Commit 40ec1807 authored by sjplimp's avatar sjplimp
Browse files 

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15681 f3b2605a-c512-4ea7-a41b-209d697bcdaa
parent bcd4dad2

examples/tad/README

+1 −1
Original line number Diff line number Diff line 
Run this example as:



mpirun -np 3 lmp_linux -partition 3x1 -in in.tad

mpirun -np 3 lmp_g++ -partition 3x1 -in in.tad



You should be able to use any number of replicas >= 3.

src/Make.py

+47 −23
Original line number Diff line number Diff line
@@ -26,7 +26,8 @@ libclasses = ("atc","awpmd","colvars","cuda","gpu","h5md", 
buildclasses = ("intel","kokkos")

makeclasses = ("cc","flags","mpi","fft","jpg","png")



setargs = ("gzip","#gzip","ffmpeg","#ffmpeg","smallbig","bigbig","smallsmall","exceptions","#exceptions")

setargs = ("gzip","#gzip","ffmpeg","#ffmpeg","smallbig","bigbig",

           "smallsmall","exceptions","#exceptions")

actionargs = ("lib-all","file","clean","exe")



gpubuildflag = 0
@@ -85,7 +86,8 @@ def switch2str(switches,switch_order): 
def compile_check(compiler,ccflags,warn):

  open("tmpauto.cpp",'w').write("int main(int, char **) {}\n")

  tmp = "%s %s -c tmpauto.cpp" % (compiler,ccflags)

  try: txt = subprocess.check_output(tmp,stderr=subprocess.STDOUT,shell=True).decode()

  try: txt = subprocess.check_output(tmp,stderr=subprocess.STDOUT,

                                     shell=True).decode()

  except subprocess.CalledProcessError as e: txt = e.output

  flag = 1

  if txt or not os.path.isfile("tmpauto.o"):
@@ -105,7 +107,8 @@ def compile_check(compiler,ccflags,warn): 
def link_check(linker,linkflags,libs,warn):

  open("tmpauto.cpp",'w').write("int main(int, char **) {}\n")

  tmp = "%s %s -o tmpauto tmpauto.cpp %s" % (linker,linkflags,libs)

  try: txt = subprocess.check_output(tmp,stderr=subprocess.STDOUT,shell=True).decode()

  try: txt = subprocess.check_output(tmp,stderr=subprocess.STDOUT,

                                     shell=True).decode()

  except subprocess.CalledProcessError as e: txt = e.output

  flag = 1

  if txt or not os.path.isfile("tmpauto"):
@@ -532,7 +535,8 @@ class Actions(object): 
    

    if caller == "file" or "file" not in self.alist:

      # make certain that 'MAKE/MINE' folder exists.

      subprocess.check_output("mkdir -p %s/MAKE/MINE" % dir.src,stderr=subprocess.STDOUT,shell=True)

      subprocess.check_output("mkdir -p %s/MAKE/MINE" % dir.src,

                              stderr=subprocess.STDOUT,shell=True)

      make.write("%s/MAKE/MINE/Makefile.auto" % dir.src,1)

      print("Created src/MAKE/MINE/Makefile.auto")
@@ -859,9 +863,12 @@ class Packages(object): 
    if self.plist: print("Installing packages ...")

    for one in self.plist:

      if one == "orig": continue

      subprocess.check_output("cd %s; make %s" % (dir.src,one),stderr=subprocess.STDOUT,shell=True)

      subprocess.check_output("cd %s; make %s" % (dir.src,one),

                              stderr=subprocess.STDOUT,shell=True)

    if self.plist and verbose:

      txt = subprocess.check_output("cd %s; make ps" % dir.src,stderr=subprocess.STDOUT,shell=True).decode()

      txt = subprocess.check_output("cd %s; make ps" % dir.src,

                                    stderr=subprocess.STDOUT,

                                    shell=True).decode()

      print("Package status after installation:")

      print(txt)
@@ -871,12 +878,16 @@ class Packages(object): 
  def uninstall(self):

    if not self.plist or self.plist[-1] != "orig": return

    print("Restoring packages to original state ...")

