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Merge pull request #2340 from rbberger/container_update 

Singularity Container definitions update
This commit is contained in:
Axel Kohlmeyer 2020-09-09 09:53:48 -04:00 committed by GitHub
parent 9f8b8529b1 6a40eba2ae
commit a51bebc9e4
No known key found for this signature in database
GPG Key ID: 4AEE18F83AFDEB23
13 changed files with 1060 additions and 83 deletions
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4
tools/singularity/centos7.def
View File

@ -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}

5
tools/singularity/centos8.def
View File

@ -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}

5
tools/singularity/fedora32_mingw.def
View File

@ -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}

68
tools/singularity/ubuntu18.04.def
View File

@ -41,6 +41,7 @@ From: ubuntu:18.04
libproj-dev \
libvtk6-dev \
libyaml-dev \
libzstd-dev \
make \
mpi-default-bin \
mpi-default-dev \
@ -70,26 +71,54 @@ From: ubuntu:18.04
xxd \
valgrind \
gdb \
zstd \
libkim-api-dev \
openkim-models
# clean cache
rm -rf /var/lib/apt/lists/*
# manually install Plumed
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
tar -xzf plumed.tar.gz
cd plumed-${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
###########################################################################
# 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
@ -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

76
tools/singularity/ubuntu18.04_amd_rocm.def
View File

@ -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

115
tools/singularity/ubuntu18.04_gpu.def
View File

@ -2,11 +2,11 @@ BootStrap: docker
From: ubuntu:18.04
%environment
export PATH=/usr/lib/ccache:/usr/local/cuda-10.2/bin:${PATH}:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64
export CUDADIR=/usr/local/cuda-10.2
export CUDA_PATH=/usr/local/cuda-10.2
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/cuda-10.2/lib64
export LIBRARY_PATH=/usr/local/cuda-10.2/lib64/stubs
export PATH=/usr/lib/ccache:/usr/local/cuda-11.0/bin:${PATH}:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64
export CUDADIR=/usr/local/cuda-11.0
export CUDA_PATH=/usr/local/cuda-11.0
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/cuda-11.0/lib64
export LIBRARY_PATH=/usr/local/cuda-11.0/lib64/stubs
%post
export DEBIAN_FRONTEND=noninteractive
apt-get update
@ -28,6 +28,8 @@ 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 \
@ -43,7 +45,6 @@ From: ubuntu:18.04
gfortran \
git \
hdf5-tools \
kmod \
less \
libblas-dev \
libeigen3-dev \
@ -54,12 +55,15 @@ 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 \
@ -81,7 +85,15 @@ From: ubuntu:18.04
wget \
xxd \
valgrind \
gdb
gdb \
zstd \
libkim-api-dev \
openkim-models
###########################################################################
# CUDA
###########################################################################
wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/cuda-ubuntu1804.pin
mv cuda-ubuntu1804.pin /etc/apt/preferences.d/cuda-repository-pin-600
@ -89,7 +101,7 @@ From: ubuntu:18.04
add-apt-repository "deb http://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/ /"
apt-get update
export CUDA_PKG_VERSION=10.2
export CUDA_PKG_VERSION=11.0
apt-get install -y --no-install-recommends \
cuda-libraries-$CUDA_PKG_VERSION \
@ -97,37 +109,90 @@ From: ubuntu:18.04
cuda-libraries-dev-$CUDA_PKG_VERSION \
cuda-minimal-build-$CUDA_PKG_VERSION \
cuda-compat-$CUDA_PKG_VERSION \
libcublas10 \
libcublas-dev
export PATH=$PATH:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64
git clone -b master-rocm-3.5 https://github.com/ROCmSoftwarePlatform/hipCUB.git
mkdir hipCUB/build
cd hipCUB/build
CXX=hipcc cmake -D BUILD_TEST=off ..
make -j4
make package
make install
libcublas-11-0 \
libcublas-dev-11-0
echo "/usr/local/nvidia/lib" >> /etc/ld.so.conf.d/nvidia.conf
echo "/usr/local/nvidia/lib64" >> /etc/ld.so.conf.d/nvidia.conf
# clean cache
rm -rf /var/lib/apt/lists/*
# add missing symlink
ln -s /usr/local/cuda-10.2 /usr/local/cuda
ln -s /usr/local/cuda-10.2/lib64/stubs/libcuda.so /usr/local/cuda-10.2/lib64/stubs/libcuda.so.1
ln -s /usr/local/cuda-11.0 /usr/local/cuda
ln -s /usr/local/cuda-11.0/lib64/stubs/libcuda.so /usr/local/cuda-11.0/lib64/stubs/libcuda.so.1
###########################################################################
# ROCm hipCUB
###########################################################################
export PATH=$PATH:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64
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
make package
make install
###########################################################################
# 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/gpu:\u@\h] \W> "
PS1="[ubuntu18.04/gpu:\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

