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README_orphan.md

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##Random Info

Rel restart, login vcellapi
sudo docker service update --force --detach=false vcellrel_activemqint
sudo docker service update --force --detach=false vcellrel_activemqsim
sudo docker service update --force --detach=false vcellrel_mongodb
sudo docker service update --force --detach=false vcellrel_db
sudo docker service update --force --detach=false vcellrel_data
sudo docker service update --force --detach=false vcellrel_sched
sudo docker service update --force --detach=false vcellrel_submit
sudo docker service update --force --detach=false vcellrel_api
(not used) sudo docker service update --force --detach=false vcellrel_opt

Alpha restart, login vcellapi-beta
sudo docker service update --force --detach=false vcellalpha_activemqint
sudo docker service update --force --detach=false vcellalpha_activemqsim
sudo docker service update --force --detach=false vcellalpha_mongodb
sudo docker service update --force --detach=false vcellalpha_db
sudo docker service update --force --detach=false vcellalpha_data
sudo docker service update --force --detach=false vcellalpha_sched
sudo docker service update --force --detach=false vcellalpha_submit
sudo docker service update --force --detach=false vcellalpha_api (not used) sudo docker service update --force --detach=false vcellalpha_opt

Build quickrun linux solvers
do this in a pristine checkout (cloned).
git clone https://github.com/virtualcell/vcell-solvers.git
cd vcell-solvers

sudo docker build --tag=frm/vcell-solvers:latest -f Dockerfile-local .
sudo docker run -it --rm -v /Users/schaff/.vcell/simdata/temp:/vcelldata frm/vcell-solvers:latest SundialsSolverStandalone_x64 /vcelldata/SimID_1460763637_0_.cvodeInput /vcelldata/SimID_1460763637_0_.ida
-----where /Users/schaff/.vcell/simdata/temp is the simulation data directory (input file) mapped to /vcelldata inside the Docker container.

Remove Broken Swarm
On each docker node that is part of broken swarm:
260 sudo systemctl stop docker.service
261 sudo rm -rf /var/lib/docker/swarm
264 sudo systemctl start docker.service
Recreate swarm
273 hostname -i (on vcellapi or vcellapi-beta)
274 sudo docker swarm init --advertise-addr {155.37.255.68 or 155.37.255.90}
276 sudo docker swarm join-token manager (to create join token command)
//On other nodes run following command to add them as managers
278 Example: sudo docker swarm join --token SWMTKN-1-18b6etsn3yn562xxxxxirf6uqnlmlmlbcvc4m5nxh-05d2jflrf5ox1z0w9y0nt1f7l 155.37.255.68:2377
//On vcellapi redeploy
sudo env $(cat /usr/local/deploy/config/server_rel_7.2.0_39_0b71a4d.config | xargs) docker stack deploy --prune -c /usr/local/deploy/config/docker-compose_0b71a4d.yml vcellrel
286 sudo docker stack ps vcellalpha | grep -i running
287 exit
288 sudo docker node update --label-add zone=INTERNAL 8yfu0lrwfkoil8k038rkm3edj
289 sudo docker node inspect | grep -i label
290 sudo docker node inspect self | grep -i label

vcellNagios monitoring
Nagios monitor calls Nagios plugin manager at vcellapi.cam.uchc.edu which executes script:
vcell@vcellapi:/usr/lib64/nagios/plugins/vcellNagios.sh (returns status info to Nagios monitor)
vcellNagios.sh source code located in github project https://github.com/virtualcell/vcell.git at location /vcell/docker/swarm/vcellNagios.sh
vcellNagios.sh calls Rel web service https://vcellapi/health?check={login,sim}
web service defined by org.vcell.rest.VCellApiApplication->
org.vcell.rest.health.HealthRestlet.HealthRestlet->
org.vcell.rest.health.HealthService(started as thread in org.vcell.rest.VCellApiMain)->
cbit.vcell.server.VCellConnection->{login,runsims}

DBBackupAndClean
vcell-node1:/opt/build/frm/dbbackupclean
//Normal, without debug
java -cp ./maven-jars/*:./vcell-server-0.0.1-SNAPSHOT.jar:./ojdbc6-11.2.0.4.jar:./ucp-11.2.0.4.jar:./vcell-oracle-0.0.1-SNAPSHOT.jar -Dvcell.server.dbDriverName=oracle.jdbc.driver.OracleDriver cbit.vcell.modeldb.DBBackupAndClean delsimsdisk vcell-db vcell /opt/build/frm/dbpw.txt vcelldborcl.cam.uchc.edu /tmp /share/apps/vcell3/users

