From 57f2abeb27f72491f5dea9ff80cb87c353b6eb15 Mon Sep 17 00:00:00 2001
From: Benjamin Wingfield <bwingfield@ebi.ac.uk>
Date: Mon, 26 Jun 2023 17:53:22 +0100
Subject: [PATCH] fix job submission output and db update
---
src/db/job/update.rs | 14 +++++++++-----
1 file changed, 9 insertions(+), 5 deletions(-)
diff --git a/src/db/job/update.rs b/src/db/job/update.rs
index b4c82c1..447c54b 100644
--- a/src/db/job/update.rs
+++ b/src/db/job/update.rs
@@ -1,3 +1,4 @@
+use std::path::Path;
use std::process::Command;
use log::info;
use rusqlite::Connection;
@@ -25,7 +26,7 @@ impl JobRequest {
info!("Updating {id} with slurm ID {slurm_id}");
conn
.execute("UPDATE job SET slurm_id = ? WHERE intervene_id = ?",
- &[&id, &slurm_id])
+ &[&slurm_id, &id])
.expect("Update");
Ok(())
@@ -44,13 +45,16 @@ impl JobRequest {
}
fn run_sbatch(&self, job_path: JobPath) -> String {
- let wd = job_path.path.parent().unwrap().to_str().unwrap();
+ let wd = job_path.path.parent().unwrap();
+ let output_path = wd.join(Path::new("%j.out"));
+ let output_str = output_path.to_str().unwrap();
+ info!("Output path: {output_str}");
let job_script_path = job_path.path.to_str().unwrap();
- let arguments = vec!["--parsable", job_script_path];
- let mut sbatch = Command::new("/usr/bin/sbatch");
+ let arguments = vec!["--parsable", "--output", output_str, job_script_path];
+
+ let mut sbatch = Command::new("sbatch");
let cmd = sbatch.args(&arguments);
- info!("Running sbatch process ");
info!("{:?}", &cmd);
let output = cmd.output().expect("failed to execute process").stdout;
--
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