sbatch: initial slurm implementation

2 files changed, 33 insertions, 0 deletions

diff --git a/default.nix b/default.nix
index 604badb..608fa9b 100644
--- a/default.nix
+++ b/default.nix
@@ -34,6 +34,11 @@ let
     strelka = callBionix ./tools/strelka.nix {};
     ascat = callBionix ./tools/ascat.nix {};
 
+    sbatch = attrs: bionix.extend (self: super: with self; rec {
+      sbatchDefs = { ppn = 1; mem = 1; walltime = "24:00:00"; partition = null; slurmFlags = null; } // attrs;
+      sbatch = attrs: (callPackage ./lib/sbatch.nix {}) (sbatchDefs // attrs);
+      exec = f: x: y: sbatch (builtins.intersectAttrs sbatchDefs x) (f (builtins.removeAttrs x (builtins.attrNames sbatchDefs)) y);
+      });
     qsub = attrs: bionix.extend (self: super: with self; rec {
       qsubDefs = { ppn = 1; mem = 1; walltime = "24:00:00"; tmpDir = "/tmp"; sleepTime = 60; queue = null; qsubFlags = null; } // attrs;
       qsub = attrs: (callPackage ./lib/qsub.nix {}) (qsubDefs // attrs);
diff --git a/lib/sbatch.nix b/lib/sbatch.nix
new file mode 100644
index 0000000..efb7654
--- /dev/null
+++ b/lib/sbatch.nix
@@ -0,0 +1,28 @@
+{stdenv, lib, writeScript, coreutils}:
+
+with lib;
+
+{ ppn, mem, walltime, partition ? null, slurmFlags ? null}:
+drv:
+  let ppnReified = if drv.multicore then ppn else 1;
+  in lib.overrideDerivation drv ({ args, builder, name, ... }: {
+    builder = stdenv.shell;
+    args = let
+      script = writeScript "sbatch-script" ''
+        #!${stdenv.shell}
+        ${builder} ${lib.escapeShellArgs args}
+      '';
+
+      sbatch = writeScript "sbatch" ''
+        #!${stdenv.shell}
+        NIX_BUILD_CORES=${toString ppnReified}
+
+        salloc -c $NIX_BUILD_CORES --mem=${toString mem}G -t ${walltime} \
+          -J "${name}" \
+          ${optionalString (partition != null) "-p ${partition}"} \
+          ${optionalString (slurmFlags != null) slurmFlags} \
+          ${script}
+      '';
+
+      in [ "-c" sbatch ];
+  })