First page of new autamus packages (#411)

* first page of new autamus packages
* retest with public images
* update docs

Signed-off-by: vsoch <vsoch@users.noreply.github.com>
Co-authored-by: vsoch <vsoch@users.noreply.github.com>

.github/workflows/test-container.yml

@@ -5,15 +5,54 @@ on:
     types: [labeled]
 
 jobs:
-  test-registry:
+  changes:
     if: ${{ github.event.label.name == 'container-recipe' }}
     runs-on: ubuntu-latest
+    outputs:
+      changed_recipes: ${{ steps.files.outputs.added_modified }}
     steps:
+      - name: Find changed recipes
+        id: files
+        uses: jitterbit/get-changed-files@b17fbb00bdc0c0f63fcf166580804b4d2cdc2a42
+        with:
+          format: 'json'
+
+  test-recipes:
+    needs:
+      - changes
+    runs-on: ubuntu-latest
+    strategy:
+      # Keep going on other deployments if anything bloops
+      fail-fast: false
+      matrix:
+        changed_recipe: ${{ fromJson(needs.changes.outputs.changed_recipes) }}
+
+    name: Check ${{ matrix.changed_recipe }}
+    steps:
+      - name: Continue
+        run: |
+          # Continue if we have a changed recipe file
+          if [[ "${{ matrix.changed_recipe }}" = registry* ]]; then
+            echo "keepgoing=true" >> $GITHUB_ENV
+          fi          
+
+      - name: Checkout
+        if: ${{ env.keepgoing == 'true' }}
+        uses: actions/checkout@v2        
+
+      - name: Make Space For Build
+        if: ${{ env.keepgoing == 'true' }}
+        run: |
+          sudo rm -rf /usr/share/dotnet
+          sudo rm -rf /opt/ghc
+
       - name: Install Dependencies
+        if: ${{ env.keepgoing == 'true' }}
         run: |
           sudo apt-get install lua5.2 liblua5.2-dev lua-filesystem lua-posix tcl tcl-dev
 
       - name: Install Lmod
+        if: ${{ env.keepgoing == 'true' }}
         run: |
           PKG_VERSION=8.4.27
           PKG_URL="https://github.com/TACC/Lmod/archive/${PKG_VERSION}.tar.gz"
@@ -23,61 +62,33 @@ jobs:
           ./configure --prefix=/usr/share && make && make install
 
       - uses: eWaterCycle/setup-singularity@v6
+        if: ${{ env.keepgoing == 'true' }}
         name: Install Singularity
         with:
           singularity-version: 3.6.4
 
-      - name: Derive number of commits
-        run: |
-            cd /opt
-            branch="${{ github.head_ref }}"
-            git config --global user.email "github-actions"
-            git config --global user.name "github-actions@noreply.github.users.com"
-            git clone -b main https://github.com/singularityhub/singularity-hpc
-            cd singularity-hpc
-            git checkout -b $branch
-            git pull origin $branch
-            commits=$(git log --oneline "$branch" ^main | wc -l)
-            echo "Found $commits since main"
-            cd registry
-            touch changes.txt
-            # Note that you can also do: git diff --name-only $branch..main .
-            # We show the count of commits as a sanity check to the developer
-            for container_yaml in $(git diff --name-only HEAD~$commits..HEAD .); do
-                echo $container_yaml >> changes.txt
-            done            
-            cat changes.txt
-
-      - name: Save changelist
-        uses: actions/upload-artifact@v2
-        with:
-          name: changes.txt
-          path: /opt/singularity-hpc/registry/changes.txt
-
       - name: Create conda environment
+        if: ${{ env.keepgoing == 'true' }}
         run: conda create --quiet -c conda-forge --name shpc spython
 
       - uses: actions/checkout@v2
+        if: ${{ env.keepgoing == 'true' }}
+
       - name: Install shpc
+        if: ${{ env.keepgoing == 'true' }}
         run: |
           export PATH="/usr/share/miniconda/bin:$PATH"
           source activate shpc
           pip install -e .
 
