Commit eca61226 authored by sjplimp's avatar sjplimp Committed by GitHub
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Merge pull request #583 from giacomofiorin/colvars-update-2017-07-19 

Update Colvars to version 2017-07-15 and support automated builds for it
parents fac3e3da ef9fb944

doc/src/PDF/colvars-refman-lammps.pdf

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lib/colvars/Install.py

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Original line number Diff line number Diff line 
#!/usr/bin/env python



# install.py tool to do a generic build of a library

# soft linked to by many of the lib/Install.py files

# used to automate the steps described in the corresponding lib/README

# Install.py tool to do automate build of Colvars



import sys,commands,os

from __future__ import print_function

import sys,os,subprocess



# help message



help = """

Syntax: python Install.py -m machine -e suffix

Syntax from src dir: make lib-colvars args="-m machine -e suffix"

Syntax from lib/colvars dir: python Install.py -m machine -e suffix



specify -m and optionally -e, order does not matter



  -m = peform a clean followed by "make -f Makefile.machine"

       machine = suffix of a lib/Makefile.* file

       machine = suffix of a lib/colvars/Makefile.* or of a

         src/MAKE/MACHINES/Makefile.* file

  -e = set EXTRAMAKE variable in Makefile.machine to Makefile.lammps.suffix

       does not alter existing Makefile.machine



Examples:



make lib-colvars args="-m g++"     # build COLVARS lib with GNU g++ compiler

"""



# print error message or help



def error(str=None):

  if not str: print help

  else: print "ERROR",str

  if not str: print(help)

  else: print("ERROR"),str

  sys.exit()



# parse args
@@ -31,17 +38,17 @@ nargs = len(args) 
if nargs == 0: error()



machine = None

extraflag = 0

extraflag = False



iarg = 0

while iarg < nargs:

  if args[iarg] == "-m":

    if iarg+2 > nargs: error()

    if iarg+2 > len(args): error()

    machine = args[iarg+1]

    iarg += 2  

  elif args[iarg] == "-e":

    if iarg+2 > nargs: error()

    extraflag = 1

    if iarg+2 > len(args): error()

    extraflag = True

    suffix = args[iarg+1]

    iarg += 2  

  else: error()
@@ -51,32 +58,85 @@ while iarg < nargs: 
cwd = os.getcwd()

lib = os.path.basename(cwd)



# create Makefile.auto as copy of Makefile.machine

# reset EXTRAMAKE if requested

def get_lammps_machine_flags(machine):

  """Parse Makefile.machine from LAMMPS, return dictionary of compiler flags"""

  if not os.path.exists("../../src/MAKE/MACHINES/Makefile.%s" % machine):

    error("Cannot locate src/MAKE/MACHINES/Makefile.%s" % machine)

  lines = open("../../src/MAKE/MACHINES/Makefile.%s" % machine,

               'r').readlines()

  machine_flags = {}

  for line in lines:

    line = line.partition('#')[0]

    line = line.rstrip()

    words = line.split()

    if (len(words) > 2):

      if ((words[0] == 'CC') or (words[0] == 'CCFLAGS') or

          (words[0] == 'SHFLAGS') or (words[0] == 'ARCHIVE') or

          (words[0] == 'ARFLAGS') or (words[0] == 'SHELL')):

        machine_flags[words[0]] = ' '.join(words[2:])

  return machine_flags



def gen_colvars_makefile_machine(machine, machine_flags):

  """Generate Makefile.machine for Colvars given the compiler flags"""

  machine_makefile = open("Makefile.%s" % machine, 'w')

  machine_makefile.write('''# -*- makefile -*- to build Colvars module with %s



COLVARS_LIB = libcolvars.a

COLVARS_OBJ_DIR =



CXX =		%s

CXXFLAGS =	%s %s

AR =		%s

ARFLAGS =	%s

SHELL =		%s



include Makefile.common



.PHONY: default clean



default: $(COLVARS_LIB) Makefile.lammps



clean:

	-rm -f $(COLVARS_OBJS) $(COLVARS_LIB)

''' % (machine, machine_flags['CC'],

       machine_flags['CCFLAGS'], machine_flags['SHFLAGS'] ,

       machine_flags['ARCHIVE'], machine_flags['ARFLAGS'],

       machine_flags['SHELL']))



if not os.path.exists("Makefile.%s" % machine):

  machine_flags = get_lammps_machine_flags(machine)

  gen_colvars_makefile_machine(machine, machine_flags)

if not os.path.exists("Makefile.%s" % machine):

  error("lib/%s/Makefile.%s does not exist" % (lib,machine))



