Merge pull request #2340 from rbberger/container_update (a51bebc9) · Commits · 郑智淋 / lammps

tools/singularity/centos7.def

+2 −2

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

		# we need to reset any module variables
		@@ -36,7 +36,7 @@ From: centos:7
		# manually install Plumed
		mkdir plumed
		cd plumed
		version=2.6.0
		version=2.6.1
		curl -L -o plumed.tar.gz https://github.com/plumed/plumed2/releases/download/v${version}/plumed-src-${version}.tgz
		tar -xzf plumed.tar.gz
		cd plumed-${version}

tools/singularity/centos8.def

+3 −2

Original line number	Diff line number	Diff line
		@@ -16,7 +16,8 @@ From: centos:8
		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 libyaml-devel openkim-models kim-api-devel
		blas-devel lapack-devel libyaml-devel openkim-models kim-api-devel \
		zstd libzstd-devel
		dnf clean all

		# we need to reset any module variables
		@@ -41,7 +42,7 @@ From: centos:8
		# manually install Plumed
		mkdir plumed
		cd plumed
		version=2.6.0
		version=2.6.1
		curl -L -o plumed.tar.gz https://github.com/plumed/plumed2/releases/download/v${version}/plumed-src-${version}.tgz
		tar -xzf plumed.tar.gz
		cd plumed-${version}

tools/singularity/fedora32_mingw.def

+3 −2

Original line number	Diff line number	Diff line
		@@ -36,7 +36,8 @@ From: fedora:32
		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 libyaml-devel openkim-models kim-api-devel
		blas-devel lapack-devel libyaml-devel openkim-models kim-api-devel \
		zstd libzstd-devel
		dnf clean all

		# enable Lmod and load MPI
		@@ -47,7 +48,7 @@ From: fedora:32
		# manually install Plumed
		mkdir plumed
		cd plumed
		version=2.6.0
		version=2.6.1
		curl -L -o plumed.tar.gz https://github.com/plumed/plumed2/releases/download/v${version}/plumed-src-${version}.tgz
		tar -xzf plumed.tar.gz
		cd plumed-${version}

tools/singularity/ubuntu18.04.def

+52 −16

Original line number	Diff line number	Diff line
		@@ -41,6 +41,7 @@ From: ubuntu:18.04
		libproj-dev \
		libvtk6-dev \
		libyaml-dev \
		libzstd-dev \
		make \
		mpi-default-bin \
		mpi-default-dev \
		@@ -70,27 +71,55 @@ From: ubuntu:18.04
		xxd \
		valgrind \
		gdb \
		zstd \
		libkim-api-dev \
		openkim-models

		# clean cache
		rm -rf /var/lib/apt/lists/*

		# manually install Plumed
		###########################################################################
		# KIM-API
		###########################################################################

		# workaround for installing files in /usr/share/doc inside of a container
		sed -i 's/path-exclude=\/usr\/share\/doc/#path-exclude=\/usr\/share\/doc/g' /etc/dpkg/dpkg.cfg.d/excludes
		apt-get install -y libkim-api-doc
		sed -i 's/#path-exclude=\/usr\/share\/doc/path-exclude=\/usr\/share\/doc/g' /etc/dpkg/dpkg.cfg.d/excludes

		# install KIM models
		KIM_API_EXAMPLES=/usr/share/doc/libkim-api-dev/examples
		gunzip $KIM_API_EXAMPLES/portable-models/LennardJones612_UniversalShifted__MO_959249795837_003/LennardJones612_UniversalShifted.params.gz
		gunzip $KIM_API_EXAMPLES/model-drivers/ex_model_driver_P_LJ/ex_model_driver_P_LJ.f90.gz

		kim-api-collections-management install system $KIM_API_EXAMPLES/model-drivers/LennardJones612__MD_414112407348_003
		kim-api-collections-management install system $KIM_API_EXAMPLES/model-drivers/ex_model_driver_P_LJ
		kim-api-collections-management install system $KIM_API_EXAMPLES/portable-models/LennardJones_Ar
		kim-api-collections-management install system $KIM_API_EXAMPLES/portable-models/ex_model_Ar_P_LJ
		kim-api-collections-management install system $KIM_API_EXAMPLES/portable-models/LennardJones612_UniversalShifted__MO_959249795837_003
		kim-api-collections-management install system $KIM_API_EXAMPLES/simulator-models/Sim_LAMMPS_LJcut_AkersonElliott_Alchemy_PbAu


		###########################################################################
		# Plumed
		###########################################################################

		export PLUMED_PKG_VERSION=2.6.1

		mkdir plumed
		cd plumed
		version=2.6.0
		curl -L -o plumed.tar.gz https://github.com/plumed/plumed2/releases/download/v${version}/plumed-src-${version}.tgz
		curl -L -o plumed.tar.gz https://github.com/plumed/plumed2/releases/download/v${PLUMED_PKG_VERSION}/plumed-src-${PLUMED_PKG_VERSION}.tgz
		tar -xzf plumed.tar.gz
		cd plumed-${version}
		cd plumed-${PLUMED_PKG_VERSION}
		./configure --disable-doc --prefix=/usr
		make
		make install
		# fix up installation for CentOS and Fedora
		# mv -v /usr/lib/pkgconfig/plumed* /usr/share/pkgconfig/
		cd ../../
		rm -rvf plumed


		###########################################################################
		# Customizations
		###########################################################################

