LAMMPS is a classical molecular dynamics code with a focus on materials modeling. It's an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.
The below instructions provide a spack recipe for building MPI capable instance of LAMMPS on the FASRC Cannon cluster.
Here we will use the GNU/GCC compiler suite together with OpenMPI.
The below instructions assume that spack is already configured to use the GCC compiler [email protected] and OpenMPI Library [email protected], as explained here.
spack env create lammps
spack env activate -p lammpsNote: In this recipe, we first install
libbsdwith the system version of the GCC compiler,[email protected], as the installation fails, if we try to add it directly to the environment and install it with[email protected].
spack install --add [email protected] % [email protected]spack add [email protected]
spack add lammps +asphere +body +class2 +colloid +compress +coreshell +dipole +granular +kokkos +kspace +manybody +mc +misc +molecule +mpiio +openmp-package +peri +python +qeq +replica +rigid +shock +snap +spin +srd +user-reaxc +user-misc % [email protected] ^ [email protected]Once all required packages are added to the environment, it can be installed with:
spack installFor example,
[lammps] [pkrastev@builds01 spack]$ spack add lammps +asphere +body +class2 +colloid +compress +coreshell +dipole +granular +kokkos +kspace +manybody +mc +misc +molecule +mpiio +openmp-package +peri +python +qeq +replica +rigid +shock +snap +spin +srd +user-reaxc +user-misc % [email protected] ^ [email protected]
==> Adding lammps%[email protected]+asphere+body+class2+colloid+compress+coreshell+dipole+granular+kokkos+kspace+manybody+mc+misc+molecule+mpiio+openmp-package+peri+python+qeq+replica+rigid+shock+snap+spin+srd+user-misc+user-reaxc ^[email protected] to environment lammps
[lammps] [pkrastev@builds01 spack]$ spack install
==> Concretized lammps%[email protected]+asphere+body+class2+colloid+compress+coreshell+dipole+granular+kokkos+kspace+manybody+mc+misc+molecule+mpiio+openmp-package+peri+python+qeq+replica+rigid+shock+snap+spin+srd+user-misc+user-reaxc ^[email protected]
- brvuawz lammps@20201029%[email protected]+asphere+body+class2+colloid+compress+coreshell~cuda~cuda_mps+dipole~exceptions~ffmpeg+granular~ipo~jpeg~kim+kokkos+kspace~latte+lib+manybody+mc+misc~mliap+molecule+mpi+mpiio~opencl+openmp+openmp-package~opt+peri~png~poems+python+qeq+replica+rigid~rocm+shock+snap+spin+srd~user-adios~user-atc~user-awpmd~user-bocs~user-cgsdk~user-colvars~user-diffraction~user-dpd~user-drude~user-eff~user-fep~user-h5md~user-intel~user-lb~user-manifold~user-meamc~user-mesodpd~user-mesont~user-mgpt+user-misc~user-mofff~user-molfile~user-netcdf~user-omp~user-phonon~user-plumed~user-ptm~user-qtb~user-reaction+user-reaxc~user-sdpd~user-smd~user-smtbq~user-sph~user-tally~user-uef~user-yaff~voronoi build_system=cmake build_type=Release fftw_precision=double generator=make lammps_sizes=smallbig arch=linux-rocky8-x86_64
[+] gfpb5mz ^[email protected]%[email protected]~doc+ncurses+ownlibs build_system=generic build_type=Release arch=linux-rocky8-x86_64
[+] yvt4hk5 ^[email protected]%[email protected]~gssapi~ldap~libidn2~librtmp~libssh~libssh2+nghttp2 build_system=autotools libs=shared,static tls=openssl arch=linux-rocky8-x86_64
[+] lvshkiv ^[email protected]%[email protected] build_system=autotools arch=linux-rocky8-x86_64
[+] enjvgjw ^[email protected]%[email protected]~symlinks+termlib abi=none build_system=autotools arch=linux-rocky8-x86_64
[+] vydxoz7 ^[email protected]%[email protected]+compat+opt build_system=autotools arch=linux-rocky8-x86_64
[+] o3gyqz4 ^[email protected]%[email protected]+mpi~openmp~pfft_patches build_system=autotools precision=double,float arch=linux-rocky8-x86_64
[+] svtpsvv ^[email protected]%[email protected]~guile build_system=generic arch=linux-rocky8-x86_64
[+] jiw5kkj ^[email protected]%[email protected]~aggressive_vectorization~compiler_warnings~cuda~debug~debug_bounds_check~debug_dualview_modify_check~deprecated_code~examples~hpx~hpx_async_dispatch~hwloc~ipo~memkind~numactl~openmp~openmptarget~pic~rocm+serial+shared~sycl~tests~threads~tuning~wrapper build_system=cmake build_type=Release cxxstd=17 generator=make intel_gpu_arch=none arch=linux-rocky8-x86_64
[e] rzl24ya ^[email protected]%[email protected]~atomics~cuda~cxx~cxx_exceptions~gpfs~internal-hwloc~internal-pmix~java~legacylaunchers~lustre~memchecker~openshmem~orterunprefix+romio+rsh~singularity+static+vt+wrapper-rpath build_system=autotools fabrics=none schedulers=none arch=linux-rocky8-x86_64
- eo7i4v4 ^[email protected]%[email protected] build_system=python_pip arch=linux-rocky8-x86_64
- p66ce3e ^[email protected]%[email protected] build_system=python_pip patches=c4369ad arch=linux-rocky8-x86_64
- uwtiq6m ^[email protected]%[email protected] build_system=generic arch=linux-rocky8-x86_64
