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Commit f5d8ba5a authored by Michael Blaschek's avatar Michael Blaschek :bicyclist:
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added singularity imgw scripts, updated base

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definition-files/almalinux/Singularity.base 0 → 100644
+ 23
− 0
View file @ f5d8ba5a
Bootstrap: docker
From: almalinux:8
%labels
maintainer IT-IMGW <it.img-wien@univie.ac.at>
%files
$PWD/definition-files/runscript /.singularity.d/runscript
$PWD/definition-files/run-help /.singularity.d/runscript.help
%post
# command prompt name
CNAME=alma8.base
# does not work goes into /.singularity.d/env/91-environment.sh
echo "export PS1=\"[IMGW-$CNAME]\w\$ \"" >> /.singularity.d/env/99-zz-custom-env.sh
# add some labels
echo "libc $(ldd --version | head -n1 | cut -d' ' -f4)" >> "$SINGULARITY_LABELS"
echo "linux $(cat /etc/os-release | grep PRETTY_NAME | cut -d'=' -f2)" >> "$SINGULARITY_LABELS"
%environment
export LANG=C.UTF-8
export LIBRARY=/usr/lib64:/lib64:/lib
export INCLUDE=/usr/include
\ No newline at end of file
definition-files/almalinux/Singularity.met 0 → 100644
+ 55
− 0
View file @ f5d8ba5a
Bootstrap: docker
From: almalinux:8
%labels
maintainer IT-IMGW <it.img-wien@univie.ac.at>
%files
$PWD/definition-files/runscript /.singularity.d/runscript
$PWD/definition-files/run-help /.singularity.d/runscript.help
%post
# Every line will be a layer in the container
# See https://fedoraproject.org/wiki/EPEL#Quickstart for powertools
yum update -y \
&& yum install -y dnf-plugins-core \
&& dnf config-manager --set-enabled powertools \
&& yum install -y epel-release \
&& yum update -y \
&& yum --enablerepo epel groupinstall -y "Development Tools" \
&& yum --enablerepo epel install -y \
curl \
findutils \
gcc-c++ \
gcc \
gcc-gfortran \
git \
gnupg2 \
hostname \
iproute \
make \
patch \
python38 \
python38-pip \
python38-setuptools \
unzip \
nco \
hdf5-devel \
netcdf-devel \
netcdf-fortran-devel \
python38-numpy-f2py \
&& rm -rf /var/cache/yum \
&& yum clean all
# This means no openmpi
# command prompt name
CNAME=alma8.met
# does not work goes into /.singularity.d/env/91-environment.sh
echo "export PS1=\"[IMGW-$CNAME]\w\$ \"" >> /.singularity.d/env/99-zz-custom-env.sh
# add some labels
echo "libc $(ldd --version | head -n1 | cut -d' ' -f4)" >> "$SINGULARITY_LABELS"
echo "linux $(cat /etc/os-release | grep PRETTY_NAME | cut -d'=' -f2)" >> "$SINGULARITY_LABELS"
%environment
export LIBRARY=/usr/lib64:/lib64:/lib
export INCLUDE=/usr/lib64/gfortran/modules:/usr/include
definition-files/almalinux/Singularity.met.ompi 0 → 100644
+ 55
− 0
View file @ f5d8ba5a
Bootstrap: docker
From: almalinux:8
%labels
maintainer IT-IMGW <it.img-wien@univie.ac.at>
%files
$PWD/definition-files/runscript /.singularity.d/runscript
$PWD/definition-files/run-help /.singularity.d/runscript.help
%post
# Every line will be a layer in the container
# See https://fedoraproject.org/wiki/EPEL#Quickstart for powertools
yum update -y \
&& yum install -y dnf-plugins-core \
&& dnf config-manager --set-enabled powertools \
&& yum install -y epel-release \
&& yum update -y \
&& yum --enablerepo epel groupinstall -y "Development Tools" \
&& yum --enablerepo epel install -y \
curl \
findutils \
gcc-c++ \
gcc \
gcc-gfortran \
git \
gnupg2 \
hostname \
iproute \
make \
patch \
python38 \
python38-pip \
python38-setuptools \
unzip \
nco \
hdf5-openmpi-devel \
netcdf-openmpi-devel \
netcdf-fortran-openmpi-devel \
python38-numpy-f2py \
&& rm -rf /var/cache/yum \
&& yum clean all
# This means no openmpi
# command prompt name
CNAME=alma8.metompi
# does not work goes into /.singularity.d/env/91-environment.sh
echo "export PS1=\"[IMGW-$CNAME]\w\$ \"" >> /.singularity.d/env/99-zz-custom-env.sh
# add some labels
echo "libc $(ldd --version | head -n1 | cut -d' ' -f4)" >> "$SINGULARITY_LABELS"
echo "linux $(cat /etc/os-release | grep PRETTY_NAME | cut -d'=' -f2)" >> "$SINGULARITY_LABELS"
%environment
export LIBRARY=/usr/lib64:/lib64:/lib
export INCLUDE=/usr/lib64/gfortran/modules:/usr/include
definition-files/almalinux/Singularity-alma8-spack → definition-files/almalinux/Singularity.spack
+ 6
− 0
View file @ f5d8ba5a
Bootstrap: docker
From: almalinux:8
#
# This is a spack development image to use for downstream development
# to be combined with the base image for two stage builds
#
%labels
MAINTAINER Spack Maintainers <maintainers@spack.io>
......@@ -68,6 +73,7 @@ From: almalinux:8
export DEBIAN_FRONTEND=noninteractive
%runscript
# Need spack entry point to allow spack builds
exec /bin/bash /opt/spack/share/spack/docker/entrypoint.bash interactive-shell "$@"
%startscript
......
