diff --git a/doc/src/Section_packages.txt b/doc/src/Section_packages.txt index ea7b41b0affe15ad12f2c1c6606888d1ea988cf3..16864bcdc47fe84a61b4d7b3b28ecb0aca32b34a 100644 --- a/doc/src/Section_packages.txt +++ b/doc/src/Section_packages.txt @@ -25,6 +25,17 @@ There are two kinds of packages in LAMMPS, standard and user packages: "Table of standard packages"_#table_standard "Table of user packages"_#table_user :ul +Either of these kinds of packages may work as is, may require some +additional code compiled located in the lib folder, or may require +an external library to be downloaded, compiled, installed, and LAMMPS +configured to know about its location and additional compiler flags. +You can often do the build of the internal or external libraries +in one step by typing "make lib-name args='...'" from the src dir, +with appropriate arguments included in args='...'. If you just type +"make lib-name" you should see a help message about supported flags +and some examples. For more details about this, please study the +tables below and the sections about the individual packages. + Standard packages are supported by the LAMMPS developers and are written in a syntax and style consistent with the rest of LAMMPS. This means the developers will answer questions about them, debug and @@ -34,7 +45,9 @@ LAMMPS. User packages have been contributed by users, and begin with the "user" prefix. If they are a single command (single file), they are typically in the user-misc package. User packages don't necessarily -meet the requirements of the standard packages. If you have problems +meet the requirements of the standard packages. This means the +developers will try to keep things working and usually can answer +technical questions about compiling the package. If you have problems using a feature provided in a user package, you may need to contact the contributor directly to get help. Information on how to submit additions you make to LAMMPS as single files or as a standard or user @@ -78,10 +91,10 @@ Package, Description, Doc page, Example, Library "COMPRESS"_#COMPRESS, I/O compression, "dump */gz"_dump.html, -, sys "CORESHELL"_#CORESHELL, adiabatic core/shell model, "Section 6.6.25"_Section_howto.html#howto_25, coreshell, - "DIPOLE"_#DIPOLE, point dipole particles, "pair_style dipole/cut"_pair_dipole.html, dipole, - -"GPU"_#GPU, GPU-enabled styles, "Section 5.3.1"_accelerate_gpu.html, WWW bench, int +"GPU"_#GPU, GPU-enabled styles, "Section 5.3.1"_accelerate_gpu.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, int "GRANULAR"_#GRANULAR, granular systems, "Section 6.6.6"_Section_howto.html#howto_6, pour, - "KIM"_#KIM, OpenKIM wrapper, "pair_style kim"_pair_kim.html, kim, ext -"KOKKOS"_#KOKKOS, Kokkos-enabled styles, "Section 5.3.3"_accelerate_kokkos.html, WWW bench, - +"KOKKOS"_#KOKKOS, Kokkos-enabled styles, "Section 5.3.3"_accelerate_kokkos.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, - "KSPACE"_#KSPACE, long-range Coulombic solvers, "kspace_style"_kspace_style.html, peptide, - "MANYBODY"_#MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, - "MC"_#MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, -, - @@ -90,7 +103,7 @@ Package, Description, Doc page, Example, Library "MOLECULE"_#MOLECULE, molecular system force fields, "Section 6.6.3"_Section_howto.html#howto_3, peptide, - "MPIIO"_#MPIIO, MPI parallel I/O dump and restart, "dump"_dump.html, -, - "MSCG"_#MSCG, multi-scale coarse-graining wrapper, "fix mscg"_fix_mscg.html, mscg, ext -"OPT"_#OPT, optimized pair styles, "Section 5.3.5"_accelerate_opt.html, WWW bench, - +"OPT"_#OPT, optimized pair styles, "Section 5.3.5"_accelerate_opt.