    subprocess.check_output("cd %s; make no-all" % dir.src,stderr=subprocess.STDOUT,shell=True)

    subprocess.check_output("cd %s; make no-all" % dir.src,

                            stderr=subprocess.STDOUT,shell=True)

    for one in self.all:

      if self.original[one]:

        subprocess.check_output("cd %s; make yes-%s" % (dir.src,one),stderr=subprocess.STDOUT,shell=True)

        subprocess.check_output("cd %s; make yes-%s" % (dir.src,one),

                                stderr=subprocess.STDOUT,shell=True)

    if verbose:

      txt = subprocess.check_output("cd %s; make ps" % dir.src,stderr=subprocess.STDOUT,shell=True).decode()

      txt = subprocess.check_output("cd %s; make ps" % dir.src,

                                    stderr=subprocess.STDOUT,

                                    shell=True).decode()

      print("Restored package status:")

      print(txt)
@@ -970,7 +981,8 @@ class Settings(object): 
  def help(self):

    return """

-s set1 set2 ...

  possible settings = gzip #gzip ffmpeg #ffmpeg smallbig bigbig smallsmall exceptions #exceptions

  possible settings = gzip #gzip ffmpeg #ffmpeg

                      smallbig bigbig smallsmall exceptions #exceptions

  alter LAMMPS ifdef settings in Makefile.auto

    only happens if new Makefile.auto is created by use of "file" action

  gzip and #gzip turn on/off LAMMPS_GZIP setting
@@ -1059,7 +1071,8 @@ class ATC(object): 
      make.setvar("EXTRAMAKE","Makefile.lammps.%s" % self.lammps)

    make.write("%s/Makefile.auto" % libdir)

    

    subprocess.check_output("cd %s; make -f Makefile.auto clean" % libdir,stderr=subprocess.STDOUT,shell=True)

    subprocess.check_output("cd %s; make -f Makefile.auto clean" %

                            libdir,stderr=subprocess.STDOUT,shell=True)

    if jmake: txt = "cd %s; make -j %d -f Makefile.auto" % (libdir,jmake.n)

    else: txt = "cd %s; make -f Makefile.auto" % libdir
@@ -1110,7 +1123,8 @@ class AWPMD(object): 
      make.setvar("EXTRAMAKE","Makefile.lammps.%s" % self.lammps)

    make.write("%s/Makefile.auto" % libdir)



    subprocess.check_output("cd %s; make -f Makefile.auto clean" % libdir,stderr=subprocess.STDOUT,shell=True)

    subprocess.check_output("cd %s; make -f Makefile.auto clean" %

                            libdir,stderr=subprocess.STDOUT,shell=True)

    if jmake: txt = "cd %s; make -j %d -f Makefile.auto" % (libdir,jmake.n)

    else: txt = "cd %s; make -f Makefile.auto" % libdir
@@ -1161,7 +1175,8 @@ class COLVARS(object): 
      make.setvar("EXTRAMAKE","Makefile.lammps.%s" % self.lammps)

    make.write("%s/Makefile.auto" % libdir)



    subprocess.check_output("cd %s; make -f Makefile.auto clean" % libdir,stderr=subprocess.STDOUT,shell=True)

    subprocess.check_output("cd %s; make -f Makefile.auto clean" %

                            libdir,stderr=subprocess.STDOUT,shell=True)

    if jmake: txt = "cd %s; make -j %d -f Makefile.auto" % (libdir,jmake.n)

    else: txt = "cd %s; make -f Makefile.auto" % libdir
@@ -1213,7 +1228,8 @@ class CUDA(object): 
          

  def build(self): 

    libdir = dir.lib + "/cuda"

    subprocess.check_output("cd %s; make clean" % libdir,stderr=subprocess.STDOUT,shell=True)

    subprocess.check_output("cd %s; make clean" % libdir,

                            stderr=subprocess.STDOUT,shell=True)

    if self.mode == "double": n = 2

    elif self.mode == "mixed": n = 3

    elif self.mode == "single": n = 1
@@ -1308,7 +1324,8 @@ class GPU(object): 
    make = "make"

    if "shannon" == platform.node(): make = "srun make"



    subprocess.check_output("cd %s; %s -f Makefile.auto clean" % (libdir,make),stderr=subprocess.STDOUT,shell=True)

    subprocess.check_output("cd %s; %s -f Makefile.auto clean" %

                            (libdir,make),stderr=subprocess.STDOUT,shell=True)

