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Merge branch 'master' into collected-small-changes

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This commit is contained in:
Axel Kohlmeyer
2021-09-26 18:12:40 -04:00
parent 9da8c932ab f3b1da83f7
commit ea030c6dd8
36 changed files with 1131 additions and 272 deletions
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2
tools/singularity/centos7.def
View File

@ -36,7 +36,7 @@ From: centos:7
# manually install Plumed
mkdir plumed
cd plumed
version=2.6.1
version=2.7.2
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}

4
tools/singularity/centos8.def
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@ -3,7 +3,7 @@ From: centos:8
%post
dnf -y install epel-release dnf-utils
dnf config-manager --set-enabled PowerTools
dnf config-manager --set-enabled powertools
dnf -y update
dnf -y install vim-enhanced git file make cmake patch which file ninja-build \
ccache gcc-c++ gcc-gfortran clang libomp-devel gdb valgrind libubsan libasan libtsan \
@ -42,7 +42,7 @@ From: centos:8
# manually install Plumed
mkdir plumed
cd plumed
version=2.6.1
version=2.7.2
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}

110
tools/singularity/rocky8.def Normal file
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@ -0,0 +1,110 @@
BootStrap: docker
From: rockylinux/rockylinux:8
%post
dnf -y install epel-release dnf-utils
dnf config-manager --set-enabled powertools
dnf -y update
dnf -y install vim-enhanced git file make cmake patch which file ninja-build \
ccache gcc-c++ gcc-gfortran clang libomp-devel gdb valgrind libubsan libasan libtsan \
eigen3-devel openblas-devel libpng-devel libjpeg-devel platform-python-devel \
openmpi-devel mpich-devel fftw-devel voro++-devel gsl-devel hdf5-devel \
netcdf-devel netcdf-cxx-devel netcdf-mpich-devel netcdf-openmpi-devel \
enchant python3-virtualenv doxygen diffutils latexmk readline-devel \
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 libyaml-devel openkim-models kim-api-devel \
zstd libzstd-devel
dnf clean 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
# manually install Plumed
mkdir plumed
cd plumed
version=2.7.2
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-${version}
./configure --disable-doc --prefix=/usr
make
make install
# fix up installation for CentOS and Fedora
mv -v /usr/lib64/pkgconfig/plumed* /usr/share/pkgconfig/
cd ../../
rm -rvf plumed
# create missing readline pkgconfig file
cat > /usr/lib64/pkgconfig/readline.pc <<EOF
prefix=/usr
exec_prefix=/usr
libdir=/usr/lib64
includedir=/usr/include
Name: Readline
Description: GNU Readline library for command line editing
URL: http://tiswww.cwru.edu/php/chet/readline/rltop.html
Version: 7.0
Requires.private: ncurses
Libs: -L\${libdir} -lreadline
Cflags: -I\${includedir}/readline
EOF
# set custom prompt indicating the container name
CUSTOM_PROMPT_ENV=/.singularity.d/env/99-zz_custom_prompt.sh
cat >$CUSTOM_PROMPT_ENV <<EOF
#!/bin/bash
PS1="[centos8:\u@\h] \W> "
EOF
chmod 755 $CUSTOM_PROMPT_ENV
%environment
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
# 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 akohlmey, rbberger

2
tools/singularity/ubuntu18.04.def
View File

@ -105,7 +105,7 @@ From: ubuntu:18.04
# Plumed
###########################################################################
export PLUMED_PKG_VERSION=2.6.1
export PLUMED_PKG_VERSION=2.7.2
mkdir plumed
cd plumed

6
tools/singularity/ubuntu18.04_amd_rocm.def
View File

@ -3,7 +3,7 @@ From: ubuntu:18.04
%environment
export PATH=/usr/lib/ccache:${PATH}:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/rocm/lib:/opt/rocm-4.3.0/llvm/lib
%post
export DEBIAN_FRONTEND=noninteractive
apt-get update
@ -94,7 +94,7 @@ From: ubuntu:18.04
###########################################################################
export PATH=$PATH:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64
git clone -b rocm-4.1.x https://github.com/ROCmSoftwarePlatform/hipCUB.git
git clone -b release/rocm-rel-4.3 https://github.com/ROCmSoftwarePlatform/hipCUB.git
mkdir hipCUB/build
cd hipCUB/build
CXX=hipcc cmake -D BUILD_TEST=off ..
@ -129,7 +129,7 @@ From: ubuntu:18.04
# Plumed
###########################################################################
export PLUMED_PKG_VERSION=2.6.1
export PLUMED_PKG_VERSION=2.7.2
mkdir plumed
cd plumed

