diff --git a/Dockerfile b/Dockerfile
index 695da712b1e6cff0a2fc341c92386a64797b4a83..08eaebb625f4c4dd4f6d9fe6b61bf07009c47b1a 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -18,7 +18,7 @@ FROM golang:1.20.0-alpine as builder
# along with this program. If not, see <https://www.gnu.org/licenses/>.
#
################################################################################
-
+# based on: https://github.com/singularityhub/singularity-docker/blob/v3.11.4-slim/Dockerfile
# alpine image with the go tools
RUN apk update && \
diff --git a/development/README.md b/development/README.md
index 22166f137d8ea8151ec804f95c52699ec744a62b..35a74b68f40ef5f3416b25b5f76f86b656ed76ae 100644
--- a/development/README.md
+++ b/development/README.md
@@ -4,7 +4,7 @@ We are going to use spack to build a container with different libraries and head
## Define a spack configuration
-We can choose some libraries and version that we need and build it into a concise image.
+We can choose some libraries and version that we need and build it into a concise image. We choose ubuntu 18.04 and spack 0.16.3, but we can build our own OS and spack version as we further invest.
This needs to be in a file called spack.yaml
```yaml
@@ -15,8 +15,8 @@ spack:
container:
images:
- os: "centos:8"
- spack: 0.17.2
+ os: "ubuntu:18.04"
+ spack: 0.16.3
format: singularity
@@ -70,7 +70,7 @@ SiFive - riscv64
u74mc
```
-convert this configuration into a singularity (apptainer) recipes
+convert this configuration into a singularity (apptainer) recipe
```bash
spack containerize > Singularity.hdf5.1.10.7
@@ -80,7 +80,7 @@ which has the following content
```singularity
Bootstrap: docker
-From: spack/centos7:0.16.3
+From: spack/ubuntu-bionic:0.16.3
Stage: build
%post
@@ -114,7 +114,7 @@ EOF
Bootstrap: docker
-From: centos:7
+From: ubuntu:18.04
Stage: final
%files from build
@@ -125,19 +125,56 @@ Stage: final
%post
# Update, install and cleanup of system packages needed at run-time
- yum update -y && yum install -y epel-release && yum update -y
- yum install -y gcc gcc-gfortran
- rm -rf /var/cache/yum && yum clean all
+ apt-get -yqq update && apt-get -yqq upgrade
+ apt-get -yqq install gcc gfortran
+ rm -rf /var/lib/apt/lists/*
# Modify the environment without relying on sourcing shell specific files at startup
cat /opt/spack-environment/environment_modifications.sh >> $SINGULARITY_ENVIRONMENT
%labels
app hdf5@1.10.7+mpi
- mpi openmpi@3.6.1
+ mpi openmpi@3.1.6
```
Then we can use that recipes to build a singularity container:
```bash
singularity build hdf5.1.10.7.sif Singularity.hdf5.1.10.7
+```
+
+
+
+## Build your first Singularity container for spack development and integration
+
+This is a much more complex build and of course configure example. We will build a Centos 7 image (or use any other) and install [spack](https://spack.readthedocs.io/en/latest/), a HPC package manager, into the container with our new favorite compiler. In a next step we can use that container and install even more packages into a development container for different apps.
+
+```bash
+# this will take some time ...
+singularity build centos7.sif definition-files/centos/Singularity-centos7
+# resulting in a 180 MB Centos root image, called centos.sif
+singularity build centos7.spack.sif definition-files/centos/Singularity-centos7-spack
+```
+The next step is to use the [definition file](definition-files/centos/Singularity-centos7-spack) and install the wanted compiler into that container
+
+```bash
+...
+# using spack for Installing
+$SPACK_ROOT/bin/spack install -y gcc@8.4.0
+# adding the compiler to the settings
+$SPACK_ROOT/bin/spack compiler add $(spack location -i gcc@8.4.0)
+...
+```
+Now we have an image that includes spack version 0.17.3 with a recent gcc @8.4.0 compiler, ready for development.
