Michael,
On 8/14/21 11:56, Michael Richardson wrote:
>
> Thank you for the reply.
>
> Christopher Schultz <ch...@christopherschultz.net> wrote:
> > On 8/12/21 11:05, Michael Richardson wrote:
> >> I am trying to deploy OSCAR-EMR
>
Wow, that still exists? I remember more than a decade ago being
asked to integrate a product at $work with that thing as a demo.
We never did, because the market seemed not to really exist. I see
you are in Canada. I know OSCAR same from McMaster University. Does
it have a good ecosystem and install base in CA? >
Yes, it's still quite popular among many Ontario (and I'm told BC)
doctors, because it has good integration with the provincial billing
system. Doctor like it because the price appears right, and doctors
don't get rich by spending money. >
There are a number of support companies that install it, but my
experience (via my wife) is that their do a rather poor job of
installation. No understanding of database encryption, replication,
or even how to enable https.
That's ... really bad.
There seems to be developer still working on it, according to the
bitbucket git commit lot. But, the public community around it seems
to have died, as far as I can tell.
That's a shame. As I have discovered through years of working with ASF
and other projects, the community is far more important than the actual
product itself. A good community can fix a bad product, but the reverse
is not true. I am a member of other communities where the project
ignores the community, which is also Not Good. Not naming any names. :)
On 8/14/21 12:53, Michael Richardson wrote:
This time, after apt-get purge tomcat9 and re-install, I seem to be in 100%
CPU before I've deployed oscar or even updated the tomcat-users.xml to
enable the manager login.
HTOP view attached at bottom.
(4 virtual CPUs, 4G of ram. KVM VM running ubuntu 18.04, on a server running
ubuntu core 20)
oscar-serv03-[~] root 276 #netstat -tan
Active Internet connections (servers and established)
Proto Recv-Q Send-Q Local Address Foreign Address State
tcp 0 0 127.0.0.53:53 0.0.0.0:* LISTEN
tcp 0 0 0.0.0.0:22 0.0.0.0:* LISTEN
tcp 0 0 127.0.0.1:3306 0.0.0.0:* LISTEN
tcp 0 0 192.168.2.13:22 192.168.2.3:56874 ESTABLISHED
tcp 0 0 192.168.2.13:22 192.168.2.3:56556 ESTABLISHED
tcp6 2 0 :::8080 :::* LISTEN
tcp6 0 0 :::22 :::* LISTEN
tcp6 747 0 192.168.2.9:8080 192.168.2.3:37450 CLOSE_WAIT
tcp6 489 0 192.168.2.9:8080 192.168.2.3:37452 ESTABLISHED
I find it weird that I have no catalina.out file:
oscar-serv03-[~] root 274 #ls -l /var/log/tomcat9
total 8
-rw-r----- 1 tomcat tomcat 5233 Aug 14 16:38 catalina.2021-08-14.log
-rw-r----- 1 tomcat tomcat 0 Aug 14 16:37 localhost.2021-08-14.log
-rw-r----- 1 tomcat tomcat 0 Aug 14 16:38 localhost_access_log.2021-08-14.txt
You must be running usingh jsvc, which creates the catalina.[date].log
file instead. No worries, there.
I include cataline.2021-08-14.log here.
Also now at: https://www.sandelman.ca/tmp/terapia9/catalina.2021-08-14.log
ubuntu says that I have a new kernel and I should reboot, so I'll do another
purge, reboot, and then reinstall again.
14-Aug-2021 16:38:02.279 INFO [main]
org.apache.catalina.startup.VersionLoggerListener.log Server version name:
Apache Tomcat/9.0.16 (Ubuntu)
14-Aug-2021 16:38:02.302 INFO [main]
org.apache.catalina.startup.VersionLoggerListener.log Server built:
Sep 11 2019 19:47:51 UTC
14-Aug-2021 16:38:02.320 INFO [main]
org.apache.catalina.startup.VersionLoggerListener.log Server version number:
9.0.16.0
14-Aug-2021 16:38:02.343 INFO [main]
org.apache.catalina.startup.VersionLoggerListener.log OS Name:
Linux
14-Aug-2021 16:38:02.345 INFO [main]
org.apache.catalina.startup.VersionLoggerListener.log OS Version:
5.4.0-80-generic
14-Aug-2021 16:38:02.348 INFO [main]
org.apache.catalina.startup.VersionLoggerListener.log Architecture:
amd64
14-Aug-2021 16:38:02.374 INFO [main]
org.apache.catalina.startup.VersionLoggerListener.log Java Home:
/usr/lib/jvm/java-11-openjdk-amd64
14-Aug-2021 16:38:02.380 INFO [main]
org.apache.catalina.startup.VersionLoggerListener.log JVM Version:
11.0.11+9-Ubuntu-0ubuntu2.18.04
14-Aug-2021 16:38:02.382 INFO [main]
org.apache.catalina.startup.VersionLoggerListener.log JVM Vendor:
Ubuntu
14-Aug-2021 16:38:02.384 INFO [main]
org.apache.catalina.startup.VersionLoggerListener.log CATALINA_BASE:
/var/lib/tomcat9
14-Aug-2021 16:38:02.385 INFO [main]
org.apache.catalina.startup.VersionLoggerListener.log CATALINA_HOME:
/usr/share/tomcat9
14-Aug-2021 16:38:02.472 INFO [main]