34
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-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
export PATH=/usr/lib/ccache:/usr/local/cuda-11.4/bin:${PATH}:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64
export CUDADIR=/usr/local/cuda-11.4
export CUDA_PATH=/usr/local/cuda-11.4
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/cuda-11.4/lib64:/opt/rocm/lib:/opt/rocm-4.3.0/llvm/lib
export LIBRARY_PATH=/usr/local/cuda-11.4/lib64/stubs
%post
export DEBIAN_FRONTEND=noninteractive
apt-get update
@ -104,23 +104,19 @@ 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=11.0
export CUDA_PKG_VERSION=11.4
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-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-$CUDA_PKG_VERSION \
libcublas-11-0 \
libcublas-dev-11-0
echo "/usr/local/nvidia/lib" >> /etc/ld.so.conf.d/nvidia.conf
echo "/usr/local/nvidia/lib64" >> /etc/ld.so.conf.d/nvidia.conf
libcublas-${CUDA_PKG_VERSION} \
libcublas-dev-${CUDA_PKG_VERSION}
# add missing symlink
ln -s /usr/local/cuda-11.0 /usr/local/cuda
ln -s /usr/local/cuda-11.0/lib64/stubs/libcuda.so /usr/local/cuda-11.0/lib64/stubs/libcuda.so.1
ln -s /usr/local/cuda-${CUDA_PKG_VERSION}/lib64/stubs/libcuda.so /usr/local/cuda-${CUDA_PKG_VERSION}/lib64/stubs/libcuda.so.1
###########################################################################
# NVIDIA OpenCL
@ -134,7 +130,7 @@ From: ubuntu:18.04
###########################################################################
export PATH=$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
git clone -b release/rocm-rel-4.3 https://github.com/ROCmSoftwarePlatform/hipCUB.git
mkdir hipCUB/build
cd hipCUB/build
CXX=hipcc cmake -D BUILD_TEST=off ..
@ -169,7 +165,7 @@ From: ubuntu:18.04
# Plumed
###########################################################################
export PLUMED_PKG_VERSION=2.6.1
export PLUMED_PKG_VERSION=2.7.2
mkdir plumed
cd plumed

2
tools/singularity/ubuntu18.04_intel_opencl.def
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@ -106,7 +106,7 @@ From: ubuntu:18.04
# Plumed
###########################################################################
export PLUMED_PKG_VERSION=2.6.1
export PLUMED_PKG_VERSION=2.7.2
mkdir plumed
cd plumed

4
tools/singularity/ubuntu18.04_nvidia.def
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@ -1,5 +1,5 @@
BootStrap: docker
From: nvidia/cuda:11.0-devel-ubuntu18.04
From: nvidia/cuda:11.4.1-devel-ubuntu18.04
%post
export DEBIAN_FRONTEND=noninteractive
@ -105,7 +105,7 @@ From: nvidia/cuda:11.0-devel-ubuntu18.04
# Plumed
###########################################################################
export PLUMED_PKG_VERSION=2.6.1
export PLUMED_PKG_VERSION=2.7.2
mkdir plumed
cd plumed

2
tools/singularity/ubuntu20.04.def
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@ -100,7 +100,7 @@ From: ubuntu:20.04
# Plumed
###########################################################################
export PLUMED_PKG_VERSION=2.6.1
export PLUMED_PKG_VERSION=2.7.2
mkdir plumed
cd plumed