+
+```bash
+
+```
+
+### Containerizing applications using spack
+
+
+## Signing and hosting containers
+
+```bash
+singularity sign
```
\ No newline at end of file
diff --git a/development/custom/build_base.sh b/development/custom/build_base.sh
index 4cccb152001e43c2c6b2c9aee6e80c37b5f9a9af..b8601e6cf9e9615a6950796cfba213d6d068804e 100755
--- a/development/custom/build_base.sh
+++ b/development/custom/build_base.sh
@@ -183,7 +183,7 @@ report "AlmaLinux 8 spack image available"
if [ $? -ne 0 ]; then
test -f $DEFPATH/almalinux/Singularity-alma8-spack
report "AlmaLinux 8 spack definition found" || exit 1
- sed "s/v0.17.3/${spackversion}/" definition-files/almalinux/Singularity-alma8-spack >Singularity-alma8-spack
+ sed "s/v0.17.3/v${spackversion}/" $DEFPATH/almalinux/Singularity-alma8-spack >Singularity-alma8-spack
singularity build alma8-spack${spackversion} Singularity-alma8-spack
report "AlmaLinux 8 spack container ready" || exit 1
fi
@@ -221,18 +221,18 @@ fi
#
# Verify containers work
# not as root
-su mblaschek -c 'singularity key list | grep IMGW'
+singularity key list | grep IMGW
report "IMGW GPG key" || exit 1
echo "Please supply GPG passphrase for your key"
-su mblaschek -c "singularity sign alma8-spack${spackversion}"
-su mblaschek -c "singularity sign alma8-spack${spackversion}-gcc${gccversion}"
-su mblaschek -c "singularity sign centos7-spack${spackversion}-gcc${gccversion}"
+singularity sign alma8-spack${spackversion}
+singularity sign alma8-spack${spackversion}-gcc${gccversion}
+singularity sign centos7-spack${spackversion}-gcc${gccversion}
#
# Upload to cloud / repository for open access
#
# Spack primary development container
-singularity push alma8-spack${spackversion} library://mblaschek/spack/alma8:${spackversion}
+singularity push alma8-spack${spackversion} library://mblaschek//spack${spackversion}/alma8:8.5.0
# Spack development container with gcc versions
-singularity push alma8-spack${spackversion}-gcc${gccversion} library://mblaschek/spack/${spackversion}/alma8/gcc:${gccversion}
-singularity push centos7-spack${spackversion}-gcc${gccversion} library://mblaschek/spack/${spackversion}/centos7/gcc:${gccversion}
+singularity push alma8-spack${spackversion}-gcc${gccversion} library://mblaschek//spack${spackversion}/alma8:${gccversion}
+singularity push centos7-spack${spackversion}-gcc${gccversion} library://mblaschek//spack${spackversion}/centos7:${gccversion}
# singularity push centos8-spack-icc${iccversion} library://mblaschek/spack/alma8/icc:${iccversion}
diff --git a/models/WRF/README.md b/models/WRF/README.md
index 543735168fdfa2b472e8d31335379b13cd9b7d2d..6ba441e7bbe8450eec5f3d711209bf701e83c045 100644
--- a/models/WRF/README.md
+++ b/models/WRF/README.md
@@ -48,3 +48,7 @@ Steps:
5. Build your own container from the WRF development container and your SRC Code.
+# Intel
+intel compiled WRF is faster
+intel-oneapi-runtime is 1.3GB
+intel-onaapi-compilers 10 GB
\ No newline at end of file
diff --git a/models/WRF/Singularity.dev b/models/WRF/Singularity.dev
deleted file mode 100644
index 9cacfeb19421ec1a4a0ea8e173373bea894582df..0000000000000000000000000000000000000000
--- a/models/WRF/Singularity.dev
+++ /dev/null
@@ -1,110 +0,0 @@
-Bootstrap: localimage
-From: alma8.base.sif
-
-%labels
-maintainer IT-IMGW <it.img-wien@univie.ac.at>
-baseimage AlmaLinux8
-
-
-%apprun downloadwrf
-WRF_VERSION=4.4.1
-if [ $# -ne 0 ]; then
- WRF_VERSION=$1
-fi
-if [ ! -f WRF-${WRF_VERSION}.tar.gz ]; then
- echo "[wrf.dev] Downloading WRF $WRF_VERSION from github:"
- curl -SL -o WRF-${WRF_VERSION}.tar.gz https://github.com/wrf-model/WRF/releases/download/v${WRF_VERSION}/v${WRF_VERSION}.tar.gz
-else
- echo "[wrf.dev] Source found: WRF-${WRF_VERSION}.tar.gz"
-fi
-
-
-%apphelp downloadwrf
-[WRF] APP: downloadwrf
-[WRF] This will download the WRF source code from GitHub. The version can be specified by an argument.
-[WRF] run: singularity run --app downloadwrf 4.4.1
-[WRF] curl -SL -o WRF-{WRF_VERSION}.tar.gz https://github.com/wrf-model/WRF/releases/download/v{WRF_VERSION}/v{WRF_VERSION}.tar.gz
-[WRF]
-
-%apprun downloadwps
-WPS_VERSION=4.4
-if [ $# -ne 0 ]; then
- WPS_VERSION=$1
-fi
-if [ ! -f WPS-${WPS_VERSION}.tar.gz ]; then
- echo "[wrf.dev] Downloading WPS $WPS_VERSION from github:"
- curl -SL -o WPS-${WPS_VERSION}.tar.gz https://github.com/wrf-model/WPS/archive/refs/tags/v${WPS_VERSION}.tar.gz
-else
- echo "[wrf.dev] Source found: WPS-${WPS_VERSION}.tar.gz"
-fi
-
-%apphelp downloadwps
-[WRF] APP: downloadwps
-[WRF] This will download the WPS source code from GitHub. The version can be specified by an argument.