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, - "PERI"_#PERI, Peridynamics models, "pair_style peri"_pair_peri.html, peri, - "POEMS"_#POEMS, coupled rigid body motion, "fix poems"_fix_poems.html, rigid, int "PYTHON"_#PYTHON, embed Python code in an input script, "python"_python.html, python, sys @@ -101,8 +114,7 @@ Package, Description, Doc page, Example, Library "SHOCK"_#SHOCK, shock loading methods, "fix msst"_fix_msst.html, -, - "SNAP"_#SNAP, quantum-fitted potential, "pair snap"_pair_snap.html, snap, - "SRD"_#SRD, stochastic rotation dynamics, "fix srd"_fix_srd.html, srd, - -"VORONOI"_#VORONOI, Voronoi tesselation, "compute voronoi/atom"_compute_voronoi_atom.html, -, ext -:tb(ea=c,ca1=l) +"VORONOI"_#VORONOI, Voronoi tesselation, "compute voronoi/atom"_compute_voronoi_atom.html, -, ext :tb(ea=c,ca1=l) [USER packages] :link(table_user),p @@ -118,7 +130,7 @@ Package, Description, Doc page, Example, Library "USER-EFF"_#USER-EFF, electron force field,"pair_style eff/cut"_pair_eff.html, USER/eff, - "USER-FEP"_#USER-FEP, free energy perturbation,"compute fep"_compute_fep.html, USER/fep, - "USER-H5MD"_#USER-H5MD, dump output via HDF5,"dump h5md"_dump_h5md.html, -, ext -"USER-INTEL"_#USER-INTEL, optimized Intel CPU and KNL styles,"Section 5.3.2"_accelerate_intel.html, WWW bench, - +"USER-INTEL"_#USER-INTEL, optimized Intel CPU and KNL styles,"Section 5.3.2"_accelerate_intel.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, - "USER-LB"_#USER-LB, Lattice Boltzmann fluid,"fix lb/fluid"_fix_lb_fluid.html, USER/lb, - "USER-MANIFOLD"_#USER-MANIFOLD, motion on 2d surfaces,"fix manifoldforce"_fix_manifoldforce.html, USER/manifold, - "USER-MEAMC"_#USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meam.html, meam, - @@ -126,7 +138,7 @@ Package, Description, Doc page, Example, Library "USER-MISC"_#USER-MISC, single-file contributions, USER-MISC/README, USER/misc, - "USER-MOLFILE"_#USER-MOLFILE, "VMD"_vmd_home molfile plug-ins,"dump molfile"_dump_molfile.html, -, ext "USER-NETCDF"_#USER-NETCDF, dump output via NetCDF,"dump netcdf"_dump_netcdf.html, -, ext -"USER-OMP"_#USER-OMP, OpenMP-enabled styles,"Section 5.3.4"_accelerate_omp.html, WWW bench, - +"USER-OMP"_#USER-OMP, OpenMP-enabled styles,"Section 5.3.4"_accelerate_omp.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, - "USER-PHONON"_#USER-PHONON, phonon dynamical matrix,"fix phonon"_fix_phonon.html, USER/phonon, - "USER-QMMM"_#USER-QMMM, QM/MM coupling,"fix qmmm"_fix_qmmm.html, USER/qmmm, ext "USER-QTB"_#USER-QTB, quantum nuclear effects,"fix qtb"_fix_qtb.html "fix qbmsst"_fix_qbmsst.html, qtb, - @@ -136,8 +148,7 @@ Package, Description, Doc page, Example, Library "USER-SMTBQ"_#USER-SMTBQ, second moment tight binding QEq potential,"pair_style smtbq"_pair_smtbq.html, USER/smtbq, - "USER-SPH"_#USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, - "USER-TALLY"_#USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, - -"USER-VTK"_#USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, -, ext -:tb(ea=c,ca1=l) +"USER-VTK"_#USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, -, ext :tb(ea=c,ca1=l) :line :line @@ -364,9 +375,12 @@ GPU package :link(GPU),h4 [Contents:] Dozens of pair styles and a version of the PPPM long-range Coulombic -solver optimized for NVIDIA GPUs. All such styles have a "gpu" as a -suffix in their style name. "Section 5.3.1"_accelerate_gpu.html gives -details of what hardware and Cuda software is required on your system, +solver optimized for GPUs. All such styles have a "gpu" as a +suffix in their style name. The GPU code can be compiled with either +CUDA or OpenCL, however the OpenCL variants are no longer actively +maintained and only the CUDA versions are regularly tested. +"Section 5.3.1"_accelerate_gpu.html gives details of what +hardware and GPU software is required on your system, and details on how to build and use this package. Its styles can be invoked at run time via the "-sf gpu" or "-suffix gpu" "command-line switches"_Section_start.html#start_6. See also the "KOKKOS"_#KOKKOS @@ -378,32 +392,41 @@ package, which has GPU-enabled styles. [Install or un-install:] Before building LAMMPS with this package, you must first build the GPU -library in lib/gpu from a set of provided C and Cuda files. You can +library in lib/gpu from a set of provided C and CUDA files. You can do this manually if you prefer; follow the instructions in -lib/gpu/README. You can also do it in one step from the lammps/src +lib/gpu/README. Please note, that the GPU library uses MPI calls, so +you have to make certain to use the same MPI library (or the STUBS +library) settings as the main