Merge pull request #35 from glotzerlab/constraints

Add submit options to the cluster configuration

doc/src/clusters/cluster.md

@@ -51,6 +51,11 @@ be one of:
 * `"slurm"`
 * `"bash"`
 
+## submit_options
+
+`cluster.submit_options`: **array** of **strings** - Scheduler submission options that
+are passed to every job on this cluster.
+
 ## partition
 
 `cluster.partition`: **array** of **tables** - Define the scheduler partitions that

doc/src/release-notes.md

@@ -7,6 +7,7 @@
 * Edit links to documentation pages.
 * New arguments to `show status` display actions that are in the requested states:
  `--completed`, `--eligible`, `--submitted`, and `--waiting`.
+* `cluster.submit_options` configuration option in `clusters.toml`.
 
 *Changed:*
 
@@ -15,6 +16,8 @@
 * `show status` hides actions with 0 directories by default. Pass `--all` to show all
   actions.
 * `clean` now cleans all caches by default.
+* Submit jobs with `--constraint="scratch"` by default on Delta.
+* Submit jobs with `--constraint="nvme"` by default on Frontier.
 
 *Fixed:*
 

src/builtin.rs

@@ -72,6 +72,7 @@ fn andes() -> Cluster {
         name: "andes".into(),
         identify: IdentificationMethod::ByEnvironment("LMOD_SYSTEM_NAME".into(), "andes".into()),
         scheduler: SchedulerType::Slurm,
+        submit_options: Vec::new(),
         partition: vec![
             // Auto-detected partitions: batch
             Partition {
@@ -92,6 +93,7 @@ fn anvil() -> Cluster {
         name: "anvil".into(),
         identify: IdentificationMethod::ByEnvironment("RCAC_CLUSTER".into(), "anvil".into()),
         scheduler: SchedulerType::Slurm,
+        submit_options: Vec::new(),
         partition: vec![
             // Auto-detected partitions: shared | wholenode | gpu
             Partition {
@@ -149,6 +151,7 @@ fn delta() -> Cluster {
         name: "delta".into(),
         identify: IdentificationMethod::ByEnvironment("LMOD_SYSTEM_NAME".into(), "Delta".into()),
         scheduler: SchedulerType::Slurm,
+        submit_options: vec!["--constraint=\"scratch\"".to_string()],
         partition: vec![
             // Auto-detected partitions: cpu | gpuA100x4
             Partition {
@@ -206,6 +209,7 @@ fn frontier() -> Cluster {
         name: "frontier".into(),
         identify: IdentificationMethod::ByEnvironment("LMOD_SYSTEM_NAME".into(), "frontier".into()),
         scheduler: SchedulerType::Slurm,
+        submit_options: vec!["--constraint=\"nvme\"".to_string()],
         partition: vec![
             // Auto-detected partitions: batch
             Partition {
@@ -225,6 +229,7 @@ fn greatlakes() -> Cluster {
         name: "greatlakes".into(),
         identify: IdentificationMethod::ByEnvironment("CLUSTER_NAME".into(), "greatlakes".into()),
         scheduler: SchedulerType::Slurm,
+        submit_options: Vec::new(),
         partition: vec![
             // Auto-detected partitions: standard | gpu_mig40,gpu | gpu.
             Partition {
@@ -295,6 +300,7 @@ fn none() -> Cluster {
         name: "none".into(),
         identify: IdentificationMethod::Always(true),
         scheduler: SchedulerType::Bash,
+        submit_options: Vec::new(),
         partition: vec![Partition {
             name: "none".into(),
             ..Partition::default()

src/cluster.rs

@@ -46,6 +46,10 @@ pub struct Cluster {
 
     /// The partitions in the cluster's queue.
     pub partition: Vec<Partition>,
+
+    /// Submit options to include in every job submitted to this cluster.
+    #[serde(default)]
+    pub submit_options: Vec<String>,
 }
 
 /// Methods to identify clusters.
@@ -400,30 +404,35 @@ mod tests {
                 identify: IdentificationMethod::Always(false),
                 scheduler: SchedulerType::Bash,
                 partition: Vec::new(),
+                submit_options: Vec::new(),
             },
             Cluster {
                 name: "cluster1".into(),
                 identify: IdentificationMethod::ByEnvironment("_row_select".into(), "a".into()),
                 scheduler: SchedulerType::Bash,
                 partition: Vec::new(),
+                submit_options: Vec::new(),
             },
             Cluster {
                 name: "cluster2".into(),
                 identify: IdentificationMethod::ByEnvironment("_row_select".into(), "b".into()),
                 scheduler: SchedulerType::Bash,
                 partition: Vec::new(),
+                submit_options: Vec::new(),
             },
             Cluster {
                 name: "cluster3".into(),
                 identify: IdentificationMethod::Always(true),
                 scheduler: SchedulerType::Bash,
                 partition: Vec::new(),
+                submit_options: Vec::new(),
             },
             Cluster {
                 name: "cluster4".into(),
                 identify: IdentificationMethod::ByEnvironment("_row_Select".into(), "b".into()),
                 scheduler: SchedulerType::Bash,
                 partition: Vec::new(),
+                submit_options: Vec::new(),
             },
         ];
         let cluster_configuration = Configuration { cluster: clusters };
@@ -591,6 +600,7 @@ mod tests {
             identify: IdentificationMethod::Always(true),
             scheduler: SchedulerType::Bash,
             partition: partitions,
+            submit_options: Vec::new(),
         };
 
