Merge branch 'copy-file' into GH-191/longleaf-batch-submission

batch/slurm_init_longleaf.sh

@@ -0,0 +1,42 @@
+echo ">>> running some useful commands 🤖, please wait"
+module purge
+module load gcc/9.3.0
+module load git
+module load git-lfs
+module load slurm
+module load anaconda3/2022.05
+conda activate flepimop-env
+export CENSUS_API_KEY="6a98b751a5a7a6fc365d14fa8e825d5785138935"  # joseph's key
+source /scratch4/struelo1/flepimop-code/slack_credentials.sh
+# export COVID_STOCHASTIC=false
+# export COVID_RESET_CHIMERICS=TRUE
+# export COVID_PATH=/scratch4/struelo1/flepimop-code/$USER/COVIDScenarioPipeline
+
+export FLEPI_STOCHASTIC_RUN=false
+export FLEPI_RESET_CHIMERICS=TRUE
+export FLEPI_PATH=/scratch4/struelo1/flepimop-code/$USER/flepiMoP
+
+echo "done ✅"
+
+echo "Doing some inference_run setup, hit enter to skip a question if not relevant or you're not planning on doing a run"
+
+export TODAY=`date --rfc-3339='date'`
+echo "Let's set up a flepiMoP run. Today is the $TODAY"
+
+echo "(1/3) Please input the validation date:"
+read input
+export VALIDATION_DATE="$input"
+echo -e ">>> set VALIDATION DATE to $VALIDATION_DATE \n"
+
+echo "(2/3) Please input the resume location (empty if no resume, or a s3:// url or a local folder):"
+read input
+export RESUME_LOCATION="$input"
+echo -e ">>> set RESUME_LOCATION to $RESUME_LOCATION \n"
+
+echo "(3/3) Please provide the Run Index for the current run:"
+read input
+export FLEPI_RUN_INDEX="$input"
+echo -e ">>> set  FLEPI_RUN_INDEX to $FLEPI_RUN_INDEX \n"
+
+echo "DONE. if no error please manually set export CONFIG_PATH=YOURCONFIGPATH.yml"
+echo "(in case of error, override manually some variables or rerun this script)"