LAMMPS code. That same applies to the +-DLAMMPS_BIGBIG, -DLAMMPS_SMALLBIG, or -DLAMMPS_SMALLSMALL define. + +You can also do it in one step from the lammps/src dir, using a command like these, which simply invoke the lib/gpu/Install.py script with the specified args: -make lib-gpu # print help message -make lib-gpu args="-m" # build GPU library 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 library +make lib-gpu # print help message +make lib-gpu args="-b" # build GPU library with default Makefile.linux +make lib-gpu args="-m xk7 -p single -o xk7.single" # create new Makefile.xk7.single, altered for single-precision +make lib-gpu args="-m mpi -p mixed -b" # build GPU library with mixed precision using settings in Makefile.mpi :pre -Note that this procedure starts with one of the existing -Makefile.machine files in lib/gpu. It allows you to alter 4 important -settings in that Makefile, via the -h, -a, -p, -e switches, -and save the new Makefile, if desired: +Note that this procedure through the '-m machine' flag starts with one of +the existing Makefile.machine files in lib/gpu. For your convenience, +machine makefiles for "mpi" and "serial" are provided, which have the +same settings as the corresponding machine makefiles in the main LAMMPS +source folder. In addition you can alter 4 important settings in that +Makefile, via the -h, -a, -p, -e switches, and also save a copy of the +new Makefile, if desired: -CUDA_HOME = where NVIDIA Cuda software is installed on your system +CUDA_HOME = where NVIDIA CUDA software is installed on your system CUDA_ARCH = what GPU hardware you have (see help message for details) CUDA_PRECISION = precision (double, mixed, single) EXTRAMAKE = which Makefile.lammps.* file to copy to Makefile.lammps :ul -If the library build is successful, 2 files should be created: -lib/gpu/libgpu.a and lib/gpu/Makefile.lammps. The latter has settings -that enable LAMMPS to link with Cuda libraries. If the settings in -Makefile.lammps for your machine are not correct, the LAMMPS build -will fail. +If the library build is successful, at least 3 files should be created: +lib/gpu/libgpu.a, lib/gpu/nvc_get_devices, and lib/gpu/Makefile.lammps. +The latter has settings that enable LAMMPS to link with CUDA libraries. +If the settings in Makefile.lammps for your machine are not correct, +the LAMMPS build will fail, and lib/gpu/Makefile.lammps may need to +be edited. You can then install/un-install the package and build LAMMPS in the usual manner: @@ -499,11 +522,13 @@ 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. -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 +make lib-kim # print help message +make lib-kim args="-b " # (re-)install KIM API lib with only example models +make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001" # ditto plus one model +make lib-kim args="-b -a everything" # install KIM API lib with all models +make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # add one model or model driver +make lib-kim args="-p /usr/local/kim-api" # use an existing KIM API installation at the provided location +make lib-kim args="-p /usr/local/kim-api -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or 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 @@ -547,7 +572,7 @@ KOKKOS package :link(KOKKOS),h4 Dozens of atom, pair, bond, angle, dihedral, improper, fix, compute styles adapted to compile using the Kokkos library which can convert -them to OpenMP or Cuda code so that they run efficiently on multicore +them to OpenMP or CUDA code so that they run efficiently on multicore CPUs, KNLs, or GPUs. All the styles have a "kk" as a suffix in their style name. "Section 5.3.3"_accelerate_kokkos.html gives details of what hardware and software is required on your system, and how to @@ -577,28 +602,28 @@ files for examples. For multicore CPUs using OpenMP: KOKKOS_DEVICES = OpenMP -KOKKOS_ARCH = HSW # HSW = Haswell, SNB = SandyBridge, BDW = Broadwell, etc +KOKKOS_ARCH = HSW # HSW = Haswell, SNB = SandyBridge, BDW = Broadwell, etc :pre For Intel KNLs using OpenMP: KOKKOS_DEVICES = OpenMP -KOKKOS_ARCH = KNL +KOKKOS_ARCH = KNL :pre -For NVIDIA