Init files

batch/SLURM_inference_job.run

@@ -28,34 +28,37 @@ which Rscript
 export PATH=~/aws-cli/bin:$PATH
 echo "***************** DONE LOADING ENVIRONMENT *****************"
 
+# If running from zsh, this ensure the compatibility of using space separated words as bash array
+setopt shwordsplit
+
 
 echo "***************** FETCHING RESUME FILES *****************"
 ### In case of resume, download or move the right files
 export LAST_JOB_OUTPUT=$(echo $LAST_JOB_OUTPUT | sed 's/\/$//')
-if [ -n "$LAST_JOB_OUTPUT" ]; then  # -n Checks if the length of a string is nonzero --> if LAST_JOB_OUTPUT is not empty, the we download the output from the last job
-	if [ $FLEPI_BLOCK_INDEX -eq 1 ]; then  # always true for slurm submissions
+if [[ -n "$LAST_JOB_OUTPUT" ]]; then  # -n Checks if the length of a string is nonzero --> if LAST_JOB_OUTPUT is not empty, the we download the output from the last job
+	if [[ $FLEPI_BLOCK_INDEX -eq 1 ]]; then  # always true for slurm submissions
 		export RESUME_RUN_INDEX=$OLD_FLEPI_RUN_INDEX
 		echo "RESUME_DISCARD_SEEDING is set to $RESUME_DISCARD_SEEDING"
-		if [ $RESUME_DISCARD_SEEDING == "true" ]; then
-			export PARQUET_TYPES="spar snpi hpar hnpi"
+		if [[ $RESUME_DISCARD_SEEDING == "true" ]]; then
+			export PARQUET_TYPES="spar snpi hpar hnpi init"
 		else
-			export PARQUET_TYPES="seed spar snpi hpar hnpi"
+			export PARQUET_TYPES="seed spar snpi hpar hnpi init"
 		fi
 	else                                 # if we are not in the first block, we need to resume from the last job, with seeding an all.
 		export RESUME_RUN_INDEX=$FLEPI_RUN_INDEX
-		export PARQUET_TYPES="seed spar snpi seir hpar hnpi hosp llik"
+		export PARQUET_TYPES="seed spar snpi seir hpar hnpi hosp llik init"
 	fi
 	for filetype in $PARQUET_TYPES
 	do
-		if [ $filetype == "seed" ]; then
+		if [[ $filetype == "seed" ]]; then
 			export extension="csv"
 		else
 			export extension="parquet"
 		fi
 		for liketype in "global" "chimeric"
 		do
 			export OUT_FILENAME=$(python -c "from gempyor import file_paths; print(file_paths.create_file_name('$FLEPI_RUN_INDEX','$FLEPI_PREFIX/$FLEPI_RUN_INDEX/$liketype/intermediate/%09d.'% $FLEPI_SLOT_INDEX,$FLEPI_BLOCK_INDEX-1,'$filetype','$extension'))")
-			if [ $FLEPI_BLOCK_INDEX -eq 1 ]; then
+			if [[ $FLEPI_BLOCK_INDEX -eq 1 ]]; then
