diff --git a/doc/src/Section_accelerate.txt b/doc/src/Section_accelerate.txt index 8812358886..bb0c93b8aa 100644 --- a/doc/src/Section_accelerate.txt +++ b/doc/src/Section_accelerate.txt @@ -233,8 +233,8 @@ set any needed options for the package via "-pk" "command-line switch"_Section_s use accelerated styles in your input via "-sf" "command-line switch"_Section_start.html#start_6 or "suffix"_suffix.html command | lmp_machine -in in.script -sf gpu :tb(c=2,s=|) -Note that the first 4 steps can be done as a single command, using the -src/Make.py tool. This tool is discussed in "Section +Note that the first 4 steps can be done as a single command with +suitable make command invocations. This is discussed in "Section 4"_Section_packages.html of the manual, and its use is illustrated in the individual accelerator sections. Typically these steps only need to be done once, to create an executable that uses one diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt index 7dc3d27b6a..f1eb225fe5 100644 --- a/doc/src/Section_commands.txt +++ b/doc/src/Section_commands.txt @@ -734,8 +734,8 @@ package"_Section_start.html#start_3. "smd/wall/surface"_fix_smd_wall_surface.html, "temp/rescale/eff"_fix_temp_rescale_eff.html, "ti/spring"_fix_ti_spring.html, -"ttm/mod"_fix_ttm.html -"wall/ees"_fix_wall_ees.html +"ttm/mod"_fix_ttm.html, +"wall/ees"_fix_wall_ees.html, "wall/region/ees"_fix_wall_ees.html :tb(c=6,ea=c) :line diff --git a/doc/src/Section_example.txt b/doc/src/Section_example.txt index 26dc3b9698..f8b39be173 100644 --- a/doc/src/Section_example.txt +++ b/doc/src/Section_example.txt @@ -49,6 +49,7 @@ Lists of both kinds of directories are given below. Lowercase directories :h4 accelerate: run with various acceleration options (OpenMP, GPU, Phi) +airebo: polyethylene with AIREBO potential balance: dynamic load balancing, 2d system body: body particles, 2d system cmap: CMAP 5-body contributions to CHARMM force field diff --git a/doc/src/Section_packages.txt b/doc/src/Section_packages.txt index 54a2685b86..c7e6e84831 100644 --- a/doc/src/Section_packages.txt +++ b/doc/src/Section_packages.txt @@ -492,14 +492,38 @@ Minnesota). [Install or un-install:] -Using this package requires the KIM library and its models -(interatomic potentials) to be downloaded and installed on your -system. The library can be downloaded and built in lib/kim or -elsewhere on your system. Details of the download, build, and install -process for KIM are given in the lib/kim/README file. +Before building LAMMPS with this package, you must first download and +build the KIM library and include the KIM models that you want to +use. You can do this manually if you prefer; follow the instructions +in lib/kim/README. You can also do it in one step from the lammps/src +dir, using a command like these, which simply invoke the +lib/kim/Install.py script with the specified args. -Once that process is complete, you can then install/un-install the -package and build LAMMPS in the usual manner: +make lib-kim # print help message +make lib-kim args="-b . none" # install KIM API lib with only example models +make lib-kim args="-b . Glue_Ercolessi_Adams_Al__MO_324507536345_001" # ditto plus one model +make lib-kim args="-b . OpenKIM" # install KIM API lib with all models +make lib-kim args="-a EAM_Dynamo_Ackland_W__MO_141627196590_002" # add one model or model driver :pre + +Note that in LAMMPS lingo, a KIM model driver is a pair style +(e.g. EAM or Tersoff). A KIM model is a pair style for a particular +element or alloy and set of parameters, e.g. EAM for Cu with a +specific EAM potential file. Also note that installing the KIM API +library with all its models, may take around 30 min to build. Of +course you only need to do that once. + +See the list of KIM model drivers here: +https://openkim.org/kim-items/model-drivers/alphabetical + +See the list of all KIM models here: +https://openkim.org/kim-items/models/by-model-drivers + +See the list of example KIM models included by default here: +https://openkim.org/kim-api +in the "What is in the KIM API source package?" section + +You can then install/un-install the package and build LAMMPS in the +usual manner: make yes-kim make machine :pre @@ -1414,7 +1438,7 @@ lib/linalg. In the latter case you also need to build the library in lib/linalg with a command like these: make lib-linalg # print help message -make lib-atc args="-m gfortran" # build with GNU Fortran compiler +make lib-linalg args="-m gfortran" # build with GNU Fortran compiler You can then install/un-install the package and build LAMMPS in the usual manner: @@ -2469,8 +2493,8 @@ step from the lammps/src dir, using a command like these, which simply invoke the lib/smd/Install.py