From a51ec03347bdd7fd0b42bd51deba03f37f0ffc2b Mon Sep 17 00:00:00 2001
From: Luca Beltrame <luca.beltrame@humanitasresearch.it>
Date: Tue, 28 Jun 2022 08:13:32 +0200
Subject: [PATCH] Use a more robust check for process completion

The approach used in the script assumes that the GPU is exclusively used
by the invoker. However, some places (like mine) treat GPUs as shared
resources. Therefore, the single presence of a process called `python`
in the process list, even if not created by the caller, will cause the
script to loop needlessly.

This change creates an array where the PIDs for each of the calculations
are stored, then uses `wait` to ensure that all the processes have ended
before moving to the next iteration.

**Note**: This adds a dependency on bash (but I'm not sure if this
script is POSIX-compatible) and requires a reasonably recent version of
it (tested with 5.0 on Debian).
---
 .../1_Signature_derivation_from_input_matrix.sh     | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/Denovo_Signature_Discovery/scripts/1_Signature_derivation_from_input_matrix.sh b/Denovo_Signature_Discovery/scripts/1_Signature_derivation_from_input_matrix.sh
index 7cf9290..71be385 100755
--- a/Denovo_Signature_Discovery/scripts/1_Signature_derivation_from_input_matrix.sh
+++ b/Denovo_Signature_Discovery/scripts/1_Signature_derivation_from_input_matrix.sh
@@ -1,4 +1,4 @@
-#!
+#!/bin/bash
 
 #### Deriving signatures from input matrix
 
@@ -73,21 +73,20 @@ for ITER in $(seq 1 $ITERS); do
 
     echo $ITER
 
+    pids=()
     for PAR in $(seq 1 $PARALLEL); do
 
         UUID=$(cat /dev/urandom | tr -dc 'A-Z0-9' | fold -w 6 | head -n 1)
         OUTPATH="${UUID}"
         mkdir -p $OUTPATH
         python $SCRIPTPATH --data $INPUTMATRIX --max_iter=$MAXITER --output_dir $OUTPATH $REGULARISATIONS --labeled --K0 $K0 > ${OUTPATH}/${UUID}_log.txt &
+        pids[${PAR}]=$!
 
     done
 
-    sleep 4
-    PYRUN=`nvidia-smi | grep -c python`
-    while [[ $PYRUN != 0 ]]; do
-        sleep 2
-        PYRUN=`nvidia-smi | grep -c python`
+    for pid in ${pids[*]}; do
+        wait $pid
     done
 
 done
-echo "NMF finished. Goodbye!"
\ No newline at end of file
+echo "NMF finished. Goodbye!"