    if jmake: txt = "cd %s; %s -j %d -f Makefile.auto" % (libdir,make,jmake.n)

    else: txt = "cd %s; %s -f Makefile.auto" % (libdir,make)
@@ -1359,7 +1376,8 @@ class H5MD(object): 
      make.setvar("EXTRAMAKE","Makefile.lammps.%s" % self.lammps)

    make.write("%s/Makefile.auto" % libdir)



    subprocess.check_output("cd %s; make clean" % libdir,stderr=subprocess.STDOUT,shell=True)

    subprocess.check_output("cd %s; make clean" % libdir,

                            stderr=subprocess.STDOUT,shell=True)

    txt = "cd %s; make" % libdir



    # if verbose, print output as build proceeds, else only print if fails
@@ -1409,7 +1427,8 @@ class MEAM(object): 
      make.setvar("EXTRAMAKE","Makefile.lammps.%s" % self.lammps)

    make.write("%s/Makefile.auto" % libdir)



    subprocess.check_output("cd %s; make -f Makefile.auto clean" % libdir,stderr=subprocess.STDOUT,shell=True)

    subprocess.check_output("cd %s; make -f Makefile.auto clean" %

                            libdir,stderr=subprocess.STDOUT,shell=True)

    # do not use -j for MEAM build, parallel build does not work

    txt = "cd %s; make -f Makefile.auto" % libdir
@@ -1460,7 +1479,8 @@ class POEMS(object): 
      make.setvar("EXTRAMAKE","Makefile.lammps.%s" % self.lammps)

    make.write("%s/Makefile.auto" % libdir)



    subprocess.check_output("cd %s; make -f Makefile.auto clean" % libdir,stderr=subprocess.STDOUT,shell=True)

    subprocess.check_output("cd %s; make -f Makefile.auto clean" % libdir,

                            stderr=subprocess.STDOUT,shell=True)

    if jmake: txt = "cd %s; make -j %d -f Makefile.auto" % (libdir,jmake.n)

    else: txt = "cd %s; make -f Makefile.auto" % libdir
@@ -1508,7 +1528,8 @@ class PYTHON(object): 
      subprocess.check_output("cd %s; cp Makefile.lammps.%s Makefile.lammps" %

                              (libdir,self.lammps))

    if not os.path.isfile("%s/Makefile.lammps.%s" % (libdir,self.lammps)):

      error("Unsuccessful creation of lib/python/Makefile.lammps.%s file" % self.lammps)

      error("Unsuccessful creation of lib/python/Makefile.lammps.%s file" %

            self.lammps)

    else: print("Created lib/python/Makefile.lammps file")



# QMMM lib
@@ -1546,7 +1567,8 @@ class QMMM(object): 
      make.setvar("EXTRAMAKE","Makefile.lammps.%s" % self.lammps)

    make.write("%s/Makefile.auto" % libdir)



    subprocess.check_output("cd %s; make -f Makefile.auto clean" % libdir,stderr=subprocess.STDOUT,shell=True)

    subprocess.check_output("cd %s; make -f Makefile.auto clean" %

                            libdir,stderr=subprocess.STDOUT,shell=True)

    if jmake: txt = "cd %s; make -j %d -f Makefile.auto" % (libdir,jmake.n)

    else: txt = "cd %s; make -f Makefile.auto" % libdir
@@ -1597,7 +1619,8 @@ class REAX(object): 
      make.setvar("EXTRAMAKE","Makefile.lammps.%s" % self.lammps)

    make.write("%s/Makefile.auto" % libdir)



    commands.getoutput("cd %s; make -f Makefile.auto clean" % libdir)

    cmd = "cd %s; make -f Makefile.auto clean" % libdir

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

    if jmake: txt = "cd %s; make -j %d -f Makefile.auto" % (libdir,jmake.n)

    else: txt = "cd %s; make -f Makefile.auto" % libdir
@@ -1643,7 +1666,8 @@ class VORONOI(object): 
    if not self.install: return

    libdir = dir.lib + "/voronoi"

    cmd = "cd %s; python install.py %s" % (libdir,self.install)

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

    txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,

                                  shell=True).decode()

    if verbose: print(txt)

    print("Created lib/voronoi library")

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