# create Makefile.auto as copy of Makefile.machine

# reset EXTRAMAKE if requested



lines = open("Makefile.%s" % machine,'r').readlines()

fp = open("Makefile.auto",'w')



for line in lines:

  words = line.split()

  if len(words) == 3 and extraflag and \

        words[0] == "EXTRAMAKE" and words[1] == '=':

    line = line.replace(words[2],"Makefile.lammps.%s" % suffix)

  print >>fp,line,



  fp.write(line)

fp.close()



# make the library via Makefile.auto



print "Building lib%s.a ..." % lib

cmd = "make -f Makefile.auto clean; make -f Makefile.auto"

txt = commands.getoutput(cmd)

print txt

try:

  import multiprocessing

  n_cpus = multiprocessing.cpu_count()

except:

  n_cpus = 1



print("Building lib%s.a ..." % lib)

cmd = ["make -f Makefile.auto clean"]

print(subprocess.check_output(cmd, shell=True).decode())

cmd = ["make -f Makefile.auto -j%d" % n_cpus]

print(subprocess.check_output(cmd, shell=True).decode())



if os.path.exists("lib%s.a" % lib): print "Build was successful"

if os.path.exists("lib%s.a" % lib): print("Build was successful")

else: error("Build of lib/%s/lib%s.a was NOT successful" % (lib,lib))

if not os.path.exists("Makefile.lammps"):

  print "lib/%s/Makefile.lammps was NOT created" % lib
 
  print("lib/%s/Makefile.lammps was NOT created" % lib)

lib/colvars/Makefile.colvars

deleted100644 → 0
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Original line number Diff line number Diff line 
# library build -*- makefile -*- for colvars module



# which file will be copied to Makefile.lammps



EXTRAMAKE = Makefile.lammps.empty



# ------ SETTINGS ------



CXX =		g++

CXXFLAGS =	-O2 -g -Wall -fPIC -funroll-loops # -DCOLVARS_DEBUG

ARCHIVE =	ar

ARCHFLAG =	-rscv

SHELL =		/bin/sh



# ------ DEFINITIONS ------



SRC = colvaratoms.cpp colvarbias_abf.cpp colvarbias_alb.cpp colvarbias.cpp  \

 colvarbias_histogram.cpp colvarbias_meta.cpp colvarbias_restraint.cpp      \

 colvarcomp_angles.cpp colvarcomp_coordnums.cpp colvarcomp.cpp              \

 colvarcomp_distances.cpp colvarcomp_protein.cpp colvarcomp_rotations.cpp   \

 colvardeps.cpp colvar.cpp colvargrid.cpp colvarmodule.cpp colvarparse.cpp  \

 colvarscript.cpp colvartypes.cpp colvarvalue.cpp



LIB = libcolvars.a

OBJ = $(SRC:.cpp=.o)

EXE = #colvars_standalone



# ------ MAKE PROCEDURE ------



default: $(LIB) $(EXE) Makefile.lammps



Makefile.lammps:

	@cp $(EXTRAMAKE) Makefile.lammps



$(LIB):	$(OBJ)

	$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)



colvars_standalone: colvars_main.o colvarproxy_standalone.o $(LIB)

	$(CXX) -o $@ $(CXXFLAGS) $^



# ------ MAKE FLAGS ------



.SUFFIXES:

.SUFFIXES: .cpp .o



.PHONY: default clean



# ------ COMPILE RULES ------



.cpp.o:

