Corrected mpirun to work with hostfiles

Author: Gabryel Mason-Williams crc99971

distrac/distrac.sh

@@ -70,9 +70,10 @@ fi
 
 ./create-mon.sh -i=$interface -f=$folder
 ./create-mgr.sh -f=$folder
-echo HOSTS:$mpiHosts
-module load openmpi/1.4.3
-mpirun -H $mpiHosts ./create-gram.sh -s=$size -n=$amount -f=$folder &
+echo HOSTS:
+cat $folder/hostfile
+module load openmpi
+mpirun --hostfile $folder/hostfile  ./create-gram.sh -s=$size -n=$amount -f=$folder &
 wait
 if ([ ! -z "$poolname" ] && [ "$rgw" = "false" ])
 then

distrac/process-hostfile.sh

@@ -20,5 +20,5 @@ esac
 done
 # Read hostfile and put the amount of hosts in amountOfHosts.num
 echo `awk -F '[,]' ' {print NF}' $hostfile` > $folder/amountOfHosts.num
-# Assign a string of hosts with commas to mpiHosts
-mpiHosts=$(cat $hostfile)
+# Convert the hostfile to a column of hosts and store in $folder/hostlist
+tr , '\n' <  $hostfile >  $folder/hostfile

distrac/remove-distrac.sh

@@ -32,13 +32,13 @@ else
     source ./uge-hostfile.sh -f=$folder
 fi
 
-module load openmpi/1.4.3
+module load openmpi
 echo "Removing Ceph"
-mpirun -H $mpiHosts ./remove-ceph.sh
+mpirun --hostfile $folder/hostfile ./remove-ceph.sh
 echo "Removing OSDs"
-mpirun -H $mpiHosts ./remove-osd.sh
+mpirun --hostfile $folder/hostfile ./remove-osd.sh
 echo "Removing GRAM"
-mpirun -H $mpiHosts ./remove-gram.sh
+mpirun --hostfile $folder/hostfile ./remove-gram.sh
 echo "Removing Temp Files"
 ./remove-temp-files.sh -f=$folder
 echo "Done"

distrac/remove-temp-files.sh

@@ -14,5 +14,6 @@ case $i in
 esac
 done
 rm $folder/ceph.*
+rm $folder/hostfile 
 rm $folder/*.num
 rmdir $folder

distrac/uge-hostfile.sh

@@ -14,11 +14,5 @@ case $i in
 esac
 done
 # Read UGE PE_HOSTFILE and extract hosts
-while read name rest
-	do 
-		hosts+=($name)
-done < <(cat $PE_HOSTFILE)
-# Put the amount of hosts in amountOfHosts.num
-echo "${#hosts[@]}"  > $folder/amountOfHosts.num
-# Assign a string of hosts with commas to mpiHosts
-mpiHosts=$(IFS=,; echo "${hosts[*]}")
+awk '{print $1 }' ${PE_HOSTFILE} | uniq > $folder/hostfile
+cat $folder/hostfile | wc -l > $folder/amountOfHosts.num