From 2564dc3619768231604f5b5f75a17df7a6f327b7 Mon Sep 17 00:00:00 2001
From: Andrew Reid <andrew.reid@nist.gov>
Date: Mon, 23 Oct 2023 10:38:18 -0400
Subject: [PATCH 1/2] Draft cluster snakefile stuff.

The "Snakefile_cluster_iteration" file manages the list of
widths, and can iterate over jobs on the cluster and then
do a (trivial) aggregation step.

The queuing_config.yaml file is a short cluster config that
removes the need to type the cluster stuff into the command
line.  It conventionally goes in
$HOME/.config/snakemake/queuing/config.yaml, and is accessed
by "snakemake <other-args> --profile=queuing".

The Snakefile has mpi stuff for the trivial aggregation rule
because the cluster-ness of it applies to all the rules.
This is clumsy, but not wrong.
---
 episodes/files/Snakefile_cluster_iteration | 24 ++++++++++++++++++++++
 episodes/files/queuing_config.yaml         |  6 ++++++
 2 files changed, 30 insertions(+)
 create mode 100644 episodes/files/Snakefile_cluster_iteration
 create mode 100644 episodes/files/queuing_config.yaml

diff --git a/episodes/files/Snakefile_cluster_iteration b/episodes/files/Snakefile_cluster_iteration
new file mode 100644
index 0000000..41a94a2
--- /dev/null
+++ b/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"
+
diff --git a/episodes/files/queuing_config.yaml b/episodes/files/queuing_config.yaml
new file mode 100644
index 0000000..7db5043
--- /dev/null
+++ b/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}

From 3cb2dfbd0a1e8c706c6923e725201bd0fea3abce Mon Sep 17 00:00:00 2001
From: Andrew Reid <andrew.reid@nist.gov>
Date: Wed, 20 Dec 2023 11:02:50 -0500
Subject: [PATCH 2/2] Adding an iterative snakefile.

No cluster shenanigans in this one, just straight-up iteration,
maybe a useful intermediate step.
---
 episodes/files/Snakefile_iterative | 13 +++++++++++++
 1 file changed, 13 insertions(+)
 create mode 100644 episodes/files/Snakefile_iterative

diff --git a/episodes/files/Snakefile_iterative b/episodes/files/Snakefile_iterative
new file mode 100644
index 0000000..8fe13f8
--- /dev/null
+++ b/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}'