script with the specified args: make lib-smd # print help message -make lib-smd args="-g -l" # download in default lib/smd/eigen-eigen-* -make lib-smd args="-h . eigen -g -l" # download in lib/smd/eigen +make lib-smd args="-g -l" # download and build in default lib/smd/eigen-eigen-* +make lib-smd args="-h . eigen -g -l" # download and build in lib/smd/eigen make lib-smd args="-h ~ eigen -g -l" # download and build in ~/eigen :pre Note that the final -l switch is to create a symbolic (soft) link diff --git a/doc/src/accelerate_gpu.txt b/doc/src/accelerate_gpu.txt index 68e9fa477a..2723b6e971 100644 --- a/doc/src/accelerate_gpu.txt +++ b/doc/src/accelerate_gpu.txt @@ -74,13 +74,8 @@ Run lammps/lib/gpu/nvc_get_devices (after building the GPU library, see below) t This requires two steps (a,b): build the GPU library, then build LAMMPS with the GPU package. -You can do both these steps in one line, using the src/Make.py script, -described in "Section 4"_Section_packages.html of the manual. -Type "Make.py -h" for help. If run from the src directory, this -command will create src/lmp_gpu using src/MAKE/Makefile.mpi as the -starting Makefile.machine: - -Make.py -p gpu -gpu mode=single arch=31 -o gpu -a lib-gpu file mpi :pre +You can do both these steps in one line as described in +"Section 4"_Section_packages.html of the manual. Or you can follow these two (a,b) steps: diff --git a/doc/src/accelerate_intel.txt b/doc/src/accelerate_intel.txt index 74ae9d9a42..9eb295e0d0 100644 --- a/doc/src/accelerate_intel.txt +++ b/doc/src/accelerate_intel.txt @@ -225,11 +225,9 @@ source /opt/intel/parallel_studio_xe_2016.3.067/psxevars.sh # or psxevars.csh for C-shell make intel_cpu_intelmpi :pre -Alternatively, the build can be accomplished with the src/Make.py -script, described in "Section 4"_Section_packages.html of the -manual. Type "Make.py -h" for help. For an example: - -Make.py -v -p intel omp -intel cpu -a file intel_cpu_intelmpi :pre +Alternatively this can be done as a single command with +suitable make command invocations. This is discussed in "Section +4"_Section_packages.html of the manual. Note that if you build with support for a Phi coprocessor, the same binary can be used on nodes with or without coprocessors installed. @@ -244,8 +242,7 @@ highly recommended for CCFLAGS and LINKFLAGS. LIB should include is required for CCFLAGS and "-qoffload" is required for LINKFLAGS. Other recommended CCFLAG options for best performance are "-O2 -fno-alias -ansi-alias -qoverride-limits fp-model fast=2 --no-prec-div". The Make.py command will add all of these -automatically. +-no-prec-div". NOTE: The vectorization and math capabilities can differ depending on the CPU. For Intel compilers, the "-x" flag specifies the type of diff --git a/doc/src/accelerate_kokkos.txt b/doc/src/accelerate_kokkos.txt index 6ccd695841..712a05300c 100644 --- a/doc/src/accelerate_kokkos.txt +++ b/doc/src/accelerate_kokkos.txt @@ -60,8 +60,7 @@ More details follow. use a C++11 compatible compiler make yes-kokkos make mpi KOKKOS_DEVICES=OpenMP # build with the KOKKOS package -make kokkos_omp # or Makefile.kokkos_omp already has variable set -Make.py -v -p kokkos -kokkos omp -o mpi -a file mpi # or one-line build via Make.py :pre +make kokkos_omp # or Makefile.kokkos_omp already has variable set :pre mpirun -np 16 lmp_mpi -k on -sf kk -in in.lj # 1 node, 16 MPI tasks/node, no threads mpirun -np 2 -ppn 1 lmp_mpi -k on t 16 -sf kk -in in.lj # 2 nodes, 1 MPI task/node, 16 threads/task @@ -82,8 +81,7 @@ use a C++11 compatible compiler KOKKOS_DEVICES = Cuda, OpenMP KOKKOS_ARCH = Kepler35 make yes-kokkos -make machine -Make.py -p kokkos -kokkos cuda arch=31 -o kokkos_cuda -a file kokkos_cuda :pre +make machine :pre mpirun -np 1 lmp_cuda -k on t 6 -sf kk -in in.lj # one MPI task, 6 threads on CPU mpirun -np 4 -ppn 1 lmp_cuda -k on t 6 -sf kk -in in.lj # ditto on 4 nodes :pre @@ -98,8 +96,7 @@ use a C++11 compatible compiler KOKKOS_DEVICES = OpenMP KOKKOS_ARCH = KNC make yes-kokkos -make machine -Make.py -p kokkos -kokkos phi -o kokkos_phi -a file mpi :pre +make machine :pre host=MIC, Intel Phi with 61 cores (240 threads/phi via 4x hardware threading): mpirun -np 1 lmp_g++ -k on t 240 -sf kk -in in.lj # 1 MPI task on 1 Phi, 1*240 = 240 @@ -135,9 +132,9 @@ mode like the USER-INTEL package supports. You must choose at build time whether to build for CPUs (OpenMP), GPUs, or Phi. -You can do any of these in one line, using the src/Make.py script, -described in "Section 4"_Section_packages.html of the manual. -Type "Make.py -h" for help. If run from the src directory, these +You can do any of these in one line, using the suitable make command +line flags as described in "Section 