	$(CXX) $(CXXFLAGS) -c $<



# ------ DEPENDENCIES ------

#

colvaratoms.o: colvaratoms.cpp colvarmodule.h colvartypes.h colvarproxy.h \

 colvarvalue.h colvarparse.h colvardeps.h colvaratoms.h

colvarbias_abf.o: colvarbias_abf.cpp colvarmodule.h colvartypes.h \

 colvarproxy.h colvarvalue.h colvar.h colvarparse.h colvardeps.h \

 colvarbias_abf.h colvarbias.h colvargrid.h

colvarbias_alb.o: colvarbias_alb.cpp colvarmodule.h colvartypes.h \

 colvarproxy.h colvarvalue.h colvarbias_alb.h colvar.h colvarparse.h \

 colvardeps.h colvarbias_restraint.h colvarbias.h

colvarbias.o: colvarbias.cpp colvarmodule.h colvartypes.h colvarproxy.h \

 colvarvalue.h colvarbias.h colvar.h colvarparse.h colvardeps.h

colvarbias_histogram.o: colvarbias_histogram.cpp colvarmodule.h \

 colvartypes.h colvarproxy.h colvarvalue.h colvar.h colvarparse.h \

 colvardeps.h colvarbias_histogram.h colvarbias.h colvargrid.h

colvarbias_meta.o: colvarbias_meta.cpp colvar.h colvarmodule.h \

 colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvardeps.h \

 colvarbias_meta.h colvarbias.h colvargrid.h

colvarbias_restraint.o: colvarbias_restraint.cpp colvarmodule.h \

 colvartypes.h colvarproxy.h colvarvalue.h colvarbias_restraint.h \

 colvarbias.h colvar.h colvarparse.h colvardeps.h

colvarcomp_angles.o: colvarcomp_angles.cpp colvarmodule.h colvartypes.h \

 colvarproxy.h colvarvalue.h colvar.h colvarparse.h colvardeps.h \

 colvarcomp.h colvaratoms.h

colvarcomp_coordnums.o: colvarcomp_coordnums.cpp colvarmodule.h \

 colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvardeps.h \

 colvaratoms.h colvar.h colvarcomp.h

colvarcomp.o: colvarcomp.cpp colvarmodule.h colvartypes.h colvarproxy.h \

 colvarvalue.h colvar.h colvarparse.h colvardeps.h colvarcomp.h \

 colvaratoms.h

colvarcomp_distances.o: colvarcomp_distances.cpp colvarmodule.h \

 colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvardeps.h \

 colvar.h colvarcomp.h colvaratoms.h

colvarcomp_protein.o: colvarcomp_protein.cpp colvarmodule.h colvartypes.h \

 colvarproxy.h colvarvalue.h colvarparse.h colvardeps.h colvar.h \

 colvarcomp.h colvaratoms.h

colvarcomp_rotations.o: colvarcomp_rotations.cpp colvarmodule.h \

 colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvardeps.h \

 colvar.h colvarcomp.h colvaratoms.h

colvar.o: colvar.cpp colvarmodule.h colvartypes.h colvarproxy.h \

 colvarvalue.h colvarparse.h colvardeps.h colvar.h colvarcomp.h \

 colvaratoms.h colvarscript.h colvarbias.h

colvardeps.o: colvardeps.cpp colvardeps.h colvarmodule.h colvartypes.h \

 colvarproxy.h colvarvalue.h colvarparse.h

colvargrid.o: colvargrid.cpp colvarmodule.h colvartypes.h colvarproxy.h \

 colvarvalue.h colvarparse.h colvardeps.h colvar.h colvarcomp.h \

 colvaratoms.h colvargrid.h

colvarmodule.o: colvarmodule.cpp colvarmodule.h colvartypes.h \

 colvarproxy.h colvarvalue.h colvarparse.h colvardeps.h colvar.h \

 colvarbias.h colvarbias_abf.h colvargrid.h colvarbias_alb.h \

 colvarbias_restraint.h colvarbias_histogram.h colvarbias_meta.h \

 colvarscript.h

colvarparse.o: colvarparse.cpp colvarmodule.h colvartypes.h colvarproxy.h \

 colvarvalue.h colvarparse.h

colvarscript.o: colvarscript.cpp colvarscript.h colvarmodule.h \

 colvartypes.h colvarproxy.h colvarvalue.h colvarbias.h colvar.h \

 colvarparse.h colvardeps.h

colvartypes.o: colvartypes.cpp colvarmodule.h colvartypes.h colvarproxy.h \

 colvarvalue.h colvarparse.h

colvarvalue.o: colvarvalue.cpp colvarmodule.h colvartypes.h colvarproxy.h \

 colvarvalue.h



# ------ CLEAN ------



clean:

	-rm *.o *~ $(LIB)

lib/colvars/Makefile.common

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Original line number Diff line number Diff line 
# Shared -*- makefile -*- for multiple architectures



# Detect settings from PYTHON package (if defined)

include ../../src/Makefile.package.settings

ifeq ($(python_SYSINC),)