		# set custom prompt indicating the container name
		CUSTOM_PROMPT_ENV=/.singularity.d/env/99-zz_custom_prompt.sh
		cat >$CUSTOM_PROMPT_ENV <<EOF
		@@ -99,6 +128,13 @@ PS1="[ubuntu18.04:\u@\h] \W> "
		EOF
		chmod 755 $CUSTOM_PROMPT_ENV


		###########################################################################
		# Cleanup
		###########################################################################
		# clean cache
		rm -rf /var/lib/apt/lists/*

		%environment
		LC_ALL=C
		export LC_ALL

tools/singularity/ubuntu18.04_amd_rocm.def

+67 −9

Original line number	Diff line number	Diff line
		@@ -2,7 +2,7 @@ BootStrap: docker
		From: ubuntu:18.04

		%environment
		export PATH=$PATH:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64
		export PATH=/usr/lib/ccache:${PATH}:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64

		%post
		export DEBIAN_FRONTEND=noninteractive
		@@ -25,7 +25,8 @@ From: ubuntu:18.04
		build-essential

		apt-get install --no-install-recommends -y software-properties-common

		add-apt-repository ppa:openkim/latest
		apt-get update
		apt-get install --no-install-recommends -y \
		bc \
		build-essential \
		@@ -41,7 +42,6 @@ From: ubuntu:18.04
		gfortran \
		git \
		hdf5-tools \
		kmod \
		less \
		libblas-dev \
		libeigen3-dev \
		@@ -52,12 +52,15 @@ From: ubuntu:18.04
		libhwloc-dev \
		libjpeg-dev \
		liblapack-dev \
		libnetcdf-dev \
		libomp-dev \
		libopenblas-dev \
		libnuma-dev \
		libpng-dev \
		libproj-dev \
		libvtk6-dev \
		libyaml-dev \
		libzstd-dev \
		make \
		mpi-default-bin \
		mpi-default-dev \
		@@ -79,30 +82,85 @@ From: ubuntu:18.04
		wget \
		xxd \
		valgrind \
		gdb
		gdb \
		zstd \
		libkim-api-dev \
		openkim-models


		###########################################################################
		# ROCm hipCUB
		###########################################################################

		export PATH=$PATH:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64
		git clone -b master-rocm-3.5 https://github.com/ROCmSoftwarePlatform/hipCUB.git
		git clone -b rocm-3.7.x https://github.com/ROCmSoftwarePlatform/hipCUB.git
		mkdir hipCUB/build
		cd hipCUB/build
		CXX=hipcc cmake -D BUILD_TEST=off ..
		make -j4
		make
		make package
		make install

		# clean cache
		rm -rf /var/lib/apt/lists/*

		###########################################################################
		# KIM-API
		###########################################################################

		# workaround for installing files in /usr/share/doc inside of a container
		sed -i 's/path-exclude=\/usr\/share\/doc/#path-exclude=\/usr\/share\/doc/g' /etc/dpkg/dpkg.cfg.d/excludes
		apt-get install -y libkim-api-doc
		sed -i 's/#path-exclude=\/usr\/share\/doc/path-exclude=\/usr\/share\/doc/g' /etc/dpkg/dpkg.cfg.d/excludes

		# install KIM models
		KIM_API_EXAMPLES=/usr/share/doc/libkim-api-dev/examples
		gunzip $KIM_API_EXAMPLES/portable-models/LennardJones612_UniversalShifted__MO_959249795837_003/LennardJones612_UniversalShifted.params.gz
		gunzip $KIM_API_EXAMPLES/model-drivers/ex_model_driver_P_LJ/ex_model_driver_P_LJ.f90.gz

		kim-api-collections-management install system $KIM_API_EXAMPLES/model-drivers/LennardJones612__MD_414112407348_003
		kim-api-collections-management install system $KIM_API_EXAMPLES/model-drivers/ex_model_driver_P_LJ
		kim-api-collections-management install system $KIM_API_EXAMPLES/portable-models/LennardJones_Ar
		kim-api-collections-management install system $KIM_API_EXAMPLES/portable-models/ex_model_Ar_P_LJ
		kim-api-collections-management install system $KIM_API_EXAMPLES/portable-models/LennardJones612_UniversalShifted__MO_959249795837_003
		kim-api-collections-management install system $KIM_API_EXAMPLES/simulator-models/Sim_LAMMPS_LJcut_AkersonElliott_Alchemy_PbAu


		###########################################################################
		# Plumed
		###########################################################################

		export PLUMED_PKG_VERSION=2.6.1

		mkdir plumed
		cd plumed
		curl -L -o plumed.tar.gz https://github.com/plumed/plumed2/releases/download/v${PLUMED_PKG_VERSION}/plumed-src-${PLUMED_PKG_VERSION}.tgz
		tar -xzf plumed.tar.gz
		cd plumed-${PLUMED_PKG_VERSION}
		./configure --disable-doc --prefix=/usr
		make
		make install
		cd ../../
		rm -rvf plumed


		###########################################################################
		# Customizations
		###########################################################################

		# 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="[ubuntu18/rocm:\u@\h] \W> "
		PS1="[ubuntu18.04/rocm:\u@\h] \W> "
		EOF
		chmod 755 $CUSTOM_PROMPT_ENV


		###########################################################################
		# Cleanup
		###########################################################################
		# clean cache
		rm -rf /var/lib/apt/lists/*

		%environment
		LC_ALL=C
		export LC_ALL

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