From 6872f3d02f7da0ecc889c4306f7e72879c2a8285 Mon Sep 17 00:00:00 2001
From: MB <michael.blaschek@univie.ac.at>
Date: Fri, 8 Sep 2023 15:58:37 +0200
Subject: [PATCH] restructured repo, gitlab ci
---
.gitlab-ci.yml | 33 +-
Makefile | 41 --
README.md | 33 +-
definition-files/Makefile | 14 +
...larity.base => Singularity.almalinux.base} | 4 +-
...gick => Singularity.almalinux.imagemagick} | 4 +-
...gularity.met => Singularity.almalinux.met} | 4 +-
...et.ompi => Singularity.almalinux.met.ompi} | 4 +-
...rity.spack => Singularity.almalinux.spack} | 2 +-
...Singularity.met => Singularity.alpine.met} | 4 +-
...loneapi => Singularity.centos.inteloneapi} | 0
...ity.texlive => Singularity.debian.texlive} | 4 +-
....dart => Singularity.micromamba.py39.dart} | 4 +-
...es => Singularity.micromamba.py39.eccodes} | 4 +-
...dev => Singularity.micromamba.py39.metdev} | 4 +-
....ompi => Singularity.micromamba.py39.ompi} | 6 +-
...> Singularity.miniconda.py39.ubuntu.18.04} | 0
...ky-8.4-OMPI => Singularity.rocky.8.4.ompi} | 0
....04.base => Singularity.ubuntu.18.04.base} | 4 +-
...> Singularity.ubuntu.18.04.base.bootstrap} | 0
...-gcc => Singularity.ubuntu.18.04.ompi.gcc} | 2 +-
....04.base => Singularity.ubuntu.20.04.base} | 0
...ngularity.ompi => Singularity.ubuntu.ompi} | 0
{.gitlabci => definition-files}/build.sh | 0
definition-files/imgw | 17 +
definition-files/runscript | 0
definition-files/{MPI => src}/mpitest.c | 0
install-singularity.sh | 469 ------------------
log.sh | 55 --
29 files changed, 86 insertions(+), 626 deletions(-)
delete mode 100644 Makefile
create mode 100644 definition-files/Makefile
rename definition-files/{almalinux/Singularity.base => Singularity.almalinux.base} (88%)
rename definition-files/{almalinux/Singularity.imagemagick => Singularity.almalinux.imagemagick} (88%)
rename definition-files/{almalinux/Singularity.met => Singularity.almalinux.met} (93%)
rename definition-files/{almalinux/Singularity.met.ompi => Singularity.almalinux.met.ompi} (93%)
rename definition-files/{almalinux/Singularity.spack => Singularity.almalinux.spack} (97%)
rename definition-files/{alpine/Singularity.met => Singularity.alpine.met} (86%)
rename definition-files/{centos/Singularity.inteloneapi => Singularity.centos.inteloneapi} (100%)
rename definition-files/{debian/Singularity.texlive => Singularity.debian.texlive} (84%)
rename definition-files/{micromamba/Singularity.py39.dart => Singularity.micromamba.py39.dart} (92%)
rename definition-files/{micromamba/Singularity.py39.eccodes => Singularity.micromamba.py39.eccodes} (87%)
rename definition-files/{micromamba/Singularity.py39.metdev => Singularity.micromamba.py39.metdev} (94%)
rename definition-files/{MPI/Singularity.py39.ompi => Singularity.micromamba.py39.ompi} (87%)
rename definition-files/{miniconda/Singularity.miniconda3-py39-4.9.2-ubuntu-18.04 => Singularity.miniconda.py39.ubuntu.18.04} (100%)
rename definition-files/{rocky/Singularity.rocky-8.4-OMPI => Singularity.rocky.8.4.ompi} (100%)
rename definition-files/{ubuntu/Singularity.18.04.base => Singularity.ubuntu.18.04.base} (83%)
rename definition-files/{ubuntu/Singularity.18.04.base.bootstrap => Singularity.ubuntu.18.04.base.bootstrap} (100%)
rename definition-files/{MPI/Singularity.ubuntu-18.04-OMPI-gcc => Singularity.ubuntu.18.04.ompi.gcc} (96%)
rename definition-files/{ubuntu/Singularity.20.04.base => Singularity.ubuntu.20.04.base} (100%)
rename definition-files/{ubuntu/Singularity.ompi => Singularity.ubuntu.ompi} (100%)
rename {.gitlabci => definition-files}/build.sh (100%)
mode change 100644 => 100755
create mode 100644 definition-files/imgw
mode change 100644 => 100755 definition-files/runscript
rename definition-files/{MPI => src}/mpitest.c (100%)
delete mode 100755 install-singularity.sh
delete mode 100644 log.sh
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index c3f2644..6bdecb0 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -3,19 +3,24 @@ image:
entrypoint: ["/bin/sh", "-c"]
variables:
- sfile: definition-files/almalinux/Singularity.base
- libarypath: almalinux:8-base
+ SFILE:
+ description: "file path of Singularity recipe file"
+ value: definition-files/Singularity.almalinux.base
+ CONTAINERTAG:
+ description: "registry name and tag, e.g. almalinux8:base"
+ value: almalinux8:base
build:
- when: manual
- script:
- - pwd
- - cp definition-files/runscript $PWD/
- - cp definition-files/run-help $PWD/
- # step 1. build the container!