 				export IN_FILENAME=$(python -c "from gempyor import file_paths; print(file_paths.create_file_name('$RESUME_RUN_INDEX','$FLEPI_PREFIX/$RESUME_RUN_INDEX/$liketype/final/',$FLEPI_SLOT_INDEX,'$filetype','$extension'))")
 			else
 				export IN_FILENAME=$OUT_FILENAME
@@ -69,18 +72,38 @@ if [ -n "$LAST_JOB_OUTPUT" ]; then  # -n Checks if the length of a string is non
                 mkdir -p $OUT_FILENAME_DIR
                 cp $LAST_JOB_OUTPUT/$IN_FILENAME $OUT_FILENAME
             fi
-		    if [ -f $OUT_FILENAME ]; then
+		    if [[ -f $OUT_FILENAME ]]; then
 				echo "Copy successful for file of type $filetype ($IN_FILENAME -> $OUT_FILENAME)"
 			else
 				echo "Could not copy file of type $filetype ($IN_FILENAME -> $OUT_FILENAME)"
-				if [ $liktype -eq "global" ]; then
-					exit 2
-				fi
 			fi
 		done
 	done
-	ls -ltr model_output
 fi
+
+if [[ $FLEPI_CONTINUATION == "TRUE" ]]; then
+    echo "We are doing a continuation"
+    export INIT_FILENAME=$(python -c "from gempyor import file_paths; print(file_paths.create_file_name('$FLEPI_RUN_INDEX','$FLEPI_PREFIX/$FLEPI_RUN_INDEX/global/intermediate/%09d.'% $FLEPI_SLOT_INDEX,$FLEPI_BLOCK_INDEX-1,'$FLEPI_CONTINUATION_FTYPE','$extension'))")
+    # in filename is always a seir file
+    export IN_FILENAME=$(python -c "from gempyor import file_paths; print(file_paths.create_file_name('$FLEPI_CONTINUATION_RUN_ID','$FLEPI_PREFIX/$FLEPI_CONTINUATION_RUN_ID/global/final/',$FLEPI_SLOT_INDEX,'seir','$extension'))")
+    if [[ $FLEPI_CONTINUATION_LOCATION == *"s3://"* ]]; then
+        aws s3 cp --quiet $FLEPI_CONTINUATION_LOCATION/$IN_FILENAME $INIT_FILENAME
+    else
+        # cp does not create directorys, so we make the directories first
+        export $OUT_FILENAME_DIR="$(dirname "${INIT_FILENAME}")"
+        mkdir -p $OUT_FILENAME_DIR
+        cp $FLEPI_CONTINUATION_LOCATION/$IN_FILENAME $INIT_FILENAME
+    fi
+    if [[ -f $INIT_FILENAME ]]; then
+        echo "CONTINUATION: Copy successful for file of type $filetype ($IN_FILENAME -> $INIT_FILENAME)"
+    else
+        echo "CONTINUATION: Could not copy file of type $filetype ($IN_FILENAME -> $INIT_FILENAME)"
+    fi
+    #Rscript $FLEPI_PATH/flepimop/main_scripts/seir_init_immuneladder.R --res_config config_SMH_R17_noBoo_lowIE_phase2_blk2.yml
+    #Rscript $FLEPI_PATH/preprocessing/seir_init_immuneladder_r17phase3_preOm.R --res_config config_SMH_R17_noBoo_lowIE_phase2_blk2.yml
+fi
+
+ls -ltr model_output
 echo "***************** DONE FETCHING RESUME FILES *****************"
 
