Merge pull request #12 from carpentries-incubator/cluster_snakefiles

Cluster snakefiles

episodes/files/Snakefile_cluster_iteration

@@ -0,0 +1,24 @@
+#
+# Run a bunch of Amdahl jobs and aggregate the output.
+#
+WIDTHS=[1,2]
+#
+def getwidth(wildcards):
+    return wildcards.sample
+
+rule plot:
+  input: expand('{size}.out',size=WIDTHS)
+  output: 'done.out'
+  resources:
+    mpi="mpirun",
+    tasks=1
+  shell: 'echo "{WIDTHS}, Done!" > done.out'
+rule iterate:
+  input: 
+  output: '{sample}.out' 
+  resources:
+    mpi="mpirun",
+    tasks=getwidth
+  shell: 
+    "module load OpenMPI; mpirun -np {resources.tasks} amdahl > {wildcards.sample}.out"
+

episodes/files/Snakefile_iterative

@@ -0,0 +1,13 @@
+#
+# Iterative example.
+#
+NAMES=['one','two','three']
+#
+rule done:
+  input: expand('{name}.out',name=NAMES)
+  output: 'done.out'
+  shell: 'echo "Done!" > done.out'
+rule iterate:
+  input: 
+  output: '{sample}.out' 
+  shell: 'echo {output} > {output}'

episodes/files/queuing_config.yaml

@@ -0,0 +1,6 @@
+#  snakemake -j 3 --cluster "sbatch -N 1 -n {resources.tasks} -p node"
+cluster: 
+  sbatch
+    --partition=node
+    --nodes=1
+    --tasks={resources.tasks}