- - /bin/bash .gitlabci/build.sh $sfile
- # step 2. push to harbor
- - singularity push ${sfile}.sif oras://harbor.wolke.img.univie.ac.at/apptainer/${librarypath}
- artifacts:
- paths:
- - ${sfile}.sif
+ when: manual
+ script:
+ - cd ./definition-files
+ # step 1. build the container!
+ - /bin/bash build.sh $SFILE
+ # step 2. push to harbor
+ - singularity push $SFILE.sif oras://harbor.wolke.img.univie.ac.at/apptainer/$CONTAINERTAG
+ # might be too big at some point
+ artifacts:
+ when: on_success
+ expire_in: 1 day
+ paths:
+ - $SFILE.sif
diff --git a/Makefile b/Makefile
deleted file mode 100644
index 5436bc4..0000000
--- a/Makefile
+++ /dev/null
@@ -1,41 +0,0 @@
-# This is a makefile for building singularity containers
-# from the definition files.
-
-CONTAINER_DIR := containers
-null :=
-
-output:
- @mkdir -p $(CONTAINER_DIR)
-
-.PHONY: alma8.base # AlmaLinux 8 Base Image
-alma8.base: output
- @if [ ! -f '$(CONTAINER_DIR)/$@.sif' ]; then \
- echo Building AlmaLinux 8 Base image: $(CONTAINER_DIR)/$@.sif;\
- sudo singularity build $(CONTAINER_DIR)/$@.sif definition-files/almalinux/Singularity.base;\
- fi
- @[ -f $(CONTAINER_DIR)/$@.sif ] && echo Exists: $(CONTAINER_DIR)/$@.sif || true
-
-.PHONY: alma8.met # AlmaLinux 8 Meteorology Image
-alma8.met: output
- @if [ ! -f $(CONTAINER_DIR)/$@.sif ]; then \
- echo Building AlmaLinux 8 Met image: $(CONTAINER_DIR)/alma8.met.sif;\
- sudo singularity build $(CONTAINER_DIR)/alma8.met.sif definition-files/almalinux/Singularity.met;\
- fi
- @[ -f $(CONTAINER_DIR)/$@.sif ] && echo Exists: $(CONTAINER_DIR)/$@.sif || true
-
-.PHONY: alma8.met.ompi # AlmaLinux 8 Meteorology OMPI Image
-alma8.met.ompi: output
- @if [ ! -f $(CONTAINER_DIR)/$@.sif ]; then \
- echo Building AlmaLinux 8 Met OMPI image: $(CONTAINER_DIR)/alma8.met.ompi.sif;\
- sudo singularity build $(CONTAINER_DIR)/alma8.met.ompi.sif definition-files/almalinux/Singularity.met.ompi;\
- fi
- @[ -f $(CONTAINER_DIR)/$@.sif ] && echo Exists: $(CONTAINER_DIR)/$@.sif || true
-
-.PHONY: help # Show make targets
-help: # Show list of target
- @echo Build Targets and helper functions:
- @grep "^.PHONY: .* #" Makefile | sed 's/\.PHONY: \(.*\) # \(.*\)/\1 \t\2/' | expand -t20
-
-.PHONY: clean # Remove all container images
-clean:
- rm -rf $(CONTAINER_DIR)/*.sif
\ No newline at end of file
diff --git a/README.md b/README.md
index f0af64d..0edfba7 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,6 @@
# Singularity / Apptainer
-A repository of definition files for building [Singularity](https://sylabs.io/guides/latest/user-guide) containers around the software applications, frameworks, and libraries you need to run on high-performance computing systems.
+A repository of definition files for building [Singularity](https://apptainer.org/docs/user/main/introduction.html) containers around the software applications, frameworks, and libraries you need to run on high-performance computing systems.
Based on [naked-singularity](https://github.com/mkandes/naked-singularity). Thanks M. Kandas
@@ -8,31 +8,20 @@ Based on [naked-singularity](https://github.com/mkandes/naked-singularity). Than
## Install Singularity / Apptainer
-Install Singularity on your Linux desktop, laptop, or virtual machine. You need *root* permissions to use and install the package.
+Install Singularity/Apptainer on your Linux desktop, laptop, or virtual machine. You need *root* permissions to use and install the package. Although there is a unprivileged installation possible, [here](https://apptainer.org/docs/admin/main/installation.html#install-unprivileged-from-pre-built-binaries).