- beehlpu ^[email protected]%[email protected] build_system=generic arch=linux-rocky8-x86_64
- dwr4bwe ^[email protected]%[email protected] build_system=generic arch=linux-rocky8-x86_64
- 5hw7nhs ^[email protected]%[email protected] build_system=python_pip patches=873745d arch=linux-rocky8-x86_64
- kqjh467 ^[email protected]%[email protected]+re2c build_system=generic arch=linux-rocky8-x86_64
[+] 7kut2tz ^[email protected]%[email protected] build_system=generic arch=linux-rocky8-x86_64
[+] 5oqjy7z ^[email protected]%[email protected]~bignuma~consistent_fpcsr+fortran~ilp64+locking+pic+shared build_system=makefile symbol_suffix=none threads=none arch=linux-rocky8-x86_64
[+] k7dhgbu ^[email protected]%[email protected]+cpanm+opcode+open+shared+threads build_system=generic patches=714e4d1 arch=linux-rocky8-x86_64
[+] gyedpff ^[email protected]%[email protected]+cxx~docs+stl build_system=autotools patches=26090f4,b231fcc arch=linux-rocky8-x86_64
[+] bd3npcq ^[email protected]%[email protected] build_system=autotools arch=linux-rocky8-x86_64
- u2hdpyq ^[email protected]%[email protected] build_system=python_pip arch=linux-rocky8-x86_64
- qkyvv7u ^[email protected]%[email protected] build_system=python_pip arch=linux-rocky8-x86_64
- zo3mqxg ^[email protected]%[email protected] build_system=python_pip arch=linux-rocky8-x86_64
- ayhpfzo ^[email protected]%[email protected]+bz2+crypt+ctypes+dbm~debug+libxml2+lzma~nis~optimizations+pic+pyexpat+pythoncmd+readline+shared+sqlite3+ssl~tkinter+uuid+zlib build_system=generic patches=13fa8bf,b0615b2,ebdca64,f2fd060 arch=linux-rocky8-x86_64
[+] xxvougl ^[email protected]%[email protected]~debug~pic+shared build_system=generic arch=linux-rocky8-x86_64
[+] 6delrmq ^[email protected]%[email protected] build_system=autotools arch=linux-rocky8-x86_64
- utxeqjk ^[email protected]%[email protected]+libbsd build_system=autotools arch=linux-rocky8-x86_64
[+] p4j7tjd ^[email protected]%[email protected] build_system=autotools arch=linux-rocky8-x86_64
[+] dhtpyny ^[email protected]%[email protected]~guile build_system=generic arch=linux-rocky8-x86_64
[+] zgocxqu ^[email protected]%[email protected] build_system=autotools arch=linux-rocky8-x86_64
[+] r4ncx2h ^[email protected]%[email protected] build_system=autotools arch=linux-rocky8-x86_64
[+] nbmdkeh ^[email protected]%[email protected]+bzip2+curses+git~libunistring+libxml2+pic+shared+tar+xz build_system=autotools arch=linux-rocky8-x86_64
[+] 4ic3bei ^[email protected]%[email protected] build_system=autotools libs=shared,static arch=linux-rocky8-x86_64
[+] vib3s6c ^[email protected]%[email protected]+pic~python+shared build_system=autotools arch=linux-rocky8-x86_64
[+] bmtzwo2 ^[email protected]%[email protected] build_system=autotools zip=pigz arch=linux-rocky8-x86_64
[+] g5ndpd7 ^[email protected]%[email protected] build_system=makefile arch=linux-rocky8-x86_64
[+] kjif3oe ^[email protected]%[email protected]+programs build_system=makefile compression=none libs=shared,static arch=linux-rocky8-x86_64
[+] vxfrf2m ^[email protected]%[email protected] build_system=autotools arch=linux-rocky8-x86_64
[+] pevl53e ^[email protected]%[email protected]~obsolete_api build_system=autotools patches=4885da3 arch=linux-rocky8-x86_64
[+] t6g7cgp ^[email protected]%[email protected]~docs+shared build_system=generic certs=mozilla arch=linux-rocky8-x86_64
[+] y4pl22s ^ca-certificates-mozilla@2023-05-30%[email protected] build_system=generic arch=linux-rocky8-x86_64
[+] gqnfuu6 ^[email protected]%[email protected] build_system=autotools patches=bbf97f1 arch=linux-rocky8-x86_64
[+] ir4yzhv ^[email protected]%[email protected]+column_metadata+dynamic_extensions+fts~functions+rtree build_system=autotools arch=linux-rocky8-x86_64
[+] 2lrosds ^[email protected]%[email protected] build_system=autotools arch=linux-rocky8-x86_64
[+] o2frdmd ^[email protected]%[email protected]~pic build_system=autotools libs=shared,static arch=linux-rocky8-x86_64
[+] /builds/pkrastev/Spack/spack/opt/spack/linux-rocky8-x86_64/gcc-12.2.0/nghttp2-1.57.0-lvshkivi7b4qjhtdvew667hctxypbszb
[+] /builds/pkrastev/Spack/spack/opt/spack/linux-rocky8-x86_64/gcc-12.2.0/zlib-ng-2.1.4-vydxoz7fvgvsutjrmly6cayjaedjyrmg
[+] /builds/pkrastev/Spack/spack/opt/spack/linux-rocky8-x86_64/gcc-12.2.0/ncurses-6.4-enjvgjww5qpxthriw5sywb7isei43bww
[+] /n/sw/helmod-rocky8/apps/Comp/gcc/12.2.0-fasrc01/openmpi/4.1.5-fasrc03 (external openmpi-4.1.5-rzl24yaivlkwvg4g5qznqm3vv32l2fh3)
[+] /builds/pkrastev/Spack/spack/opt/spack/linux-rocky8-x86_64/gcc-12.2.0/gmake-4.4.1-svtpsvvjlmcqaoikxzgv7tn65gm5qkd2
[+] /builds/pkrastev/Spack/spack/opt/spack/linux-rocky8-x86_64/gcc-12.2.0/bzip2-1.0.8-xxvougl2pg4l2ovlb763elztdhdigg4c
[+] /builds/pkrastev/Spack/spack/opt/spack/linux-rocky8-x86_64/gcc-8.5.0/libmd-1.0.4-zgocxqucujk4t6egi7imbdmsmk6kf7hm
