d97010481bcf72f263f4a6a21010e46bf667c272
angie
  Thu Jan 13 11:45:32 2022 -0800
Shorten time limit for matOptimize cluster run to 2 hours (probably could be 1) because it usually doesn't recognize when it's done.

diff --git src/hg/utils/otto/sarscov2phylo/usherClusterRun.sh src/hg/utils/otto/sarscov2phylo/usherClusterRun.sh
index ae2e336..6eb0965 100755
--- src/hg/utils/otto/sarscov2phylo/usherClusterRun.sh
+++ src/hg/utils/otto/sarscov2phylo/usherClusterRun.sh
@@ -1,158 +1,158 @@
 #!/bin/bash
 set -beEu -x -o pipefail
 
 #	Do not modify this script, modify the source tree copy:
 #	kent/src/hg/utils/otto/sarscov2phylo/usherClusterRun.sh
 
 usage() {
     echo "usage: $0 today"
 }
 
 if [ $# != 1 ]; then
   usage
   exit 1
 fi
 
 today=$1
 
 ottoDir=/hive/data/outside/otto/sarscov2phylo
 scriptDir=$(dirname "${BASH_SOURCE[0]}")
 source $scriptDir/util.sh
 
 usherDir=~angie/github/usher
 usher=$usherDir/build/usher
 matUtils=$usherDir/build/matUtils
 
 cd $ottoDir/$today
 
 # 32 cluster jobs, 16 threads each --> 1/2 capacity of ku cluster.  (for many hours)
 jobCount=32
 threadCount=16
 
 sampleCount=$(vcfSamples new.masked.vcf.gz | wc -l)
 samplesPerJob=$(( ($sampleCount + ($jobCount-1)) / $jobCount ))
 
 echo $sampleCount samples, $jobCount jobs, $samplesPerJob samples per job
 for ((i=0;  $i < $jobCount;  i++)); do
     startIx=$(( 10 + ($i * $samplesPerJob) ))
     if [ $i == $(( $jobCount - 1 )) ]; then
         endIx=$(( 9 + $sampleCount ))
     else
         endIx=$(( 9 + (($i+1) * $samplesPerJob) ))
     fi
     echo job $i, genotype columns $startIx-$endIx
     zcat new.masked.vcf.gz \
     | cut -f 1-9,$startIx-$endIx \
     | gzip -c \
         > new.$i.masked.vcf.gz
     vcfSamples new.$i.masked.vcf.gz | wc -l
 done
 
 cat > runUsher.sh <<EOF
 #!/bin/bash
 set -beEu
 vcf=\$1
 pbIn=\$2
 pbOut=\$3
 log=\$4
 /cluster/home/angie/github/usher/build/usher -u -T $threadCount -A -e 5 -v \$vcf -i \$pbIn -o \$pbOut >& \$log
 EOF
 chmod a+x runUsher.sh
 
 cp /dev/null jobList
 for ((i=0;  $i < $jobCount;  i++)); do
     echo "./runUsher.sh new.$i.masked.vcf.gz prevRenamed.pb {check out exists preTrim.$i.pb} usher.addNew.$i.log" >> jobList
 done
 
 ssh ku "cd $ottoDir/$today && para -cpu=$threadCount -ram=16g -retries=5 -priority=10 make jobList"
 
 # Make a combined log (updateCombinedTree.sh looks there for sequences with excessively high EPPs)
 cat usher.addNew.*.log > usher.addNew.log
 
 # Merge 32 protobufs into 1
 time $matUtils merge -T 8 --input-mat-1 preTrim.0.pb --input-mat-2 preTrim.1.pb -o merged.0.1.pb &
 $matUtils merge -T 8 --input-mat-1 preTrim.2.pb --input-mat-2 preTrim.3.pb -o merged.2.3.pb &
 $matUtils merge -T 8 --input-mat-1 preTrim.4.pb --input-mat-2 preTrim.5.pb -o merged.4.5.pb &
 $matUtils merge -T 8 --input-mat-1 preTrim.6.pb --input-mat-2 preTrim.7.pb -o merged.6.7.pb &
 $matUtils merge -T 8 --input-mat-1 preTrim.8.pb --input-mat-2 preTrim.9.pb -o merged.8.9.pb &
 $matUtils merge -T 8 --input-mat-1 preTrim.10.pb --input-mat-2 preTrim.11.pb -o merged.10.11.pb &
 $matUtils merge -T 8 --input-mat-1 preTrim.12.pb --input-mat-2 preTrim.13.pb -o merged.12.13.pb &
 $matUtils merge -T 8 --input-mat-1 preTrim.14.pb --input-mat-2 preTrim.15.pb -o merged.14.15.pb &
 wait
 
 time $matUtils merge -T 8 --input-mat-1 preTrim.16.pb --input-mat-2 preTrim.17.pb -o merged.16.17.pb &
 $matUtils merge -T 8 --input-mat-1 preTrim.18.pb --input-mat-2 preTrim.19.pb -o merged.18.19.pb &
 $matUtils merge -T 8 --input-mat-1 preTrim.20.pb --input-mat-2 preTrim.21.pb -o merged.20.21.pb &
 $matUtils merge -T 8 --input-mat-1 preTrim.22.pb --input-mat-2 preTrim.23.pb -o merged.22.23.pb &
 $matUtils merge -T 8 --input-mat-1 preTrim.24.pb --input-mat-2 preTrim.25.pb -o merged.24.25.pb &
 $matUtils merge -T 8 --input-mat-1 preTrim.26.pb --input-mat-2 preTrim.27.pb -o merged.26.27.pb &
 $matUtils merge -T 8 --input-mat-1 preTrim.28.pb --input-mat-2 preTrim.29.pb -o merged.28.29.pb &
 $matUtils merge -T 8 --input-mat-1 preTrim.30.pb --input-mat-2 preTrim.31.pb -o merged.30.31.pb &
 wait
 