-There is a general install script that installs version 3.5.3 (can be easily changed to 3.8 or 3.9) from source, but there are also binary packages build for modern OS (Server OS).
-e.g. Red Hat, Arch, ...
+Use the instructions from [apptainer](https://apptainer.org/docs/admin/main/installation.html)
-more informaiton on building from source can be found here: [Installing Singularity Documentation](https://sylabs.io/guides/3.6/admin-guide/installation.html#)
-
-```bash
-# Centos / Red Hat
-sudo yum update -y && \
- sudo yum install -y epel-release && \
- sudo yum update -y && \
- sudo yum install -y singularity
-
-# Arch / Manjaro
-sudo pamac install singularity-container
-
-# Manual using this script (builds from source)
-sudo ./install-singularity.sh install
+```sh title='Apptainer install instructions'
+# Red Hat Based
+sudo yum install -y epel-release
+sudo yum install -y apptainer
+# Ubuntu
+sudo add-apt-repository -y ppa:apptainer/ppa
+sudo apt update
+sudo apt install -y apptainer
```
-e.g. Ubuntu does not have the package in the repos, but a deb file exists in the releases. See below.
-
-Please note that these versions can vary substantially. Please check that at least version 3.5 is available or for newer distributions use **apptainer**.
-
### prebuild binary releases
If you can not find singularity or apptainer in your repos, there are prebuild packages available as well. Go to the github release [singularity](https://github.com/sylabs/singularity/releases) or [apptainer](https://github.com/apptainer/apptainer/releases) page.
diff --git a/definition-files/Makefile b/definition-files/Makefile
new file mode 100644
index 0000000..405d7b0
--- /dev/null
+++ b/definition-files/Makefile
@@ -0,0 +1,14 @@
+
+SFILES := $(wildcard Singularity.*)
+
+%.sif:%
+ sudo singularity build $@ $<
+
+$(addsuffix .sif, $(SFILES)): $(SFILES)
+
+.PHONY: list
+list:
+ @LC_ALL=C $(MAKE) -pRrq -f $(firstword $(MAKEFILE_LIST)) : 2>/dev/null | awk -v RS= -F: '/(^|\n)# Files(\n|$$)/,/(^|\n)# Finished Make data base/ {if ($$1 !~ "^[#.]") {print $$1}}' | sort | grep -E -v -e '^[^[:alnum:]]' -e '^$@$$'
+
+clean:
+ rm -f *.sif
\ No newline at end of file
diff --git a/definition-files/almalinux/Singularity.base b/definition-files/Singularity.almalinux.base
similarity index 88%
rename from definition-files/almalinux/Singularity.base
rename to definition-files/Singularity.almalinux.base
index 9bc6aae..427b388 100644
--- a/definition-files/almalinux/Singularity.base
+++ b/definition-files/Singularity.almalinux.base
@@ -5,8 +5,8 @@ From: almalinux:8
maintainer IT-IMGW <it.img-wien@univie.ac.at>
%files
- runscript /.singularity.d/runscript
- run-help /.singularity.d/runscript.help
+ ./runscript /.singularity.d/runscript
+ ./run-help /.singularity.d/runscript.help
%post
# command prompt name
diff --git a/definition-files/almalinux/Singularity.imagemagick b/definition-files/Singularity.almalinux.imagemagick
similarity index 88%
rename from definition-files/almalinux/Singularity.imagemagick
rename to definition-files/Singularity.almalinux.imagemagick
index 8b3744e..a6c36f1 100644
--- a/definition-files/almalinux/Singularity.imagemagick
+++ b/definition-files/Singularity.almalinux.imagemagick
@@ -5,8 +5,8 @@ From: almalinux:8
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
+ ./runscript /.singularity.d/runscript
+ ./run-help /.singularity.d/runscript.help
%post
dnf update -y \
diff --git a/definition-files/almalinux/Singularity.met b/definition-files/Singularity.almalinux.met
similarity index 93%
rename from definition-files/almalinux/Singularity.met
rename to definition-files/Singularity.almalinux.met
index 53e21f1..9b31f3a 100644
--- a/definition-files/almalinux/Singularity.met
+++ b/definition-files/Singularity.almalinux.met
@@ -5,8 +5,8 @@ From: almalinux:8
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
+ ./runscript /.singularity.d/runscript
+ ./run-help /.singularity.d/runscript.help
%post
# Every line will be a layer in the container
diff --git a/definition-files/almalinux/Singularity.met.ompi b/definition-files/Singularity.almalinux.met.ompi
similarity index 93%
rename from definition-files/almalinux/Singularity.met.ompi
rename to definition-files/Singularity.almalinux.met.ompi
