Merge pull request #16 from CALeDNA/develop

smart js2 flavor sizing

autoscale.sh

@@ -4,7 +4,7 @@
 JS2AUTOSCALING="/home/ubuntu/t-rex-monitor/js2-autoscaling.sh"
 CONFIG="/home/ubuntu/crux/crux/vars/crux_vars.sh"
 SETUP_CONFIG="/home/ubuntu/t-rex-monitor/vm_vars.sh"
-QUEUES=("/etc/ben/queue/qc.ini" "/etc/ben/queue/assign.ini" "/etc/ben/queue/ecopcr.ini" "/etc/ben/queue/blast.ini" "/etc/ben/queue/ac.ini" "/etc/ben/queue/newick.ini" "/etc/ben/queue/tronko.ini")
+QUEUES=("/etc/ben/queue/qc.ini" "/etc/ben/queue/assign.ini" "/etc/ben/queue/assignxl.ini" "/etc/ben/queue/ecopcr.ini" "/etc/ben/queue/blast.ini" "/etc/ben/queue/ac.ini" "/etc/ben/queue/newick.ini" "/etc/ben/queue/tronko.ini")
 
 cd /home/ubuntu/t-rex-monitor
 

js2-autoscaling.sh

@@ -17,8 +17,8 @@ while getopts "b:c:d" opt; do
     esac
 done
 
-source $CONFIG
-# gets JSCRED, SSHKEY, NETWORK, SECURITY, SSHCONFIG
+source $CONFIG # gets JSCRED, SSHKEY, NETWORK, SECURITY, SSHCONFIG
+
 VMNAME="${BENSERVER##*/ben-}"
 
 declare -A MAXVM_MAP
@@ -31,6 +31,7 @@ MAXVM_MAP=(
     ["tronko"]=$MAX_TRONKO
     ["qc"]=$MAX_QC
     ["assign"]=$MAX_ASSIGN
+    ["assignxl"]=$MAX_ASSIGNXL
 )
 
 MAXVM="${MAXVM_MAP[${VMNAME}]}"
@@ -117,7 +118,7 @@ else # Scale Up
                 n="$availVM"
             fi
 
-            if [[ $BENSERVER == *assign* ]]; then
+            if [[ $BENSERVER == *assignxl* ]]; then
                 FLAVOR="m3.xl" # need more RAM for tronko assign
             fi
 

main/setup_instance.sh

@@ -11,7 +11,6 @@ SECURITY=""
 VOLUME=""
 VMNAME="chunk"
 VMNUMBER=0
-SETUP_CONFIG="/home/ubuntu/t-rex-monitor/vm_vars.sh"
 while getopts "u:f:i:k:j:n:m:b:s:w:v:c:" opt; do
     case $opt in
         u) USER="$OPTARG"
@@ -57,7 +56,6 @@ START=$VMNUMBER
 END=$(( VMNUMBER + NUMINSTANCES))
 
 source $JSCRED
-source $SETUP_CONFIG
 
 
 # create and start an instance

scheduler/ben.sh

@@ -55,7 +55,13 @@ do
     if [[ -v SERVER_MAP[${BENSERVER}] ]]; then
         # add socket connection to add job after
         BENSERVERSECOND="${SERVER_MAP[${BENSERVER}]}"
-        /etc/ben/ben client -r $host -n 0 --remote-path $REMOTE_PATH -s $BENSERVERSECOND --remote-socket $BENSERVERSECOND -d
+        /etc/ben/ben client -r "$host" -n 0 --remote-path "$REMOTE_PATH" -s "$BENSERVERSECOND" --remote-socket "$BENSERVERSECOND" -d
+
+        # add assign XL socket
+        if [[ $BENSERVERSECOND == *assign* ]]; then
+            BENSERVERSECOND="${BENSERVERSECOND}xl"
+            /etc/ben/ben client -r "$host" -n 0 --remote-path "$REMOTE_PATH" -s "$BENSERVERSECOND" --remote-socket "$BENSERVERSECOND" -d
+        fi
     fi
     counter=$(( 10#$counter + 1 ))
 done

scheduler/main_ben_setup.sh

@@ -24,6 +24,7 @@ sudo cp jobs/ben-jobs.service jobs/ben-jobs.timer supabase/ben-supabase.service
 /etc/ben/ben server --snapshot /etc/ben/queue/tronko.ini -s /tmp/ben-tronko -d
 /etc/ben/ben server --snapshot /etc/ben/queue/qc.ini -s /tmp/ben-qc -d
 /etc/ben/ben server --snapshot /etc/ben/queue/assign.ini -s /tmp/ben-assign -d
+/etc/ben/ben server --snapshot /etc/ben/queue/assignxl.ini -s /tmp/ben-assignxl -d
 
 sudo systemctl enable ben-logs.service
 sudo systemctl enable ben-jobs.service

scheduler/servers/ben-assignxl-server.service

@@ -0,0 +1,16 @@
+[Unit]
+Description=Ben Assign XL Job Scheduler Server
+After=network-online.target
+
+[Service]
+User=ubuntu
+Type=forking
+WorkingDirectory=/home/ubuntu/t-rex-monitor/scheduler/servers
+Environment="PATH=/usr/local/bin:/usr/bin:/bin:/home/ubuntu/miniconda/envs/webhook/bin"
+ExecStart=/bin/bash ./ben-servers.sh "assignxl" "/tmp/ben-assignxl"
+TimeoutSec=600
+Restart=no
+RestartSec=5s
+
+[Install]
+WantedBy=multi-user.target

vm_vars.sh.sample

@@ -23,4 +23,5 @@ MAX_AC=5
 MAX_NEWICK=5
 MAX_TRONKO=5
 MAX_QC=5
-MAX_ASSIGN=5
+MAX_ASSIGN=5
+MAX_ASSIGNXL=2