69
tools/singularity/ubuntu18.04_intel_opencl.def
View File

@ -4,8 +4,10 @@ From: ubuntu:18.04
%post
export DEBIAN_FRONTEND=noninteractive
apt-get update
apt-get upgrade --no-install-recommends -y
apt-get install --no-install-recommends -y software-properties-common
add-apt-repository ppa:openkim/latest
apt-get update
apt-get upgrade --no-install-recommends -y
apt-get install --no-install-recommends -y \
bc \
build-essential \
@ -38,6 +40,8 @@ From: ubuntu:18.04
libpng-dev \
libproj-dev \
libvtk6-dev \
libyaml-dev \
libzstd-dev \
make \
mpi-default-bin \
mpi-default-dev \
@ -61,24 +65,79 @@ From: ubuntu:18.04
wget \
xxd \
valgrind \
gdb
gdb \
zstd \
libkim-api-dev \
openkim-models
###########################################################################
# Intel OpenCL
###########################################################################
add-apt-repository ppa:intel-opencl/intel-opencl
apt-get update
apt-get install -y intel-opencl-icd
# 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/intel:\u@\h] \W> "
PS1="[ubuntu18.04/intel:\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

70
tools/singularity/ubuntu18.04_nvidia.def
View File

@ -1,11 +1,13 @@
BootStrap: docker
From: nvidia/cuda:10.2-devel-ubuntu18.04
From: nvidia/cuda:11.0-devel-ubuntu18.04
%post
export DEBIAN_FRONTEND=noninteractive
apt-get update
apt-get upgrade --no-install-recommends -y
apt-get install --no-install-recommends -y software-properties-common
add-apt-repository ppa:openkim/latest
apt-get update
apt-get upgrade --no-install-recommends -y
apt-get install --no-install-recommends -y \
bc \
build-essential \
@ -38,6 +40,8 @@ From: nvidia/cuda:10.2-devel-ubuntu18.04
libpng-dev \
libproj-dev \
libvtk6-dev \
libyaml-dev \
libzstd-dev \
make \
mpi-default-bin \
mpi-default-dev \
@ -61,23 +65,77 @@ From: nvidia/cuda:10.2-devel-ubuntu18.04
wget \
xxd \
valgrind \
gdb
gdb \
zstd \
libkim-api-dev \
openkim-models
###########################################################################
# NVIDIA OpenCL
###########################################################################
mkdir -p /etc/OpenCL/vendors
echo "libnvidia-opencl.so.1" > /etc/OpenCL/vendors/nvidia.icd
# 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/nvidia:\u@\h] \W> "
PS1="[ubuntu18.04/nvidia:\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

66
tools/singularity/ubuntu20.04.def
View File

@ -41,6 +41,7 @@ From: ubuntu:20.04
libproj-dev \
libvtk6-dev \
libyaml-dev \
libzstd-dev \
make \
mpi-default-bin \
mpi-default-dev \
@ -66,26 +67,52 @@ From: ubuntu:20.04
xxd \
valgrind \
gdb \
zstd \
libkim-api-dev \
openkim-models
# clean cache
rm -rf /var/lib/apt/lists/*
###########################################################################
# KIM-API
###########################################################################
# manually install Plumed
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
tar -xzf plumed.tar.gz
cd plumed-${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
# 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
@ -95,6 +122,13 @@ PS1="[ubuntu20.04:\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

