From 3d3dbe701e22f5d8989e184cf11b5f95e35a3c7e Mon Sep 17 00:00:00 2001
From: Samuel Hanot <samuel.hanot@pasteur.fr>
Date: Tue, 13 Mar 2018 11:15:39 +0100
Subject: [PATCH] make recursive_gmconvert.sh get the number of gaussians from
an array. This opens the door to reading num of gaussians lists from a file
---
recursive_gmconvert.sh | 36 +++++++++++++++++++++++-------------
1 file changed, 23 insertions(+), 13 deletions(-)
diff --git a/recursive_gmconvert.sh b/recursive_gmconvert.sh
index 0b37711..e8c6b8a 100755
--- a/recursive_gmconvert.sh
+++ b/recursive_gmconvert.sh
@@ -18,8 +18,8 @@ Optional arguments:
#defaults
map_name=
threshold=
-n_gaussians=
-n_gaussians0=
+ng=
+ng0=
N=
i0=1
serial=0
@@ -29,8 +29,8 @@ do
case "$opt" in
f) map_name="$OPTARG";;
t) threshold="$OPTARG";;
- n) n_gaussians="$OPTARG";;
- 0) n_gaussians0="$OPTARG";;
+ n) ng="$OPTARG";;
+ 0) ng0="$OPTARG";;
N) N="$OPTARG";;
i) i0="$OPTARG";;
s) serial=1;;
@@ -44,17 +44,29 @@ do
done
#check that necessary options were set
-if [[ ! -e "$map_name" ]] || [[ -z "$threshold" ]] || [[ -z "$n_gaussians" ]] || [[ -z "$N" ]]
+if [[ ! -e "$map_name" ]] || [[ -z "$threshold" ]] || [[ -z "$ng" ]] || [[ -z "$N" ]]
then
usage
exit 1
fi
-if [[ -z "$n_gaussians0" ]]
+if [[ -z "$ng0" ]]
then
- n_gaussians0=$n_gaussians
+ ng0=$ng
fi
+num_gaussians=()
+for ((i=$i0 ; i<=N ; i++))
+do
+ if ((i==1))
+ then
+ num_gaussians+=$ng0
+ else
+ num_gaussians+=$ng
+ fi
+done
+
+
MaxArraySize=100000
get_max_jobs(){
echo ${MaxArraySize}
@@ -71,12 +83,10 @@ map_name=$(basename $map_name)
cd $map_root_dir
-
mkdir -p converged
-for ((i=$i0 ; i<=N ; i++))
+for ((i=$i0 ; i<=${#num_gaussians} ; i++))
do
- echo "i=$i"
- n=$((i))
+ n=${num_gaussians[$i]}
jobname=${map_name}_${n}
n_jobs=1
@@ -86,7 +96,7 @@ do
then
${gmconvert} -imap ${map_name} -zth ${threshold} -oimap threshold.map -ogmm /dev/null -ng 0
fi
- echo ${profile_cmd} ${gmconvert} -imap ${map_name} -ogmm $n/${n}_0.gmm -ng ${n_gaussians0} -zth ${threshold}
+ echo ${profile_cmd} ${gmconvert} -imap ${map_name} -ogmm $n/${n}_0.gmm -ng ${ng0} -zth ${threshold}
echo ${gmconvert} -igmm $n/${n}_0.gmm -imap ${map_name} -omap /dev/null
else
n_prev=$((i-1))
@@ -97,7 +107,7 @@ do
n_jobs=$((n_jobs + $(awk '/NGAUSS/{s+=$3}END{print s}' ${gmm_file}) ))
done
echo echo ${gmm_name} '$((SLURM_ARRAY_TASK_ID-1+offset))' \> 'tmp_$((SLURM_ARRAY_TASK_ID+offset)).txt'
- echo ${profile_cmd} ${gmconvert} -imap ${map_name} -gmml 'tmp_$((SLURM_ARRAY_TASK_ID+offset)).txt' -ogmm $n/${n}_'$((SLURM_ARRAY_TASK_ID-1+offset))'.gmm -ng ${n_gaussians} -zth ${threshold}
+ echo ${profile_cmd} ${gmconvert} -imap ${map_name} -gmml 'tmp_$((SLURM_ARRAY_TASK_ID+offset)).txt' -ogmm $n/${n}_'$((SLURM_ARRAY_TASK_ID-1+offset))'.gmm -ng ${ng} -zth ${threshold}
echo ${gmconvert} -igmm $n/${n}_'$((SLURM_ARRAY_TASK_ID-1+offset)).gmm' -imap ${map_name} -gmml 'tmp_$((SLURM_ARRAY_TASK_ID+offset)).txt' -omap /dev/null
fi > commands_$i.sh
mkdir -p $n
--
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