 echo "***************** RUNNING INFERENCE_MAIN.R *****************"
@@ -100,20 +123,20 @@ echo "Rscript $FLEPI_PATH/flepimop/main_scripts/inference_slot.R --config $CONFI
                                                                  --python python
                                                                  --rpath Rscript
                                                                  --is-resume $RESUME_RUN # Is this run a resume
-                                                                 --is-interactive FALSE # Is this run an interactive run" > $LOG_FILE 2>&1 &
+                                                                 --is-interactive FALSE # Is this run an interactive run" #> $LOG_FILE 2>&1 &
 
-Rscript $FLEPI_PATH/flepimop/main_scripts/inference_slot.R -p $FLEPI_PATH --config $CONFIG_PATH --run_id $FLEPI_RUN_INDEX --npi_scenarios $FLEPI_NPI_SCENARIOS --outcome_scenarios $FLEPI_OUTCOME_SCENARIOS --jobs 1 --iterations_per_slot $FLEPI_ITERATIONS_PER_SLOT --this_slot $FLEPI_SLOT_INDEX --this_block 1 --stoch_traj_flag $FLEPI_STOCHASTIC_RUN --is-resume $RESUME_RUN --is-interactive FALSE > $LOG_FILE 2>&1
+Rscript $FLEPI_PATH/flepimop/main_scripts/inference_slot.R -p $FLEPI_PATH --config $CONFIG_PATH --run_id $FLEPI_RUN_INDEX --npi_scenarios $FLEPI_NPI_SCENARIOS --outcome_scenarios $FLEPI_OUTCOME_SCENARIOS --jobs 1 --iterations_per_slot $FLEPI_ITERATIONS_PER_SLOT --this_slot $FLEPI_SLOT_INDEX --this_block 1 --stoch_traj_flag $FLEPI_STOCHASTIC_RUN --is-resume $RESUME_RUN --is-interactive FALSE #> $LOG_FILE 2>&1
 dvc_ret=$?
-if [ $dvc_ret -ne 0 ]; then
+if [[ $dvc_ret -ne 0 ]]; then
         echo "Error code returned from inference_slot.R: $dvc_ret"
 fi
 echo "***************** DONE RUNNING INFERENCE_SLOT.R *****************"
 
 
 echo "***************** UPLOADING RESULT TO S3 (OR NOT) *****************"
 ## copy to s3 if necessary:
-if [ $S3_UPLOAD == "true" ]; then
-    for type in "seir" "hosp" "llik" "spar" "snpi" "hnpi" "hpar"
+if [[ $S3_UPLOAD == "true" ]]; then
+    for type in "seir" "hosp" "llik" "spar" "snpi" "hnpi" "hpar" "init"
     do
         export FILENAME=$(python -c "from gempyor import file_paths; print(file_paths.create_file_name('$FLEPI_RUN_INDEX','$FLEPI_PREFIX/$FLEPI_RUN_INDEX/chimeric/intermediate/%09d.'% $FLEPI_SLOT_INDEX,$FLEPI_BLOCK_INDEX,'$type','parquet'))")
         aws s3 cp --quiet $FILENAME $S3_RESULTS_PATH/$FILENAME
@@ -128,12 +151,12 @@ if [ $S3_UPLOAD == "true" ]; then
             export FILENAME=$(python -c "from gempyor import file_paths; print(file_paths.create_file_name('$FLEPI_RUN_INDEX','$FLEPI_PREFIX/$FLEPI_RUN_INDEX/global/intermediate/%09d.'% $FLEPI_SLOT_INDEX,$FLEPI_BLOCK_INDEX,'$type','csv'))")
         aws s3 cp --quiet $FILENAME $S3_RESULTS_PATH/$FILENAME
     done
-        for type in "seir" "hosp" "llik" "spar" "snpi" "hnpi" "hpar" "memprof"
+        for type in "seir" "hosp" "llik" "spar" "snpi" "hnpi" "hpar" "memprof" "init"
     do
         export FILENAME=$(python -c "from gempyor import file_paths; print(file_paths.create_file_name('$FLEPI_RUN_INDEX','$FLEPI_PREFIX/$FLEPI_RUN_INDEX/global/intermediate/%09d.'% $FLEPI_SLOT_INDEX,$FLEPI_BLOCK_INDEX,'$type','parquet'))")
         aws s3 cp --quiet $FILENAME $S3_RESULTS_PATH/$FILENAME
     done
-        for type in "seir" "hosp" "llik" "spar" "snpi" "hnpi" "hpar" "memprof"
+        for type in "seir" "hosp" "llik" "spar" "snpi" "hnpi" "hpar" "memprof" "init"
     do
         export FILENAME=$(python -c "from gempyor import file_paths; print(file_paths.create_file_name('$FLEPI_RUN_INDEX','$FLEPI_PREFIX/$FLEPI_RUN_INDEX/global/final/', $FLEPI_SLOT_INDEX,'$type','parquet'))")
         aws s3 cp --quiet $FILENAME $S3_RESULTS_PATH/$FILENAME
@@ -149,7 +172,7 @@ echo "***************** DONE UPLOADING RESULT TO S3 (OR NOT) *****************"
 