definition-files/alpine/Singularity.met 0 → 100644
+ 34
− 0
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Bootstrap: docker
From: alpine
%labels
MAINTAINER Michael Blaschek <michael.blaschek@univie.ac.at>
%files
$PWD/definition-files/runscript /.singularity.d/runscript
$PWD/definition-files/run-help /.singularity.d/runscript.help
%post
apk add --no-cache build-base \
curl \
gcc \
gcc-gfortran \
make \
cdo \
nco \
hdf5-dev \
hdf5-fortran \
netcdf-dev \
netcdf-fortran
# command prompt name
CNAME=u18.04.base
# does not work goes into /.singularity.d/env/91-environment.sh
echo "export PS1=\"[IMGW-$CNAME]\w\$ \"" >> /.singularity.d/env/99-zz-custom-env.sh
# add some labels
echo "libc $(ldd --version | head -n1 | cut -d' ' -f4)" >> "$SINGULARITY_LABELS"
echo "linux $(cat /etc/os-release | grep PRETTY_NAME | cut -d'=' -f2)" >> "$SINGULARITY_LABELS"
%environment
export LANG=C.UTF-8
export LIBRARY=/usr/lib64:/lib64:/lib
export INCLUDE=/usr/include
\ No newline at end of file
definition-files/micromamba/Singularity.conda-py39-dev-debian deleted 100644 → 0
+ 0
− 26
View file @ 1d65e712
Bootstrap: docker
From: mambaorg/micromamba:latest
%help
Micromamba conda environment with
Python 3.9.13 and the latest eccodes (binary+py)
https://pypi.org/project/eccodes/
%labels
maintainer M. Blaschek
mail michael.blaschek@univie.ac.at
date 7.10.2022
python 3.9.13
eccodes 2.27.0
gcc 9.5.0
gfortran 9.5.0
%post
micromamba -q install -y -n base -c conda-forge eccodes=2.27.0 cdo nco netcdf4 hdf5 openmpi=4.0.5 gcc=9.5.0 gfortran=9.5.0 python=3.9.13 &&
/opt/conda/bin/pip install eccodes && /opt/conda/bin/pip cache purge &&
micromamba clean --all --yes
%environment
LIBRARY=/opt/conda/lib
INCLUDE=/opt/conda/include
BIN=/opt/conda/bin
SHARE=/opt/conda/share
%test
/opt/conda/bin/python3 -m eccodes selfcheck
definition-files/micromamba/Singularity.py39.dart 0 → 100644
+ 53
− 0
View file @ f5d8ba5a
Bootstrap: docker
From: mambaorg/micromamba:latest
%labels
maintainer IT-IMGW <it.img-wien@univie.ac.at>
%files
$PWD/definition-files/runscript /.singularity.d/runscript
$PWD/definition-files/run-help /.singularity.d/runscript.help
%post
apt -y update && apt -y install \
build-essential \
git \
tcsh \
csh \
ksh \
m4 \
libtool \
automake \
autoconf \
&& apt -y clean
micromamba -q install -y -n base -c conda-forge \
eccodes=2.27.0 \
cdo \
nco \
netcdf4 \
hdf5 \
openmpi=4.0.5 \
gcc=9.5.0 \
gfortran=9.5.0 \
python=3.9.13 &&
/opt/conda/bin/pip install eccodes && /opt/conda/bin/pip cache purge &&
micromamba clean --all --yes
# command prompt name
CNAME=m.dart
# does not work goes into /.singularity.d/env/91-environment.sh
echo "export PS1=\"[IMGW-$CNAME]\w\$ \"" >> /.singularity.d/env/99-zz-custom-env.sh
# add some labels
echo "libc $(ldd --version | head -n1 | cut -d' ' -f4)" >> "$SINGULARITY_LABELS"
echo "linux $(cat /etc/os-release | grep PRETTY_NAME | cut -d'=' -f2)" >> "$SINGULARITY_LABELS"
%test
python -m eccodes selfcheck
gfortran --version
gcc --version
ncks --version
cdo --version
%environment
export PATH=/opt/conda/bin:$PATH
export LIBRARY=/opt/conda/lib:/usr/lib64:/lib64:/lib