         let cpu_resources = Resources {
@@ -728,6 +738,7 @@ name = "b"
         assert_eq!(cluster.name, "a");
         assert_eq!(cluster.identify, IdentificationMethod::Always(true));
         assert_eq!(cluster.scheduler, SchedulerType::Bash);
+        assert!(cluster.submit_options.is_empty());
         assert_eq!(
             cluster.partition,
             vec![Partition {
@@ -748,6 +759,7 @@ name = "b"
 name = "a"
 identify.by_environment = ["b", "c"]
 scheduler = "slurm"
+submit_options = ["option1", "option2"]
 
 [[cluster.partition]]
 name = "d"
@@ -777,6 +789,7 @@ account_suffix = "-gpu"
             IdentificationMethod::ByEnvironment("b".into(), "c".into())
         );
         assert_eq!(cluster.scheduler, SchedulerType::Slurm);
+        assert_eq!(cluster.submit_options, vec!["option1", "option2"]);
         assert_eq!(
             cluster.partition,
             vec![Partition {

src/scheduler/bash.rs

@@ -539,6 +539,7 @@ mod tests {
             scheduler: SchedulerType::Bash,
             identify: IdentificationMethod::Always(false),
             partition: Vec::new(),
+            submit_options: Vec::new(),
         };
         let script = Bash::new(cluster, launchers)
             .make_script(&action, &directories)

src/scheduler/slurm.rs

@@ -115,6 +115,11 @@ impl Scheduler for Slurm {
         let minutes = (total + 59) / 60;
         let _ = writeln!(preamble, "#SBATCH --time={minutes}");
 
+        // Add global cluster submit options first so that users can override them.
+        for option in &self.cluster.submit_options {
+            let _ = writeln!(preamble, "#SBATCH {option}");
+        }
+
         // Use provided submission options
         if let Some(submit_options) = action.submit_options.get(&self.cluster.name) {
             if let Some(ref account) = submit_options.account {
@@ -299,6 +304,7 @@ mod tests {
             identify: IdentificationMethod::Always(false),
             scheduler: SchedulerType::Slurm,
             partition: vec![Partition::default()],
+            submit_options: Vec::new(),
         };
 
         let slurm = Slurm::new(cluster, launchers.by_cluster("cluster"));
@@ -323,6 +329,27 @@ mod tests {
         assert!(script.contains("#SBATCH --time=180"));
     }
 
+    #[test]
+    #[parallel]
+    fn cluster_submit_options() {
+        let (action, directories, mut slurm) = setup();
+        slurm.cluster.submit_options = vec!["--option=value".to_string()];
+
+        let script = slurm
+            .make_script(&action, &directories)
+            .expect("valid script");
+        println!("{script}");
+
+        assert!(script.contains("#SBATCH --job-name=action"));
+        assert!(script.contains("#SBATCH --ntasks=1"));
+        assert!(!script.contains("#SBATCH --account"));
+        assert!(script.contains("#SBATCH --partition=partition"));
+        assert!(!script.contains("#SBATCH --cpus-per-task"));
+        assert!(!script.contains("#SBATCH --gpus-per-task"));
+        assert!(script.contains("#SBATCH --time=180"));
+        assert!(script.contains("#SBATCH --option=value"));
+    }
+
     #[test]
     #[parallel]
     fn ntasks() {
@@ -421,6 +448,7 @@ mod tests {
             name: "cluster".into(),
             identify: IdentificationMethod::Always(false),
             scheduler: SchedulerType::Slurm,
+            submit_options: Vec::new(),
             partition: vec![Partition {
                 memory_per_cpu: Some("a".into()),
                 ..Partition::default()
@@ -447,6 +475,7 @@ mod tests {
             name: "cluster".into(),
             identify: IdentificationMethod::Always(false),
             scheduler: SchedulerType::Slurm,
+            submit_options: Vec::new(),
             partition: vec![Partition {
                 memory_per_gpu: Some("b".into()),
                 ..Partition::default()
@@ -475,6 +504,7 @@ mod tests {
             name: "cluster".into(),
             identify: IdentificationMethod::Always(false),
             scheduler: SchedulerType::Slurm,
+            submit_options: Vec::new(),
             partition: vec![Partition {
                 cpus_per_node: Some(10),
                 ..Partition::default()
@@ -503,6 +533,7 @@ mod tests {
             name: "cluster".into(),
             identify: IdentificationMethod::Always(false),
             scheduler: SchedulerType::Slurm,
+            submit_options: Vec::new(),
             partition: vec![Partition {
                 gpus_per_node: Some(5),
                 ..Partition::default()