6
tools/singularity/ubuntu20.04_amd_rocm.def
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@ -3,7 +3,7 @@ From: ubuntu:20.04
%environment
export PATH=/usr/lib/ccache:${PATH}:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/rocm/lib:/opt/rocm-4.2.0/llvm/lib
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/rocm/lib:/opt/rocm-4.3.0/llvm/lib
%post
export DEBIAN_FRONTEND=noninteractive
apt-get update
@ -91,7 +91,7 @@ From: ubuntu:20.04
###########################################################################
export PATH=$PATH:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64
git clone -b rocm-4.1.x https://github.com/ROCmSoftwarePlatform/hipCUB.git
git clone -b release/rocm-rel-4.3 https://github.com/ROCmSoftwarePlatform/hipCUB.git
mkdir hipCUB/build
cd hipCUB/build
CXX=hipcc cmake -D BUILD_TEST=off ..
@ -126,7 +126,7 @@ From: ubuntu:20.04
# Plumed
###########################################################################
export PLUMED_PKG_VERSION=2.6.1
export PLUMED_PKG_VERSION=2.7.2
mkdir plumed
cd plumed

34
tools/singularity/ubuntu20.04_gpu.def
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@ -2,11 +2,11 @@ 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:/opt/rocm/lib:/opt/rocm-4.2.0/llvm/lib
export LIBRARY_PATH=/usr/local/cuda-11.0/lib64/stubs
export PATH=/usr/lib/ccache:/usr/local/cuda-11.4/bin:${PATH}:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64
export CUDADIR=/usr/local/cuda-11.4
export CUDA_PATH=/usr/local/cuda-11.4
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/cuda-11.4/lib64:/opt/rocm/lib:/opt/rocm-4.3.0/llvm/lib
export LIBRARY_PATH=/usr/local/cuda-11.4/lib64/stubs
%post
export DEBIAN_FRONTEND=noninteractive
apt-get update
@ -101,23 +101,19 @@ From: ubuntu:20.04
add-apt-repository "deb http://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/ /"
apt-get update
export CUDA_PKG_VERSION=11.0
export CUDA_PKG_VERSION=11.4
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-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-$CUDA_PKG_VERSION \
libcublas-11-0 \
libcublas-dev-11-0
echo "/usr/local/nvidia/lib" >> /etc/ld.so.conf.d/nvidia.conf
echo "/usr/local/nvidia/lib64" >> /etc/ld.so.conf.d/nvidia.conf
libcublas-${CUDA_PKG_VERSION} \
libcublas-dev-${CUDA_PKG_VERSION}
# add missing symlink
ln -s /usr/local/cuda-11.0 /usr/local/cuda
ln -s /usr/local/cuda-11.0/lib64/stubs/libcuda.so /usr/local/cuda-11.0/lib64/stubs/libcuda.so.1
ln -s /usr/local/cuda-${CUDA_PKG_VERSION}/lib64/stubs/libcuda.so /usr/local/cuda-${CUDA_PKG_VERSION}/lib64/stubs/libcuda.so.1
###########################################################################
# NVIDIA OpenCL
@ -131,7 +127,7 @@ From: ubuntu:20.04
###########################################################################
export PATH=$PATH:/opt/rocm/bin:/opt/rocm/profiler/bin:/opt/rocm/opencl/bin/x86_64
git clone -b rocm-4.2.x https://github.com/ROCmSoftwarePlatform/hipCUB.git
git clone -b release/rocm-rel-4.3 https://github.com/ROCmSoftwarePlatform/hipCUB.git
mkdir hipCUB/build
cd hipCUB/build
CXX=hipcc cmake -D BUILD_TEST=off ..
@ -166,7 +162,7 @@ From: ubuntu:20.04
# Plumed
###########################################################################
export PLUMED_PKG_VERSION=2.6.1
export PLUMED_PKG_VERSION=2.7.2
mkdir plumed
cd plumed

2
tools/singularity/ubuntu20.04_intel_opencl.def
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@ -99,7 +99,7 @@ From: ubuntu:20.04
# Plumed
###########################################################################
export PLUMED_PKG_VERSION=2.6.1
export PLUMED_PKG_VERSION=2.7.2
mkdir plumed
cd plumed

4
tools/singularity/ubuntu20.04_nvidia.def
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@ -1,5 +1,5 @@
BootStrap: docker
From: nvidia/cuda:11.0-devel-ubuntu20.04
From: nvidia/cuda:11.4.1-devel-ubuntu20.04
%post
export DEBIAN_FRONTEND=noninteractive
@ -102,7 +102,7 @@ From: nvidia/cuda:11.0-devel-ubuntu20.04
# Plumed
###########################################################################
export PLUMED_PKG_VERSION=2.6.1
export PLUMED_PKG_VERSION=2.7.2
mkdir plumed
cd plumed