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Merge branch 'master' into feature-cnt

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This commit is contained in:
Axel Kohlmeyer
2020-06-12 05:53:17 -04:00
parent 0bc1c3b2a2 22ed175632
commit cf5c748fb4
572 changed files with 83637 additions and 10156 deletions
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38
tools/singularity/centos7.def
View File

@ -11,9 +11,43 @@ 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
blas-devel lapack-devel libyaml-devel openkim-models kim-api-devel
yum 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=2.6.0
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-${version}
./configure --disable-doc --prefix=/usr
make
make install
# fix up installation for CentOS and Fedora
mv -v /usr/lib/pkgconfig/plumed* /usr/share/pkgconfig/
cd ../../
rm -rvf plumed
# set custom prompt indicating the container name
CUSTOM_PROMPT_ENV=/.singularity.d/env/99-zz_custom_prompt.sh
cat >$CUSTOM_PROMPT_ENV <<EOF
@ -46,7 +80,7 @@ EOF
. /etc/profile
module load mpi
# restrict OpenMPI to shared memory comm by default
OMPI_MCA_btl="sm,self"
OMPI_MCA_btl="tcp,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

38
tools/singularity/centos8.def
View File

@ -16,9 +16,43 @@ 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
blas-devel lapack-devel libyaml-devel openkim-models kim-api-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=2.6.0
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-${version}
./configure --disable-doc --prefix=/usr
make
make install
# fix up installation for CentOS and Fedora
mv -v /usr/lib64/pkgconfig/plumed* /usr/share/pkgconfig/
cd ../../
rm -rvf plumed
# set custom prompt indicating the container name
CUSTOM_PROMPT_ENV=/.singularity.d/env/99-zz_custom_prompt.sh
cat >$CUSTOM_PROMPT_ENV <<EOF
@ -51,7 +85,7 @@ EOF
. /etc/profile
module load mpi
# restrict OpenMPI to shared memory comm by default
OMPI_MCA_btl="sm,self"
OMPI_MCA_btl="tcp,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

24
tools/singularity/fedora32_mingw.def
View File

@ -35,9 +35,29 @@ 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
blas-devel lapack-devel libyaml-devel openkim-models kim-api-devel
dnf clean all
# enable Lmod and load MPI
source /usr/share/lmod/lmod/init/profile
module purge
module load mpi
# 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-${version}
./configure --disable-doc --prefix=/usr
make
make install
# fix up installation for CentOS and Fedora
mv -v /usr/lib64/pkgconfig/plumed* /usr/share/pkgconfig/
cd ../../
rm -rvf plumed
# set custom prompt indicating the container name
CUSTOM_PROMPT_ENV=/.singularity.d/env/99-zz_custom_prompt.sh
cat >$CUSTOM_PROMPT_ENV <<EOF
@ -66,7 +86,7 @@ EOF
. /etc/profile
module load mpi
# restrict OpenMPI to shared memory comm by default
OMPI_MCA_btl="sm,self"
OMPI_MCA_btl="tcp,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

2
tools/singularity/ubuntu16.04.def
View File

@ -29,7 +29,7 @@ EOF
LC_ALL=C
export LC_ALL
# restrict OpenMPI to shared memory comm by default
OMPI_MCA_btl="sm,self"
OMPI_MCA_btl="tcp,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

24
tools/singularity/ubuntu18.04.def
View File

@ -4,6 +4,9 @@ From: ubuntu:18.04
%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 \
@ -66,11 +69,28 @@ From: ubuntu:18.04
wget \
xxd \
valgrind \
gdb
gdb \
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-${version}
./configure --disable-doc --prefix=/usr
make
make install
# fix up installation for CentOS and Fedora
# mv -v /usr/lib/pkgconfig/plumed* /usr/share/pkgconfig/
cd ../../
rm -rvf plumed
# set custom prompt indicating the container name
CUSTOM_PROMPT_ENV=/.singularity.d/env/99-zz_custom_prompt.sh
cat >$CUSTOM_PROMPT_ENV <<EOF
@ -84,7 +104,7 @@ EOF
export LC_ALL
export PATH=/usr/lib/ccache:$PATH
# restrict OpenMPI to shared memory comm by default
OMPI_MCA_btl="sm,self"
OMPI_MCA_btl="tcp,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

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

@ -90,7 +90,7 @@ EOF
LC_ALL=C
export LC_ALL
# restrict OpenMPI to shared memory comm by default
OMPI_MCA_btl="sm,self"
OMPI_MCA_btl="tcp,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

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

@ -117,7 +117,7 @@ EOF
LC_ALL=C
export LC_ALL
# restrict OpenMPI to shared memory comm by default
OMPI_MCA_btl="sm,self"
OMPI_MCA_btl="tcp,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

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

@ -83,7 +83,7 @@ EOF
LC_ALL=C
export LC_ALL
# restrict OpenMPI to shared memory comm by default
OMPI_MCA_btl="sm,self"
OMPI_MCA_btl="tcp,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

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

@ -82,7 +82,7 @@ EOF
LC_ALL=C
export LC_ALL
# restrict OpenMPI to shared memory comm by default
OMPI_MCA_btl="sm,self"
OMPI_MCA_btl="tcp,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

26
tools/singularity/ubuntu20.04.def
View File

@ -4,6 +4,9 @@ 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 \
@ -62,11 +65,28 @@ From: ubuntu:20.04
wget \
xxd \
valgrind \
gdb
gdb \
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-${version}
./configure --disable-doc --prefix=/usr
make
make install
# fix up installation for CentOS and Fedora
# mv -v /usr/lib/pkgconfig/plumed* /usr/share/pkgconfig/
cd ../../
rm -rvf plumed
# set custom prompt indicating the container name
CUSTOM_PROMPT_ENV=/.singularity.d/env/99-zz_custom_prompt.sh
cat >$CUSTOM_PROMPT_ENV <<EOF
@ -75,12 +95,12 @@ PS1="[ubuntu20.04:\u@\h] \W> "
EOF
chmod 755 $CUSTOM_PROMPT_ENV
%environment
LC_ALL=C
export LC_ALL
export PATH=/usr/lib/ccache:$PATH
# restrict OpenMPI to shared memory comm by default
OMPI_MCA_btl="sm,self"
OMPI_MCA_btl="tcp,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