4"_Section_packages.html of the +manual. If run from the src directory, these commands will create src/lmp_kokkos_omp, lmp_kokkos_cuda, and lmp_kokkos_phi. Note that the OMP and PHI options use src/MAKE/Makefile.mpi as the starting Makefile.machine. The CUDA diff --git a/doc/src/accelerate_omp.txt b/doc/src/accelerate_omp.txt index 81b7a5adc2..fa7bef1a52 100644 --- a/doc/src/accelerate_omp.txt +++ b/doc/src/accelerate_omp.txt @@ -23,8 +23,7 @@ one or more 16-core nodes. More details follow. use -fopenmp with CCFLAGS and LINKFLAGS in Makefile.machine make yes-user-omp make mpi # build with USER-OMP package, if settings added to Makefile.mpi -make omp # or Makefile.omp already has settings -Make.py -v -p omp -o mpi -a file mpi # or one-line build via Make.py :pre +make omp # or Makefile.omp already has settings :pre lmp_mpi -sf omp -pk omp 16 < in.script # 1 MPI task, 16 threads mpirun -np 4 lmp_mpi -sf omp -pk omp 4 -in in.script # 4 MPI tasks, 4 threads/task @@ -40,14 +39,11 @@ each MPI task running on a CPU. The lines above illustrate how to include/build with the USER-OMP package in two steps, using the "make" command. Or how to do it with -one command via the src/Make.py script, described in "Section -4"_Section_packages.html of the manual. Type "Make.py -h" for -help. +one command as described in "Section 4"_Section_packages.html of the manual. Note that the CCFLAGS and LINKFLAGS settings in Makefile.machine must include "-fopenmp". Likewise, if you use an Intel compiler, the -CCFLAGS setting must include "-restrict". The Make.py command will -add these automatically. +CCFLAGS setting must include "-restrict". [Run with the USER-OMP package from the command line:] diff --git a/doc/src/accelerate_opt.txt b/doc/src/accelerate_opt.txt index 5a2a5eac0a..845264b522 100644 --- a/doc/src/accelerate_opt.txt +++ b/doc/src/accelerate_opt.txt @@ -21,8 +21,7 @@ Here is a quick overview of how to use the OPT package. More details follow. make yes-opt -make mpi # build with the OPT package -Make.py -v -p opt -o mpi -a file mpi # or one-line build via Make.py :pre +make mpi # build with the OPT package :pre lmp_mpi -sf opt -in in.script # run in serial mpirun -np 4 lmp_mpi -sf opt -in in.script # run in parallel :pre @@ -35,13 +34,10 @@ None. The lines above illustrate how to build LAMMPS with the OPT package in two steps, using the "make" command. Or how to do it with one command -via the src/Make.py script, described in "Section -4"_Section_packages.html of the manual. Type "Make.py -h" for -help. +as described in "Section 4"_Section_packages.html of the manual. Note that if you use an Intel compiler to build with the OPT package, the CCFLAGS setting in your Makefile.machine must include "-restrict". -The Make.py command will add this automatically. [Run with the OPT package from the command line:] diff --git a/doc/src/neigh_modify.txt b/doc/src/neigh_modify.txt index 5c149d892d..c4544cb29b 100644 --- a/doc/src/neigh_modify.txt +++ b/doc/src/neigh_modify.txt @@ -109,7 +109,8 @@ atoms in the specified group. This can be useful for models where a large portion of the simulation is particles that do not interact with other particles or with each other via pairwise interactions. The group specified with this option must also be specified via the -"atom_modify first"_atom_modify.html command. +"atom_modify first"_atom_modify.html command. Note that specifying +"all" as the group-ID effectively turns off the {include} option. The {exclude} option turns off pairwise interactions between certain pairs of atoms, by not including them in the neighbor list. These are @@ -213,5 +214,5 @@ space. [Default:] The option defaults are delay = 10, every = 1, check = yes, once = no, -cluster = no, include = all, exclude = none, page = 100000, one = -2000, and binsize = 0.0. +cluster = no, include = all (same as no include option defined), +exclude = none, page = 100000, one = 2000, and binsize = 0.0. diff --git a/examples/README b/examples/README index 0b037f5c38..dc622ef7c4 100644 --- a/examples/README +++ b/examples/README @@ -58,7 +58,7 @@ These are the sample problems and their output in the various sub-directories: accelerate: use of all the various accelerator packages -airebo: example for using AIREBO and AIREBO-M +airebo: polyethylene with AIREBO potential balance: dynamic load balancing, 2d system body: body particles, 2d system cmap: CMAP 5-body contributions to CHARMM force field diff --git a/lib/Install.py b/lib/Install.py index 18b426f928..29270560a6 100644 --- a/lib/Install.py +++ b/lib/Install.py @@ -9,12 +9,21 @@ import sys,commands,os # help message help = """ -Syntax: python Install.py -m machine -e suffix - specify -m and optionally -e, order