 # TODO: MV here ? what to do about integration_dump.pkl e.g ?
 echo "***************** COPYING RESULTS TO RESULT DIRECTORY *****************"
-for type in "seir" "hosp" "llik" "spar" "snpi" "hnpi" "hpar"
+for type in "seir" "hosp" "llik" "spar" "snpi" "hnpi" "hpar" "init"
 do
     export FILENAME=$(python -c "from gempyor import file_paths; print(file_paths.create_file_name('$FLEPI_RUN_INDEX','$FLEPI_PREFIX/$FLEPI_RUN_INDEX/chimeric/intermediate/%09d.'% $FLEPI_SLOT_INDEX,$FLEPI_BLOCK_INDEX,'$type','parquet'))")
     export $OUT_FILENAME_DIR="$(dirname "${FS_RESULTS_PATH}/${FILENAME}")"
@@ -170,14 +193,14 @@ do
     mkdir -p $OUT_FILENAME_DIR
     cp --parents $FILENAME $FS_RESULTS_PATH
 done
-for type in "seir" "hosp" "llik" "spar" "snpi" "hnpi" "hpar" "memprof"
+for type in "seir" "hosp" "llik" "spar" "snpi" "hnpi" "hpar" "memprof" "init"
 do
     export FILENAME=$(python -c "from gempyor import file_paths; print(file_paths.create_file_name('$FLEPI_RUN_INDEX','$FLEPI_PREFIX/$FLEPI_RUN_INDEX/global/intermediate/%09d.'% $FLEPI_SLOT_INDEX,$FLEPI_BLOCK_INDEX,'$type','parquet'))")
     export $OUT_FILENAME_DIR="$(dirname "${FS_RESULTS_PATH}/${FILENAME}")"
     mkdir -p $OUT_FILENAME_DIR
     cp --parents $FILENAME $FS_RESULTS_PATH
 done
-    for type in "seir" "hosp" "llik" "spar" "snpi" "hnpi" "hpar" "memprof"
+    for type in "seir" "hosp" "llik" "spar" "snpi" "hnpi" "hpar" "memprof" "init"
 do
     export FILENAME=$(python -c "from gempyor import file_paths; print(file_paths.create_file_name('$FLEPI_RUN_INDEX','$FLEPI_PREFIX/$FLEPI_RUN_INDEX/global/final/', $FLEPI_SLOT_INDEX,'$type','parquet'))")
     export $OUT_FILENAME_DIR="$(dirname "${FS_RESULTS_PATH}/${FILENAME}")"
@@ -204,5 +227,6 @@ echo "DONE EVERYTHING."
 # --> THIS DOES NOT WORK
 #mv slurm-$SLURM_ARRAY_JOB_ID_${SLURM_ARRAY_TASK_ID}.out $FS_RESULTS_PATH/slurm-$SLURM_ARRAY_JOB_ID_${SLURM_ARRAY_TASK_ID}.out
 