[+] /builds/pkrastev/Spack/spack/opt/spack/linux-rocky8-x86_64/gcc-12.2.0/re2c-2.2-7kut2tz4mzisyoxxpdzw5fsoserrhg5b
[+] /builds/pkrastev/Spack/spack/opt/spack/linux-rocky8-x86_64/gcc-12.2.0/openssl-3.1.3-t6g7cgpe6j762uy7k6tywuvoehrpoxlr
[+] /builds/pkrastev/Spack/spack/opt/spack/linux-rocky8-x86_64/gcc-12.2.0/util-linux-uuid-2.38.1-2lrosds6dyqiwq2dqezt4rfxpilyw7mx
[+] /builds/pkrastev/Spack/spack/opt/spack/linux-rocky8-x86_64/gcc-12.2.0/pkgconf-1.9.5-bd3npcqaivwm7xw6ryfdx4ngkhsqvw5y
[+] /builds/pkrastev/Spack/spack/opt/spack/linux-rocky8-x86_64/gcc-12.2.0/fftw-3.3.10-o3gyqz4xr6icuwhvkij36gelql4w7zhe
[+] /builds/pkrastev/Spack/spack/opt/spack/linux-rocky8-x86_64/gcc-12.2.0/xz-5.4.1-o2frdmd6pdpc5shh4b7ceuh6m3r24tky
[+] /builds/pkrastev/Spack/spack/opt/spack/linux-rocky8-x86_64/gcc-12.2.0/libxcrypt-4.4.35-pevl53etfet57jj6otonswfahl4lpgln
[+] /builds/pkrastev/Spack/spack/opt/spack/linux-rocky8-x86_64/gcc-12.2.0/libiconv-1.17-4ic3bei7fcc3od6alzc4xhoag6tovpc6
[+] /builds/pkrastev/Spack/spack/opt/spack/linux-rocky8-x86_64/gcc-12.2.0/pigz-2.7-g5ndpd7evf6ikjvebjge3twqrifi3pio
[+] /builds/pkrastev/Spack/spack/opt/spack/linux-rocky8-x86_64/gcc-12.2.0/openblas-0.3.24-5oqjy7z5brnhphx4cutohw242bfxnk7m
[+] /builds/pkrastev/Spack/spack/opt/spack/linux-rocky8-x86_64/gcc-12.2.0/kokkos-3.7.02-jiw5kkjl63zeyy45klhoojvcbc2yndbq
[+] /builds/pkrastev/Spack/spack/opt/spack/linux-rocky8-x86_64/gcc-12.2.0/readline-8.2-gqnfuu6cimjmva7lm3226ajtlbbf33wb
[+] /builds/pkrastev/Spack/spack/opt/spack/linux-rocky8-x86_64/gcc-12.2.0/zstd-1.5.5-kjif3oebskvl7e2ctnhmfjeyllpfdb44
[+] /builds/pkrastev/Spack/spack/opt/spack/linux-rocky8-x86_64/gcc-12.2.0/libffi-3.4.4-vxfrf2modrtt52i565y3vtph64q7kdgi
[+] /builds/pkrastev/Spack/spack/opt/spack/linux-rocky8-x86_64/gcc-8.5.0/libbsd-0.11.6-p4j7tjdjyqh53iyoeeui2npoompdw33g
[+] /builds/pkrastev/Spack/spack/opt/spack/linux-rocky8-x86_64/gcc-12.2.0/curl-8.4.0-yvt4hk57jtntsqm3n3jund52c5b6j3yf
[+] /builds/pkrastev/Spack/spack/opt/spack/linux-rocky8-x86_64/gcc-12.2.0/libxml2-2.10.3-vib3s6cnyl2yvtxwpneekgtl2wrbbhmr
[+] /builds/pkrastev/Spack/spack/opt/spack/linux-rocky8-x86_64/gcc-12.2.0/gdbm-1.23-r4ncx2hr7cny6evxb65xredi36qykaee
[+] /builds/pkrastev/Spack/spack/opt/spack/linux-rocky8-x86_64/gcc-12.2.0/sqlite-3.43.2-ir4yzhvm3qpqqtznwpyzb6i34emgbtzw
[+] /builds/pkrastev/Spack/spack/opt/spack/linux-rocky8-x86_64/gcc-12.2.0/tar-1.34-bmtzwo27cebonnqmsq7bmgff334itq4a
==> Installing expat-2.5.0-utxeqjkqdtzrd4hj6thql2awuuyn6nu2 [28/42]
==> No binary for expat-2.5.0-utxeqjkqdtzrd4hj6thql2awuuyn6nu2 found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/6f/6f0e6e01f7b30025fa05c85fdad1e5d0ec7fd35d9f61b22f34998de11969ff67.tar.bz2
==> No patches needed for expat
==> expat: Executing phase: 'autoreconf'
==> expat: Executing phase: 'configure'
==> expat: Executing phase: 'build'
==> expat: Executing phase: 'install'
==> expat: Successfully installed expat-2.5.0-utxeqjkqdtzrd4hj6thql2awuuyn6nu2
Stage: 0.32s. Autoreconf: 0.00s. Configure: 11.32s. Build: 5.61s. Install: 0.60s. Post-install: 0.06s. Total: 18.07s
[+] /builds/pkrastev/Spack/spack/opt/spack/linux-rocky8-x86_64/gcc-12.2.0/expat-2.5.0-utxeqjkqdtzrd4hj6thql2awuuyn6nu2
[+] /builds/pkrastev/Spack/spack/opt/spack/linux-rocky8-x86_64/gcc-12.2.0/cmake-3.27.7-gfpb5mzafl4j7znv6r3z7v3n65y4lmhd
[+] /builds/pkrastev/Spack/spack/opt/spack/linux-rocky8-x86_64/gcc-12.2.0/gettext-0.22.3-nbmdkehmpboc6ujcs7i4h7nkzchrtmlz
==> Installing python-3.11.6-ayhpfzopafuhgnbm76kgzhcwzzj3bgk6 [31/42]
==> No binary for python-3.11.6-ayhpfzopafuhgnbm76kgzhcwzzj3bgk6 found: installing from source
==> Fetching https://www.python.org/ftp/python/3.11.6/Python-3.11.6.tgz
==> Applied patch /builds/pkrastev/Spack/spack/var/spack/repos/builtin/packages/python/python-3.7.4+-distutils-C++-testsuite.patch
==> Applied patch /builds/pkrastev/Spack/spack/var/spack/repos/builtin/packages/python/python-3.11-distutils-C++.patch
==> Applied patch /builds/pkrastev/Spack/spack/var/spack/repos/builtin/packages/python/tkinter-3.11.patch
==> Applied patch /builds/pkrastev/Spack/spack/var/spack/repos/builtin/packages/python/rpath-non-gcc.patch
==> Ran patch() for python
==> python: Executing phase: 'configure'
==> python: Executing phase: 'build'
==> python: Executing phase: 'install'
==> python: Successfully installed python-3.11.6-ayhpfzopafuhgnbm76kgzhcwzzj3bgk6
Stage: 2.25s. Configure: 1m 13.81s. Build: 21.41s. Install: 21.77s. Post-install: 1.42s. Total: 2m 0.87s
[+] /builds/pkrastev/Spack/spack/opt/spack/linux-rocky8-x86_64/gcc-12.2.0/python-3.11.6-ayhpfzopafuhgnbm76kgzhcwzzj3bgk6
==> Installing ninja-1.11.1-kqjh467ra53zkcgsfw2f2seztreu6cn7 [32/42]
==> No binary for ninja-1.11.1-kqjh467ra53zkcgsfw2f2seztreu6cn7 found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/31/31747ae633213f1eda3842686f83c2aa1412e0f5691d1c14dbbcc67fe7400cea.tar.gz
==> No patches needed for ninja