-      - name: Download changelist
-        uses: actions/download-artifact@v2
-        with:
-          name: changes.txt
-
       - name: Run module tests
+        if: ${{ env.keepgoing == 'true' }}
         run: |
           export PATH="/usr/share/miniconda/bin:$PATH"
-
           source activate shpc
           cd registry
-          for container_yaml in $(cat ../changes.txt); do
-              module=$(dirname $container_yaml)
-              module=$(echo "${module/registry\//}")
-              echo "Testing $module"
-              shpc test --template ../shpc/tests/test-registry-module.sh --commands $module
-          done
+          container_yaml="${{ matrix.changed_recipe }}"
+          module=$(dirname $container_yaml)
+          module=$(echo "${module/registry\//}")
+          echo "Testing $module"
+          shpc test --template ../shpc/tests/test-registry-module.sh --commands $module

docs/getting_started/developer-guide.rst

@@ -71,9 +71,8 @@ for others to use. You should:
 4. You should generally choose smaller images (if possible) and define aliases (entrypoints) for the commands that you think would be useful.
 
 A shell entrypoint for the container will be generated automatically.
-When you open a pull request, if your branch prefix starts with ``recipe`` the PR
-will test your recipe automatically. If you forget, you can ask a maintainer to apply
-the ``container-recipe`` label and it will test accordingly.
+When you open a pull request, a maintainer can apply
+the ``container-recipe`` label and it will test your new or updated recipes accordingly.
 Once your recipe is added to the repository, the versions will be automatically
 updated with a nightly run. This means that you can pull the repository to get
 updated recipes, and then check for updates (the bot to do this is not developed yet):

registry/ghcr.io/autamus/ed/container.yaml

@@ -0,0 +1,11 @@
+docker: ghcr.io/autamus/ed
+url: https://github.com/orgs/autamus/packages/container/package/ed
+maintainer: "@vsoch"
+description: "GNU ed is a line-oriented text editor used to create, display, modify and otherwise manipulate text files, both interactively and via shell scripts https://www.gnu.org/software/ed."
+latest:
+  "1.4": sha256:ec791627353859a7569abd79c9b1e1f01032e2a363afc925a85849b60e5aec27
+tags:
+  "1.4": sha256:ec791627353859a7569abd79c9b1e1f01032e2a363afc925a85849b60e5aec27
+aliases:
+  ed: /opt/view/bin/ed
+  red: /opt/view/bin/red

registry/ghcr.io/autamus/emacs/container.yaml

@@ -0,0 +1,13 @@
+docker: ghcr.io/autamus/emacs
+url: https://github.com/orgs/autamus/packages/container/package/emacs
+maintainer: "@vsoch"
+description: The Emacs programmable text editor. https://www.gnu.org/software/emacs
+latest:
+  "27.2": sha256:a1fa851f9dbd3ba0474fd8f0365f23ba5cedc46095c5f6dedfa5fd433652a84a
+tags:
+  "27.2": sha256:a1fa851f9dbd3ba0474fd8f0365f23ba5cedc46095c5f6dedfa5fd433652a84a
+aliases:
+  ebrowse: /opt/view/bin/ebrowse
+  emacs: /opt/view/bin/emacs
+  emacsclient: /opt/view/bin/emacsclient
+  etags: /opt/view/bin/etags

registry/ghcr.io/autamus/gawk/container.yaml

@@ -0,0 +1,10 @@
+docker: ghcr.io/autamus/gawk
+url: https://github.com/orgs/autamus/packages/container/package/gawk
+maintainer: '@vsoch'
+description: gawk is the GNU implementation of awk. The awk utility interprets a special-purpose programming language that makes it possible to handle simple data-reformatting jobs with just a few lines of code. https://www.gnu.org/software/gawk/
+latest:
+  5.10.0: sha256:502eebe2f9a93ce7bb06fc6f97f8ce8dd76802a380ade9b4c71f0d3f15ef0a45
+tags:
+  5.10.0: sha256:502eebe2f9a93ce7bb06fc6f97f8ce8dd76802a380ade9b4c71f0d3f15ef0a45
+aliases:
+  gawk: /opt/view/bin/gawk

registry/ghcr.io/autamus/htop/container.yaml

@@ -0,0 +1,10 @@
+docker: ghcr.io/autamus/htop
+url: https://github.com/orgs/autamus/packages/container/package/htop
+maintainer: '@vsoch'
+description: htop is an interactive text-mode process viewer for Unix systems. https://github.com/hishamhm/htop
+latest:
+  2.2.0: sha256:017e8c7e87614dddb1fd01fb1892d40947501596504bf4d27af71c677d122851
+tags:
+  2.2.0: sha256:017e8c7e87614dddb1fd01fb1892d40947501596504bf4d27af71c677d122851
+aliases:
+  htop: /opt/view/bin/htop

