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/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:]