==> ninja: Executing phase: 'configure'
==> ninja: Executing phase: 'install'
==> ninja: Successfully installed ninja-1.11.1-kqjh467ra53zkcgsfw2f2seztreu6cn7
Stage: 0.24s. Configure: 28.56s. Install: 0.01s. Post-install: 0.08s. Total: 29.06s
[+] /builds/pkrastev/Spack/spack/opt/spack/linux-rocky8-x86_64/gcc-12.2.0/ninja-1.11.1-kqjh467ra53zkcgsfw2f2seztreu6cn7
==> Installing py-pip-23.1.2-uwtiq6mvi75v6eztiwl35ehuwvdjlzvq [33/42]
==> No binary for py-pip-23.1.2-uwtiq6mvi75v6eztiwl35ehuwvdjlzvq found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/3e/3ef6ac33239e4027d9a5598a381b9d30880a1477e50039db2eac6e8a8f6d1b18
==> No patches needed for py-pip
==> py-pip: Executing phase: 'install'
==> py-pip: Successfully installed py-pip-23.1.2-uwtiq6mvi75v6eztiwl35ehuwvdjlzvq
Stage: 0.27s. Install: 2.75s. Post-install: 0.23s. Total: 3.38s
[+] /builds/pkrastev/Spack/spack/opt/spack/linux-rocky8-x86_64/gcc-12.2.0/py-pip-23.1.2-uwtiq6mvi75v6eztiwl35ehuwvdjlzvq
==> Installing py-wheel-0.41.2-dwr4bwera5xqx3tcjni2xwle35yni2xv [34/42]
==> No binary for py-wheel-0.41.2-dwr4bwera5xqx3tcjni2xwle35yni2xv found: installing from source
==> Fetching https://files.pythonhosted.org/packages/py3/w/wheel/wheel-0.41.2-py3-none-any.whl
==> No patches needed for py-wheel
==> py-wheel: Executing phase: 'install'
==> py-wheel: Successfully installed py-wheel-0.41.2-dwr4bwera5xqx3tcjni2xwle35yni2xv
Stage: 0.96s. Install: 0.57s. Post-install: 0.07s. Total: 1.73s
[+] /builds/pkrastev/Spack/spack/opt/spack/linux-rocky8-x86_64/gcc-12.2.0/py-wheel-0.41.2-dwr4bwera5xqx3tcjni2xwle35yni2xv
==> Installing py-setuptools-68.0.0-beehlpujcxge7rergkdu2sqtd3juztlx [35/42]
==> No binary for py-setuptools-68.0.0-beehlpujcxge7rergkdu2sqtd3juztlx found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/11/11e52c67415a381d10d6b462ced9cfb97066179f0e871399e006c4ab101fc85f
==> No patches needed for py-setuptools
==> py-setuptools: Executing phase: 'install'
==> py-setuptools: Successfully installed py-setuptools-68.0.0-beehlpujcxge7rergkdu2sqtd3juztlx
Stage: 0.10s. Install: 0.97s. Post-install: 0.13s. Total: 1.33s
[+] /builds/pkrastev/Spack/spack/opt/spack/linux-rocky8-x86_64/gcc-12.2.0/py-setuptools-68.0.0-beehlpujcxge7rergkdu2sqtd3juztlx
==> Installing py-flit-core-3.9.0-zo3mqxgcedttrjdp3s3e44ws3og4zn53 [36/42]
==> No binary for py-flit-core-3.9.0-zo3mqxgcedttrjdp3s3e44ws3og4zn53 found: installing from source
==> Fetching https://files.pythonhosted.org/packages/source/f/flit-core/flit_core-3.9.0.tar.gz
==> No patches needed for py-flit-core
==> py-flit-core: Executing phase: 'install'
==> py-flit-core: Successfully installed py-flit-core-3.9.0-zo3mqxgcedttrjdp3s3e44ws3og4zn53
Stage: 0.92s. Install: 0.81s. Post-install: 0.09s. Total: 1.94s
[+] /builds/pkrastev/Spack/spack/opt/spack/linux-rocky8-x86_64/gcc-12.2.0/py-flit-core-3.9.0-zo3mqxgcedttrjdp3s3e44ws3og4zn53
==> Installing py-cython-0.29.36-p66ce3exy7gg5fta3sfefwwwh6lwc2w2 [37/42]
==> No binary for py-cython-0.29.36-p66ce3exy7gg5fta3sfefwwwh6lwc2w2 found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/41/41c0cfd2d754e383c9eeb95effc9aa4ab847d0c9747077ddd7c0dcb68c3bc01f.tar.gz
==> Applied patch /builds/pkrastev/Spack/spack/var/spack/repos/builtin/packages/py-cython/5712.patch
==> py-cython: Executing phase: 'install'
==> py-cython: Successfully installed py-cython-0.29.36-p66ce3exy7gg5fta3sfefwwwh6lwc2w2
Stage: 0.46s. Install: 58.86s. Post-install: 0.15s. Total: 59.59s
[+] /builds/pkrastev/Spack/spack/opt/spack/linux-rocky8-x86_64/gcc-12.2.0/py-cython-0.29.36-p66ce3exy7gg5fta3sfefwwwh6lwc2w2
==> Installing py-packaging-23.1-qkyvv7uu42txcfawduemltgl7ddjy4jn [38/42]
==> No binary for py-packaging-23.1-qkyvv7uu42txcfawduemltgl7ddjy4jn found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/a3/a392980d2b6cffa644431898be54b0045151319d1e7ec34f0cfed48767dd334f.tar.gz
==> No patches needed for py-packaging
==> py-packaging: Executing phase: 'install'
==> py-packaging: Successfully installed py-packaging-23.1-qkyvv7uu42txcfawduemltgl7ddjy4jn
Stage: 0.26s. Install: 0.76s. Post-install: 0.07s. Total: 1.23s
[+] /builds/pkrastev/Spack/spack/opt/spack/linux-rocky8-x86_64/gcc-12.2.0/py-packaging-23.1-qkyvv7uu42txcfawduemltgl7ddjy4jn
==> Installing py-mpi4py-3.1.4-eo7i4v4wgy35fuvmf76aygklxnxzkbs2 [39/42]
==> No binary for py-mpi4py-3.1.4-eo7i4v4wgy35fuvmf76aygklxnxzkbs2 found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/17/17858f2ebc623220d0120d1fa8d428d033dde749c4bc35b33d81a66ad7f93480.tar.gz
==> No patches needed for py-mpi4py
==> py-mpi4py: Executing phase: 'install'
==> py-mpi4py: Successfully installed py-mpi4py-3.1.4-eo7i4v4wgy35fuvmf76aygklxnxzkbs2
Stage: 1.40s. Install: 49.94s. Post-install: 0.08s. Total: 51.58s
[+] /builds/pkrastev/Spack/spack/opt/spack/linux-rocky8-x86_64/gcc-12.2.0/py-mpi4py-3.1.4-eo7i4v4wgy35fuvmf76aygklxnxzkbs2