index e5fa895..983b468 100644
--- a/definition-files/almalinux/Singularity.met.ompi
+++ b/definition-files/Singularity.almalinux.met.ompi
@@ -5,8 +5,8 @@ From: almalinux:8
maintainer IT-IMGW <it.img-wien@univie.ac.at>
%files
- $PWD/definition-files/runscript /.singularity.d/runscript
- $PWD/definition-files/run-help /.singularity.d/runscript.help
+ ./runscript /.singularity.d/runscript
+ ./run-help /.singularity.d/runscript.help
%post
# Every line will be a layer in the container
diff --git a/definition-files/almalinux/Singularity.spack b/definition-files/Singularity.almalinux.spack
similarity index 97%
rename from definition-files/almalinux/Singularity.spack
rename to definition-files/Singularity.almalinux.spack
index b2494ae..824fa9e 100644
--- a/definition-files/almalinux/Singularity.spack
+++ b/definition-files/Singularity.almalinux.spack
@@ -75,7 +75,7 @@ From: almalinux:8
export DEBIAN_FRONTEND=noninteractive
%runscript
- # Need spack entry point to allow spack builds
+ # Need spack entry point to allow spack builds
exec /bin/bash /opt/spack/share/spack/docker/entrypoint.bash interactive-shell "$@"
%startscript
diff --git a/definition-files/alpine/Singularity.met b/definition-files/Singularity.alpine.met
similarity index 86%
rename from definition-files/alpine/Singularity.met
rename to definition-files/Singularity.alpine.met
index 7da3717..7ae30de 100644
--- a/definition-files/alpine/Singularity.met
+++ b/definition-files/Singularity.alpine.met
@@ -5,8 +5,8 @@ From: alpine
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
+ ./runscript /.singularity.d/runscript
+ ./run-help /.singularity.d/runscript.help
%post
apk add --no-cache build-base \
diff --git a/definition-files/centos/Singularity.inteloneapi b/definition-files/Singularity.centos.inteloneapi
similarity index 100%
rename from definition-files/centos/Singularity.inteloneapi
rename to definition-files/Singularity.centos.inteloneapi
diff --git a/definition-files/debian/Singularity.texlive b/definition-files/Singularity.debian.texlive
similarity index 84%
rename from definition-files/debian/Singularity.texlive
rename to definition-files/Singularity.debian.texlive
index 9c767e2..6a31cee 100644
--- a/definition-files/debian/Singularity.texlive
+++ b/definition-files/Singularity.debian.texlive
@@ -5,8 +5,8 @@ From: texlive/texlive:latest
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
+ ./runscript /.singularity.d/runscript
+ ./run-help /.singularity.d/runscript.help
%post
# command prompt name
diff --git a/definition-files/micromamba/Singularity.py39.dart b/definition-files/Singularity.micromamba.py39.dart
similarity index 92%
rename from definition-files/micromamba/Singularity.py39.dart
rename to definition-files/Singularity.micromamba.py39.dart
index a42fb4b..b6936e9 100644
--- a/definition-files/micromamba/Singularity.py39.dart
+++ b/definition-files/Singularity.micromamba.py39.dart
@@ -5,8 +5,8 @@ From: mambaorg/micromamba:latest
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
+ ./runscript /.singularity.d/runscript
+ ./run-help /.singularity.d/runscript.help
%post
apt -y update && apt -y install \
diff --git a/definition-files/micromamba/Singularity.py39.eccodes b/definition-files/Singularity.micromamba.py39.eccodes
similarity index 87%
rename from definition-files/micromamba/Singularity.py39.eccodes
rename to definition-files/Singularity.micromamba.py39.eccodes
index ad82c2d..4d8d82a 100644
--- a/definition-files/micromamba/Singularity.py39.eccodes
+++ b/definition-files/Singularity.micromamba.py39.eccodes
@@ -7,8 +7,8 @@ From: mambaorg/micromamba:latest
eccodes 2.27.0
%files
- $PWD/definition-files/runscript /.singularity.d/runscript
- $PWD/definition-files/run-help /.singularity.d/runscript.help
+ ./runscript /.singularity.d/runscript
+ ./run-help /.singularity.d/runscript.help
%post
micromamba -q install -y -n base -c conda-forge eccodes=2.27.0 python=3.9.13 &&
diff --git a/definition-files/micromamba/Singularity.py39.metdev b/definition-files/Singularity.micromamba.py39.metdev
similarity index 94%
rename from definition-files/micromamba/Singularity.py39.metdev
rename to definition-files/Singularity.micromamba.py39.metdev
index 8f1ab7f..82e4cfe 100644
