restructured repo, gitlab ci

6872f3d0 · Michael Blaschek · 1939a97a · 6872f3d0 · 1939a97a · 6872f3d0
Commit 6872f3d0 authored 1 year ago by Michael Blaschek
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -3,19 +3,24 @@ image:
  entrypoint: ["/bin/sh", "-c"]
 variables:
-    sfile: definition-files/almalinux/Singularity.base
+  SFILE:
-    libarypath: almalinux:8-base
+    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
+  when: manual
-    script:
+  script:
-        - pwd
+    - cd ./definition-files
-        - cp definition-files/runscript $PWD/
+    # step 1. build the container!
-        - cp definition-files/run-help $PWD/
+    - /bin/bash build.sh $SFILE
-        # step 1. build the container!
+    # step 2. push to harbor
-        - /bin/bash .gitlabci/build.sh $sfile
+    - singularity push $SFILE.sif oras://harbor.wolke.img.univie.ac.at/apptainer/$CONTAINERTAG
-        # step 2. push to harbor
+  # might be too big at some point
-        - singularity push ${sfile}.sif oras://harbor.wolke.img.univie.ac.at/apptainer/${librarypath}
+  artifacts:
-    artifacts:
+    when: on_success
-        paths:
+    expire_in: 1 day
-            - ${sfile}.sif
+    paths:
+      - $SFILE.sif
--- a/Makefile
+++ b/Makefile
-# 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
--- a/README.md
+++ b/README.md
 # 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).
+Use the instructions from [apptainer](https://apptainer.org/docs/admin/main/installation.html)
-e.g. Red Hat, Arch, ...
-more informaiton on building from source can be found here: [Installing Singularity Documentation](https://sylabs.io/guides/3.6/admin-guide/installation.html#)
+```sh title='Apptainer install instructions'
+# Red Hat Based
-```bash
+sudo yum install -y epel-release
-# Centos / Red Hat
+sudo yum install -y apptainer
-sudo yum update -y && \
+# Ubuntu
-    sudo yum install -y epel-release && \
+sudo add-apt-repository -y ppa:apptainer/ppa
-    sudo yum update -y && \
+sudo apt update
-    sudo yum install -y singularity
+sudo apt install -y apptainer
-# Arch / Manjaro
-sudo pamac install singularity-container
-# Manual using this script (builds from source)
-sudo ./install-singularity.sh install
 ```
-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.

--- a/definition-files/Makefile
+++ b/definition-files/Makefile
+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
--- a/definition-files/almalinux/Singularity.base
+++ b/definition-files/almalinux/Singularity.base
@@ -5,8 +5,8 @@ From: almalinux:8
    maintainer IT-IMGW <it.img-wien@univie.ac.at>
 %files
-    runscript /.singularity.d/runscript
+    ./runscript /.singularity.d/runscript
-    run-help /.singularity.d/runscript.help
+    ./run-help /.singularity.d/runscript.help
 %post
    # command prompt name

--- a/definition-files/almalinux/Singularity.imagemagick
+++ b/definition-files/almalinux/Singularity.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
+    ./runscript /.singularity.d/runscript
-    $PWD/definition-files/run-help /.singularity.d/runscript.help
+    ./run-help /.singularity.d/runscript.help
 %post
    dnf update -y \

--- a/definition-files/almalinux/Singularity.met
+++ b/definition-files/almalinux/Singularity.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
+    ./runscript /.singularity.d/runscript
-    $PWD/definition-files/run-help /.singularity.d/runscript.help
+    ./run-help /.singularity.d/runscript.help
 %post
    # Every line will be a layer in the container

--- a/definition-files/almalinux/Singularity.met.ompi
+++ b/definition-files/almalinux/Singularity.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
+    ./runscript /.singularity.d/runscript
-    $PWD/definition-files/run-help /.singularity.d/runscript.help
+    ./run-help /.singularity.d/runscript.help
 %post
    # Every line will be a layer in the container

--- a/definition-files/almalinux/Singularity.spack
+++ b/definition-files/almalinux/Singularity.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

--- a/definition-files/alpine/Singularity.met
+++ b/definition-files/alpine/Singularity.met
@@ -5,8 +5,8 @@ From: alpine
    MAINTAINER Michael Blaschek <michael.blaschek@univie.ac.at>
 %files
-    $PWD/definition-files/runscript /.singularity.d/runscript
+    ./runscript /.singularity.d/runscript
-    $PWD/definition-files/run-help /.singularity.d/runscript.help
+    ./run-help /.singularity.d/runscript.help
 %post
    apk add --no-cache build-base \

--- a/definition-files/centos/Singularity.inteloneapi
+++ b/definition-files/centos/Singularity.inteloneapi
--- a/definition-files/debian/Singularity.texlive
+++ b/definition-files/debian/Singularity.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
+    ./runscript /.singularity.d/runscript
-    $PWD/definition-files/run-help /.singularity.d/runscript.help
+    ./run-help /.singularity.d/runscript.help
 %post
    # command prompt name

--- a/definition-files/micromamba/Singularity.py39.dart
+++ b/definition-files/micromamba/Singularity.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
+    ./runscript /.singularity.d/runscript
-    $PWD/definition-files/run-help /.singularity.d/runscript.help
+    ./run-help /.singularity.d/runscript.help
 %post
    apt -y update && apt -y install \

--- a/definition-files/micromamba/Singularity.py39.eccodes
+++ b/definition-files/micromamba/Singularity.py39.eccodes
@@ -7,8 +7,8 @@ From: mambaorg/micromamba:latest
    eccodes 2.27.0
 %files
-    $PWD/definition-files/runscript /.singularity.d/runscript
+    ./runscript /.singularity.d/runscript
-    $PWD/definition-files/run-help /.singularity.d/runscript.help
+    ./run-help /.singularity.d/runscript.help
 %post
    micromamba -q install -y -n base -c conda-forge eccodes=2.27.0 python=3.9.13 &&

--- a/definition-files/micromamba/Singularity.py39.metdev
+++ b/definition-files/micromamba/Singularity.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
+    ./runscript /.singularity.d/runscript
-    $PWD/definition-files/run-help /.singularity.d/runscript.help
+    ./run-help /.singularity.d/runscript.help
 %apprun install-ipykernel
    # install current container as kernel

--- a/definition-files/MPI/Singularity.py39.ompi
+++ b/definition-files/MPI/Singularity.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
+    ./runscript /.singularity.d/runscript
-    $PWD/definition-files/run-help /.singularity.d/runscript.help
+    ./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

--- a/definition-files/miniconda/Singularity.miniconda3-py39-4.9.2-ubuntu-18.04
+++ b/definition-files/miniconda/Singularity.miniconda3-py39-4.9.2-ubuntu-18.04
--- a/definition-files/rocky/Singularity.rocky-8.4-OMPI
+++ b/definition-files/rocky/Singularity.rocky-8.4-OMPI
--- a/definition-files/ubuntu/Singularity.18.04.base
+++ b/definition-files/ubuntu/Singularity.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
+    ./runscript /.singularity.d/runscript
-    $PWD/definition-files/run-help /.singularity.d/runscript.help
+    ./run-help /.singularity.d/runscript.help
 %post
    # command prompt name

--- a/definition-files/ubuntu/Singularity.18.04.base.bootstrap
+++ b/definition-files/ubuntu/Singularity.18.04.base.bootstrap