==> Installing py-pyproject-metadata-0.7.1-u2hdpyqmxrrs54rhmddn6rwbawbqvn4z [40/42]
==> No binary for py-pyproject-metadata-0.7.1-u2hdpyqmxrrs54rhmddn6rwbawbqvn4z found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/0a/0a94f18b108b9b21f3a26a3d541f056c34edcb17dc872a144a15618fed7aef67.tar.gz
==> No patches needed for py-pyproject-metadata
==> py-pyproject-metadata: Executing phase: 'install'
==> py-pyproject-metadata: Successfully installed py-pyproject-metadata-0.7.1-u2hdpyqmxrrs54rhmddn6rwbawbqvn4z
Stage: 0.23s. Install: 0.96s. Post-install: 0.07s. Total: 1.40s
[+] /builds/pkrastev/Spack/spack/opt/spack/linux-rocky8-x86_64/gcc-12.2.0/py-pyproject-metadata-0.7.1-u2hdpyqmxrrs54rhmddn6rwbawbqvn4z
==> Installing py-numpy-1.26.1-5hw7nhsp23hc6m35emvtzzuficgf5745 [41/42]
==> No binary for py-numpy-1.26.1-5hw7nhsp23hc6m35emvtzzuficgf5745 found: installing from source
==> Fetching https://files.pythonhosted.org/packages/source/n/numpy/numpy-1.26.1.tar.gz
==> Applied patch /builds/pkrastev/Spack/spack/var/spack/repos/builtin/packages/py-numpy/check_executables.patch
==> py-numpy: Executing phase: 'install'
==> py-numpy: Successfully installed py-numpy-1.26.1-5hw7nhsp23hc6m35emvtzzuficgf5745
Stage: 1.56s. Install: 1m 10.30s. Post-install: 0.34s. Total: 1m 12.37s
[+] /builds/pkrastev/Spack/spack/opt/spack/linux-rocky8-x86_64/gcc-12.2.0/py-numpy-1.26.1-5hw7nhsp23hc6m35emvtzzuficgf5745
==> Installing lammps-20201029-brvuawzoq5ge6ak27a7474ziesqmbbq4 [42/42]
==> No binary for lammps-20201029-brvuawzoq5ge6ak27a7474ziesqmbbq4 found: installing from source
==> Fetching https://mirror.spack.io/_source-cache/archive/75/759705e16c1fedd6aa6e07d028cc0c78d73c76b76736668420946a74050c3726.tar.gz
==> No patches needed for lammps
==> lammps: Executing phase: 'cmake'
==> lammps: Executing phase: 'build'
==> lammps: Executing phase: 'install'
==> lammps: Successfully installed lammps-20201029-brvuawzoq5ge6ak27a7474ziesqmbbq4
Stage: 8.79s. Cmake: 8.14s. Build: 2m 12.32s. Install: 1.78s. Post-install: 0.21s. Total: 2m 31.51s
[+] /builds/pkrastev/Spack/spack/opt/spack/linux-rocky8-x86_64/gcc-12.2.0/lammps-20201029-brvuawzoq5ge6ak27a7474ziesqmbbq4
==> Updating view at /builds/pkrastev/Spack/spack/var/spack/environments/lammps/.spack-env/view
==> Warning: Skipping external package: [email protected]%[email protected]~atomics~cuda~cxx~cxx_exceptions~gpfs~internal-hwloc~internal-pmix~java~legacylaunchers~lustre~memchecker~openshmem~orterunprefix+romio+rsh~singularity+static+vt+wrapper-rpath build_system=autotools fabrics=none schedulers=none arch=linux-rocky8-x86_64/rzl24ya[lammps] [pkrastev@builds01 spack]$ spack find
==> In environment lammps
==> Root specs
[email protected]
-- no arch / [email protected] ------------------------------------------
[email protected]%[email protected]
-- no arch / [email protected] -----------------------------------------
lammps%[email protected] +asphere+body+class2+colloid+compress+coreshell+dipole+granular+kokkos+kspace+manybody+mc+misc+molecule+mpiio+openmp-package+peri+python+qeq+replica+rigid+shock+snap+spin+srd+user-misc+user-reaxc
==> Installed packages
-- linux-rocky8-x86_64 / [email protected] ------------------------------
[email protected] [email protected] [email protected]
-- linux-rocky8-x86_64 / [email protected] -----------------------------
[email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected]
[email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected]
ca-certificates-mozilla@2023-05-30 [email protected] lammps@20201029 [email protected] [email protected] [email protected] [email protected] [email protected] [email protected]
[email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected]
[email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected] [email protected]
==> 47 installed packagesOnce the environment is installed, all installed packages in the LAMMPS environment are available on the PATH, e.g.,:
[lammps] [pkrastev@builds01 ~]$ lmp -h
Large-scale Atomic/Molecular Massively Parallel Simulator - 29 Oct 2020
Usage example: lmp -var t 300 -echo screen -in in.alloy
List of command line options supported by this LAMMPS executable:
-echo none/screen/log/both : echoing of input script (-e)
-help : print this help message (-h)
-in filename : read input from file, not stdin (-i)
-kokkos on/off ... : turn KOKKOS mode on or off (-k)
-log none/filename : where to send log output (-l)
-mpicolor color : which exe in a multi-exe mpirun cmd (-m)
-nocite : disable writing log.cite file (-nc)
-package style ... : invoke package command (-pk)
-partition size1 size2 ... : assign partition sizes (-p)
-plog basename : basename for partition logs (-pl)
-pscreen basename : basename for partition screens (-ps)
-restart2data rfile dfile ... : convert restart to data file (-r2data)
-restart2dump rfile dgroup dstyle dfile ...