--- a/definition-files/micromamba/Singularity.py39.metdev
+++ b/definition-files/Singularity.micromamba.py39.metdev
@@ -5,8 +5,8 @@ From: mambaorg/micromamba:latest
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
+ ./runscript /.singularity.d/runscript
+ ./run-help /.singularity.d/runscript.help
%apprun install-ipykernel
# install current container as kernel
diff --git a/definition-files/MPI/Singularity.py39.ompi b/definition-files/Singularity.micromamba.py39.ompi
similarity index 87%
rename from definition-files/MPI/Singularity.py39.ompi
rename to definition-files/Singularity.micromamba.py39.ompi
index 96f0a87..53b8522 100644
--- a/definition-files/MPI/Singularity.py39.ompi
+++ b/definition-files/Singularity.micromamba.py39.ompi
@@ -5,8 +5,8 @@ From: mambaorg/micromamba:latest
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
+ ./runscript /.singularity.d/runscript
+ ./run-help /.singularity.d/runscript.help
%apprun mpitest
@@ -18,7 +18,7 @@ From: mambaorg/micromamba:latest
exec mpirun -np $nproc mpitest.x
%appfiles mpitest
- ./definition-files/MPI/mpitest.c ./mpitest.c
+ ./src/mpitest.c ./mpitest.c
%appinstall mpitest
export PATH=/opt/conda/bin:$PATH
diff --git a/definition-files/miniconda/Singularity.miniconda3-py39-4.9.2-ubuntu-18.04 b/definition-files/Singularity.miniconda.py39.ubuntu.18.04
similarity index 100%
rename from definition-files/miniconda/Singularity.miniconda3-py39-4.9.2-ubuntu-18.04
rename to definition-files/Singularity.miniconda.py39.ubuntu.18.04
diff --git a/definition-files/rocky/Singularity.rocky-8.4-OMPI b/definition-files/Singularity.rocky.8.4.ompi
similarity index 100%
rename from definition-files/rocky/Singularity.rocky-8.4-OMPI
rename to definition-files/Singularity.rocky.8.4.ompi
diff --git a/definition-files/ubuntu/Singularity.18.04.base b/definition-files/Singularity.ubuntu.18.04.base
similarity index 83%
rename from definition-files/ubuntu/Singularity.18.04.base
rename to definition-files/Singularity.ubuntu.18.04.base
index 6aa685d..64843c0 100644
--- a/definition-files/ubuntu/Singularity.18.04.base
+++ b/definition-files/Singularity.ubuntu.18.04.base
@@ -5,8 +5,8 @@ From: ubuntu:18.04
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
+ ./runscript /.singularity.d/runscript
+ ./run-help /.singularity.d/runscript.help
%post
# command prompt name
diff --git a/definition-files/ubuntu/Singularity.18.04.base.bootstrap b/definition-files/Singularity.ubuntu.18.04.base.bootstrap
similarity index 100%
rename from definition-files/ubuntu/Singularity.18.04.base.bootstrap
rename to definition-files/Singularity.ubuntu.18.04.base.bootstrap
diff --git a/definition-files/MPI/Singularity.ubuntu-18.04-OMPI-gcc b/definition-files/Singularity.ubuntu.18.04.ompi.gcc
similarity index 96%
rename from definition-files/MPI/Singularity.ubuntu-18.04-OMPI-gcc
rename to definition-files/Singularity.ubuntu.18.04.ompi.gcc
index d9dadb3..c8df976 100644
--- a/definition-files/MPI/Singularity.ubuntu-18.04-OMPI-gcc
+++ b/definition-files/Singularity.ubuntu.18.04.ompi.gcc
@@ -2,7 +2,7 @@ Bootstrap: library
From: mblaschek/imgw/ubuntu:18.04
%files
- definition-files/MPI/mpitest.c /opt
+ ./src/mpitest.c /opt
%environment
export OMPI_DIR=/opt/ompi
diff --git a/definition-files/ubuntu/Singularity.20.04.base b/definition-files/Singularity.ubuntu.20.04.base
similarity index 100%
rename from definition-files/ubuntu/Singularity.20.04.base
rename to definition-files/Singularity.ubuntu.20.04.base
diff --git a/definition-files/ubuntu/Singularity.ompi b/definition-files/Singularity.ubuntu.ompi
similarity index 100%
rename from definition-files/ubuntu/Singularity.ompi
rename to definition-files/Singularity.ubuntu.ompi
diff --git a/.gitlabci/build.sh b/definition-files/build.sh
old mode 100644
new mode 100755
similarity index 100%
rename from .gitlabci/build.sh
rename to definition-files/build.sh
diff --git a/definition-files/imgw b/definition-files/imgw
new file mode 100644
index 0000000..96c9645
--- /dev/null
+++ b/definition-files/imgw
@@ -0,0 +1,17 @@
+#!/bin/bash
+# By MB
+# IMGW introduction on the container environment
+
+cat <<EOF
+
+IMGW - Institut für Meteorologie und Geophysik
+Universität Wien
+Österreich
+
+Department of Meteorology and Geophysics
+
+Welcome inside a IMGW container!