-[WRF] run: singularity run --app downloadwps 4.4
-[WRF] curl -SL -o WPS-{WPS_VERSION}.tar.gz https://github.com/wrf-model/WPS/archive/refs/tags/v{WPS_VERSION}.tar.gz
-[WRF]
-
-%post
-# Every line will be a layer in the container
-# See https://fedoraproject.org/wiki/EPEL#Quickstart for powertools
-# yum --enablerepo epel groupinstall -y "Development Tools" \
-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 install -y \
- curl wget \
- file \
- findutils \
- gcc-c++ \
- gcc \
- gcc-gfortran \
- glibc.i686 libgcc.i686 \
- libpng-devel jasper-libs jasper-devel \
- m4 make perl cmake \
- flex flex-devel bison bison-devel \
- libcurl-devel \
- libxml2 libxml2-devel perl-XML-LibXML ImageMagick \
- python3 python3-pip python3-devel \
- tar bash tcsh time which zlib zlib-devel \
- git \
- gnupg2 \
- hostname \
- iproute \
- patch \
- openmpi-devel \
- openmpi \
- hdf5-openmpi-devel \
- hdf5-openmpi-static \
- netcdf-openmpi-devel \
- netcdf-openmpi-static \
- netcdf-fortran-openmpi-devel \
- netcdf-fortran-openmpi-static \
- openblas-devel.x86_64 \
- openblas-openmp.x86_64 \
-&& rm -rf /var/cache/yum \
-&& yum clean all \
-&& dnf clean all \
-&& rm -rf /usr/share/doc \
-&& rm -rf /usr/share/man \
-&& ln -s /usr/include/openmpi-x86_64/ /usr/lib64/openmpi/include
-
-# command prompt name
-CNAME=wrf.dev
-# 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
-# not sure why that does not happen as default
-echo "export PKG_CONFIG_PATH=/usr/lib64/openmpi/lib/pkgconfig/" >> $SINGULARITY_ENVIRONMENT
-
-%environment
-export LD_LIBRARY_PATH=/usr/lib64/openmpi/lib:/usr/lib64:/lib64:/lib
-export PATH=/usr/lib64/openmpi/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
-export LIBRARY=/usr/lib64/openmpi/lib:/usr/lib64:/lib64:/lib
-export INCLUDE=/usr/include/openmpi-x86_64/:/usr/lib64/gfortran/modules/openmpi:/usr/include
-export NETCDF=/usr/lib64/openmpi
-export NETCDF_ROOT=/usr/lib64/openmpi
-export HDF5_ROOT=/usr/lib64/openmpi
-export JASPERINC=/usr/include/jasper/
-export JASPERLIB=/usr/lib64/
diff --git a/models/WRF/Singularity.wrf b/models/WRF/Singularity.wrf
index 8efe12b27e3396ae82bf6e8a74003bd9a4c609a7..e2191d7278f9a82477ec776d3f84a31caecf840a 100644
--- a/models/WRF/Singularity.wrf
+++ b/models/WRF/Singularity.wrf
@@ -93,5 +93,6 @@ Stage: final
echo "export PS1=\"[IMGW-$CNAME]\w\$ \"" >> /.singularity.d/env/99-zz-custom-env.sh
%environment
+ export LC_ALL=C
export PATH=/wrf/bin:$PATH
export WRF_BUILD_TARGET=em_real
diff --git a/models/WRF/scripts/run-help b/models/WRF/scripts/run-help
index ef55af8e76ed7a6503989a4c2f2aeaa934a7816f..17d6d76e9b032c648cd5b5c72a023cc29603caa4 100644
--- a/models/WRF/scripts/run-help
+++ b/models/WRF/scripts/run-help
@@ -16,6 +16,11 @@ bind special directories
development using includes and libraries from inside the container
> ./image.sif gfortran -I\$INCLUDE -L\$LIBRARY -o test.x test.f90
+Directory not found?
+As a defaut singularity only mounts your home into the container. So you need access to other directories inside the container:
+> export SINGULARITY_BIND="/path1,/path2"
+> ./image.sif
+
WRF Simulations - Example
default run files are located in /wrf/run
executables are located in /wrf/bin