export INCLUDE=/opt/conda/include:/usr/include
definition-files/micromamba/Singularity.conda-py39-eccodes-debian → definition-files/micromamba/Singularity.py39.eccodes
+ 31
− 0
View file @ f5d8ba5a
Bootstrap: docker
From: mambaorg/micromamba:latest
%help
Micromamba conda environment with
Python 3.9.13 and the latest eccodes (binary+py)
https://pypi.org/project/eccodes/
%labels
maintainer M. Blaschek
mail michael.blaschek@univie.ac.at
date 7.10.2022
maintainer IT-IMGW <it.img-wien@univie.ac.at>
python 3.9.13
eccodes 2.27.0
%files
$PWD/definition-files/runscript /.singularity.d/runscript
$PWD/definition-files/run-help /.singularity.d/runscript.help
%post
micromamba -q install -y -n base -c conda-forge eccodes=2.27.0 python=3.9.13 &&
/opt/conda/bin/pip install eccodes && /opt/conda/bin/pip cache purge &&
micromamba clean --all --yes
# command prompt name
CNAME=m.eccodes
# does not work goes into /.singularity.d/env/91-environment.sh
echo "export PS1=\"[IMGW-$CNAME]\w\$ \"" >> /.singularity.d/env/99-zz-custom-env.sh
# add some labels
echo "libc $(ldd --version | head -n1 | cut -d' ' -f4)" >> "$SINGULARITY_LABELS"
echo "linux $(cat /etc/os-release | grep PRETTY_NAME | cut -d'=' -f2)" >> "$SINGULARITY_LABELS"
%test
python -m eccodes selfcheck
%environment
export PATH=/opt/conda/bin:$PATH
export LIBRARY=/opt/conda/lib
export INCLUDE=/opt/conda/include
\ No newline at end of file
definition-files/micromamba/Singularity.py39.metdev 0 → 100644
+ 78
− 0
View file @ f5d8ba5a
Bootstrap: docker
From: mambaorg/micromamba:latest
%labels
maintainer IT-IMGW <it.img-wien@univie.ac.at>
%files
$PWD/definition-files/runscript /.singularity.d/runscript
$PWD/definition-files/run-help /.singularity.d/runscript.help
%apprun install-ipykernel
# install current container as kernel
mkdir -p $HOME/.local/share/jupyter/kernels/metdev-py3
cat <<EOF >$HOME/.local/share/jupyter/kernels/metdev-py3/kernel.json
{
"language": "python",
"argv": ["singularity",
"exec",
"$SINGULARITY_CONTAINER",
"/opt/conda/bin/python3",
"-m",
"ipykernel",
"-f",
"{connection_file}"
],
"display_name": "sPy 3 (metdev)"
}
EOF
echo "Kernel written: $HOME/.local/share/jupyter/kernels/metdev-py3"
%post
micromamba -q install -y -n base -c conda-forge \
python=3.9.13 \
eccodes=2.27.0 \
ipykernel \
nco \
cdo \
pandas \
xarray \
dask \
numba \
scipy \
netcdf4 \
h5py \
hdf5 \
distributed \
proj \
h5netcdf \
matplotlib \
zarr \
metpy \
cartopy \
&& /opt/conda/bin/pip install eccodes && /opt/conda/bin/pip cache purge &&
micromamba clean --all --yes
# command prompt name
CNAME=m.metdev
# does not work goes into /.singularity.d/env/91-environment.sh
echo "export PS1=\"[IMGW-$CNAME]\w\$ \"" >> /.singularity.d/env/99-zz-custom-env.sh
# add some labels
echo "libc $(ldd --version | head -n1 | cut -d' ' -f4)" >> "$SINGULARITY_LABELS"
echo "linux $(cat /etc/os-release | grep PRETTY_NAME | cut -d'=' -f2)" >> "$SINGULARITY_LABELS"
# add App help information
echo -e "Apps: \n- install-ipykernel Install IPython Kernel to local user\n" >> /.singularity.d/runscript.help
%test
# Check eccodes lib functionality
python -m eccodes selfcheck
# Check cartopy
# Check netcdf
# Check hdf5
%environment
