| building and deploying two scripts | |
| vcell/docker/build/build.sh (building portable self contained container with vcell software) | |
| vcell/docker/swarm/deploy.sh (add configuration for deployment specific installation, install and restart services (stack)) | |
| administration | |
| vcell/docker/swarm/cli.py | |
| invoke (login to vcell-node1 as vcell, /opt/build/vcell/docker/swarm/cli.py) | |
| dont reboot more than one Docker swarm "manager" node at a time. | |
| (vcellapi, vcell-node1, vcell-node2) | |
| or (vcellapi-beta, vcell-node3, vcell-node4) | |
| curl https://vcellapi.cam.uchc.edu/api/v0/health?check=login | |
| admin logs for docker daemons | |
| on each swarm node: | |
| sudo docker event log | |
| for debugging slurm jobs, look in the Slurm log for that job (Slurm Job Name is "V_REL_{simid}_{jobid}_{taskid}"): | |
| log file is /share/apps/vcell3/htclogs/V_REL_{simid}_{jobid}_{taskid}.slurm.log | |
| submission script is /share/apps/vcell3/htclogs/V_REL_{simid}_{jobid}_{taskid}.slurm.sub | |
| open https://vcellapi.cam.uchc.edu/api/v0/biomodel (ugly api browser for vcell REST services ... incomplete coverage of API). | |
| for activemq website: | |
| [vcell@vcell-node1 ~ 13] $ sudo docker service ls | grep activemq | |
| nndtf3phq7v7 vcellrel_activemqint replicated 1/1 webcenter/activemq:5.14.3 *:30005->61616/tcp, *:30006->8161/tcp | |
| mbniasxc2byn vcellrel_activemqsim replicated 1/1 webcenter/activemq:5.14.3 *:8161->8161/tcp, *:61616->61616/tcp | |
| open http://vcellapi.cam.uchc.edu:30006 (for vcellrel_activemqint ... note port mappings above) | |
| open http://vcellapi.cam.uchc.edu:8161 (for vcellrel_activemqsim ... note port mappings above) | |
| Nagios logs (http://nagios.cam.uchc.edu/nagios/). | |
| open http://elk.cam.uchc.edu:5601/ | |
| there are two other "docker stacks" for monitoring and debugging. | |
| 1) very lightweight graphical view of which containers run on which nodes ... equivalent to "sudo docker stack ps <stack_name> (vcellrel, vcellalpha)" | |
| 2) more interesting dashboard for resources used by docker containers (cadvisor, influxdb, graphana) ... see Frank to enable this stack (some configuration required). | |
| log4j xml file for each container specifying the logging levels on a java package granularity | |
| for vcell-api | |
| look in <vcell-root>/docker/build/Dockerfile-api-dev | |
| WORKDIR /usr/local/app | |
| COPY ./docker/build/vcell-api.log4j.xml . | |
| (vcell api java code can find the log4j configuration at /usr/local/app ... a path inside the container) | |
| ENTRYPOINT java \ | |
| ... | |
| -Djava.util.logging.manager=org.apache.logging.log4j.jul.LogManager \ | |
| -Dlog4j.configurationFile=/usr/local/app/vcell-api.log4j.xml \ | |
| ... | |
| what happens when the events that I want to see are not logged to stdout or log4j (so wont get to ELK)? | |
| copy log4j xml file out, change logging level, copy back in ... within 5 seconds the new log configuration will take effect. | |
| sudo docker cp 7e8c543f6211:/usr/local/app/vcell-api.log4j.xml /tmp/local.xml | |
| sudo docker cp 7e8c543f6211:/usr/local/app/vcell-api.log4j.xml /tmp/local.xml | |
| REBOOTING: | |
| TODO: | |
| find a way of storing some info from HTC logs in ELK. | |
| NAGIOS server is not showing VCell services. (see http://nagios.cam.uchc.edu/nagios/ ... vcell critical) | |