GPUs using Cuda: +For NVIDIA GPUs using CUDA: KOKKOS_DEVICES = Cuda KOKKOS_ARCH = Pascal60,Power8 # P100 hosted by an IBM Power8, etc -KOKKOS_ARCH = Kepler37,Power8 # K80 hosted by an IBM Power8, etc +KOKKOS_ARCH = Kepler37,Power8 # K80 hosted by an IBM Power8, etc :pre For GPUs, you also need these 2 lines in your Makefile.machine before the CC line is defined, in this case for use with OpenMPI mpicxx. The 2 lines define a nvcc wrapper compiler, which will use nvcc for -compiling Cuda files or use a C++ compiler for non-Kokkos, non-Cuda +compiling CUDA files or use a C++ compiler for non-Kokkos, non-CUDA files. KOKKOS_ABSOLUTE_PATH = $(shell cd $(KOKKOS_PATH); pwd) export OMPI_CXX = $(KOKKOS_ABSOLUTE_PATH)/config/nvcc_wrapper -CC = mpicxx +CC = mpicxx :pre Once you have an appropriate Makefile.machine, you can install/un-install the package and build LAMMPS in the usual manner. @@ -734,6 +759,12 @@ MEAM package :link(MEAM),h4 A pair style for the modified embedded atom (MEAM) potential. +Please note that the MEAM package has been superseded by the +"USER-MEAMC"_#USER-MEAMC package, which is a direct translation +of the MEAM package to C++. USER-MEAMC contains additional +optimizations making it run faster than MEAM on most machines, +while providing the identical features and USER interface. + [Author:] Greg Wagner (Northwestern U) while at Sandia. [Install or un-install:] @@ -744,9 +775,10 @@ follow the instructions in lib/meam/README. You can also do it in one step from the lammps/src dir, using a command like these, which simply invoke the lib/meam/Install.py script with the specified args: -make lib-meam # print help message -make lib-meam args="-m gfortran" # build with GNU Fortran compiler -make lib-meam args="-m ifort" # build with Intel ifort compiler :pre +make lib-meam # print help message +make lib-meam args="-m mpi" # build with default Fortran compiler compatible with your MPI library +make lib-meam args="-m serial" # build with compiler compatible with "make serial" (GNU Fortran) +make lib-meam args="-m ifort" # build with Intel Fortran compiler using Makefile.ifort :pre The build should produce two files: lib/meam/libmeam.a and lib/meam/Makefile.lammps. The latter is copied from an existing @@ -789,6 +821,9 @@ A variety of compute, fix, pair, dump styles with specialized capabilities that don't align with other packages. Do a directory listing, "ls src/MISC", to see the list of commands. +NOTE: the MISC package contains styles that require using the +-restrict flag, when compiling with Intel compilers. + [Install or un-install:] make yes-misc @@ -902,9 +937,9 @@ University of Chicago. Before building LAMMPS with this package, you must first download and build the MS-CG library. Building the MS-CG library and using it from -LAMMPS requires a C++11 compatible compiler, and that LAPACK and GSL -(GNU Scientific Library) libraries be installed on your machine. See -the lib/mscg/README and MSCG/Install files for more details. +LAMMPS requires a C++11 compatible compiler and that the GSL +(GNU Scientific Library) headers and libraries are installed on your +machine. See the lib/mscg/README and MSCG/Install files for more details. Assuming these libraries are in place, you can do the download and build of MS-CG manually if you prefer; follow the instructions in @@ -912,15 +947,16 @@ lib/mscg/README. You can also do it in one step from the lammps/src dir, using a command like these, which simply invoke the lib/mscg/Install.py script with the specified args: -make lib-mscg # print help message -make lib-mscg args="-g -b -l" # download and build in default lib/mscg/MSCG-release-master -make lib-mscg args="-h . MSCG -g -b -l" # download and build in lib/mscg/MSCG -make lib-mscg args="-h ~ MSCG -g -b -l" # download and build in ~/mscg :pre +make lib-mscg # print help message +make lib-mscg args="-b -m serial" # download and build in lib/mscg/MSCG-release-master + # with the settings compatible with "make serial" +make lib-mscg args="-b -m mpi" # download and build in lib/mscg/MSCG-release-master + # with the settings compatible with "make mpi" +make lib-mscg args="-p /usr/local/mscg-release" # use the existing MS-CG installation in /usr/local/mscg-release :pre -Note that the final -l switch is to create 2 symbolic (soft) links, -"includelink" and "liblink", in lib/mscg to point to the MS-CG src -dir. When LAMMPS builds it will use these links. You should not need -to edit the lib/mscg/Makefile.lammps file. +Note that 2 symbolic (soft) links, "includelink" and "liblink", will be created in lib/mscg +to point to the MS-CG src/installation dir. When LAMMPS is built in src it will use these links. +You should not need to edit the lib/mscg/Makefile.lammps file. You can then install/un-install the package and build LAMMPS in the usual manner: @@ -966,11 +1002,11 @@ make no-opt make machine :pre NOTE: The compile flag "-restrict" must be used to build LAMMPS with -the OPT package. It should be added to the CCFLAGS line of your -Makefile.machine. See Makefile.opt in src/MAKE/OPTIONS for an -example. +the OPT package when using Intel compilers. It should be added to +the CCFLAGS line of your Makefile.machine. See Makefile.opt in +src/MAKE/OPTIONS for an example. -CCFLAGS: add -restrict :ul +CCFLAGS: add -restrict for Intel compilers :ul [Supporting info:] @@ -1039,9 +1075,10 @@ follow the instructions in lib/poems/README. You can also do it in one step from the lammps/src dir, using a command like these, which simply invoke the lib/poems/Install.py script with the specified args: -make lib-poems # print help message -make lib-poems args="-m g++" # build with GNU g++ compiler -make lib-poems args="-m icc" # build with Intel icc compiler :pre +make lib-poems # print help message +make lib-poems args="-m serial" # build with GNU g++ compiler (settings as with "make serial") +make lib-poems args="-m mpi" # build with default MPI C++ compiler (settings as with "make mpi") +make lib-poems args="-m icc" # build with Intel icc compiler :pre The build should produce two files: lib/poems/libpoems.a and lib/poems/Makefile.lammps. The latter is copied from an existing @@ -1151,9 +1188,10 @@ follow the instructions in lib/reax/README. You can also do it in one step from the lammps/src dir, using a command like these, which simply invoke the lib/reax/Install.py script with the specified args: -make lib-reax # print help message -make lib-reax args="-m gfortran" # build with GNU Fortran compiler -make lib-reax args="-m ifort" # build with Intel ifort compiler :pre +make lib-reax # print help message +make lib-reax args="-m serial" # build with GNU Fortran compiler (settings as with "make serial") +make lib-reax args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi") +make lib-reax args="-m ifort" # build with Intel ifort compiler :pre The build should produce two files: lib/reax/libreax.a and lib/reax/Makefile.lammps. The latter is copied from an existing @@ -1370,15 +1408,15 @@ one step from the lammps/src dir, using a command like these, which simply invoke the lib/voronoi/Install.py script with the specified args: -make lib-voronoi # print help message -make lib-voronoi args="-g -b -l" # download and build in default lib/voronoi/voro++-0.4.6 -make lib-voronoi args="-h . voro++ -g -b -l" # download and build in lib/voronoi/voro++ -make lib-voronoi args="-h ~ voro++ -g -b -l" # download and build in ~/voro++ :pre +make lib-voronoi # print help message +make lib-voronoi args="-b" # download and build the default version in lib/voronoi/voro++-<version> +make lib-voronoi args="-p $HOME/voro++" # use existing Voro++ installation in $HOME/voro++ +make lib-voronoi args="-b -v voro++0.4.6" # download and build the 0.4.6 version in lib/voronoi/voro++-0.4.6 :pre -Note that the final -l switch is to create 2 symbolic (soft) links, -"includelink" and "liblink", in lib/voronoi to point to the Voro++ src -dir. When LAMMPS builds it will use these links. You should not need -to edit the lib/voronoi/Makefile.lammps file. +Note that 2 symbolic (soft) links, "includelink" and "liblink", are +created in lib/voronoi to point to the Voro++ src dir. When LAMMPS +builds in src it will use these links. You should not need to edit +the lib/voronoi/Makefile.lammps file. You can then