[WIP] setonix script

README.md

@@ -97,10 +97,12 @@ macOS amd64 (Intel) and arm64 (M-Series) will work, but CPU-only.
 
 Windows users will need to use WSL2 or Docker Desktop with Git Bash.
 
-## Setup
+## Clone
 
 Clone this repository to a machine that meets the [system requirements](#system-requirements).
 
+Setonix note: a good place for this is either `$MYSOFTWARE` or `/software/projects/pawsey1094/${USER}/`
+
 ```bash
 git clone https://github.com/MWATelescope/mwa-demo.git
 cd mwa-demo
@@ -113,13 +115,16 @@ to check for updates right before the workshop starts with a `git pull`.
 
 Download demo data (from Pawsey). You should be in the root of the repository.
 
+Setonix note: if you intend to expand this demo further, you can change `$outdir` to `$MYSCRATCH` in `demo/00_env.sh` and `source demo/00_env.sh`
+
 ```bash
-mkdir -p demo/data/1121334536/raw
-curl -L -o demo/data/1121334536/raw/1121334536_20150719094841_gpubox20_00.fits 'https://projects.pawsey.org.au/mwa-demo/1121334536_20150719094841_gpubox20_00.fits'
-mkdir -p demo/data/1303134032/raw
-curl -L -o demo/data/1303134032/raw/1303134032_20210422134116_gpubox20_01.fits 'https://projects.pawsey.org.au/mwa-demo/1303134032_20210422134116_gpubox20_01.fits'
-mkdir -p demo/data/1341914000/raw
-curl -L -o demo/data/1341914000/raw/1341914000_20220715095302_ch137_000.fits 'https://projects.pawsey.org.au/mwa-demo/1341914000_20220715095302_ch137_000.fits'
+export outdir=${outdir:-${PWD}/demo/data/}
+mkdir -p ${outdir}/1121334536/raw
+curl -L -o ${outdir}/1121334536/raw/1121334536_20150719094841_gpubox20_00.fits 'https://projects.pawsey.org.au/mwa-demo/1121334536_20150719094841_gpubox20_00.fits'
+mkdir -p ${outdir}/1303134032/raw
+curl -L -o ${outdir}/1303134032/raw/1303134032_20210422134116_gpubox20_01.fits 'https://projects.pawsey.org.au/mwa-demo/1303134032_20210422134116_gpubox20_01.fits'
+mkdir -p ${outdir}/1341914000/raw
+curl -L -o ${outdir}/1341914000/raw/1341914000_20220715095302_ch137_000.fits 'https://projects.pawsey.org.au/mwa-demo/1341914000_20220715095302_ch137_000.fits'
 ```
 
 Alternatively , you can download the same demo data in your browser [here](https://curtin-my.sharepoint.com/:u:/g/personal/285446d_curtin_edu_au/EQF1Dl93KixAimsD7wi7TcYBjAUs7Y6LO08An5rKSB2cmg?e=nMtGhu) and extract it to the `demo/data` directory.
@@ -258,7 +263,7 @@ Most HPC environments don't allow you to run Docker (for security reasons).
 You can however run Docker images in Singularity.
 
 ```bash
-singularity exec -B$PWD -W$PWD --cleanenv docker://mwatelescope/mwa-demo:latest /bin/bash
+singularity exec -B$PWD -B${outdir:-$PWD} -W$PWD --cleanenv docker://mwatelescope/mwa-demo:latest /bin/bash
 ```
 
 </details>

demo/00_setonix.sh

@@ -0,0 +1,55 @@
+#!/bin/bash
+# shellcheck disable=SC2139
+
+export outdir=${outdir:=${MYSCRATCH}/}
+module use /software/projects/pawsey1094/setonix/2024.05/modules/zen3/gcc/12.2.0
+module load hyperdrive/default birli/default giant-squid/default hyperbeam/default wsclean/default mwalib/default singularity/default
+module load py-pip/default py-numpy/default
+pip install --user \
+    importlib_metadata==8.2.0 \
+    kneed==0.8.5 \
+    matplotlib==3.7.5 \
+    maturin[patchelf]==1.7.0 \
+    numpy==1.24.4 \
+    pandas==2.0.3 \
+    pip==24.2 \
+    pyuvdata==2.4.5 \
+    pyvo==1.5.2 \
+    seaborn==0.13.2 \
+    psutil==6.0.0 \
+    git+https://github.com/mwilensky768/SSINS.git@master \
+    git+https://github.com/PaulHancock/Aegean.git \
+    git+https://github.com/tjgalvin/fits_warp.git \
+    git+https://github.com/d3v-null/mwa_qa.git@dev
+
+export singularity_base="singularity exec"
+export docker_img=${docker_img:="mwatelescope/mwa-demo:latest"}
+
+export bindir=${PWD}/bin/
+export PATH=${PATH}:${bindir}
+mkdir -p ${bindir}
+rm ${bindir}*
+while IFS='|' read -r bin argv; do
+    # strip spaces
+    bin=$(echo "$bin" | tr -d '[:space:]')
+    if command -v "$bin" &>/dev/null; then
+        echo "$bin already exists, skipping"
+        continue
+    else
+        echo "$bin not found, creating ${bindir}$bin"
+    fi
+    echo "#!/bin/bash" >"${bindir}$bin"
+    echo "$singularity_base $argv $docker_img $bin \"\$@\"" >>"${bindir}$bin"
+    chmod +x "${bindir}$bin"
+done <<-EoF
+birli
+giant-squid | -e MWA_ASVO_API_KEY=\$MWA_ASVO_API_KEY
+hyperdrive  | -e MWA_BEAM_FILE=\$MWA_BEAM_FILE
+jq
+wsclean
+python
+plot_calqa.py
+plot_prepvisqa.py
+run_calqa.py
+run_prepvisqa.py
+EoF

demo/02_download.sh

@@ -56,3 +56,15 @@ echo ""
 echo " -> download a job"
 echo "giant-squid download jobid"
 echo ""
+
+echo " -> download a bunch of obsids with the script at the bottom of 02_download.sh"
+exit 0
+
+giant-squid list $obsids_csv --states ready --json | jq -r $'.[]|[.jobId,.obsid]|@tsv' | while IFS=$'\t' read -r jobid obsid; do
+    echo jobid=$jobid obsid=$obsid
+    mkdir -p $outdir/$obsid/raw;
+    cd $_;
+    if eval ls -1 ${obsid}_2*.fits; then continue; fi
+    giant-squid download $jobid;
+    cd -;
+done