Improved sync with HPC and added config for longer runs

.run_configs/fau_woody/executor.sh

@@ -4,7 +4,7 @@ sbatch <<EOT
 #!/bin/bash -l
 
 #SBATCH --job-name="$2"
-#SBATCH --time=03:00:00
+#SBATCH --time=08:00:00
 #SBATCH --mail-user="$USER_EMAIL"
 #SBATCH --mail-type=ALL
 #SBATCH --output=../../results/hpc_logs/%j_$2.out

.run_configs/fau_woody/executor_short.sh

@@ -0,0 +1,23 @@
+#!/bin/bash
+
+sbatch <<EOT
+#!/bin/bash -l
+
+#SBATCH --job-name="$2"
+#SBATCH --time=03:00:00
+#SBATCH --mail-user="$USER_EMAIL"
+#SBATCH --mail-type=ALL
+#SBATCH --output=../../results/hpc_logs/%j_$2.out
+#SBATCH --ntasks=5
+
+# load module
+module load python/3.9-anaconda
+
+# Make sure poetry is in path
+export PATH="$HOME/.local/bin:$PATH"
+
+echo "Starting job $2"
+echo "Running command: $1"
+eval "$1"
+echo "Finished job $2"
+EOT

.run_configs/fau_woody/result_sync.sh

@@ -15,7 +15,7 @@ REMOTE_PATH="~/projects/gaitmap-bench"
 # To do this safely without deleting any commits locally, we actually use git and not rsync for this.
 echo "Syncing git directory"
 git remote add _woody "$USERNAME"@woody.nhr.fau.de:"$REMOTE_PATH"
-git pull _woody "$(git branch --show-current)" --rebase || exit 1
+git pull _woody "$(git branch --show-current)" --rebase --autostash || exit 1
 git remote remove _woody
 
 # Use rsync to sync the results directory from the remote machine