: convert restart to dump file (-r2dump)
-reorder topology-specs : processor reordering (-r)
-screen none/filename : where to send screen output (-sc)
-suffix gpu/intel/opt/omp : style suffix to apply (-sf)
-var varname value : set index style variable (-v)
OS: Linux 4.18.0-425.10.1.el8_7.x86_64 on x86_64
Compiler: GNU C++ 12.2.0 with OpenMP 4.5
C++ standard: C++17
MPI v3.1: Open MPI v4.1.5, package: Open MPI [email protected] Distribution, ident: 4.1.5, repo rev: v4.1.5, Feb 23, 2023
Active compile time flags:
-DLAMMPS_GZIP
-DLAMMPS_SMALLBIG
sizeof(smallint): 32-bit
sizeof(imageint): 32-bit
sizeof(tagint): 32-bit
sizeof(bigint): 64-bit
Installed packages:
ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GRANULAR KOKKOS KSPACE
MANYBODY MC MISC MOLECULE MPIIO PERI PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN
SRD USER-MISC USER-REAXC
List of individual style options included in this LAMMPS executable
* Atom styles:
angle angle/kk angle/kk/device angle/kk/host atomic
atomic/kk atomic/kk/device atomic/kk/host body
bond bond/kk bond/kk/device bond/kk/host charge
charge/kk charge/kk/device charge/kk/host dipole
ellipsoid full full/kk full/kk/device full/kk/host
hybrid hybrid/kk line molecular molecular/kk
molecular/kk/device molecular/kk/host peri
sphere sphere/kk sphere/kk/device sphere/kk/host
spin template tri
* Integrate styles:
respa verlet verlet/kk verlet/kk/device
verlet/kk/host verlet/split
* Minimize styles:
cg cg/kk cg/kk/device cg/kk/host fire
fire/old hftn quickmin sd spin
spin/cg spin/lbfgs
* Pair styles:
adp agni airebo airebo/morse atm
beck body/nparticle body/rounded/polygon
body/rounded/polyhedron bop born born/coul/dsf
born/coul/dsf/cs born/coul/long born/coul/long/cs
born/coul/msm born/coul/wolf born/coul/wolf/cs brownian
brownian/poly buck buck/coul/cut buck/coul/cut/kk
buck/coul/cut/kk/device buck/coul/cut/kk/host buck/coul/long
buck/coul/long/cs buck/coul/long/kk
buck/coul/long/kk/device buck/coul/long/kk/host buck/coul/msm
buck/kk buck/kk/device buck/kk/host buck/long/coul/long
buck/mdf colloid comb comb3 cosine/squared
coul/cut coul/cut/kk coul/cut/kk/device coul/cut/kk/host
coul/debye coul/debye/kk coul/debye/kk/device
coul/debye/kk/host coul/diel coul/dsf coul/dsf/kk
coul/dsf/kk/device coul/dsf/kk/host coul/long
coul/long/cs coul/long/kk coul/long/kk/device
coul/long/kk/host coul/msm coul/shield coul/slater/cut
coul/slater/long coul/streitz coul/wolf coul/wolf/cs
coul/wolf/kk coul/wolf/kk/device coul/wolf/kk/host
reax dpd dpd/tstat drip dsmc
e3b eam eam/alloy eam/alloy/kk
eam/alloy/kk/device eam/alloy/kk/host eam/cd
eam/cd/old eam/fs eam/fs/kk eam/fs/kk/device
eam/fs/kk/host eam/kk eam/kk/device eam/kk/host edip
edip/multi eim extep gauss gauss/cut
gayberne gran/hertz/history gran/hooke
gran/hooke/history gran/hooke/history/kk
gran/hooke/history/kk/device gran/hooke/history/kk/host granular
gw gw/zbl hbond/dreiding/lj
hbond/dreiding/morse hybrid hybrid/kk hybrid/overlay
hybrid/overlay/kk ilp/graphene/hbn
kolmogorov/crespi/full kolmogorov/crespi/z lcbop
lebedeva/z lennard/mdf line/lj list lj96/cut
lj/charmm/coul/charmm lj/charmm/coul/charmm/implicit
lj/charmm/coul/charmm/implicit/kk
lj/charmm/coul/charmm/implicit/kk/device
lj/charmm/coul/charmm/implicit/kk/host lj/charmm/coul/charmm/kk
lj/charmm/coul/charmm/kk/device lj/charmm/coul/charmm/kk/host
lj/charmm/coul/long lj/charmm/coul/long/kk
lj/charmm/coul/long/kk/device lj/charmm/coul/long/kk/host
lj/charmm/coul/msm lj/charmmfsw/coul/charmmfsh
lj/charmmfsw/coul/long lj/class2 lj/class2/coul/cut
lj/class2/coul/cut/kk lj/class2/coul/cut/kk/device
lj/class2/coul/cut/kk/host lj/class2/coul/long
lj/class2/coul/long/cs lj/class2/coul/long/kk
lj/class2/coul/long/kk/device lj/class2/coul/long/kk/host lj/class2/kk
lj/class2/kk/device lj/class2/kk/host lj/cubic
lj/cut lj/cut/coul/cut lj/cut/coul/cut/kk
lj/cut/coul/cut/kk/device lj/cut/coul/cut/kk/host
lj/cut/coul/debye lj/cut/coul/debye/kk
lj/cut/coul/debye/kk/device lj/cut/coul/debye/kk/host lj/cut/coul/dsf
lj/cut/coul/dsf/kk lj/cut/coul/dsf/kk/device
lj/cut/coul/dsf/kk/host lj/cut/coul/long
lj/cut/coul/long/cs lj/cut/coul/long/kk
lj/cut/coul/long/kk/device lj/cut/coul/long/kk/host lj/cut/coul/msm
lj/cut/coul/wolf lj/cut/dipole/cut
lj/cut/dipole/long lj/cut/kk lj/cut/kk/device
lj/cut/kk/host lj/cut/tip4p/cut lj/cut/tip4p/long
lj/expand lj/expand/coul/long lj/expand/kk
lj/expand/kk/device lj/expand/kk/host lj/gromacs
lj/gromacs/coul/gromacs lj/gromacs/coul/gromacs/kk
lj/gromacs/coul/gromacs/kk/device lj/gromacs/coul/gromacs/kk/host
lj/gromacs/kk lj/gromacs/kk/device lj/gromacs/kk/host
lj/long/coul/long lj/long/dipole/long
lj/long/tip4p/long lj/mdf lj/sf/dipole/sf lj/smooth
lj/smooth/linear lj/sf local/density lubricate
lubricateU lubricateU/poly lubricate/poly meam/spline meam/sw/spline
mie/cut momb morse morse/kk morse/kk/device
morse/kk/host morse/smooth/linear nb3b/harmonic nm/cut
nm/cut/coul/cut nm/cut/coul/long peri/eps peri/lps
peri/pmb peri/ves polymorphic python reax/c
reax/c/kk reax/c/kk/device reax/c/kk/host rebo
resquared snap snap/kk snap/kk/device snap/kk/host
soft spin/dipole/cut spin/dipole/long spin/dmi
spin/exchange spin/magelec spin/neel srp sw
sw/kk sw/kk/device sw/kk/host table table/kk
table/kk/device table/kk/host tersoff tersoff/kk
tersoff/kk/device tersoff/kk/host tersoff/mod tersoff/mod/c
tersoff/mod/kk tersoff/mod/kk/device tersoff/mod/kk/host
tersoff/table tersoff/zbl tersoff/zbl/kk tersoff/zbl/kk/device
tersoff/zbl/kk/host tip4p/cut tip4p/long tri/lj
ufm vashishta vashishta/kk vashishta/kk/device
vashishta/kk/host vashishta/table yukawa yukawa/colloid
yukawa/kk yukawa/kk/device yukawa/kk/host zbl
zbl/kk zbl/kk/device zbl/kk/host zero
* Bond styles:
class2 class2/kk class2/kk/device class2/kk/host
fene fene/expand fene/kk fene/kk/device fene/kk/host
gromos harmonic harmonic/kk harmonic/kk/device
harmonic/kk/host harmonic/shift harmonic/shift/cut
hybrid morse nonlinear quartic special
table zero
* Angle styles:
charmm charmm/kk charmm/kk/device charmm/kk/host
class2 class2/kk class2/kk/device class2/kk/host
cosine cosine/delta cosine/kk cosine/kk/device
cosine/kk/host cosine/periodic cosine/shift cosine/shift/exp
cosine/squared dipole fourier fourier/simple harmonic
harmonic/kk harmonic/kk/device harmonic/kk/host
hybrid quartic table zero
* Dihedral styles:
charmm charmm/kk charmm/kk/device charmm/kk/host
charmmfsw class2 class2/kk class2/kk/device
class2/kk/host cosine/shift/exp fourier harmonic
harmonic/kk harmonic/kk/device harmonic/kk/host
helix hybrid multi/harmonic nharmonic opls
opls/kk opls/kk/device opls/kk/host quadratic spherical
table table/cut zero
* Improper styles:
class2 class2/kk class2/kk/device class2/kk/host
cossq cvff distance fourier harmonic
harmonic/kk harmonic/kk/device harmonic/kk/host
hybrid ring umbrella zero
* KSpace styles:
ewald ewald/dipole ewald/dipole/spin ewald/disp
msm msm/cg pppm pppm/cg pppm/dipole
pppm/dipole/spin pppm/disp pppm/disp/tip4p pppm/kk
pppm/kk/device pppm/kk/host pppm/stagger pppm/tip4p
* Fix styles
accelerate/cos adapt addforce addtorque append/atoms
atom/swap ave/atom ave/chunk ave/correlate
ave/correlate/long ave/histo ave/histo/weight
ave/time aveforce balance bond/break bond/create
bond/create/angle bond/swap box/relax cmap
controller deform deform/kk deform/kk/device
deform/kk/host deposit ave/spatial ave/spatial/sphere
drag dt/reset efield ehex
electron/stopping enforce2d enforce2d/kk
enforce2d/kk/device enforce2d/kk/host evaporate
external ffl filter/corotate flow/gauss freeze
freeze/kk freeze/kk/device freeze/kk/host gcmc
gld gle gravity gravity/kk
gravity/kk/device gravity/kk/host grem halt
heat hyper/global hyper/local imd indent
ipi langevin langevin/kk langevin/kk/device
langevin/kk/host langevin/spin lineforce momentum
momentum/chunk momentum/kk momentum/kk/device momentum/kk/host
move msst neb neb/spin nph
nph/asphere nph/body nph/kk nph/kk/device nph/kk/host
nph/sphere nphug npt npt/asphere npt/body
npt/cauchy npt/kk npt/kk/device npt/kk/host npt/sphere
numdiff nve nve/asphere nve/asphere/noforce
nve/body nve/kk nve/kk/device nve/kk/host nve/limit
nve/line nve/noforce nve/sphere nve/sphere/kk
nve/sphere/kk/device nve/sphere/kk/host nve/spin
nve/tri nvk nvt nvt/asphere nvt/body
nvt/kk nvt/kk/device nvt/kk/host nvt/sllod nvt/sphere
oneway orient/bcc orient/eco orient/fcc pafi
pimd planeforce pour precession/spin press/berendsen
print propel/self property/atom property/atom/kk
python/invoke python python/move qeq/comb qeq/dynamic
qeq/dynamic qeq/fire qeq/fire qeq/point qeq/point
qeq/reax qeq/reax/kk qeq/reax/kk/device qeq/reax/kk/host
qeq/shielded qeq/shielded qeq/slater qeq/slater rattle
reax/c/bonds reax/c/bonds/kk reax/c/bonds/kk/device
reax/c/bonds/kk/host reax/c/species reax/c/species/kk
reax/c/species/kk/device reax/c/species/kk/host recenter
restrain rhok rigid rigid/nph rigid/nph/small
rigid/npt rigid/npt/small rigid/nve rigid/nve/small rigid/nvt
rigid/nvt/small rigid/small setforce setforce/kk
setforce/kk/device setforce/kk/host setforce/spin
shake smd spring spring/chunk spring/rg
spring/self srd store/force store/state temp/berendsen
temp/csld temp/csvr temp/rescale tfmc
thermal/conductivity ti/spring tmd ttm
ttm/mod tune/kspace vector viscosity viscous
wall/body/polygon wall/body/polyhedron wall/colloid
wall/ees wall/gran wall/gran/region wall/harmonic
wall/lj1043 wall/lj126 wall/lj93 wall/lj93/kk
wall/lj93/kk/device wall/lj93/kk/host wall/morse
wall/piston wall/reflect wall/reflect/kk wall/reflect/kk/device
wall/reflect/kk/host wall/reflect/stochastic wall/region
wall/region/ees wall/srd widom
* Compute styles:
ackland/atom adf aggregate/atom angle angle/local
angmom/chunk basal/atom body/local bond bond/local
centro/atom centroid/stress/atom chunk/atom
chunk/spread/atom cluster/atom cna/atom cnp/atom
com com/chunk contact/atom coord/atom coord/atom/kk
coord/atom/kk/device coord/atom/kk/host damage/atom
dihedral dihedral/local dilatation/atom dipole/chunk displace/atom
entropy/atom erotate/asphere erotate/rigid erotate/sphere
erotate/sphere/atom event/displace fragment/atom global/atom
group/group gyration gyration/chunk gyration/shape
gyration/shape/chunk heat/flux hexorder/atom hma
improper improper/local inertia/chunk ke ke/atom
ke/rigid momentum msd msd/chunk msd/nongauss
omega/chunk orientorder/atom orientorder/atom/kk
orientorder/atom/kk/device orientorder/atom/kk/host pair
pair/local pe pe/atom plasticity/atom pressure
pressure/cylinder property/atom property/chunk property/local
rdf reduce reduce/chunk reduce/region rigid/local
slice sna/atom snad/atom snap snav/atom
spin stress/atom stress/mop stress/mop/profile
temp temp/asphere temp/body temp/chunk temp/com
temp/cs temp/deform temp/kk temp/kk/device temp/kk/host
temp/partial temp/profile temp/ramp temp/region temp/rotate
temp/sphere ti torque/chunk vacf vcm/chunk
viscosity/cos
* Region styles:
block block/kk block/kk/device block/kk/host cone
cylinder intersect plane prism sphere
union
* Dump styles:
atom atom/gz atom/mpiio atom/zstd cfg
cfg/gz cfg/mpiio cfg/zstd custom custom/gz
custom/mpiio custom/zstd dcd image local
local/gz local/zstd movie xtc xyz
xyz/gz xyz/mpiio xyz/zstd
* Command styles
balance change_box create_atoms create_bonds create_box
delete_atoms delete_bonds reset_ids displace_atoms hyper
info minimize neb neb/spin prd
read_data read_dump read_restart replicate rerun
reset_atom_ids reset_mol_ids run set tad
temper temper/grem temper/npt velocity write_coeff
write_data write_dump write_restartYou can run LAMMPS interactively in both serial and parallel mode. This assumes you have requested an interactive session first, as explained here.
Serial
[lammps] [pkrastev@builds01 Fort]$ lmp -in in.demo
LAMMPS (29 Oct 2020)
using 1 OpenMP thread(s) per MPI task
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (16.795962 16.795962 16.795962)
1 by 1 by 1 MPI processor grid
Created 4000 atoms
create_atoms CPU = 0.001 seconds
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 12 12 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Setting up Verlet run ...
Unit style : lj
Current step : 0
Time step : 0.005
Per MPI rank memory allocation (min/avg/max) = 3.763 | 3.763 | 3.763 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6139081 -5.0199732
100 0.75715334 -5.7581426 0 -4.6226965 0.20850222
Loop time of 0.168767 on 1 procs for 100 steps with 4000 atoms
Performance: 255973.752 tau/day, 592.532 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.13874 | 0.13874 | 0.13874 | 0.0 | 82.21
Neigh | 0.023646 | 0.023646 | 0.023646 | 0.0 | 14.01
Comm | 0.003051 | 0.003051 | 0.003051 | 0.0 | 1.81
Output | 2.8434e-05 | 2.8434e-05 | 2.8434e-05 | 0.0 | 0.02
Modify | 0.0027839 | 0.0027839 | 0.0027839 | 0.0 | 1.65
Other | | 0.0005168 | | | 0.31
Nlocal: 4000.00 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5754.00 ave 5754 max 5754 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 150362.0 ave 150362 max 150362 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 150362
Ave neighs/atom = 37.590500
Neighbor list builds = 5
Dangerous builds not checked
Total wall time: 0:00:00
Parallel (e.g., 4 MPI tasks)
[lammps] [pkrastev@builds01 Fort]$ mpirun -np 4 lmp -in in.demo
LAMMPS (29 Oct 2020)
using 1 OpenMP thread(s) per MPI task
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (16.795962 16.795962 16.795962)
1 by 2 by 2 MPI processor grid
Created 4000 atoms
create_atoms CPU = 0.002 seconds
Neighbor list info ...
update every 20 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 2.8
ghost atom cutoff = 2.8
binsize = 1.4, bins = 12 12 12
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d/newton
bin: standard
Setting up Verlet run ...
Unit style : lj
Current step : 0
Time step : 0.005
Per MPI rank memory allocation (min/avg/max) = 3.224 | 3.224 | 3.224 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6139081 -5.0199732
100 0.75715334 -5.7581426 0 -4.6226965 0.20850222
Loop time of 0.0526894 on 4 procs for 100 steps with 4000 atoms
Performance: 819898.804 tau/day, 1897.914 timesteps/s
99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.034334 | 0.035334 | 0.036511 | 0.4 | 67.06
Neigh | 0.006092 | 0.0061221 | 0.0061656 | 0.0 | 11.62
Comm | 0.0090592 | 0.01032 | 0.011391 | 0.8 | 19.59
Output | 2.6026e-05 | 2.9345e-05 | 3.4108e-05 | 0.0 | 0.06
Modify | 0.00065987 | 0.00070476 | 0.0007444 | 0.0 | 1.34
Other | | 0.0001791 | | | 0.34
Nlocal: 1000.00 ave 1019 max 980 min
Histogram: 1 0 0 0 0 2 0 0 0 1
Nghost: 2858.75 ave 2881 max 2844 min
Histogram: 1 1 0 0 1 0 0 0 0 1
Neighs: 37590.5 ave 38013 max 37269 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Total # of neighbors = 150362
Ave neighs/atom = 37.590500
Neighbor list builds = 5
Dangerous builds not checked
Total wall time: 0:00:00
Example input file in.demo (3d Lennard-Jones melt)
[lammps] [pkrastev@builds01 Fort]$ cat in.demo
# 3d Lennard-Jones melt
units lj
atom_style atomic
atom_modify map hash
lattice fcc 0.8442
region box block 0 10 0 10 0 10
create_box 1 box
create_atoms 1 box
mass 1 1.0
velocity all create 1.44 87287 loop geom
pair_style lj/cut 2.5
pair_coeff 1 1 1.0 1.0 2.5
neighbor 0.3 bin
neigh_modify delay 0 every 20 check no
fix 1 all nve
variable eng equal pe
variable vy atom vy
run 100
Example batch job submission script
Below is an example batch-job submission script using the LAMMPS spack environment.
#!/bin/bash
#SBATCH -J lammps_test # job name
#SBATCH -o lammps_test.out # standard output file
#SBATCH -e lammps_test.err # standard error file
#SBATCH -p shared # partition
#SBATCH -n 4 # ntasks
#SBATCH -t 00:30:00 # time in HH:MM:SS
#SBATCH --mem-per-cpu=500 # memory in megabytes
# --- Activate the LAMMPS Spack environment., e.g., ---
### NOTE: Replace <PATH TO> with the actual path to your spack installation
. <PATH TO>/spack/share/spack/setup-env.sh
spack env activate lammps
# --- Run the executable ---
srun -n $SLURM_NTASKS --mpi=pmix lmp -in in.demo