From d9b6e7bc43a7848fba5783e92415887a5ab9b4c8 Mon Sep 17 00:00:00 2001
From: "christoph.stritt@unibas.ch" <christoph.stritt@unibas.ch>
Date: Tue, 16 Jan 2024 12:29:46 +0100
Subject: [PATCH] cluster config again
---
assembly/cluster/config.yaml | 6 +++---
assembly/config/cluster_config.yaml | 29 -----------------------------
2 files changed, 3 insertions(+), 32 deletions(-)
delete mode 100644 assembly/config/cluster_config.yaml
diff --git a/assembly/cluster/config.yaml b/assembly/cluster/config.yaml
index a8eb216..e4ec829 100644
--- a/assembly/cluster/config.yaml
+++ b/assembly/cluster/config.yaml
@@ -9,9 +9,9 @@ cluster:
--output=logs/{rule}/{rule}-{wildcards}-%j.stdout
--error=logs/{rule}/{rule}-{wildcards}-%j.stderr
default-resources:
- - partition=scicore
- - qos=1day
- - time=12:00:00
+ - partition='scicore'
+ - qos='1day'
+ - time='12:00:00'
- mem_mb=20000
restart-times: 3
max-jobs-per-second: 10
diff --git a/assembly/config/cluster_config.yaml b/assembly/config/cluster_config.yaml
deleted file mode 100644
index e4f0748..0000000
--- a/assembly/config/cluster_config.yaml
+++ /dev/null
@@ -1,29 +0,0 @@
-cluster:
- mkdir -p logs/{rule} &&
- sbatch
- --partition={resources.partition}
- --qos={resources.qos}
- --cpus-per-task={threads}
- --mem={resources.mem_mb}
- --job-name=assemblySMK-{rule}-{wildcards}
- --output=logs/{rule}/{rule}-{wildcards}-%j.stdout
- --error=logs/{rule}/{rule}-{wildcards}-%j.stderr
-default-resources:
- - "partition='scicore'"
- - "qos='1day'"
- - "time=12:00:00"
- - "mem_mb=20000"
-restart-times: 3
-max-jobs-per-second: 10
-max-status-checks-per-second: 1
-local-cores: 1
-latency-wait: 60
-jobs: 500
-keep-going: True
-rerun-incomplete: True
-printshellcmds: True
-scheduler: greedy
-use-conda: True
-
-
-# https://github.com/jdblischak/smk-simple-slurm
--
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