export LANG=C.UTF-8
export PATH=/opt/conda/bin:$PATH
export LIBRARY=/opt/conda/lib
export INCLUDE=/opt/conda/include
\ No newline at end of file
definition-files/run-help 0 → 100644
+ 20
− 0
View file @ f5d8ba5a
Singularity/Apptainer container
(c) Department of Meteorology and Geophysics
University of Vienna
interactive shell
> singularity shell image.sif
> ./image.sif
run a command inside the container
> ./image.sif [cmd] [args]
bind special directories
> export SINGULARITY_BIND=/this/is/not/a/typical/linux/path
> ./image.sif ls /this/is/not/a/typical/linux/path
development using includes and libraries from inside the container
> ./image.sif gfortran -I\$INCLUDE -L\$LIBRARY -o test.x test.f90
Ask for help: it.img-wien@univie.ac.at
Gitlab: https://gitlab.phaidra.org/imgw/singularity
definition-files/runscript 0 → 100644
+ 12
− 0
View file @ f5d8ba5a
#!/bin/sh
# overwrite any existing runscript
# add IMGW customized PROMPT_COMMAND
if [ $# -gt 0 ]; then
# run cmd line options
exec "$@"
else
# interactive
echo "Welcome inside an IMGW container!"
echo "Get help: singularity run-help $SINGULARITY_NAME"
exec /.singularity.d/actions/shell "$@"
fi
\ No newline at end of file
definition-files/ubuntu/Singularity.ubuntu-18.04 → definition-files/ubuntu/Singularity.18.04.base
+ 16
− 19
View file @ f5d8ba5a
......@@ -3,20 +3,9 @@ MirrorURL: http://at.archive.ubuntu.com/ubuntu
OSVersion: bionic
%labels
APPLICATION_NAME ubuntu
APPLICATION_VERSION 18.04
APPLICATION_URL https://www.ubuntu.com
AUTHOR_NAME Michael Blaschek
AUTHOR_EMAIL michael.blaschek@univie.ac.at
LAST_UPDATED 20211118
%setup
maintainer IT-IMGW <it.img-wien@univie.ac.at>
%environment
# Set operating system mirror URL
export MIRRORURL='http://at.archive.ubuntu.com/ubuntu'
......@@ -24,7 +13,8 @@ OSVersion: bionic
export OSVERSION='bionic'
# Set system locale
export LC_ALL='C'
#export LC_ALL='C'
export LANG=C.UTF-8
# Set debian frontend interface
export DEBIAN_FRONTEND='noninteractive'
......@@ -38,7 +28,8 @@ OSVersion: bionic
export OSVERSION='bionic'
# Set system locale
export LC_ALL=C
# export LC_ALL=C
export LANG=C.UTF-8
# Set debian frontend interface
export DEBIAN_FRONTEND='noninteractive'
......@@ -91,9 +82,15 @@ OSVersion: bionic
# Update database for mlocate
updatedb
# command prompt name
CNAME=u18.04.base
# does not work goes into /.singularity.d/env/91-environment.sh
echo "export PS1=\"[IMGW-$CNAME]\w\$ \"" >> /.singularity.d/env/99-zz-custom-env.sh
# add some labels
echo "libc $(ldd --version | head -n1 | cut -d' ' -f4)" >> "$SINGULARITY_LABELS"
echo "linux $(cat /etc/os-release | grep PRETTY_NAME | cut -d'=' -f2)" >> "$SINGULARITY_LABELS"
%files
%runscript
%test
%environment
export LANG=C.UTF-8
export LIBRARY=/usr/lib64:/lib64:/lib
export INCLUDE=/usr/include
\ No newline at end of file
definition-files/ubuntu/Singularity.ubuntu-20.04 → definition-files/ubuntu/Singularity.20.04.base
+ 17
− 17
View file @ f5d8ba5a
......@@ -2,18 +2,10 @@ Bootstrap: debootstrap
MirrorURL: http://at.archive.ubuntu.com/ubuntu
OSVersion: focal
%labels
APPLICATION_NAME ubuntu
APPLICATION_VERSION 20.04