COLVARS_PYTHON_INCFLAGS =

else

COLVARS_PYTHON_INCFLAGS = -DCOLVARS_PYTHON $(python_SYSINC)

endif



# Detect debug settings

ifeq ($(COLVARS_DEBUG),)

COLVARS_DEBUG_INCFLAGS =

else

COLVARS_DEBUG_INCFLAGS= -DCOLVARS_DEBUG

endif



COLVARS_INCFLAGS = $(COLVARS_DEBUG_INCFLAGS) $(COLVARS_PYTHON_INCFLAGS)





.SUFFIXES:

.SUFFIXES: .cpp .o



COLVARS_SRCS = \

        colvaratoms.cpp \

        colvarbias_abf.cpp \

        colvarbias_alb.cpp \

        colvarbias.cpp \

        colvarbias_histogram.cpp \

        colvarbias_meta.cpp \

        colvarbias_restraint.cpp \

        colvarcomp_angles.cpp \

        colvarcomp_coordnums.cpp \

        colvarcomp.cpp \

        colvarcomp_distances.cpp \

        colvarcomp_protein.cpp \

        colvarcomp_rotations.cpp \

        colvar.cpp \

        colvardeps.cpp \

        colvargrid.cpp \

        colvarmodule.cpp \

        colvarparse.cpp \

        colvarproxy.cpp \

        colvarscript.cpp \

        colvartypes.cpp \

        colvarvalue.cpp



COLVARS_OBJS = $(COLVARS_SRCS:.cpp=.o)



.cpp.o:

	$(CXX) $(CXXFLAGS) $(COLVARS_INCFLAGS) -c $<



$(COLVARS_LIB):	Makefile.deps $(COLVARS_OBJS)

	$(AR) $(ARFLAGS) $(COLVARS_LIB) $(COLVARS_OBJS)





Makefile.deps: $(COLVARS_SRCS)

	@echo > $@

	@for src in $^ ; do \

	  obj=`basename $$src .cpp`.o ; \

	  $(CXX) -MM $(COLVARS_INCFLAGS) \

	    -MT '$$(COLVARS_OBJ_DIR)'$$obj $$src >> $@ ; \

	  done



include Makefile.deps

lib/colvars/Makefile.deps

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$(COLVARS_OBJ_DIR)colvaratoms.o: colvaratoms.cpp colvarmodule.h \