170
tools/singularity/ubuntu20.04_amd_rocm.def Normal file
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@ -0,0 +1,170 @@
BootStrap: docker
From: ubuntu:20.04
%environment
export PATH=/usr/lib/ccache:/usr/local/cuda-11.0/bin:${PATH}:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64
%post
export DEBIAN_FRONTEND=noninteractive
apt-get update
apt-get upgrade --no-install-recommends -y
apt-get install -y --no-install-recommends curl libnuma-dev gnupg
curl -sL http://repo.radeon.com/rocm/apt/debian/rocm.gpg.key | apt-key add -
# AMD is using xenial folder also for focal
printf "deb [arch=amd64] http://repo.radeon.com/rocm/apt/debian/ xenial main" > /etc/apt/sources.list.d/rocm.list
apt-get update
apt-get install --no-install-recommends -y \
kmod \
file \
sudo \
libelf1 \
rocm-dev \
rocm-libs \
build-essential
apt-get install --no-install-recommends -y software-properties-common
add-apt-repository ppa:openkim/latest
apt-get update
apt-get install --no-install-recommends -y \
bc \
build-essential \
ccache \
clang \
cmake \
cmake-curses-gui \
curl \
doxygen \
enchant \
g++ \
gcc \
gfortran \
git \
hdf5-tools \
less \
libblas-dev \
libeigen3-dev \
libenchant-dev \
libfftw3-dev \
libgsl-dev \
libhdf5-serial-dev \
libhwloc-dev \
libjpeg-dev \
liblapack-dev \
libnetcdf-dev \
libomp-dev \
libopenblas-dev \
libnuma-dev \
libpng-dev \
libproj-dev \
libvtk6-dev \
libyaml-dev \
libzstd-dev \
make \
mpi-default-bin \
mpi-default-dev \
ninja-build \
python3-dev \
python3-pip \
python3-pkg-resources \
python3-setuptools \
python3-virtualenv \
rsync \
ssh \
vim-nox \
virtualenv \
voro++-dev \
wget \
xxd \
valgrind \
gdb \
zstd \
libkim-api-dev \
openkim-models
###########################################################################
# ROCm hipCUB
###########################################################################
export PATH=$PATH:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64
git clone -b rocm-3.7.x https://github.com/ROCmSoftwarePlatform/hipCUB.git
mkdir hipCUB/build
cd hipCUB/build
CXX=hipcc cmake -D BUILD_TEST=off ..
make
make package
make install
###########################################################################
# 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="[ubuntu20.04/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
# tell OpenMPI to not try using Infiniband
OMPI_MCA_btl="^openib"
# 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
Author rbberger, akohlmey

203
tools/singularity/ubuntu20.04_gpu.def Normal file
View File

@ -0,0 +1,203 @@
BootStrap: docker
From: ubuntu:20.04
%environment
export PATH=/usr/lib/ccache:/usr/local/cuda-11.0/bin:${PATH}:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64
export CUDADIR=/usr/local/cuda-11.0
export CUDA_PATH=/usr/local/cuda-11.0
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/cuda-11.0/lib64
export LIBRARY_PATH=/usr/local/cuda-11.0/lib64/stubs
%post
export DEBIAN_FRONTEND=noninteractive
apt-get update
apt-get upgrade --no-install-recommends -y
apt-get install -y --no-install-recommends curl libnuma-dev gnupg
curl -sL http://repo.radeon.com/rocm/apt/debian/rocm.gpg.key | apt-key add -
# AMD is using xenial folder also for focal
printf "deb [arch=amd64] http://repo.radeon.com/rocm/apt/debian/ xenial main" > /etc/apt/sources.list.d/rocm.list
apt-get update
apt-get install --no-install-recommends -y \
kmod \
file \
sudo \
libelf1 \
rocm-dev \
rocm-libs \
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 \
ccache \
clang \
cmake \
cmake-curses-gui \
curl \
doxygen \
enchant \
g++ \
gcc \
gfortran \
git \
hdf5-tools \
less \
libblas-dev \
libeigen3-dev \
libenchant-dev \
libfftw3-dev \
libgsl-dev \
libhdf5-serial-dev \
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 \
ninja-build \
python3-dev \
python3-pip \
python3-pkg-resources \
python3-setuptools \
python3-virtualenv \
rsync \
ssh \
vim-nox \
virtualenv \
voro++-dev \
wget \
xxd \
valgrind \
gdb \
zstd \
libkim-api-dev \
openkim-models
###########################################################################
# CUDA
###########################################################################
wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/cuda-ubuntu2004.pin
mv cuda-ubuntu2004.pin /etc/apt/preferences.d/cuda-repository-pin-600
apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/7fa2af80.pub
add-apt-repository "deb http://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/ /"
apt-get update
export CUDA_PKG_VERSION=11.0
apt-get install -y --no-install-recommends \
cuda-libraries-$CUDA_PKG_VERSION \
cuda-command-line-tools-$CUDA_PKG_VERSION \
cuda-libraries-dev-$CUDA_PKG_VERSION \
cuda-minimal-build-$CUDA_PKG_VERSION \
cuda-compat-$CUDA_PKG_VERSION \
libcublas-11-0 \
libcublas-dev-11-0
echo "/usr/local/nvidia/lib" >> /etc/ld.so.conf.d/nvidia.conf
echo "/usr/local/nvidia/lib64" >> /etc/ld.so.conf.d/nvidia.conf
# add missing symlink
ln -s /usr/local/cuda-11.0 /usr/local/cuda
ln -s /usr/local/cuda-11.0/lib64/stubs/libcuda.so /usr/local/cuda-11.0/lib64/stubs/libcuda.so.1
###########################################################################
# ROCm hipCUB
###########################################################################
export PATH=$PATH:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64
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
make package
make install
###########################################################################
# 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="[ubuntu20.04/gpu:\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
# tell OpenMPI to not try using Infiniband
OMPI_MCA_btl="^openib"
# 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
Author rbberger, akohlmey

