add hpc stuff

README.md

@@ -236,6 +236,23 @@ stdenv.mkDerivation {
 }
 ```
 
+### [`makeSquashFs`](./lib/make-squashfs)
+
+builds a squashfs image from the given derivations
+
+example
+```nix
+makeSquashFs {
+  filename = "my-image"; # optional
+  storeContents = [ foo bar ];
+}
+```
+
+### [`makeHpcDist`](./lib/make-hpc-dist)
+
+create a packaged nix distribution with the given packages in it for weird HPC systems. go read the
+source to find out what it does; i don't recommend using this if you're not me
+
 ## development
 
 structure of this repo

default.nix

@@ -12,6 +12,9 @@
 
       gitSource = prev.callPackage ./lib/git-source {};
 
+      makeSquashFs = prev.callPackage ./lib/make-squashfs {};
+      makeHpcDist = final.callPackage ./lib/make-hpc-dist {};
+
       ghidra_headless = prev.ghidra.override {
         openjdk17 = prev.openjdk17_headless;
       };

lib/make-hpc-dist/default.nix

@@ -0,0 +1,119 @@
+{
+  mkShell,
+  runCommand,
+  stdenvNoCC,
+  vmTools,
+  writeClosure,
+  writeText,
+
+  bash,
+  cacert,
+  coreutils,
+  lix,
+  singularity,
+
+  makeSquashFs,
+
+  diskSize ? 1024,
+  memSize ? 1024
+}:
+{
+  contents,
+  startupScript ? "exec ${bash}/bin/bash -i"
+}:
+let
+  base-container = runCommand "empty.sif.d" {
+    buildInputs = [ coreutils ];
+  } ''
+    mkdir "$out"
+    cd "$out"
+    mkdir -p proc sys dev nix etc bin usr/bin .singularity.d
+    ln -s /etc/sh bin/sh
+    ln -s /etc/env usr/bin/env
+    ln -s /etc/runscript .singularity.d/runscript
+  '';
+  container-image = vmTools.runInLinuxVM (
+    runCommand "singularity-empty-image" {
+      buildInputs = [ base-container singularity ];
+    } ''
+      export HOME=/tmp
+      cp -r "${base-container}" "/tmp/container"
+      cd "/tmp"
+      find container -type d -exec chmod 755 {} \;
+
+      mkdir -p /var/lib/singularity/mnt/session
+      echo "root:x:0:0:System administrator:/root:/bin/sh" > /etc/passwd
+      echo > /etc/resolv.conf
+      ${singularity}/bin/singularity build "$out/empty.sif" "container/"
+    '');
+
+  deps = [ coreutils bash cacert ];
+
+  startupScriptFile = writeText "singularity-startup-script" startupScript;
+
+  shell = stdenvNoCC.mkDerivation {
+    name = "shell";
+    propagatedBuildInputs = deps ++ contents;
+    unpackPhase = "true";
+    installPhase = ''
+      mkdir -p "$out/bin"
+      printf '#!${bash}/bin/bash\n' > "$out/bin/startup.sh"
+      export >> "$out/bin/startup.sh"
+      cat "${startupScriptFile}" >> "$out/bin/startup.sh"
+      chmod +x "$out/bin/startup.sh"
+    '';
+  };
+
+  base-etc = runCommand "singularity-etc" {
+    buildInputs = [ coreutils bash cacert ];
+  } ''
+    mkdir "$out"
+    ln -s "${shell}/bin/startup.sh" "$out/runscript"
+    ln -s "${bash}/bin/bash" "$out/sh"
+    ln -s "${coreutils}/bin/env" "$out/env"
+
+    mkdir -p "$out/ssl/certs"
+    ln -s "${cacert}/etc/ssl/certs/ca-bundle.crt" "$out/ssl/certs/ca-bundle.crt"
+    ln -s "${cacert}/etc/ssl/certs/ca-bundle.crt" "$out/ssl/certs/ca-certificates.crt"
+
+    touch "$out/localtime"
+    touch "$out/resolv.conf"
+  '';
+
+
+  squashfs = makeSquashFs { filename = "nix-store"; storeContents = [ shell ]; };
+
+  startCommand = writeText "run-container.sh" ''
+    #!/usr/bin/env bash
+    set -euo pipefail
+
+    module load singularity/3.10.3
+
+    temp_dir="$(mktemp -d)"
+    mkdir -p "$TMPDIR/empty"
+    function __cleanup {
+      echo cleaning up
+      rsync -r --delete -- "$TMPDIR/empty/." "$temp_dir/."
+      rmdir "$temp_dir"
+      echo done
+    }
+    trap __cleanup EXIT
+
+    cp -r etc nix-store.squashfs "$temp_dir"
+
+    chmod +w "$temp_dir/etc"
+    chmod +w "$temp_dir/etc/resolv.conf"
+    chmod +w "$temp_dir/etc/localtime"
+    cat /etc/localtime > $temp_dir/etc/localtime
+    cat /etc/resolv.conf > $temp_dir/etc/resolv.conf
+
+    singularity run -B "/work:/work,/scratch:/scratch,$temp_dir/nix-store.squashfs:/nix/store:image-src=/,$temp_dir/etc:/etc" --pid --uts --ipc container-base.sif
+  '';
+in runCommand "hpc-files.d" {} ''
+  mkdir "$out"
+  cp "${squashfs}" "$out/nix-store.squashfs"
+  cp -r "${base-etc}" "$out/etc"
+  cp "${container-image}/empty.sif" "$out/container-base.sif"
+  cp "${startCommand}" "$out/run-container.sh"
+  chmod +x "$out/run-container.sh"
+''

lib/make-squashfs/default.nix

@@ -0,0 +1,23 @@
+{
+  squashfsTools,
+
+  closureInfo,
+  runCommand
+}:
+{
+  filename ? "image",
+  storeContents ? [],
+  comp ? "xz -Xdict-size 100%"
+}:
+let
+  compFlag = if comp == null then "-no-compression" else "-comp ${comp}";
+in runCommand "${filename}.squashfs" {
+  nativeBuildInputs = [ squashfsTools ];
+} ''
+  closureInfo=${closureInfo { rootPaths = storeContents; }}
+  cp $closureInfo/registration nix-path-registration
+
+  mksquashfs nix-path-registration $(cat $closureInfo/store-paths) $out \
+      -no-hardlinks -keep-as-directory -all-root -b 1048576 ${compFlag} \
+      -processors $NIX_BUILD_CORES
+''