registry/ghcr.io/autamus/py-libensemble/container.yaml

@@ -0,0 +1,8 @@
+docker: ghcr.io/autamus/py-libensemble
+url: https://github.com/orgs/autamus/packages/container/package/py-libensemble
+maintainer: '@vsoch'
+description: Library for managing ensemble-like collections of computations. 
+latest:
+  "0.7.2": sha256:ac19eb043b9b185e299616ed642d0b9f350c2373ac8b3bb3c415439b89cc8801
+tags:
+  "0.7.2": sha256:ac19eb043b9b185e299616ed642d0b9f350c2373ac8b3bb3c415439b89cc8801

registry/ghcr.io/autamus/py-petsc4py/container.yaml

@@ -0,0 +1,8 @@
+docker: ghcr.io/autamus/py-petsc4py 
+url: https://github.com/orgs/autamus/packages/container/package/py-petsc4py
+maintainer: '@vsoch'
+description: This package provides Python bindings for the PETSc package. 
+latest:
+  "3.15.1": sha256:4a6b58e25f765f191c2ddad01ed33f4dee4de953ef7e59ff1f31e4e6d0c23f8a
+tags:
+  "3.15.1": sha256:4a6b58e25f765f191c2ddad01ed33f4dee4de953ef7e59ff1f31e4e6d0c23f8a

registry/ghcr.io/autamus/rempi/container.yaml

@@ -0,0 +1,13 @@
+docker: ghcr.io/autamus/rempi
+url: https://github.com/orgs/autamus/packages/container/package/rempi
+maintainer: '@vsoch'
+description: ReMPI is a record-and-replay tool for MPI applications.
+latest:
+  "1.1.0": sha256:13f3ae61146c389b0fef9e6e1f331a8f229cc15c886a215c9437249301903400
+tags:
+  "1.1.0": sha256:13f3ae61146c389b0fef9e6e1f331a8f229cc15c886a215c9437249301903400
+aliases:
+  rempi: /opt/view/bin/rempi
+  rempi_record: /opt/view/bin/rempi_record
+  rempi_replay: /opt/view/bin/rempi_replay
+  reset: /opt/view/bin/reset

registry/ghcr.io/autamus/rsync/container.yaml

@@ -0,0 +1,11 @@
+docker: ghcr.io/autamus/rsync
+url: https://github.com/orgs/autamus/packages/container/package/rsync
+maintainer: '@vsoch'
+description: An open source utility that provides fast incremental file transfer. https://rsync.samba.org/
+latest:
+  "3.2.2": sha256:99c4780710b1d844ca8998dea4c59b2d3b54c28ac206dc3ee580ca2c34f455d1
+tags:
+  "3.2.2": sha256:99c4780710b1d844ca8998dea4c59b2d3b54c28ac206dc3ee580ca2c34f455d1
+aliases:
+  rsync: /opt/view/bin/rsync
+  rsync-ssl: /opt/view/bin/rsync-ssl

registry/ghcr.io/autamus/scr/container.yaml

@@ -0,0 +1,46 @@
+docker: ghcr.io/autamus/scr
+url: https://github.com/orgs/autamus/packages/container/package/scr
+maintainer: '@vsoch'
+description: SCR caches checkpoint data in storage on the compute nodes of a Linux cluster to provide a fast, scalable checkpoint/restart capability for MPI codes.
+latest:
+  "3.0.rc.1": sha256:86b2b8c8b530e17b01714be42e37aaa85061015aefd7683fa3332cd0aa61e958
+tags:
+  "3.0.rc.1": sha256:86b2b8c8b530e17b01714be42e37aaa85061015aefd7683fa3332cd0aa61e958s
+aliases:
+  scancel: /opt/view/bin/scancel
+  scontrol: /opt/view/bin/scontrol
+  scp: /opt/view/bin/scp
+  scr_check_node: /opt/view/bin/scr_check_node
+  scr_ckpt_interval.py: /opt/view/bin/scr_ckpt_interval.py
+  scr_copy: /opt/view/bin/scr_copy
+  scr_crc32: /opt/view/bin/scr_crc32
+  scr_env: /opt/view/bin/scr_env
+  scr_flush_file: /opt/view/bin/scr_flush_file
+  scr_get_jobstep_id: /opt/view/bin/scr_get_jobstep_id
+  scr_glob_hosts: /opt/view/bin/scr_glob_hosts
+  scr_halt: /opt/view/bin/scr_halt
+  scr_halt_cntl: /opt/view/bin/scr_halt_cntl
+  scr_index: /opt/view/bin/scr_index
+  scr_inspect: /opt/view/bin/scr_inspect
+  scr_kill_jobstep: /opt/view/bin/scr_kill_jobstep
+  scr_list_dir: /opt/view/bin/scr_list_dir
+  scr_list_down_nodes: /opt/view/bin/scr_list_down_nodes
+  scr_log_event: /opt/view/bin/scr_log_event
+  scr_log_transfer: /opt/view/bin/scr_log_transfer
+  scr_nodes_file: /opt/view/bin/scr_nodes_file
+  scr_postrun: /opt/view/bin/scr_postrun
+  scr_prefix: /opt/view/bin/scr_prefix
+  scr_prerun: /opt/view/bin/scr_prerun
+  scr_print: /opt/view/bin/scr_print
+  scr_rebuild_partner: /opt/view/bin/scr_rebuild_partner
+  scr_rebuild_rs: /opt/view/bin/scr_rebuild_rs
+  scr_rebuild_xor: /opt/view/bin/scr_rebuild_xor
+  scr_retries_halt: /opt/view/bin/scr_retries_halt
+  scr_run: /opt/view/bin/scr_run
+  scr_scavenge: /opt/view/bin/scr_scavenge
+  scr_srun: /opt/view/bin/scr_srun
+  scr_test_datemanip: /opt/view/bin/scr_test_datemanip
+  scr_test_runtime: /opt/view/bin/scr_test_runtime
+  scr_watchdog: /opt/view/bin/scr_watchdog
+  scrlog.py: /opt/view/bin/scrlog.py
+  scrontab: /opt/view/bin/scrontab