145
tools/singularity/ubuntu20.04_intel_opencl.def Normal file
View File

@ -0,0 +1,145 @@
BootStrap: docker
From: ubuntu:20.04
%post
export DEBIAN_FRONTEND=noninteractive
apt-get update
apt-get install --no-install-recommends -y software-properties-common
add-apt-repository ppa:openkim/latest
apt-get update
apt-get upgrade --no-install-recommends -y
apt-get install --no-install-recommends -y \
bc \
build-essential \
ccache \
clang \
cmake \
cmake-curses-gui \
curl \
doxygen \
enchant \
g++ \
gcc \
gfortran \
git \
hdf5-tools \
less \
libblas-dev \
libeigen3-dev \
libenchant-dev \
libfftw3-dev \
libgsl-dev \
libhdf5-serial-dev \
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 \
ninja-build \
python3-dev \
python3-pip \
python3-pkg-resources \
python3-setuptools \
python3-virtualenv \
rsync \
ssh \
vim-nox \
virtualenv \
voro++-dev \
wget \
xxd \
valgrind \
gdb \
zstd \
libkim-api-dev \
openkim-models
###########################################################################
# Intel OpenCL
###########################################################################
add-apt-repository ppa:intel-opencl/intel-opencl
apt-get update
apt-get install -y intel-opencl-icd
###########################################################################
# 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="[ubuntu20.04/intel:\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
# tell OpenMPI to not try using Infiniband
OMPI_MCA_btl="^openib"
# 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
Author rbberger, akohlmey

147
tools/singularity/ubuntu20.04_nvidia.def Normal file
View File

@ -0,0 +1,147 @@
BootStrap: docker
From: nvidia/cuda:11.0-devel-ubuntu20.04
%post
export DEBIAN_FRONTEND=noninteractive
apt-get update
apt-get install --no-install-recommends -y software-properties-common
add-apt-repository ppa:openkim/latest
apt-get update
apt-get upgrade --no-install-recommends -y
apt-get install --no-install-recommends -y \
bc \
build-essential \
ccache \
clang \
clinfo \
cmake \
cmake-curses-gui \
curl \
doxygen \
enchant \
g++ \
gcc \
gfortran \
git \
hdf5-tools \
less \
libblas-dev \
libeigen3-dev \
libenchant-dev \
libfftw3-dev \
libgsl-dev \
libhdf5-serial-dev \
libhwloc-dev \
libjpeg-dev \
liblapack-dev \
libomp-dev \
libopenblas-dev \
libnuma-dev \
libpng-dev \
libproj-dev \
libvtk6-dev \
libyaml-dev \
libzstd-dev \
make \
mpi-default-bin \
mpi-default-dev \
ninja-build \
ocl-icd-libopencl1 \
ocl-icd-opencl-dev \
python3-dev \
python3-pip \
python3-pkg-resources \
python3-setuptools \
python3-virtualenv \
rsync \
ssh \
vim-nox \
virtualenv \
voro++-dev \
wget \
xxd \
valgrind \
gdb \
zstd \
libkim-api-dev \
openkim-models
###########################################################################
# NVIDIA OpenCL
###########################################################################
mkdir -p /etc/OpenCL/vendors
echo "libnvidia-opencl.so.1" > /etc/OpenCL/vendors/nvidia.icd
###########################################################################
# 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="[ubuntu20.04/nvidia:\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
# tell OpenMPI to not try using Infiniband
OMPI_MCA_btl="^openib"
# 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
Author rbberger, akohlmey