//Normal, without debug, single user only
java -Xms200m -Xmx1500m -cp ./maven-jars/*:./vcell-server-0.0.1-SNAPSHOT.jar:./ojdbc6-11.2.0.4.jar:./ucp-11.2.0.4.jar:./vcell-oracle-0.0.1-SNAPSHOT.jar -Dvcell.server.dbDriverName=oracle.jdbc.driver.OracleDriver cbit.vcell.modeldb.DBBackupAndClean delsimsdisk2 vcell-db vcell /opt/build/frm/dbpw.txt vcelldborcl.cam.uchc.edu /tmp /share/apps/vcell3/users Juliajessica

//With debug (note: eclipse debug config: vcell-server,vcell-node1,30301)
java -agentlib:jdwp=transport=dt_socket,server=y,address=30301,suspend=y -cp ./maven-jars/*:./vcell-server-0.0.1-SNAPSHOT.jar:./ojdbc6-11.2.0.4.jar:./ucp-11.2.0.4.jar:./vcell-oracle-0.0.1-SNAPSHOT.jar -Dvcell.server.dbDriverName=oracle.jdbc.driver.OracleDriver cbit.vcell.modeldb.DBBackupAndClean delsimsdisk vcell-db vcell /opt/build/frm/dbpw.txt vcelldborcl.cam.uchc.edu /tmp /share/apps/vcell3/users

//DBBackupAndClean Scheduled Task (vcell-db.cam.uchc.edu->'scheduled task'->'Task Scheduler Library'->cleanAndBackupDB->properties->Actions->'Edit...') Program/script: "C:\Program Files (x86)\Java\jre1.8.0_121\bin\java.exe" Add arguments: -jar DBBackupAndClean_Ampli.jar cleanandbackup vcell-db vcell cbittech vcelldborcl.cam.uchc.edu \cfs05\vcell\temp \cfs03\shared\archive\vcell\VCDBdumps Start in: C:\fromDBS3

useful commands

docker stack services local
ID                  NAME                MODE                REPLICAS            IMAGE                               PORTS
5hrlf3u1kdgr        local_visualizer    replicated          1/1                 dockersamples/visualizer:stable     *:30013->8080/tcp
cflee8p55yph        local_mongodb       replicated          1/1                 schaff/vcell-mongo:7.0.0-alpha.4    *:27020->27017/tcp
evpnt4b10dbs        local_activemq      replicated          1/1                 webcenter/activemq:5.14.3           *:61619->61616/tcp
tpo0wfjmgqeo        local_api           replicated          1/1                 schaff/vcell-api:7.0.0-alpha.4      *:30014->8000/tcp,*:8083->8080/tcp
xkb1tp4znjha        local_master        replicated          1/1                 schaff/vcell-master:7.0.0-alpha.4   *:30012->8000/tcp
docker stack ps local
ID               NAME                   IMAGE                               NODE                    DESIRED STATE   CURRENT STATE           ERROR  PORTS
mlvxxlvxedvh     local_master.1         schaff/vcell-master:7.0.0-alpha.4   linuxkit-025000000001   Running         Running 4 minutes ago
z164vsxiorox     local_api.1            schaff/vcell-api:7.0.0-alpha.4      linuxkit-025000000001   Running         Running 4 minutes ago
y0v50e8r31ce      \_ local_api.1        schaff/vcell-api:7.0.0-alpha.4      linuxkit-025000000001   Shutdown        Shutdown 4 minutes ago
9pjpi1lvi46r     local_visualizer.1     dockersamples/visualizer:stable     linuxkit-025000000001   Running         Running 25 minutes ago
3gdwdlijfxdz     local_mongodb.1        schaff/vcell-mongo:7.0.0-alpha.4    linuxkit-025000000001   Running         Running 26 minutes ago
k2hyfkcyqwpx     local_activemq.1       webcenter/activemq:5.14.3           linuxkit-025000000001   Running         Running 26 minutes ago
w059r4hbdgq9     local_master.1         schaff/vcell-master:7.0.0-alpha.4   linuxkit-025000000001   Shutdown        Shutdown 4 minutes ago
deploy schaff$ docker service ls
ID                  NAME                MODE                REPLICAS            IMAGE                               PORTS
evpnt4b10dbs        local_activemq      replicated          1/1                 webcenter/activemq:5.14.3           *:61619->61616/tcp
tpo0wfjmgqeo        local_api           replicated          1/1                 schaff/vcell-api:7.0.0-alpha.4      *:30014->8000/tcp,*:8083->8080/tcp
xkb1tp4znjha        local_master        replicated          1/1                 schaff/vcell-master:7.0.0-alpha.4   *:30012->8000/tcp
cflee8p55yph        local_mongodb       replicated          1/1                 schaff/vcell-mongo:7.0.0-alpha.4    *:27020->27017/tcp
5hrlf3u1kdgr        local_visualizer    replicated          1/1                 dockersamples/visualizer:stable     *:30013->8080/tcp
docker service logs -f local_api
curl --verbose --insecure "https://vcellapi.cam.uchc.edu/admin/jobs?completed=false&stopped=false&serverId=REL" | jq '.'
(see AdminJobsRestlet for details)