+unsetopt shwordsplit
 
 wait

batch/SLURM_inference_runner.sh

@@ -128,12 +128,12 @@ if [ $S3_UPLOAD == "true" ]; then
             export FILENAME=$(python -c "from gempyor import file_paths; print(file_paths.create_file_name('$FLEPI_RUN_INDEX','$FLEPI_PREFIX/$FLEPI_RUN_INDEX/global/intermediate/%09d.'% $FLEPI_SLOT_INDEX,$FLEPI_BLOCK_INDEX,'$type','csv'))")
         aws s3 cp --quiet $FILENAME $S3_RESULTS_PATH/$FILENAME
     done
-        for type in "seir" "hosp" "llik" "spar" "snpi" "hnpi" "hpar"
+        for type in "seir" "hosp" "llik" "spar" "snpi" "hnpi" "hpar" "memprof"
     do
         export FILENAME=$(python -c "from gempyor import file_paths; print(file_paths.create_file_name('$FLEPI_RUN_INDEX','$FLEPI_PREFIX/$FLEPI_RUN_INDEX/global/intermediate/%09d.'% $FLEPI_SLOT_INDEX,$FLEPI_BLOCK_INDEX,'$type','parquet'))")
         aws s3 cp --quiet $FILENAME $S3_RESULTS_PATH/$FILENAME
     done
-        for type in "seir" "hosp" "llik" "spar" "snpi" "hnpi" "hpar"
+        for type in "seir" "hosp" "llik" "spar" "snpi" "hnpi" "hpar" "memprof"
     do
         export FILENAME=$(python -c "from gempyor import file_paths; print(file_paths.create_file_name('$FLEPI_RUN_INDEX','$FLEPI_PREFIX/$FLEPI_RUN_INDEX/global/final/', $FLEPI_SLOT_INDEX,'$type','parquet'))")
         aws s3 cp --quiet $FILENAME $S3_RESULTS_PATH/$FILENAME
@@ -170,14 +170,14 @@ do
     mkdir -p $OUT_FILENAME_DIR
     cp --parents $FILENAME $FS_RESULTS_PATH
 done
-for type in "seir" "hosp" "llik" "spar" "snpi" "hnpi" "hpar"
+for type in "seir" "hosp" "llik" "spar" "snpi" "hnpi" "hpar" "memprof"
 do
     export FILENAME=$(python -c "from gempyor import file_paths; print(file_paths.create_file_name('$FLEPI_RUN_INDEX','$FLEPI_PREFIX/$FLEPI_RUN_INDEX/global/intermediate/%09d.'% $FLEPI_SLOT_INDEX,$FLEPI_BLOCK_INDEX,'$type','parquet'))")
     export $OUT_FILENAME_DIR="$(dirname "${FS_RESULTS_PATH}/${FILENAME}")"
     mkdir -p $OUT_FILENAME_DIR
     cp --parents $FILENAME $FS_RESULTS_PATH
 done
-    for type in "seir" "hosp" "llik" "spar" "snpi" "hnpi" "hpar"
+    for type in "seir" "hosp" "llik" "spar" "snpi" "hnpi" "hpar" "memprof"
 do
     export FILENAME=$(python -c "from gempyor import file_paths; print(file_paths.create_file_name('$FLEPI_RUN_INDEX','$FLEPI_PREFIX/$FLEPI_RUN_INDEX/global/final/', $FLEPI_SLOT_INDEX,'$type','parquet'))")
     export $OUT_FILENAME_DIR="$(dirname "${FS_RESULTS_PATH}/${FILENAME}")"

batch/SLURM_postprocess_runner.run

@@ -19,14 +19,17 @@ conda activate flepimop-env
 which python
 which Rscript
 
+# aws cli to export plots (location according to instruction)
+export PATH=~/aws-cli/bin:$PATH
+
 # move all the slurm logs into the right folder:
 mv slurm-$SLURM_ARRAY_JOB_ID_${SLURM_ARRAY_TASK_ID}.out $FS_RESULTS_PATH/slurm-$SLURM_ARRAY_JOB_ID_${SLURM_ARRAY_TASK_ID}.out
 
 curl \
   -H "Title: $FLEPI_RUN_INDEX Done ✅" \
   -H "Priority: urgent" \
   -H "Tags: warning,snail" \
-  -d "TODO say how many failure and stuff" \
+  -d "Hopefully the results look alright" \
   ntfy.sh/flepimop_alerts
 
 # get the slack credentials
@@ -37,3 +40,8 @@ mkdir pplot
 
 source $FLEPI_PATH/batch/postprocessing-scripts.sh
 
+cp -R pplot $FS_RESULTS_PATH
+if [[ $S3_UPLOAD == "true" ]]; then
+    aws s3 cp --quiet pplot $S3_RESULTS_PATH/pplot
+fi
+