registry/ghcr.io/autamus/tasmanian/container.yaml

@@ -0,0 +1,11 @@
+docker: ghcr.io/autamus/tasmanian
+url: https://github.com/orgs/autamus/packages/container/package/tasmanian
+maintainer: '@vsoch'
+description: The Toolkit for Adaptive Stochastic Modeling and Non-Intrusive ApproximatioN is a robust library for high dimensional integration and interpolation as well as parameter calibration.  https://tasmanian.ornl.gov
+latest:
+  "7.5": sha256:0fe2ce4fc12320415f2c032976ec15eaf2f4120ad888fbb72b8b70a99a2e04ea
+tags:
+  "7.5": sha256:0fe2ce4fc12320415f2c032976ec15eaf2f4120ad888fbb72b8b70a99a2e04ea
+aliases:
+  tasgrid: /opt/view/bin/tasgrid
+

registry/ghcr.io/autamus/tau/container.yaml

@@ -0,0 +1,8 @@
+docker: ghcr.io/autamus/tau
+url: https://github.com/orgs/autamus/packages/container/package/tau
+maintainer: '@vsoch'
+description: A portable profiling and tracing toolkit for performance analysis of parallel programs written in Fortran, C, C++, UPC, Java, Python.
+latest:
+  2.30.1: sha256:b98fb90c2261594a3c5682cd049fcbd15c55b581f374187af74af8db20614715
+tags:
+  2.30.1: sha256:b98fb90c2261594a3c5682cd049fcbd15c55b581f374187af74af8db20614715

registry/ghcr.io/autamus/trilinos/container.yaml

@@ -0,0 +1,8 @@
+docker: ghcr.io/autamus/trilinos
+url: https://github.com/orgs/autamus/packages/container/package/trilinos
+maintainer: '@vsoch'
+description: The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. A unique design feature of Trilinos is its focus on packages. 
+latest:
+  13.0.1: sha256:69c55ce5c908da160da0242cbfe2a201f12f13c2781ea9a78c1eea06b783bdb2
+tags:
+  13.0.1: sha256:69c55ce5c908da160da0242cbfe2a201f12f13c2781ea9a78c1eea06b783bdb2

registry/ghcr.io/autamus/turbine/container.yaml

@@ -0,0 +1,13 @@
+docker: ghcr.io/autamus/turbine
+url: https://github.com/orgs/autamus/packages/container/package/turbine
+maintainer: '@vsoch'
+description: Turbine is the Swift/T runtime 
+latest:
+  1.3.0: sha256:076739ee1f6754f6cbf43dcdaedf021410529c195a671ca099b3a3e11160b611 
+tags:
+  1.3.0: sha256:076739ee1f6754f6cbf43dcdaedf021410529c195a671ca099b3a3e11160b611 
+aliases:
+  turbine: /opt/view/bin/turbine
+  turbine-pilot: /opt/view/bin/turbine-pilot
+  turbine-read-doubles: /opt/view/bin/turbine-read-doubles
+  turbine-write-doubles: /opt/view/bin/turbine-write-doubles

