ALL":
+      for package in packstd:
+        if package not in list: list.append(package)
+      for package in packuser:
+        if package not in list: list.append(package)
+    elif entry == "STANDARD":
+      for package in packstd:
+        if package not in list: list.append(package)
+    elif entry == "USER":
+      for package in packuser:
+        if package not in list: list.append(package)
+    elif entry in packstd:
+      if entry not in list: list.append(entry)
+    elif entry in packuser:
+      if entry not in list: list.append(entry)
+    elif "USER-" + entry in packuser:
+      if "USER-" + entry not in list: list.append("USER-" + entry)
+    else: error("Invalid package %s to install" % entry.lower())
+
+  installed_packages = detect_installed_packages()
+  for package in list:
+    if package not in installed_packages: install_package(package)
+
+# -e switch
+# add explicitly named libs to list first, so can include arg1/arg2
+# if -i, add needed libs to list
+# if none named, add libs for installed packages to list
+# use Makefile.arg1 and Makefile.lammps.arg1/arg2 if specified
+# force rebuild by doing clean first
+    
+if extflag:
+  print "Building external libraries ..."
+
+  list = {}
+  packages_with_flags = reparse_packages(extpackages)
+  for package in packages_with_flags:
+    upper = package.upper()
+    if upper in extlibs and upper not in list:
+      list[upper] = packages_with_flags[package]
+    upper = "USER-" + upper
+    if upper in extlibs and upper not in list:
+      list[upper] = packages_with_flags[package]
+
+  if infiles:
+    for package in packneed:
+      if package in extlibs and package not in list: list[package] = []
+  if not extpackages:
+    installed_packages = detect_installed_packages()
+    for package in installed_packages:
+      if package in extlibs and package not in list: list[package] = []
+    
+  for package in list:
+    lib = extlibs[package]
+    print "  lib/%s/lib%s.a for package %s ..." % (lib,lib,package)
+    args = list[package]
+
+    # makefile = Makefile by default unless arg1 specified
+    
+    makefile = "Makefile"
+    if args: makefile = "Makefile.%s" % args[0]
+    if not os.path.isfile("%s/%s/%s" % (libdir,lib,makefile)):
+      error("%s for external lib %s does not exist" % (makefile,lib))
+
+    # no makefile_lammps by default unless arg2 or arg1 specified
+      
+    makefile_lammps = ""
+    if args and len(args) == 2:
+      makefile_lammps = "Makefile.lammps.%s" % args[1]
+      if not os.path.isfile("%s/%s/%s" % (libdir,lib,makefile_lammps)):
+        error("%s for external lib %s does not exist" % (makefile,lib))
+    elif args:
+      makefile_lammps = "Makefile.lammps.%s" % args[0]
+
+    # target lib file
+    # KLUDGE for cuda, since it is liblammpscuda.a instead of libcuda.a
+      
+    libfile = "%s/%s/lib%s.a" % (libdir,lib,lib)
+    if lib == "cuda": libfile = "%s/%s/liblammpscuda.a" % (libdir,lib)
+    
+    # remove lib file
+
+    if os.path.exists(libfile): os.remove(libfile)
+    
+    # make clean
+
+    print "    cleaning ..."
+    cmd = "cd %s/%s; make -f %s clean" % (libdir,lib,makefile)
+    output = commands.getoutput(cmd)
+
+    # build the external lib and check if successful
+      
+    print "    building ..."
+    cmd = "cd %s/%s; make %s -f %s" % (libdir,lib,makestr,makefile)
+    output = commands.getoutput(cmd)
+    if os.path.exists(libfile):
+      print "  successfully built lib/%s/lib%s.a" % (lib,lib)
+    else:
+      print output
+      error("Build of lib/%s/lib%s.a was unsuccessful" % (lib,lib))
+
+    # if it exists, copy makefile_lammps to Makefile.lammps
+
+    if makefile_lammps:
+      if os.path.isfile("%s/%s/%s" % (libdir,lib,makefile_lammps)):
+        cmd = "cd %s/%s; cp %s Makefile.lammps" % (libdir,lib,makefile_lammps) 
+        commands.getoutput(cmd)
+
+# -n switch
+# create newdir with exactly the needed src files for scripts
+# newdir has support files and STUBS and MAKE, but no package dirs
+# insure Makefile.package and Makefile.package.settings are correct by
+#   installing all needed packages in newdir, then delete package dirs
+
+if newdir:
+  print "Creating %s ..." % newdir
+  if os.path.exists(newdir): error("Directory %s already exists" % newdir)
+  os.mkdir(newdir)
+  os.mkdir(newdir + "/MAKE")
+  os.mkdir(newdir + "/STUBS")
+    
+  for file in support:
+    commands.getoutput("cp %s/%s %s" % (srcdir,file,newdir))
+
+  files = glob.glob("%s/MAKE/Makefile.*" % srcdir)
+  fstr = " ".join(files)
+  commands.getoutput("cp %s %s/MAKE" % (fstr,newdir))
+
+  commands.getoutput("cp %s/STUBS/Makefile %s/STUBS" % (srcdir,newdir))
+  commands.getoutput("cp %s/STUBS/mpi.c %s/STUBS" % (srcdir,newdir))
+  commands.getoutput("cp %s/STUBS/mpi.h %s/STUBS" % (srcdir,newdir))
+
+  for package in packneed:
+    os.mkdir("%s/%s" % (newdir,package))
+    commands.getoutput("cp %s/%s/* %s/%s" % (srcdir,package,newdir,package))
+    commands.getoutput("cd %s; make yes-%s" % (newdir,package.lower()))
+    commands.getoutput("rm -r %s/%s" % (newdir,package))
+
+  commands.getoutput("rm -r %s/*.cpp" % (newdir))
+  commands.getoutput("rm -r %s/*.h" % (newdir))
+    
+  for file in creq:
+    if cfiles[file]: file = cfiles[file] + "/" + file
+    commands.getoutput("cp %s/%s %s" % (srcdir,file,newdir))
+  for file in hreq:
+    if hfiles[file]: file = hfiles[file] + "/" + file
+    commands.getoutput("cp %s/%s %s" % (srcdir,file,newdir))
+
+# -b switch
+# build LAMMPS in src or newdir
+# assumes external package libs are already built
+# build STUBS lib if needed and not already built
+    
+if build:
+  print "Building LAMMPS for %s ..." % build
+  if newdir: builddir = newdir
+  else: builddir = srcdir
+
+  makefile = "%s/MAKE/Makefile.%s" % (builddir,build)
+  if not os.path.exists(makefile):
+    error("%s does not exist" % makefile)
+
+  txt = open(makefile,"r").read()
+  if "../STUBS" in txt:
+    if not os.path.exists("%s/STUBS/libmpi.a" % builddir):
+      cmd = "cd %s/STUBS; make" % builddir
+      output = commands.getoutput(cmd)
+      if os.path.exists("%s/STUBS/libmpi.a" % builddir):
+        print "Successfully built STUBS/libmpi.a"
+      else:
+        print output
+        error("Build of STUBS/libmpi.a was unsuccessful")
+    
+  if os.path.exists("%s/lmp_%s" % (builddir,build)):
+    os.remove("%s/lmp_%s" % (builddir,build))
+  cmd = "cd %s; make %s %s" % (builddir,makestr,build)
+  output = commands.getoutput(cmd)
+  if os.path.exists("%s/lmp_%s" % (builddir,build)):
+    print "Successfully built %s/lmp_%s" % (builddir,build)
+  else:
+    print output
+    error("Build of %s/lmp_%s was unsuccessful" % (builddir,build))