 colvars_version.h colvartypes.h colvarproxy.h colvarvalue.h \

 colvarparse.h colvaratoms.h colvardeps.h

$(COLVARS_OBJ_DIR)colvarbias_abf.o: colvarbias_abf.cpp colvarmodule.h \

 colvars_version.h colvartypes.h colvarproxy.h colvarvalue.h colvar.h \

 colvarparse.h colvardeps.h colvarbias_abf.h colvarbias.h colvargrid.h

$(COLVARS_OBJ_DIR)colvarbias_alb.o: colvarbias_alb.cpp colvarmodule.h \

 colvars_version.h colvartypes.h colvarproxy.h colvarvalue.h \

 colvarbias_alb.h colvar.h colvarparse.h colvardeps.h colvarbias.h

$(COLVARS_OBJ_DIR)colvarbias.o: colvarbias.cpp colvarmodule.h \

 colvars_version.h colvartypes.h colvarproxy.h colvarvalue.h colvarbias.h \

 colvar.h colvarparse.h colvardeps.h

$(COLVARS_OBJ_DIR)colvarbias_histogram.o: colvarbias_histogram.cpp \

 colvarmodule.h colvars_version.h colvartypes.h colvarproxy.h \

 colvarvalue.h colvar.h colvarparse.h colvardeps.h colvarbias_histogram.h \

 colvarbias.h colvargrid.h

$(COLVARS_OBJ_DIR)colvarbias_meta.o: colvarbias_meta.cpp colvar.h \

 colvarmodule.h colvars_version.h colvartypes.h colvarproxy.h \

 colvarvalue.h colvarparse.h colvardeps.h colvarbias_meta.h colvarbias.h \

 colvargrid.h

$(COLVARS_OBJ_DIR)colvarbias_restraint.o: colvarbias_restraint.cpp \

 colvarmodule.h colvars_version.h colvartypes.h colvarproxy.h \

 colvarvalue.h colvarbias_restraint.h colvarbias.h colvar.h colvarparse.h \

 colvardeps.h

$(COLVARS_OBJ_DIR)colvarcomp_angles.o: colvarcomp_angles.cpp \

 colvarmodule.h colvars_version.h colvartypes.h colvarproxy.h \

 colvarvalue.h colvar.h colvarparse.h colvardeps.h colvarcomp.h \

 colvaratoms.h

$(COLVARS_OBJ_DIR)colvarcomp_coordnums.o: colvarcomp_coordnums.cpp \

 colvarmodule.h colvars_version.h colvartypes.h colvarproxy.h \

 colvarvalue.h colvarparse.h colvaratoms.h colvardeps.h colvar.h \

 colvarcomp.h

$(COLVARS_OBJ_DIR)colvarcomp.o: colvarcomp.cpp colvarmodule.h \

 colvars_version.h colvartypes.h colvarproxy.h colvarvalue.h colvar.h \

 colvarparse.h colvardeps.h colvarcomp.h colvaratoms.h

$(COLVARS_OBJ_DIR)colvarcomp_distances.o: colvarcomp_distances.cpp \

 colvarmodule.h colvars_version.h colvartypes.h colvarproxy.h \

 colvarvalue.h colvarparse.h colvar.h colvardeps.h colvarcomp.h \

 colvaratoms.h

$(COLVARS_OBJ_DIR)colvarcomp_protein.o: colvarcomp_protein.cpp \

 colvarmodule.h colvars_version.h colvartypes.h colvarproxy.h \

 colvarvalue.h colvarparse.h colvar.h colvardeps.h colvarcomp.h \

 colvaratoms.h

$(COLVARS_OBJ_DIR)colvarcomp_rotations.o: colvarcomp_rotations.cpp \

 colvarmodule.h colvars_version.h colvartypes.h colvarproxy.h \

 colvarvalue.h colvarparse.h colvar.h colvardeps.h colvarcomp.h \

 colvaratoms.h

$(COLVARS_OBJ_DIR)colvar.o: colvar.cpp colvarmodule.h colvars_version.h \

 colvartypes.h colvarproxy.h colvarvalue.h colvarparse.h colvar.h \

 colvardeps.h colvarcomp.h colvaratoms.h colvarscript.h colvarbias.h

$(COLVARS_OBJ_DIR)colvardeps.o: colvardeps.cpp colvardeps.h \

 colvarmodule.h colvars_version.h colvartypes.h colvarproxy.h \

 colvarvalue.h colvarparse.h

$(COLVARS_OBJ_DIR)colvargrid.o: colvargrid.cpp colvarmodule.h \

 colvars_version.h colvartypes.h colvarproxy.h colvarvalue.h \

 colvarparse.h colvar.h colvardeps.h colvarcomp.h colvaratoms.h \

 colvargrid.h

$(COLVARS_OBJ_DIR)colvarmodule.o: colvarmodule.cpp colvarmodule.h \

 colvars_version.h colvartypes.h colvarproxy.h colvarvalue.h \

 colvarparse.h colvar.h colvardeps.h colvarbias.h colvarbias_abf.h \

 colvargrid.h colvarbias_alb.h colvarbias_histogram.h colvarbias_meta.h \

 colvarbias_restraint.h colvarscript.h colvaratoms.h

$(COLVARS_OBJ_DIR)colvarparse.o: colvarparse.cpp colvarmodule.h \

 colvars_version.h colvartypes.h colvarproxy.h colvarvalue.h \

 colvarparse.h

$(COLVARS_OBJ_DIR)colvarproxy.o: colvarproxy.cpp colvarmodule.h \

 colvars_version.h colvartypes.h colvarproxy.h colvarvalue.h \

 colvarscript.h colvarbias.h colvar.h colvarparse.h colvardeps.h \

 colvaratoms.h

$(COLVARS_OBJ_DIR)colvarscript.o: colvarscript.cpp colvarscript.h \

 colvarmodule.h colvars_version.h colvartypes.h colvarproxy.h \

 colvarvalue.h colvarbias.h colvar.h colvarparse.h colvardeps.h

$(COLVARS_OBJ_DIR)colvartypes.o: colvartypes.cpp colvarmodule.h \

 colvars_version.h colvartypes.h colvarproxy.h colvarvalue.h \

 colvarparse.h

$(COLVARS_OBJ_DIR)colvarvalue.o: colvarvalue.cpp colvarmodule.h \

 colvars_version.h colvartypes.h colvarproxy.h colvarvalue.h

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