does not matter +Syntax from src dir: make lib-libname args="-m machine -e suffix" +Syntax from lib dir: python Install.py -m machine -e suffix + +libname = name of lib dir (e.g. atc, colvars, h5md, meam, poems, etc) +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 -e = set EXTRAMAKE variable in Makefile.machine to Makefile.lammps.suffix does not alter existing Makefile.machine + +Examplesx: + +make lib-colvars args="-m g++" # build COLVARS lib with GNU g++ compiler +make lib-meam args="-m ifort" # build MEAM lib with Intel ifort compiler """ # print error message or help diff --git a/lib/gpu/Install.py b/lib/gpu/Install.py index d396be5e1a..c6cd1f3021 100644 --- a/lib/gpu/Install.py +++ b/lib/gpu/Install.py @@ -8,14 +8,17 @@ import sys,os,re,commands # help message help = """ -Syntax: python Install.py -i isuffix -h hdir -a arch -p precision -e esuffix -m -o osuffix - specify one or more options, order does not matter - copies an existing Makefile.isuffix in lib/gpu to Makefile.auto - optionally edits these variables in Makefile.auto: - CUDA_HOME, CUDA_ARCH, CUDA_PRECISION, EXTRAMAKE - optionally uses Makefile.auto to build the GPU library -> libgpu.a - and to copy a Makefile.lammps.esuffix -> Makefile.lammps - optionally copies Makefile.auto to a new Makefile.osuffix +Syntax from src dir: make lib-gpu args="-i isuffix -h hdir -a arch -p precision -e esuffix -m -o osuffix" +Syntax from lib dir: python Install.py -i isuffix -h hdir -a arch -p precision -e esuffix -m -o osuffix + +specify one or more options, order does not matter + +copies an existing Makefile.isuffix in lib/gpu to Makefile.auto +optionally edits these variables in Makefile.auto: + CUDA_HOME, CUDA_ARCH, CUDA_PRECISION, EXTRAMAKE +optionally uses Makefile.auto to build the GPU library -> libgpu.a + and to copy a Makefile.lammps.esuffix -> Makefile.lammps +optionally copies Makefile.auto to a new Makefile.osuffix -i = use Makefile.isuffix as starting point, copy to Makefile.auto default isuffix = linux @@ -34,6 +37,12 @@ Syntax: python Install.py -i isuffix -h hdir -a arch -p precision -e esuffix -m also copies EXTRAMAKE file -> Makefile.lammps -e can set which Makefile.lammps.esuffix file is copied -o = copy final Makefile.auto to Makefile.osuffix + +Examples: + +make lib-gpu args="-m" # build GPU lib with default Makefile.linux +make lib-gpu args="-i xk7 -p single -o xk7.single" # create new Makefile.xk7.single, altered for single-precision +make lib-gpu args="-i xk7 -p single -o xk7.single -m" # ditto, also build GPU lib """ # print error message or help diff --git a/lib/kim/Install.py b/lib/kim/Install.py index bcd22dcbb3..1405cc5fad 100644 --- a/lib/kim/Install.py +++ b/lib/kim/Install.py @@ -1,150 +1,232 @@ #!/usr/bin/env python -# install.py tool to setup the kim-api library +# install.pa tool to setup the kim-api library # used to automate the steps described in the README file in this dir - -import sys,os,re,urllib,commands +from __future__ import print_function +import sys,os,re,subprocess +try: from urllib.request import urlretrieve as geturl +except: from urllib import urlretrieve as geturl help = """ -Syntax: install.py -v version -c kim-dir -b kim-model-name -a kim-name - specify one or more options, order does not matter - -v = version of kim-api to download and work with - default = kim-api-v1.8.2 (current as of June 2017) - -c = create Makefile.KIM_DIR within lammps lib/kim to configure lammps - for use with the kim-api library installed at "kim-dir" (absolute - path). default = this dir - -b = build kim-api and kim model where kim-model-name can be a specific - openkim.org model name (such as - "EAM_Dynamo_Ackland_W__MO_141627196590_002") or the keyword - "OpenKIM" to install all compatible models from the openkim.org - site. - -a = add kim-name openkim.org item (model driver or model) to existing - kim-api instalation. +Syntax from src dir: make lib-kim args="-v version -b kim-install-dir kim-name -a kim-name" +Syntax from lib dir: python Install.py -v version -b kim-install-dir kim-name -a kim-name + +specify one or more options, order does not matter + + -v = version of KIM API library to use + default = kim-api-v1.8.2 (current as of June 2017) + -b = download and build KIM API library with KIM models + kim-dir = where to install/build the KIM API library + use "." to install in lib/kim + kim-name = none to install only the example KIM models + kim-name = KIM model name (see example below) + examples + kim-name = OpenKIM to install all models + from the openkim.org site (this can take 30 minutes or more) + -a = add single KIM model or model driver with kim-name + to existing KIM API lib (see example below) + +Examples: + +make lib-kim args="-b . none" # install KIM API lib with only example models +make lib-kim args="-b . Glue_Ercolessi_Adams_Al__MO_324507536345_001" # ditto plus one model +make lib-kim args="-b . OpenKIM" # install KIM API lib with all models +make lib-kim args="-a EAM_Dynamo_Ackland_W__MO_141627196590_002" # add one model or model driver + +See the list of KIM model drivers here: +https://openkim.org/kim-items/model-drivers/alphabetical + +See the list of all KIM models here: +https://openkim.org/kim-items/models/by-model-drivers + +See the list of example KIM models included by default here: +https://openkim.org/kim-api +in the "What is in the KIM API source package?" section """ def error(): - print help + print(help) sys.exit() # parse args -args = sys.argv +args = sys.argv[1:] +nargs = len(args) +if nargs == 0: error() thisdir = os.environ['PWD'] -dir = thisdir version = "kim-api-v1.8.2" -dirflag = 0 -buildflag = 0 -addflag = 0 +buildflag = False +addflag = False -iarg = 1 +iarg = 0 while iarg < len(args): if args[iarg] == "-v": if iarg+2 > len(args): error() version = args[iarg+1] iarg += 2 - elif args[iarg] == "-c": - dirflag = 1 - if iarg+2 > len(args): error() - dir = args[iarg+1] - iarg += 2 elif args[iarg] == "-b": - buildflag = 1 - if iarg+2 > len(args): error() - modelname = args[iarg+1] - iarg += 2 + buildflag = True + if iarg+3 > len(args): error() + dir = args[iarg+1] + modelname = args[iarg+2] + iarg += 3 elif args[iarg] == "-a": - addflag = 1 + addflag = True if iarg+2 > len(args): error() addmodelname = args[iarg+1] iarg += 2 else: error() thisdir = os.path.abspath(thisdir) -dir = os.path.abspath(dir) url = "https://s3.openkim.org/kim-api/%s.tgz" % version -# download and unpack tarball +# download KIM tarball, unpack, build KIM +# either in lib/kim or user-requested location +if buildflag: -if not os.path.isfile("%s/Makefile.KIM_DIR" % thisdir): - open("%s/Makefile.KIM_DIR" % thisdir, 'w').write("KIM_INSTALL_DIR=%s" % dir) - open("%s/Makefile.KIM_Config" % thisdir, 'w').write("include %s/lib/kim-api/Makefile.KIM_Config" % dir) - print "Created %s/Makefile.KIM_DIR : using %s" % (thisdir,dir) -else: - if dirflag == 1: - open("%s/Makefile.KIM_DIR" % thisdir, 'w').write("KIM_INSTALL_DIR=%s" % dir) - open("%s/Makefile.KIM_Config" % thisdir, 'w').write("include %s/lib/kim-api/Makefile.KIM_Config" % dir) - print "Updated %s/Makefile.KIM_DIR : using %s" % (thisdir,dir) + # set install directory + dir = os.path.join(os.path.abspath(dir), "installed-" + version) -if buildflag == 1: - # download kim-api - print "Downloading kim-api tarball ..." - urllib.urlretrieve(url,"%s/%s.tgz" % (thisdir,version)) - print "Unpacking kim-api tarball ..." + # check to see if an installed kim-api already exists and wipe it out. + + if os.path.isdir(dir): + print("kim-api is already installed at %s.\nRemoving it for re-install" % dir) + cmd = "rm -rf %s" % dir + subprocess.check_output(cmd,shell=True) + + # configure LAMMPS to use kim-api to be installed + + with open("%s/Makefile.KIM_DIR" % thisdir, 'w') as mkfile: + mkfile.write("KIM_INSTALL_DIR=%s\n\n" % dir) + mkfile.write(".DUMMY: print_dir\n\n") + mkfile.write("print_dir:\n") + mkfile.write(" @printf $(KIM_INSTALL_DIR)\n") + + with open("%s/Makefile.KIM_Config" % thisdir, 'w') as cfgfile: + cfgfile.write("include %s/lib/kim-api/Makefile.KIM_Config" % dir) + + print("Created %s/Makefile.KIM_DIR : using %s" % (thisdir,dir)) + + # download entire kim-api tarball + + print("Downloading kim-api tarball ...") + geturl(url,"%s/%s.tgz" % (thisdir,version)) + print("Unpacking kim-api tarball ...") cmd = "cd %s; rm -rf %s; tar zxvf %s.tgz" % (thisdir,version,version) - txt = commands.getstatusoutput(cmd) - if txt[0] != 0: error() + subprocess.check_output(cmd,shell=True) # configure kim-api - print "Configuring kim-api ..." + + print("Configuring kim-api ...") cmd = "cd %s/%s; ./configure --prefix='%s'" % (thisdir,version,dir) - txt = commands.getstatusoutput(cmd) - print txt[1] - if txt[0] != 0: error() + subprocess.check_output(cmd,shell=True) # build kim-api - print "Configuring model : %s" % modelname - cmd = "cd %s/%s; make add-%s" % (thisdir,version,modelname) - txt = commands.getstatusoutput(cmd) - print txt[1] - if txt[0] != 0: error() - # - print "Building kim-api ..." + + print("Configuring model : %s" % modelname) + if modelname == "none": + cmd = "cd %s/%s; make add-examples" % (thisdir,version) + else: + if modelname == "OpenKIM": + print("configuring all OpenKIM models, this will take a while ...") + cmd = "cd %s/%s; make add-examples; make add-%s" % \ + (thisdir,version,modelname) + subprocess.check_output(cmd,shell=True) + + print("Building kim-api ...") cmd = "cd %s/%s; make" % (thisdir,version) - txt = commands.getstatusoutput(cmd) - print txt[1] - if txt[0] != 0: error() + subprocess.check_output(cmd,shell=True) # install kim-api - print "Installing kim-api ..." + + print("Installing kim-api ...") cmd = "cd %s/%s; make install" % (thisdir,version) - txt = commands.getstatusoutput(cmd) - print txt[1] - if txt[0] != 0: error() - # + subprocess.check_output(cmd,shell=True) + cmd = "cd %s/%s; make install-set-default-to-v1" %(thisdir,version) - txt = commands.getstatusoutput(cmd) - print txt[1] - if txt[0] != 0: error() + subprocess.check_output(cmd,shell=True) # remove source files - print "Removing kim-api source and build files ..." - cmd = "cd %s; rm -rf %s; rm -rf %s.tgz" % (thisdir,version,version) - txt = commands.getstatusoutput(cmd) - print txt[1] - if txt[0] != 0: error() -if addflag == 1: - # download model + print("Removing kim-api source and build files ...") + cmd = "cd %s; rm -rf %s; rm -rf %s.tgz" % (thisdir,version,version) + subprocess.check_output(cmd,shell=True) + +# add a single model (and possibly its driver) to existing KIM installation + +if addflag: + + # get location of installed kim-api + + if not os.path.isfile("%s/Makefile.KIM_DIR" % thisdir): + print("kim-api is not installed") + error() + else: + cmd = "cd %s; make -f Makefile.KIM_DIR print_dir" % thisdir + dir = subprocess.check_output(cmd,shell=True)[1] + + # download single model + # try first via urllib + # if fails (probably due to no SSL support), use wget + + print("Downloading item tarball ...") url = "https://openkim.org/download/%s.tgz" % addmodelname - print "Downloading item tarball ..." - urllib.urlretrieve(url,"%s/%s.tgz" % (thisdir,addmodelname)) - print "Unpacking item tarball ..." + geturl(url,"%s/%s.tgz" % (thisdir,addmodelname)) + + print("Unpacking item tarball ...") cmd = "cd %s; tar zxvf %s.tgz" % (thisdir,addmodelname) - txt = commands.getstatusoutput(cmd) - if txt[0] != 0: error() - # - print "Building item ..." + subprocess.check_output(cmd,shell=True) + + print("Building item ...") cmd = "cd %s/%s; make; make install" %(thisdir,addmodelname) - txt = commands.getstatusoutput(cmd) - print txt[1] - if txt[0] != 0: error() - # - print "Removing kim item source and build files ..." + try: + txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) + except subprocess.CalledProcessError as e: + + # Error: but first, check to see if it needs a driver + firstRunOutput = e.output.decode() + + cmd = "cd %s/%s; make kim-item-type" % (thisdir,addmodelname) + txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) + txt = txt.decode().strip() + if txt == "ParameterizedModel": + + # Get and install driver + + cmd = "cd %s/%s; make model-driver-name" % (thisdir,addmodelname) + txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) + adddrivername = txt.decode().strip() + print("First installing model driver: %s" % adddrivername) + cmd = "cd %s; python Install.py -a %s" % (thisdir,adddrivername) + try: + txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) + except subprocess.CalledProcessError as e: + print(e.output) + sys.exit() + + # now install the model that needed the driver + + print("Now installing model : %s" % addmodelname) + cmd = "cd %s; python Install.py -a %s" % (thisdir,addmodelname) + try: + txt = subprocess.check_output(cmd,stderr=subprocess.STDOUT,shell=True) + except subprocess.CalledProcessError as e: + print(e.output) + sys.exit() + print(txt.decode()) + sys.exit() + else: + print(firstRunOutput) + print("Error, unable to build and install OpenKIM item: %s" \ + % addmodelname) + sys.exit() + + # success the first time + + print(txt) + print("Removing kim item source and build files ...") cmd = "cd %s; rm -rf %s; rm -rf %s.tgz" %(thisdir,addmodelname,addmodelname) - txt = commands.getstatusoutput(cmd) - print txt[1] - if txt[0] != 0: error() + subprocess.check_output(cmd,shell=True) diff --git a/lib/kim/README b/lib/kim/README index 00d6ea8fad..7a4230dc25 100644 --- a/lib/kim/README +++ b/lib/kim/README @@ -8,14 +8,16 @@ James Sethna (Cornell U). Ryan Elliott is the main developer for the KIM API and he also maintains the code that implements the pair_style kim command. -To download, build, and install the KIM API on your system, follow -these steps. You can use the install.py script to automate these steps. +You can type "make lib-kim" from the src directory to see help on +how to download and build this library via make commands, or you can +do the same thing by typing "python Install.py" from within this +directory, or you can do it manually by following the instructions +below. ----------------- Instructions: - 1. Configure lammps for use with the kim-api library installed in this directory $ printf "KIM_INSTALL_DIR=${PWD}\n" > ./Makefile.KIM_DIR @@ -65,7 +67,7 @@ $ rm -rf EAM_Johnson_NearestNeighbor_Cu__MO_887933271505_001.tgz When these steps are complete you can build LAMMPS with the KIM package installed: -$ cd ../../src +$ cd lammpos/src $ make yes-kim $ make g++ (or whatever target you wish) diff --git a/lib/linalg/Install.py b/lib/linalg/Install.py index c7076ca52f..560afecec4 100644 --- a/lib/linalg/Install.py +++ b/lib/linalg/Install.py @@ -8,9 +8,15 @@ import sys,commands,os # help message help = """ -Syntax: python Install.py -m machine +Syntax from src dir: make lib-linalg args="-m machine" +Syntax from lib dir: python Install.py -m machine + -m = peform a clean followed by "make -f Makefile.machine" machine = suffix of a lib/Makefile.* file + +Example: + +make lib-linalg args="-m gfortran" # build with GNU Fortran compiler """ # print error message or help diff --git a/lib/mscg/Install.py b/lib/mscg/Install.py index e547232614..7b10be189f 100644 --- a/lib/mscg/Install.py +++ b/lib/mscg/Install.py @@ -8,8 +8,11 @@ import sys,os,re,commands # help message help = """ -Syntax: python Install.py -h hpath hdir -g -b [suffix] -l - specify one or more options, order does not matter +Syntax from src dir: make lib-mscg args="-h hpath hdir -g -b [suffix] -l" +Syntax from lib dir: python Install.py -h hpath hdir -g -b [suffix] -l + +specify one or more options, order does not matter + -h = set home dir of MS-CG to be hpath/hdir hpath can be full path, contain '~' or '.' chars default hpath = . = lib/mscg @@ -22,6 +25,10 @@ Syntax: python Install.py -h hpath hdir -g -b [suffix] -l optional suffix specifies which src/Make/Makefile.suffix to use default suffix = g++_simple -l = create 2 softlinks (includelink,liblink) in lib/mscg to MS-CG src dir + +Example: + +make lib-mscg args="-g -b -l" # download/build in lib/mscg/MSCG-release-master """ # settings diff --git a/lib/smd/Install.py b/lib/smd/Install.py index dc0a3187ce..0fa05375db 100644 --- a/lib/smd/Install.py +++ b/lib/smd/Install.py @@ -3,13 +3,19 @@ # Install.py tool to download, unpack, and point to the Eigen library # used to automate the steps described in the README file in this dir -import sys,os,re,glob,commands +from __future__ import print_function +import sys,os,re,glob,subprocess +try: from urllib.request import urlretrieve as geturl +except: from urllib import urlretrieve as geturl # help message help = """ -Syntax: python Install.py -h hpath hdir -g -l - specify one or more options, order does not matter +Syntax from src dir: make lib-smd args="-h hpath hdir -g -l" +Syntax from lib dir: python Install.py -h hpath hdir -g -l + +specify one or more options, order does not matter + -h = set home dir of Eigen to be hpath/hdir hpath can be full path, contain '~' or '.' chars default hpath = . = lib/smd @@ -19,18 +25,23 @@ Syntax: python Install.py -h hpath hdir -g -l hpath must already exist if hdir already exists, it will be deleted before unpack -l = create softlink (includelink) in lib/smd to Eigen src dir + +Example: + +make lib-smd args="-g -l" # download/build in default lib/smd/eigen-eigen-* """ # settings -url = "http://bitbucket.org/eigen/eigen/get/3.3.3.tar.gz" +version = '3.3.4' +url = "http://bitbucket.org/eigen/eigen/get/%s.tar.gz" % version tarball = "eigen.tar.gz" # 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() # expand to full path name @@ -73,26 +84,26 @@ if not os.path.isdir(homepath): error("Eigen path does not exist") # glob to find name of dir it unpacks to if grabflag: - print "Downloading Eigen ..." - cmd = "curl -L %s > %s/%s" % (url,homepath,tarball) - print cmd - print commands.getoutput(cmd) + print("Downloading Eigen ...") + geturl(url,"%s/%s" % (homepath,tarball)) - print "Unpacking Eigen tarball ..." + print("Unpacking Eigen tarball ...") edir = glob.glob("%s/eigen-eigen-*" % homepath) for one in edir: - if os.path.isdir(one): commands.getoutput("rm -rf %s" % one) - cmd = "cd %s; tar zxvf %s" % (homepath,tarball) - commands.getoutput(cmd) + if os.path.isdir(one): + subprocess.check_output("rm -rf %s" % one,shell=True) + cmd = 'cd "%s"; tar -xzvf %s' % (homepath,tarball) + subprocess.check_output(cmd,shell=True) if homedir != "ee": - if os.path.exists(homedir): commands.getoutput("rm -rf %s" % homedir) + if os.path.exists(homedir): + subprocess.check_output("rm -rf %s" % homedir,shell=True) edir = glob.glob("%s/eigen-eigen-*" % homepath) os.rename(edir[0],"%s/%s" % (homepath,homedir)) # create link in lib/smd to Eigen src dir if linkflag: - print "Creating link to Eigen files" + print("Creating link to Eigen files") if os.path.isfile("includelink") or os.path.islink("includelink"): os.remove("includelink") if homedir == "ee": @@ -100,4 +111,4 @@ if linkflag: linkdir = edir[0] else: linkdir = "%s/%s" % (homepath,homedir) cmd = "ln -s %s includelink" % linkdir - commands.getoutput(cmd) + subprocess.check_output(cmd,shell=True) diff --git a/lib/voronoi/Install.py b/lib/voronoi/Install.py index 7d847183b3..1c4bc5cb6d 100644 --- a/lib/voronoi/Install.py +++ b/lib/voronoi/Install.py @@ -2,14 +2,19 @@ # Install.py tool to download, unpack, build, and link to the Voro++ library # used to automate the steps described in the README file in this dir - -import sys,os,re,urllib,commands +from __future__ import print_function +import sys,os,re,subprocess +try: from urllib.request import urlretrieve as geturl +except: from urllib import urlretrieve as geturl # help message help = """ -Syntax: python Install.py -v version -h hpath hdir -g -b -l - specify one or more options, order does not matter +Syntax from src dir: make lib-voronoi args="-v version -h hpath hdir -g -b -l" +Syntax from lib dir: python Install.py -v version -h hpath hdir -g -b -l + +specify one or more options, order does not matter + -v = version of Voro++ to download and build default version = voro++-0.4.6 (current as of Jan 2015) -h = set home dir of Voro++ to be hpath/hdir @@ -22,6 +27,10 @@ Syntax: python Install.py -v version -h hpath hdir -g -b -l if hdir already exists, it will be deleted before unpack -b = build Voro++ library in its src dir -l = create 2 softlinks (includelink,liblink) in lib/voronoi to Voro++ src dir + +Example: + +make lib-voronoi args="-g -b -l" # download/build in lib/voronoi/voro++-0.4.6 """ # settings @@ -32,8 +41,8 @@ url = "http://math.lbl.gov/voro++/download/dir/%s.tar.gz" % version # 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() # expand to full path name @@ -51,9 +60,9 @@ if nargs == 0: error() homepath = "." homedir = version -grabflag = 0 -buildflag = 0 -linkflag = 0 +grabflag = False +buildflag = False +linkflag = False iarg = 0 while iarg < nargs: @@ -67,13 +76,13 @@ while iarg < nargs: homedir = args[iarg+2] iarg += 3 elif args[iarg] == "-g": - grabflag = 1 + grabflag = True iarg += 1 elif args[iarg] == "-b": - buildflag = 1 + buildflag = True iarg += 1 elif args[iarg] == "-l": - linkflag = 1 + linkflag = True iarg += 1 else: error() @@ -84,35 +93,38 @@ homedir = "%s/%s" % (homepath,homedir) # download and unpack Voro++ tarball if grabflag: - print "Downloading Voro++ ..." - urllib.urlretrieve(url,"%s/%s.tar.gz" % (homepath,version)) + print("Downloading Voro++ ...") + geturl(url,"%s/%s.tar.gz" % (homepath,version)) - print "Unpacking Voro++ tarball ..." + print("Unpacking Voro++ tarball ...") if os.path.exists("%s/%s" % (homepath,version)): - commands.getoutput("rm -rf %s/%s" % (homepath,version)) - cmd = "cd %s; tar zxvf %s.tar.gz" % (homepath,version) - commands.getoutput(cmd) + cmd = 'rm -rf "%s/%s"' % (homepath,version) + subprocess.check_output(cmd,shell=True) + cmd = 'cd "%s"; tar -xzvf %s.tar.gz' % (homepath,version) + subprocess.check_output(cmd,shell=True) if os.path.basename(homedir) != version: - if os.path.exists(homedir): commands.getoutput("rm -rf %s" % homedir) + if os.path.exists(homedir): + cmd = 'rm -rf "%s"' % homedir + subprocess.check_output(cmd,shell=True) os.rename("%s/%s" % (homepath,version),homedir) # build Voro++ if buildflag: - print "Building Voro++ ..." - cmd = "cd %s; make" % homedir - txt = commands.getoutput(cmd) - print txt + print("Building Voro++ ...") + cmd = 'cd "%s"; make' % homedir + txt = subprocess.check_output(cmd,shell=True) + print(txt) # create 2 links in lib/voronoi to Voro++ src dir if linkflag: - print "Creating links to Voro++ include and lib files" + print("Creating links to Voro++ include and lib files") 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") - cmd = "ln -s %s/src includelink" % homedir - commands.getoutput(cmd) - cmd = "ln -s %s/src liblink" % homedir - commands.getoutput(cmd) + cmd = ['ln -s "%s/src" includelink' % homedir, 'includelink'] + subprocess.check_output(cmd,shell=True) + cmd = ['ln -s "%s/src" liblink' % homedir] + subprocess.check_output(cmd,shell=True) diff --git a/src/Makefile b/src/Makefile index c7b20dcb13..3d1085e0be 100644 --- a/src/Makefile +++ b/src/Makefile @@ -116,7 +116,8 @@ help: @echo 'make package-overwrite replace package files with src files' @echo 'make package-diff (pd) diff src files against package files' @echo '' - @echo 'make lib-package download/build/install a package library' + @echo 'make lib-package help for download/build/install a package library' + @echo 'make lib-package args="..." download/build/install a package library' @echo 'make purge purge obsolete copies of source files' @echo '' @echo 'make machine build LAMMPS for machine'