APPLICATION_URL https://www.ubuntu.com
AUTHOR_NAME Michael Blaschek
AUTHOR_EMAIL michael.blaschek@univie.ac.at
LAST_UPDATED 20211118
%labels
maintainer IT-IMGW <it.img-wien@univie.ac.at>
%setup
%environment
......@@ -24,7 +16,8 @@ OSVersion: focal
export OSVERSION='focal'
# Set system locale
export LC_ALL='C'
#export LC_ALL='C'
export LANG=C.UTF-8
# Set debian frontend interface
export DEBIAN_FRONTEND='noninteractive'
......@@ -38,7 +31,8 @@ OSVersion: focal
export OSVERSION='focal'
# Set system locale
export LC_ALL=C
#export LC_ALL=C
export LANG=C.UTF-8
# Set debian frontend interface
export DEBIAN_FRONTEND='noninteractive'
......@@ -91,9 +85,15 @@ OSVersion: focal
# Update database for mlocate
updatedb
# command prompt name
CNAME=u20.04.base
# does not work goes into /.singularity.d/env/91-environment.sh
echo "export PS1=\"[IMGW-$CNAME]\w\$ \"" >> /.singularity.d/env/99-zz-custom-env.sh
# add some labels
echo "libc $(ldd --version | head -n1 | cut -d' ' -f4)" >> "$SINGULARITY_LABELS"
echo "linux $(cat /etc/os-release | grep PRETTY_NAME | cut -d'=' -f2)" >> "$SINGULARITY_LABELS"
%files
%runscript
%test
%environment
export LANG=C.UTF-8
export LIBRARY=/usr/lib64:/lib64:/lib
export INCLUDE=/usr/include
\ No newline at end of file
definition-files/ubuntu/Singularity.ompi 0 → 100644
+ 66
− 0
View file @ f5d8ba5a
Bootstrap: docker
From: ubuntu:18.04
%labels
maintainer IT-IMGW <it.img-wien@univie.ac.at>
%environment
# Point to OMPI binaries, libraries, man pages
export OMPI_DIR=/opt/ompi
export PATH="$OMPI_DIR/bin:$PATH"
export LD_LIBRARY_PATH="$OMPI_DIR/lib:$LD_LIBRARY_PATH"
export MANPATH="$OMPI_DIR/share/man:$MANPATH"
export LANG=C.UTF-8
%post
echo "Installing required packages..."
apt-get update && apt-get install -y wget git bash gcc gfortran g++ make file
echo "Installing Open MPI"
export OMPI_DIR=/opt/ompi
export OMPI_VERSION=4.0.5
export OMPI_URL="https://download.open-mpi.org/release/open-mpi/v4.0/openmpi-$OMPI_VERSION.tar.bz2"
mkdir -p /tmp/ompi
mkdir -p /opt
# Download
cd /tmp/ompi && wget -O openmpi-$OMPI_VERSION.tar.bz2 $OMPI_URL && tar -xjf openmpi-$OMPI_VERSION.tar.bz2
# Compile and install
cd /tmp/ompi/openmpi-$OMPI_VERSION && ./configure --prefix=$OMPI_DIR && make -j8 install
# Set env variables so we can compile our application
export PATH=$OMPI_DIR/bin:$PATH
export LD_LIBRARY_PATH=$OMPI_DIR/lib:$LD_LIBRARY_PATH
echo "Compiling the MPI application..."
cat<<EOF>/opt/mpitest.c
/*
* Usage:
* mpicc mpitest.c -o mpitest
* mpirun -np 2 -H `hostname` ./mpitest
*/
#include <stdio.h>
#include <mpi.h>
int main(int argc, char *argv[])
{
int rank, size, h_len;
char hostname[MPI_MAX_PROCESSOR_NAME];
MPI_Init(&argc, &argv);
// get rank of this proces
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
// get total process number
MPI_Comm_size(MPI_COMM_WORLD, &size);
MPI_Get_processor_name(hostname, &h_len);
printf("Start! rank:%d size: %d at %s\n", rank, size,hostname);
//do something
printf("Done! rank:%d size: %d at %s\n", rank, size,hostname);
MPI_Finalize();
return 0;
}
EOF
cd /opt && mpicc -o mpitest mpitest.c
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