install/un-install the package and build LAMMPS in the usual manner: @@ -1420,7 +1458,8 @@ from the lammps/src dir, using a command like these, which simply invoke the lib/atc/Install.py script with the specified args: make lib-atc # print help message -make lib-atc args="-m g++" # build with GNU g++ compiler +make lib-atc args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial") +make lib-atc args="-m mpi" # build with default MPI compiler (settings as with "make mpi") make lib-atc args="-m icc" # build with Intel icc compiler :pre The build should produce two files: lib/atc/libatc.a and @@ -1437,8 +1476,10 @@ can either exist on your system, or you can use the files provided in 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-linalg args="-m gfortran" # build with GNU Fortran compiler +make lib-linalg # print help message +make lib-linalg args="-m serial" # build with GNU Fortran compiler (settings as with "make serial") +make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi") +make lib-linalg args="-m gfortran" # build with GNU Fortran compiler :pre You can then install/un-install the package and build LAMMPS in the usual manner: @@ -1478,9 +1519,10 @@ follow the instructions in lib/awpmd/README. You can also do it in one step from the lammps/src dir, using a command like these, which simply invoke the lib/awpmd/Install.py script with the specified args: -make lib-awpmd # print help message -make lib-awpmd args="-m g++" # build with GNU g++ compiler -make lib-awpmd args="-m icc" # build with Intel icc compiler :pre +make lib-awpmd # print help message +make lib-awpmd args="-m serial" # build with GNU g++ compiler and MPI STUBS (settings as with "make serial") +make lib-awpmd args="-m mpi" # build with default MPI compiler (settings as with "make mpi") +make lib-awpmd args="-m icc" # build with Intel icc compiler :pre The build should produce two files: lib/awpmd/libawpmd.a and lib/awpmd/Makefile.lammps. The latter is copied from an existing @@ -1496,8 +1538,10 @@ these can either exist on your system, or you can use the files provided in 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 # print help message +make lib-linalg args="-m serial" # build with GNU Fortran compiler (settings as with "make serial") +make lib-linalg args="-m mpi" # build with default MPI Fortran compiler (settings as with "make mpi") +make lib-linalg args="-m gfortran" # build with GNU Fortran compiler :pre You can then install/un-install the package and build LAMMPS in the usual manner: @@ -1590,9 +1634,11 @@ Restraints. A "fix colvars"_fix_colvars.html command is implemented which wraps a COLVARS library, which implements these methods. simulations. -[Authors:] Axel Kohlmeyer (Temple U). The COLVARS library was written -by Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA) and -Jerome Henin (LISM, CNRS, Marseille, France). +[Authors:] The COLVARS library is written and maintained by +Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA) +and Jerome Henin (LISM, CNRS, Marseille, France), originally for +the NAMD MD code, but with portability in mind. Axel Kohlmeyer +(Temple U) provided the interface to LAMMPS. [Install or un-install:] @@ -1604,7 +1650,9 @@ which simply invoke the lib/colvars/Install.py script with the specified args: make lib-colvars # print help message -make lib-colvars args="-m g++" # build with GNU g++ compiler :pre +make lib-colvars args="-m serial" # build with GNU g++ compiler (settings as with "make serial") +make lib-colvars args="-m mpi" # build with default MPI compiler (settings as with "make mpi") +make lib-colvars args="-m g++-debug" # build with GNU g++ compiler and colvars debugging enabled :pre The build should produce two files: lib/colvars/libcolvars.a and lib/colvars/Makefile.lammps. The latter is copied from an existing @@ -1892,7 +1940,12 @@ Also see the "KOKKOS"_#KOKKOS, "OPT"_#OPT, and "USER-OMP"_#USER-OMP packages, which have styles optimized for CPUs and KNLs. You need to have an Intel compiler, version 14 or higher to take full -advantage of this package. +advantage of this package. While compilation with GNU compilers is +supported, performance