registry/ghcr.io/autamus/umap/container.yaml

@@ -0,0 +1,8 @@
+docker: ghcr.io/autamus/umap
+url: https://github.com/orgs/autamus/packages/container/package/umap
+maintainer: '@vsoch'
+description: Umap is a library that provides an mmap()-like interface to a simple, user-space page fault handler based on the userfaultfd Linux feature (starting with 4.3 linux kernel).
+latest:
+  2.1.0: sha256:b81554c3aba70bf5d093ff8a9c76d504757a70aa9c9415c219cfe831c46a8edd
+tags:
+  2.1.0: sha256:b81554c3aba70bf5d093ff8a9c76d504757a70aa9c9415c219cfe831c46a8edd

registry/ghcr.io/autamus/unifyfs/container.yaml

@@ -0,0 +1,12 @@
+docker: ghcr.io/autamus/unifyfs
+url: https://github.com/orgs/autamus/packages/container/package/unifyfs
+maintainer: '@vsoch'
+description: User level file system that enables applications to use node-local storage as burst buffers for shared files.
+latest:
+  "0.9.2": sha256:401d1041f3daf9b1fb52306fce6fbc58df48a64ba225da752f8d3b16da85e65a
+tags:
+  "0.9.2": sha256:401d1041f3daf9b1fb52306fce6fbc58df48a64ba225da752f8d3b16da85e65a
+aliases:
+  unifyfs: /opt/view/bin/unifyfs
+  unifyfs-config: /opt/view/bin/unifyfs-config
+  unifyfsd: /opt/view/bin/unifyfsd

registry/ghcr.io/autamus/upcxx/container.yaml

@@ -0,0 +1,13 @@
+docker: ghcr.io/autamus/upcxx
+url: https://github.com/orgs/autamus/packages/container/package/upcxx
+maintainer: '@vsoch'
+description: UPC++ is a C++ library that supports Partitioned Global Address Space (PGAS) programming, and is designed to interoperate smoothly and efficiently with MPI, OpenMP, CUDA and AMTs.
+latest:
+  "2021.3.0": sha256:0b537157644529a8fe20a95e0bef31ab7e6801b7433898a17f2c37a97c4d6883
+tags:
+  "2021.3.0": sha256:0b537157644529a8fe20a95e0bef31ab7e6801b7433898a17f2c37a97c4d6883
+aliases:
+  upcxx: /opt/view/bin/upcxx
+  upcxx-meta: /opt/view/bin/upcxx-meta
+  upcxx-run: /opt/view/bin/upcxx-run
+  upcxx.sh: /opt/view/bin/upcxx.sh

registry/ghcr.io/autamus/veloc/container.yaml

@@ -0,0 +1,15 @@
+docker: ghcr.io/autamus/veloc
+url: https://github.com/orgs/autamus/packages/container/package/veloc
+maintainer: '@vsoch'
+description: Very-Low Overhead Checkpointing System. VELOC is a multi-level checkpoint-restart runtime for HPC supercomputing infrastructures 
+latest:
+  "1.4": sha256:05677f36265c1bdf14977688f12b8e4a96261be80cc8ecce38796e2e46e82c96
+tags:
+  "1.4": sha256:05677f36265c1bdf14977688f12b8e4a96261be80cc8ecce38796e2e46e82c96
+aliases:
+  veloc-backend: /opt/view/bin/veloc-backend
+  veloc_check_node: /opt/view/bin/veloc_check_node
+  veloc_env: /opt/view/bin/veloc_env
+  veloc_glob_hosts: /opt/view/bin/veloc_glob_hosts
+  veloc_jsrun: /opt/view/bin/veloc_jsrun
+  veloc_list_down_nodes: /opt/view/bin/veloc_list_down_nodes

registry/ghcr.io/autamus/zfp/container.yaml

@@ -0,0 +1,8 @@
+docker: ghcr.io/autamus/zfp
+url: https://github.com/orgs/autamus/packages/container/package/zfp
+maintainer: '@vsoch'
+description: zfp is a compressed number format for multidimensional floating-point and integer arrays.
+latest:
+  "0.5.5": sha256:3a441ab9099713a500171cd7a9aaa48460b1101c834520dab5637c9419ce20b7
+tags:
+  "0.5.5": sha256:3a441ab9099713a500171cd7a9aaa48460b1101c834520dab5637c9419ce20b7