 time $matUtils merge -T 8 --input-mat-1 merged.0.1.pb --input-mat-2 merged.2.3.pb -o merged.0.3.pb &
 $matUtils merge -T 8 --input-mat-1 merged.4.5.pb --input-mat-2 merged.6.7.pb -o merged.4.7.pb &
 $matUtils merge -T 8 --input-mat-1 merged.8.9.pb --input-mat-2 merged.10.11.pb -o merged.8.11.pb &
 $matUtils merge -T 8 --input-mat-1 merged.12.13.pb --input-mat-2 merged.14.15.pb -o merged.12.15.pb &
 $matUtils merge -T 8 --input-mat-1 merged.16.17.pb --input-mat-2 merged.18.19.pb -o merged.16.19.pb &
 $matUtils merge -T 8 --input-mat-1 merged.20.21.pb --input-mat-2 merged.22.23.pb -o merged.20.23.pb &
 $matUtils merge -T 8 --input-mat-1 merged.24.25.pb --input-mat-2 merged.26.27.pb -o merged.24.27.pb &
 $matUtils merge -T 8 --input-mat-1 merged.28.29.pb --input-mat-2 merged.30.31.pb -o merged.28.31.pb &
 wait
 
 time $matUtils merge -T 16 --input-mat-1 merged.0.3.pb --input-mat-2 merged.4.7.pb -o merged.0.7.pb &
 $matUtils merge -T 16 --input-mat-1 merged.8.11.pb --input-mat-2 merged.12.15.pb -o merged.8.15.pb &
 $matUtils merge -T 16 --input-mat-1 merged.16.19.pb --input-mat-2 merged.20.23.pb -o merged.16.23.pb &
 $matUtils merge -T 16 --input-mat-1 merged.24.27.pb --input-mat-2 merged.28.31.pb -o merged.24.31.pb &
 wait
 
 time $matUtils merge -T 32 --input-mat-1 merged.0.7.pb --input-mat-2 merged.8.15.pb -o merged.0.15.pb &
 time $matUtils merge -T 32 --input-mat-1 merged.16.23.pb --input-mat-2 merged.24.31.pb -o merged.16.31.pb &
 wait
 
 time $matUtils merge -T 64 --input-mat-1 merged.0.15.pb --input-mat-2 merged.16.31.pb -o merged.pb
 
 # Mask Delta deletion sites where spurious "mutations" called by sloppy genome assembly pipelines
 # wreak havoc otherwise.
 $scriptDir/maskDelta.sh merged.pb merged.deltaMasked.pb
 
 # Optimize on the cluster too, with Cheng's MPI-parallelized matOptimize
 # Reserve parasol nodes with a "cluster run" of sleep commands
 mkdir -p reserveKuNodes
 cd reserveKuNodes
 jobCount=16
 threadCount=16
-reserveHours=8
+reserveHours=2
 reserveSeconds=$((3600 * $reserveHours))
 cp /dev/null jobList
 for ((i=0;  $i < $jobCount;  i++)); do
     echo "sleep $reserveSeconds" >> jobList
 done
 ssh ku "cd $ottoDir/$today/reserveKuNodes && para create -cpu=$threadCount jobList && para push"
 
 # Wait for all jobs to start (i.e. all nodes to be reserved):
 echo "Waiting for parasol to assign ku nodes"
-while (( $(ssh ku "parasol list jobs | grep $USER" | awk '$2 != "none"' | wc -l) < $jobCount )); do
+while (( $(ssh ku "parasol list jobs | grep $USER | grep sleep" | awk '$2 != "none"' | wc -l) < $jobCount )); do
     sleep 10
 done
 
 # Make hostfile for mpirun
 cd $ottoDir/$today
 ssh ku "parasol list jobs | grep $USER | grep sleep" \
 | awk '{print $2;}' \
 | sort \
 | uniq -c \
 | awk '{print $2, "slots=" '$threadCount'*$1;}' \
     > hostfile
 
 # mpirun matOptimize on first host in hostfile
 headNode=$(head -1 hostfile | awk '{print $1;}')
 radius=8
 ssh $headNode "cd $ottoDir/$today && \
-               $scriptDir/kuRunMatOptimize.sh -T $threadCount -r $radius \
+               $scriptDir/kuRunMatOptimize.sh -T $threadCount -r $radius -M $reserveHours \
                    -S move_log.cluster -i merged.deltaMasked.pb \
                    -o gisaidAndPublic.$today.masked.preTrim.pb \
                    >& matOptimize.cluster.log"
 
 # Release the ku nodes by stopping the parasol batch
-ssh ku "cd $ottoDir/$today/reserveKuNodes && para stop"
+ssh ku "cd $ottoDir/$today/reserveKuNodes && para stop || true"