WIP: postprocessing pipeline

Now each run is executed in a independent folder

garlic/stages/control.nix

@@ -19,7 +19,10 @@ stdenv.mkDerivation {
     cat > $out <<EOF
     #!/bin/sh
     for n in \$(seq 1 ${toString loops}); do
+      mkdir "\$n"
+      cd "\$n"
       ${stageProgram nextStage}
+      cd ..
     done
     EOF
     chmod +x $out

garlic/stages/sbatch.nix

@@ -14,6 +14,7 @@
 , ntasks ? null
 , ntasksPerNode ? null
 , ntasksPerSocket ? null
+, cpusPerTask ? null
 , nodes ? null
 , exclusive ? true # By default we run in exclusive mode
 , qos ? null
@@ -60,6 +61,7 @@ stdenv.mkDerivation rec {
     + sbatchOpt "ntasks" ntasks
     + sbatchOpt "ntasks-per-node" ntasksPerNode
     + sbatchOpt "ntasks-per-socket" ntasksPerSocket
+    + sbatchOpt "cpus-per-task" cpusPerTask
     + sbatchOpt "nodes" nodes
     + sbatchOpt "chdir" chdir
     + sbatchOpt "output" output

garlic/stages/srun.nix

@@ -8,6 +8,8 @@
 , cpuBind
 , nixPrefix
 , srunOptions ? ""
+, output ? "stdout.log"
+, error ? "stderr.log"
 }:
 
 with garlicTools;
@@ -23,6 +25,8 @@ stdenv.mkDerivation rec {
     exec ${slurm}/bin/srun \
       --mpi=pmi2 \
       --cpu-bind=${cpuBind} \
+      --output=${output} \
+      --error=${error} \
       ${srunOptions} \
       ${nixPrefix}${stageProgram nextStage}
     EOF