+
+
+Please try the following
+EOF
\ No newline at end of file
diff --git a/definition-files/runscript b/definition-files/runscript
old mode 100644
new mode 100755
diff --git a/definition-files/MPI/mpitest.c b/definition-files/src/mpitest.c
similarity index 100%
rename from definition-files/MPI/mpitest.c
rename to definition-files/src/mpitest.c
diff --git a/install-singularity.sh b/install-singularity.sh
deleted file mode 100755
index 1247be7..0000000
--- a/install-singularity.sh
+++ /dev/null
@@ -1,469 +0,0 @@
-#!/usr/bin/env bash
-# ======================================================================
-# NAME
-#
-# install-singularity.sh
-#
-# DESCRIPTION
-#
-# A bash shell utility to help you work with Singularity (and the
-# definition files within the monkey-singularity repository) on your
-# Linux desktop, laptop, or virtual machine.
-#
-# USAGE
-#
-# Install Singularity from source.
-#
-# ./install-singularity.sh install
-#
-# LAST UPDATED
-#
-# Thursday, Nov 18th, 2021
-# Based on MKandas naked-singularity
-#
-# ----------------------------------------------------------------------
-
-source log.sh
-
-# ----------------------------------------------------------------------
-# monkey::install
-#
-# Installs Singularity from source [or via rpm].
-#
-# Globals:
-#
-# N/A
-#
-# Arguments:
-#
-# @
-#
-# Returns:
-#
-# True (0) if Singularity is installed sucessfully.
-# False (1) if the installation of Singularity fails.
-#
-# ----------------------------------------------------------------------
-
-monkey::install() {
-
- local singularity_version='3.5.3'
- local go_version='1.15.6'
- local use_rpm='false'
- local rpm_repo='epel'
-
- local os_release_id=''
- local os_release_version_id=''
-
- while (("${#}" > 0)); do
- case "${1}" in
- -s | --singularity )
- singularity_version="${2}"
- shift 2
- ;;
- -g | --go )
- go_version="${2}"
- shift 2
- ;;
- -r | --rpm )
- use_rpm='true'
- shift 1
- ;;
- -e | --enable-repo )
- rpm_repo="${2}"
- shift 2
- ;;
- *)
- log::error "Command-line option ${1} not recognized or not supported."
- return 1
- esac
- done
-
- log::output 'Checking if Singularity is already installed ...'
- singularity --version > /dev/null 2>&1
- if [[ "${?}" -eq 0 ]]; then
- log::error "Singularity is installed: $(singularity --version)"
- return 1
- else
- log::output 'Singularity is not installed.'
- fi
-
- log::output 'Parsing /etc/os-release to identify operating system ...'
- if [[ -f '/etc/os-release' ]]; then
-
- grep '^ID=' /etc/os-release > /dev/null 2>&1
- if [[ "${?}" -eq 0 ]]; then
- grep '^ID=' /etc/os-release | grep '"' > /dev/null 2>&1
- if [[ "${?}" -eq 0 ]]; then
- os_release_id="$(grep '^ID=' /etc/os-release | cut -d '"' -f 2)"
- else
- os_release_id="$(grep '^ID=' /etc/os-release | cut -d '=' -f 2)"
- fi
- log::output "Operating system identified as ${os_release_id}."
- else
- log::error '/etc/os-release does not contain ID parameter.'
- return 1
- fi
-
- grep '^VERSION_ID=' /etc/os-release > /dev/null 2>&1
- if [[ "${?}" -eq 0 ]]; then
- grep '^VERSION_ID=' /etc/os-release | grep '"' > /dev/null 2>&1
- if [[ "${?}" -eq 0 ]]; then
- os_release_version_id="$(grep '^VERSION_ID=' /etc/os-release | cut -d '"' -f 2)"
- else
- os_release_version_id="$(grep '^VERSION_ID=' /etc/os-release | cut -d '=' -f 2)"
- fi
- log::output "Operating system version identified as ${os_release_version_id}."
- else
- log::error '/etc/os-release does not contain VERSION_ID parameter.'
- return 1
- fi
-
- else
-
- log::error '/etc/os-release does not exist.'
- return 1
-
- fi
-
- if [[ "${os_release_id}" = 'centos' ]]; then
-
- log::output 'Running yum update ...'
- yum -y update
-
- log::output 'Installing Singularity dependencies ...'
- yum -y groupinstall 'Development Tools'
- yum -y install epel-release
- yum -y install openssl-devel
- yum -y install libuuid-devel
- yum -y install libseccomp-devel
- yum -y install wget
- yum -y install squashfs-tools
- yum -y install cryptsetup
- yum -y install debootstrap
-
- elif [[ "${os_release_id}" = 'ubuntu' ]]; then
-
- log::output 'Running apt-get update ...'
- apt-get -y update
-
- log::output 'Installing Singularity dependencies ...'
- apt-get -y install build-essential
- apt-get -y install libssl-dev
- apt-get -y install uuid-dev
- apt-get -y install libgpgme-dev
- apt-get -y install squashfs-tools
- apt-get -y install libseccomp-dev
- apt-get -y install wget
- apt-get -y install pkg-config
- apt-get -y install git
- apt-get -y install cryptsetup-bin
- apt-get -y install debootstrap
- apt-get -y install yum-utils
-
- # https://github.com/hpcng/singularity/issues/241
- echo '%_var /var' > ~/.rpmmacros
- echo '%_dbpath %{_var}/lib/rpm' >> ~/.rpmmacros
-
- else
-
- log::error 'Operating system not recognized or not supported.'
- return 1
-
- fi
-
- if [[ "${os_release_id}" = 'centos' && "${use_rpm}" = 'true' ]]; then
-
- log::output 'Installing Singularity ...'
- yum -y install --enablerepo="${rpm_repo}" singularity-"${singularity_version}"
-
- else # build and install singularity from source
-
- mkdir -p /tmp/go
- cd /tmp/go
-
- log::output 'Installing Go ...'
- export CGO_ENABLED=0
- wget https://dl.google.com/go/go1.4-bootstrap-20171003.tar.gz
- tar -xf go1.4-bootstrap-20171003.tar.gz
- mv go 1.4
- cd 1.4/src
- ./make.bash
-
- export GOROOT_BOOTSTRAP='/tmp/go/1.4'
-
- cd /tmp/go
-
- export CGO_ENABLED=1
- git clone https://go.googlesource.com/go "${go_version}"
- cd "${go_version}"
- git checkout "go${go_version}"
- cd src
- ./all.bash
-
- export GOROOT="/tmp/go/${go_version}"
- export PATH="${GOROOT}/bin:${PATH}"
-
- cd /tmp
-
- log::output 'Installing Singularity ...'
- wget "https://github.com/hpcng/singularity/releases/download/v${singularity_version}/singularity-${singularity_version}.tar.gz"
- tar -xf "singularity-${singularity_version}.tar.gz"
- cd singularity
- ./mconfig #--prefix=/opt/singularity <- include prefix as used-defined option?
- make -C ./builddir
- make -C ./builddir install
-
- fi
-
- # Prepend the path of the install directory of Singularity to PATH
- # because not all secure_paths in /etc/sudoers may include it. If it
- # is not included as one of the secure_paths by default, then the
- # final install test below will fail erroneously, even when
- # Singularity has been installed successfully.
- #
- # https://unix.stackexchange.com/questions/8646/why-are-path-variables-different-when-running-via-sudo-and-su
- export PATH="/usr/local/bin:${PATH}"
-
- log::output 'Checking if Singularity was installed successully ...'
- singularity --version
- if [[ "${?}" -ne 0 ]]; then
- log::error 'Singularity installation failed!'
- return 1
- fi
-
- log::output 'Singularity was installed successfully!'
-
- return 0
-
-}
-
-# ----------------------------------------------------------------------
-# monkey::uninstall
-#
-# Removes an existing source [or rpm-based] installation of Singularity.
-#
-# Globals:
-#
-# N/A
-#
-# Arguments:
-#
-# @
-#
-# Returns:
-#
-# True (0) if Singularity is uninstalled and removed sucessfully.
-# False (1) if the removal of Singularity fails.
-#
-# ----------------------------------------------------------------------
-
-monkey::uninstall() {
-
- local singularity_prefix='/usr/local'
- local use_rpm='false'
-
- local os_release_id=''
- local os_release_version_id=''
-
- while (("${#}" > 0)); do
- case "${1}" in
- -p | --prefix )
- singularity_prefix="${2}"
- shift 2
- ;;
- -r | --rpm )
- use_rpm='true'
- shift 1
- ;;
- *)
- log::error "Command-line option ${1} not recognized or not supported."
- return 1
- esac
- done
-
- log::output 'Checking if Singularity is already installed ...'
- singularity --version > /dev/null 2>&1
- if [[ "${?}" -eq 0 ]]; then
- log::output "Singularity is installed: $(singularity --version)"
- else
- log::error 'Singularity is not installed.'
- return 1
- fi
-
- log::output 'Parsing /etc/os-release to identify operating system ...'
- if [[ -f '/etc/os-release' ]]; then
-
- grep '^ID=' /etc/os-release > /dev/null 2>&1
- if [[ "${?}" -eq 0 ]]; then
- grep '^ID=' /etc/os-release | grep '"' > /dev/null 2>&1
- if [[ "${?}" -eq 0 ]]; then
- os_release_id="$(grep '^ID=' /etc/os-release | cut -d '"' -f 2)"
- else
- os_release_id="$(grep '^ID=' /etc/os-release | cut -d '=' -f 2)"
- fi
- log::output "Operating system identified as ${os_release_id}."
- else
- log::error '/etc/os-release does not contain ID parameter.'
- return 1
- fi
-
- grep '^VERSION_ID=' /etc/os-release > /dev/null 2>&1
- if [[ "${?}" -eq 0 ]]; then
- grep '^VERSION_ID=' /etc/os-release | grep '"' > /dev/null 2>&1
- if [[ "${?}" -eq 0 ]]; then
- os_release_version_id="$(grep '^VERSION_ID=' /etc/os-release | cut -d '"' -f 2)"
- else
- os_release_version_id="$(grep '^VERSION_ID=' /etc/os-release | cut -d '=' -f 2)"
- fi
- log::output "Operating system version identified as ${os_release_version_id}."