will be suboptimal. + +NOTE: the USER-INTEL package contains styles that require using the +-restrict flag, when compiling with Intel compilers. + [Author:] Mike Brown (Intel). @@ -1909,17 +1962,17 @@ For CPUs: OPTFLAGS = -xHost -O2 -fp-model fast=2 -no-prec-div -qoverride-limits CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload \ - -fno-alias -ansi-alias -restrict $(OPTFLAGS) +-fno-alias -ansi-alias -restrict $(OPTFLAGS) LINKFLAGS = -g -qopenmp $(OPTFLAGS) -LIB = -ltbbmalloc -ltbbmalloc_proxy +LIB = -ltbbmalloc -ltbbmalloc_proxy :pre For KNLs: OPTFLAGS = -xMIC-AVX512 -O2 -fp-model fast=2 -no-prec-div -qoverride-limits CCFLAGS = -g -qopenmp -DLAMMPS_MEMALIGN=64 -no-offload \ - -fno-alias -ansi-alias -restrict $(OPTFLAGS) +-fno-alias -ansi-alias -restrict $(OPTFLAGS) LINKFLAGS = -g -qopenmp $(OPTFLAGS) -LIB = -ltbbmalloc +LIB = -ltbbmalloc :pre Once you have an appropriate Makefile.machine, you can install/un-install the package and build LAMMPS in the usual manner. @@ -2224,11 +2277,15 @@ CPUs. [Author:] Axel Kohlmeyer (Temple U). -NOTE: The compile flags "-restrict" and "-fopenmp" must be used to -build LAMMPS with the USER-OMP package, as well as the link flag -"-fopenmp". They should be added to the CCFLAGS and LINKFLAGS lines -of your Makefile.machine. See src/MAKE/OPTIONS/Makefile.omp for an -example. +NOTE: To enable multi-threading support the compile flag "-fopenmp" +and the link flag "-fopenmp" (for GNU compilers, you have to look up +the equivalent flags for other compilers) must be used to build LAMMPS. +When using Intel compilers, also the "-restrict" flag is required. +The USER-OMP package can be compiled without enabling OpenMP; then +all code will be compiled as serial and the only improvement over the +regular styles are some data access optimization. These flags should +be added to the CCFLAGS and LINKFLAGS lines of your Makefile.machine. +See src/MAKE/OPTIONS/Makefile.omp for an example. Once you have an appropriate Makefile.machine, you can install/un-install the package and build LAMMPS in the usual manner: @@ -2241,7 +2298,7 @@ make machine :pre make no-user-omp make machine :pre -CCFLAGS: add -fopenmp and -restrict +CCFLAGS: add -fopenmp (and -restrict when using Intel compilers) LINKFLAGS: add -fopenmp :ul [Supporting info:] @@ -2310,12 +2367,14 @@ without changes to LAMMPS itself. Before building LAMMPS with this package, you must first build the QMMM library in lib/qmmm. You can do this manually if you prefer; -follow the first two steps explained in lib/colvars/README. You can +follow the first two steps explained in lib/qmmm/README. You can also do it in one step from the lammps/src dir, using a command like -these, which simply invoke the lib/colvars/Install.py script with the +these, which simply invoke the lib/qmmm/Install.py script with the specified args: make lib-qmmm # print help message +make lib-qmmm args="-m serial" # build with GNU Fortran compiler (settings as in "make serial") +make lib-qmmm args="-m mpi" # build with default MPI compiler (settings as in "make mpi") make lib-qmmm args="-m gfortran" # build with GNU Fortran compiler :pre The build should produce two files: lib/qmmm/libqmmm.a and @@ -2492,15 +2551,13 @@ follow the instructions in lib/smd/README. You can also do it in one 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 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 +make lib-smd # print help message +make lib-smd args="-b" # download and build in default lib/smd/eigen-eigen-... +make lib-smd args="-p /usr/include/eigen3" # use existing Eigen installation in /usr/include/eigen3 :pre -Note that the final -l switch is to create a symbolic (soft) link -named "includelink" in lib/smd to point to the Eigen dir. When LAMMPS -builds it will use this link. You should not need to edit the -lib/smd/Makefile.lammps file. +Note that a symbolic (soft) link named "includelink" is created in +lib/smd to point to the Eigen dir. When LAMMPS builds it will use +this link. You should not need to edit the lib/smd/Makefile.lammps file. You can then install/un-install the package and build LAMMPS in the usual manner: