Merge pull request #2074 from akohlmey/singularity-update (af1aa034) · Commits · 郑智淋 / lammps

.github/CODEOWNERS

+1 −0

Original line number	Original line	Diff line number	Diff line
	@@ -115,6 +115,7 @@ src/min* @sjplimp @stanmoore1
	# tools		# tools
	tools/msi2lmp/* @akohlmey		tools/msi2lmp/* @akohlmey
	tools/emacs/* @HaoZeke		tools/emacs/* @HaoZeke
			tools/singularity/* @akohlmey @rbberger

	# cmake		# cmake
	cmake/* @junghans @rbberger		cmake/* @junghans @rbberger

tools/singularity/README.md

+1 −1

Original line number	Original line	Diff line number	Diff line
	@@ -48,7 +48,6 @@ make
	\| ------------------------------ \| ---------------------------------------------- \|		\| ------------------------------ \| ---------------------------------------------- \|
	\| centos7.def \| CentOS 7.x with EPEL enabled, no LaTeX \|		\| centos7.def \| CentOS 7.x with EPEL enabled, no LaTeX \|
	\| centos8.def \| CentOS 8.x with EPEL enabled \|		\| centos8.def \| CentOS 8.x with EPEL enabled \|
	\| fedora30_mingw.def \| Fedora 30 with MinGW cross-compiler toolchain \|
	\| fedora32_mingw.def \| Fedora 32 with MinGW cross-compiler toolchain \|		\| fedora32_mingw.def \| Fedora 32 with MinGW cross-compiler toolchain \|
	\| ubuntu16.04.def \| Ubuntu 16.04LTS with MPI == OpenMPI, no LaTeX \|		\| ubuntu16.04.def \| Ubuntu 16.04LTS with MPI == OpenMPI, no LaTeX \|
	\| ubuntu18.04.def \| Ubuntu 18.04LTS with MPI == OpenMPI \|		\| ubuntu18.04.def \| Ubuntu 18.04LTS with MPI == OpenMPI \|
	@@ -57,3 +56,4 @@ make
	\| ubuntu18.04_nvidia.def \| Ubuntu 18.04LTS with Nvidia CUDA 10.2 toolkit \|		\| ubuntu18.04_nvidia.def \| Ubuntu 18.04LTS with Nvidia CUDA 10.2 toolkit \|
	\| ubuntu18.04_intel_opencl.def \| Ubuntu 18.04LTS with Intel OpenCL runtime \|		\| ubuntu18.04_intel_opencl.def \| Ubuntu 18.04LTS with Intel OpenCL runtime \|
	\| ubuntu20.04.def \| Ubuntu 20.04LTS with MPI == OpenMPI \|		\| ubuntu20.04.def \| Ubuntu 20.04LTS with MPI == OpenMPI \|
			\| ------------------------------ \| ---------------------------------------------- \|

tools/singularity/centos7.def

+15 −1

Original line number	Original line	Diff line number	Diff line
	@@ -11,9 +11,18 @@ From: centos:7
	hdf5-devel python36-virtualenv python36-pip python-pip \		hdf5-devel python36-virtualenv python36-pip python-pip \
	netcdf-devel netcdf-cxx-devel netcdf-mpich-devel netcdf-openmpi-devel \		netcdf-devel netcdf-cxx-devel netcdf-mpich-devel netcdf-openmpi-devel \
	python-virtualenv fftw-devel voro++-devel eigen3-devel gsl-devel openblas-devel enchant \		python-virtualenv fftw-devel voro++-devel eigen3-devel gsl-devel openblas-devel enchant \
	blas-devel lapack-devel		blas-devel lapack-devel libyaml-devel
	yum clean all		yum clean all

			# set custom prompt indicating the container name
			CUSTOM_PROMPT_ENV=/.singularity.d/env/99-zz_custom_prompt.sh
			cat >$CUSTOM_PROMPT_ENV <<EOF
			#!/bin/bash
			PS1="[centos7:\u@\h] \W> "
			EOF
			chmod 755 $CUSTOM_PROMPT_ENV


	%environment		%environment
	LC_ALL=C		LC_ALL=C
	export LC_ALL		export LC_ALL
	@@ -36,6 +45,11 @@ From: centos:7
	# load MPI by default		# load MPI by default
	. /etc/profile		. /etc/profile
	module load mpi		module load mpi
			# restrict OpenMPI to shared memory comm by default
			OMPI_MCA_btl="sm,self"
			# do not warn about unused components as this messes up testing
			OMPI_MCA_btl_base_warn_component_unused="0"
			export OMPI_MCA_btl OMPI_MCA_btl_base_warn_component_unused

	%labels		%labels
	Author akohlmey, rbberger		Author akohlmey, rbberger

tools/singularity/centos8.def

+16 −2

Original line number	Original line	Diff line number	Diff line
	@@ -10,15 +10,24 @@ From: centos:8
	eigen3-devel openblas-devel libpng-devel libjpeg-devel platform-python-devel \		eigen3-devel openblas-devel libpng-devel libjpeg-devel platform-python-devel \
	openmpi-devel mpich-devel fftw-devel voro++-devel gsl-devel hdf5-devel \		openmpi-devel mpich-devel fftw-devel voro++-devel gsl-devel hdf5-devel \
	netcdf-devel netcdf-cxx-devel netcdf-mpich-devel netcdf-openmpi-devel \		netcdf-devel netcdf-cxx-devel netcdf-mpich-devel netcdf-openmpi-devel \
	enchant python3-virtualenv doxygen \		enchant python3-virtualenv doxygen diffutils \
	texlive-latex-fonts texlive-pslatex texlive-collection-latexrecommended \		texlive-latex-fonts texlive-pslatex texlive-collection-latexrecommended \
	texlive-latex texlive-latexconfig doxygen-latex texlive-collection-latex \		texlive-latex texlive-latexconfig doxygen-latex texlive-collection-latex \
	texlive-latex-bin texlive-lualatex-math texlive-fncychap texlive-tabulary \		texlive-latex-bin texlive-lualatex-math texlive-fncychap texlive-tabulary \
	texlive-framed texlive-wrapfig texlive-upquote texlive-capt-of \		texlive-framed texlive-wrapfig texlive-upquote texlive-capt-of \
	texlive-needspace texlive-titlesec texlive-anysize texlive-dvipng \		texlive-needspace texlive-titlesec texlive-anysize texlive-dvipng \
	blas-devel lapack-devel		blas-devel lapack-devel libyaml-devel
	dnf clean all		dnf clean all

			# set custom prompt indicating the container name
			CUSTOM_PROMPT_ENV=/.singularity.d/env/99-zz_custom_prompt.sh
			cat >$CUSTOM_PROMPT_ENV <<EOF
			#!/bin/bash
			PS1="[centos8:\u@\h] \W> "
			EOF
			chmod 755 $CUSTOM_PROMPT_ENV


	%environment		%environment
	LC_ALL=C		LC_ALL=C
	export LC_ALL		export LC_ALL
	@@ -41,6 +50,11 @@ From: centos:8
	# load MPI by default		# load MPI by default
	. /etc/profile		. /etc/profile
	module load mpi		module load mpi
			# restrict OpenMPI to shared memory comm by default
			OMPI_MCA_btl="sm,self"
			# do not warn about unused components as this messes up testing
			OMPI_MCA_btl_base_warn_component_unused="0"
			export OMPI_MCA_btl OMPI_MCA_btl_base_warn_component_unused

	%labels		%labels
	Author akohlmey, rbberger		Author akohlmey, rbberger

tools/singularity/fedora30_mingw.def

deleted100644 → 0

+0 −65

Original line number	Original line	Diff line number	Diff line
	BootStrap: docker
	From: fedora:30

	%post
	dnf -y update
	dnf -y install vim-enhanced git file make cmake patch which file Lmod \
	ninja-build clang libomp-devel libubsan libasan libtsan \
	dos2unix findutils rsync python-devel libjpeg-devel libpng-devel \
	ccache gcc-c++ gcc-gfortran gdb valgrind eigen3-devel openblas-devel \
	openmpi-devel mpich-devel fftw-devel voro++-devel gsl-devel hdf5-devel \
	netcdf-devel netcdf-cxx-devel netcdf-mpich-devel netcdf-openmpi-devel \
	mingw-filesystem-base mingw32-nsis mingw-binutils-generic \
	mingw32-filesystem mingw32-pkg-config \
	mingw64-filesystem mingw64-pkg-config \
	mingw32-crt mingw32-headers mingw32-binutils \
	mingw64-crt mingw64-headers mingw64-binutils \
	mingw32-cpp mingw32-gcc mingw32-gcc-gfortran mingw32-gcc-c++ \
	mingw64-cpp mingw64-gcc mingw64-gcc-gfortran mingw64-gcc-c++ \
	mingw32-libgomp mingw64-libgomp \
	mingw32-winpthreads mingw64-winpthreads \
	mingw32-winpthreads-static mingw64-winpthreads-static \
	mingw32-eigen3 mingw64-eigen3 \
	mingw32-libjpeg-turbo mingw64-libjpeg-turbo \
	mingw32-libjpeg-turbo-static mingw64-libjpeg-turbo-static \
	mingw32-libpng mingw64-libpng \
	mingw32-libpng-static mingw64-libpng-static \
	mingw32-zlib mingw64-zlib \
	mingw32-zlib-static mingw64-zlib-static \
	mingw32-expat mingw64-expat \
	mingw64-expat-static mingw32-expat-static \
	mingw32-sqlite-static mingw64-sqlite-static \
	enchant python3-virtualenv doxygen \
	texlive-latex-fonts texlive-pslatex texlive-collection-latexrecommended \
	texlive-latex texlive-latexconfig doxygen-latex texlive-collection-latex \
	texlive-latex-bin texlive-lualatex-math texlive-fncychap texlive-tabulary \
	texlive-framed texlive-wrapfig texlive-upquote texlive-capt-of \
	texlive-needspace texlive-titlesec texlive-anysize texlive-dvipng \
	blas-devel lapack-devel
	dnf clean all

	%environment
	LC_ALL=C
	export LC_ALL

	# we need to reset any module variables
	# inherited from the host.
	unset __LMOD_REF_COUNT__LMFILES_
	unset __LMOD_REF_COUNT_PATH
	unset __LMOD_REF_COUNT_LD_LIBRARY_PATH
	unset __LMOD_REF_COUNT_MANPATH
	unset __LMOD_REF_COUNT_MODULEPATH
	unset __LMOD_REF_COUNT_LOADEDMODULES
	unset _LMFILES_
	unset MODULEPATH
	unset MODULESHOME
	unset MODULEPATH_ROOT
	unset LOADEDMODULES
	unset LMOD_SYSTEM_DEFAULT_MODULES

	# load MPI by default
	. /etc/profile
	module load mpi

	%labels
	Author akohlmey, rbberger

Original line number	Original line	Diff line number	Diff line
	@@ -48,7 +48,6 @@ make
	\| ------------------------------ \| ---------------------------------------------- \|		\| ------------------------------ \| ---------------------------------------------- \|
	\| centos7.def \| CentOS 7.x with EPEL enabled, no LaTeX \|		\| centos7.def \| CentOS 7.x with EPEL enabled, no LaTeX \|
	\| centos8.def \| CentOS 8.x with EPEL enabled \|		\| centos8.def \| CentOS 8.x with EPEL enabled \|
	\| fedora30_mingw.def \| Fedora 30 with MinGW cross-compiler toolchain \|
	\| fedora32_mingw.def \| Fedora 32 with MinGW cross-compiler toolchain \|		\| fedora32_mingw.def \| Fedora 32 with MinGW cross-compiler toolchain \|
	\| ubuntu16.04.def \| Ubuntu 16.04LTS with MPI == OpenMPI, no LaTeX \|		\| ubuntu16.04.def \| Ubuntu 16.04LTS with MPI == OpenMPI, no LaTeX \|
	\| ubuntu18.04.def \| Ubuntu 18.04LTS with MPI == OpenMPI \|		\| ubuntu18.04.def \| Ubuntu 18.04LTS with MPI == OpenMPI \|
	@@ -57,3 +56,4 @@ make
	\| ubuntu18.04_nvidia.def \| Ubuntu 18.04LTS with Nvidia CUDA 10.2 toolkit \|		\| ubuntu18.04_nvidia.def \| Ubuntu 18.04LTS with Nvidia CUDA 10.2 toolkit \|
	\| ubuntu18.04_intel_opencl.def \| Ubuntu 18.04LTS with Intel OpenCL runtime \|		\| ubuntu18.04_intel_opencl.def \| Ubuntu 18.04LTS with Intel OpenCL runtime \|
	\| ubuntu20.04.def \| Ubuntu 20.04LTS with MPI == OpenMPI \|		\| ubuntu20.04.def \| Ubuntu 20.04LTS with MPI == OpenMPI \|
			\| ------------------------------ \| ---------------------------------------------- \|

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