- else
- log::error '/etc/os-release does not contain VERSION_ID parameter.'
- return 1
- fi
-
- else
-
- log::error '/etc/os-release does not exist.'
- return 1
-
- fi
-
- log::output 'Uninstalling Singularity ...'
- if [[ "${os_release_id}" = 'centos' && "${use_rpm}" = 'true' ]]; then
-
- yum -y remove singularity
-
- else # remove source-based install
-
- rm -rf "${singularity_prefix}/libexec/singularity"
- rm -rf "${singularity_prefix}/var/singularity"
- rm -rf "${singularity_prefix}/etc/singularity"
- rm -rf "${singularity_prefix}/bin/singularity"
- rm -rf "${singularity_prefix}/bin/run-singularity"
- rm -rf "${singularity_prefix}/etc/bash_completion.d/singularity"
-
- fi
-
- log::output 'Checking if Singularity was uninstalled successfully ...'
- which singularity
- if [[ "${?}" -eq 0 ]]; then
- log::error 'Singularity was NOT uninstalled!'
- return 1
- fi
-
- log::output 'Singularity was uninstalled successfully!'
-
- return 0
-
-}
-
-# ----------------------------------------------------------------------
-# monkey::help
-#
-# Prints information on how to use this script to standard output.
-#
-# Globals:
-#
-# N/A
-#
-# Arguments:
-#
-# N/A
-#
-# Returns:
-#
-# True (0) always.
-#
-# ----------------------------------------------------------------------
-
-monkey::help() {
-
- log::output 'USAGE: install-singularity.sh <command> [options] {value}'
- log::output ''
-
- return 0
-
-}
-
-# ----------------------------------------------------------------------
-# monkey::main
-#
-# Controls the execution of the script.
-#
-# Globals:
-#
-# @
-#
-# Arguments:
-#
-# @
-#
-# Returns:
-#
-# True (0) if the script executes without issue.
-# False (1) if the script fails to executre properly.
-#
-# ----------------------------------------------------------------------
-
-monkey::main() {
-
- local monkey_command=''
-
- # If at least one command-line argument was provided by the user,
- # then start parsing the command-line arguments. Otherwise, throw
- # an error.
- if (( "${#}" > 0 )); then
-
- monkey_command="${1}"
- shift 1
-
- if [[ "${monkey_command}" = 'install' ]]; then
-
- monkey::install "${@}"
- if [[ "${?}" -ne 0 ]]; then
- log::error 'Failed to run install command.'
- exit 1
- fi
-
- elif [[ "${monkey_command}" = 'uninstall' ]]; then
-
- monkey::uninstall "${@}"
- if [[ "${?}" -ne 0 ]]; then
- log::error 'Failed to run uninstall command.'
- exit 1
- fi
-
- elif [[ "${monkey_command}" = 'help' || \
- "${monkey_command}" = '-h' || \
- "${monkey_command}" = '--help' ]]; then
-
- monkey::help
- if [[ "${?}" -ne 0 ]]; then
- log::error 'Failed to run help command.'
- exit 1
- fi
-
- else
-
- log::error 'Command not recognized or not supported.'
- exit 1
-
- fi
-
- else
-
- log::error 'No command-line arguments were provided.'
- exit 1
-
- fi
-
- exit 0
-
-}
-
-# ----------------------------------------------------------------------
-
-monkey::main "${@}"
-
-# ======================================================================
diff --git a/log.sh b/log.sh
deleted file mode 100644
index 24ac853..0000000
--- a/log.sh
+++ /dev/null
@@ -1,55 +0,0 @@
-#!/usr/bin/env bash
-# ======================================================================
-#
-# NAME
-#
-# log.sh
-#
-# DESCRIPTION
-#
-# A library of bash functions for writing formatted log messages to
-# standard output and standard error.
-#
-# USAGE
-#
-# If you would like to use this library in your bash script, then
-# source it at the beginning of your bash script.
-#
-# source log.sh
-#
-# Once the library has been sourced, you can call functions from the
-# library in your bash script.
-#
-# AUTHOR
-#
-# Marty Kandes, Ph.D.
-# Computational & Data Science Research Specialist
-# High-Performance Computing User Services Group
-# San Diego Supercomputer Center
-# University of California, San Diego
-#
-# LAST UPDATED
-#
-# Monday, December 28th, 2020
-#
-# ----------------------------------------------------------------------
-
-log::output() {
-
- echo "${@}" >&1
-
-}
-
-log::error() {
-
- echo "ERROR :: ${@}" >&2
-
-}
-
-log::warning() {
-
- echo "WARNING :: ${@}" >&2
-
-}
-
-# ======================================================================
--
GitLab