org.apache.catalina.startup.VersionLoggerListener.log Command line argument:
--add-opens=java.base/java.lang=ALL-UNNAMED
14-Aug-2021 16:38:02.478 INFO [main]
org.apache.catalina.startup.VersionLoggerListener.log Command line argument:
--add-opens=java.base/java.io=ALL-UNNAMED
14-Aug-2021 16:38:02.499 INFO [main]
org.apache.catalina.startup.VersionLoggerListener.log Command line argument:
--add-opens=java.rmi/sun.rmi.transport=ALL-UNNAMED
14-Aug-2021 16:38:02.501 INFO [main]
org.apache.catalina.startup.VersionLoggerListener.log Command line argument:
-Djava.util.logging.config.file=/var/lib/tomcat9/conf/logging.properties
14-Aug-2021 16:38:02.504 INFO [main]
org.apache.catalina.startup.VersionLoggerListener.log Command line argument:
-Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
14-Aug-2021 16:38:02.509 INFO [main]
org.apache.catalina.startup.VersionLoggerListener.log Command line argument:
-Djava.awt.headless=true
14-Aug-2021 16:38:02.512 INFO [main]
org.apache.catalina.startup.VersionLoggerListener.log Command line argument:
-XX:+UseG1GC
14-Aug-2021 16:38:02.513 INFO [main]
org.apache.catalina.startup.VersionLoggerListener.log Command line argument:
-Djdk.tls.ephemeralDHKeySize=2048
14-Aug-2021 16:38:02.529 INFO [main]
org.apache.catalina.startup.VersionLoggerListener.log Command line argument:
-Djava.protocol.handler.pkgs=org.apache.catalina.webresources
14-Aug-2021 16:38:02.531 INFO [main]
org.apache.catalina.startup.VersionLoggerListener.log Command line argument:
-Dorg.apache.catalina.security.SecurityListener.UMASK=0027
14-Aug-2021 16:38:02.532 INFO [main]
org.apache.catalina.startup.VersionLoggerListener.log Command line argument:
-Dignore.endorsed.dirs=
14-Aug-2021 16:38:02.534 INFO [main]
org.apache.catalina.startup.VersionLoggerListener.log Command line argument:
-Dcatalina.base=/var/lib/tomcat9
14-Aug-2021 16:38:02.536 INFO [main]
org.apache.catalina.startup.VersionLoggerListener.log Command line argument:
-Dcatalina.home=/usr/share/tomcat9
14-Aug-2021 16:38:02.537 INFO [main]
org.apache.catalina.startup.VersionLoggerListener.log Command line argument:
-Djava.io.tmpdir=/tmp
14-Aug-2021 16:38:02.551 INFO [main]
org.apache.catalina.core.AprLifecycleListener.lifecycleEvent Loaded APR based
Apache Tomcat Native library [1.2.21] using APR version [1.6.3].
14-Aug-2021 16:38:02.553 INFO [main]
org.apache.catalina.core.AprLifecycleListener.lifecycleEvent APR capabilities:
IPv6 [true], sendfile [true], accept filters [false], random [true].
14-Aug-2021 16:38:02.554 INFO [main]
org.apache.catalina.core.AprLifecycleListener.lifecycleEvent APR/OpenSSL
configuration: useAprConnector [false], useOpenSSL [true]
14-Aug-2021 16:38:02.676 INFO [main]
org.apache.catalina.core.AprLifecycleListener.initializeSSL OpenSSL
successfully initialized [OpenSSL 1.1.1 11 Sep 2018]
14-Aug-2021 16:38:03.322 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing
ProtocolHandler ["http-nio-8080"]
14-Aug-2021 16:38:04.066 INFO [main] org.apache.catalina.startup.Catalina.load
Server initialization in [12,268] milliseconds
14-Aug-2021 16:38:05.601 INFO [main]
org.apache.catalina.core.StandardService.startInternal Starting service
[Catalina]
14-Aug-2021 16:38:05.621 INFO [main]
org.apache.catalina.core.StandardEngine.startInternal Starting Servlet engine:
[Apache Tomcat/9.0.16 (Ubuntu)]
14-Aug-2021 16:38:05.760 INFO [main]
org.apache.catalina.startup.HostConfig.deployDescriptor Deploying deployment
descriptor [/etc/tomcat9/Catalina/localhost/docs.xml]
14-Aug-2021 16:38:06.052 WARNING [main]
org.apache.catalina.startup.HostConfig.deployDescriptor The path attribute with
value [/docs] in deployment descriptor
[/etc/tomcat9/Catalina/localhost/docs.xml] has been ignored
Okay, all that looks fine to me, except the "9.0.16" part. That version
is *very/8 old. I see you are running Ubuntu: are you running the latest
release? That 9.0.16 number if rinning a bell about an older release
which was capped at 9.0.16. YOu might want to consider upgrading
everything once you figure all of this out. No need to muddy the waters
quite, yet, though.
A few more things:
1. It takes 12 seconds to initialize the server? That seems ... slow. Is
this on Amazon? What instance type? The memory size 3.75GiB is ringing a
bell, too.
2. You shouldn't have the "docs" project depployed on a production system.
3. I don't see any message "Deploying deployment descriptor
blah/blah/oscar/blah"
PID USER PRI NI VIRT RES SHR S CPU% MEM% TIME+ Command
28648 tomcat 20 0 4011M 112M 32844 S 110. 2.9 9:59.52
/usr/lib/jvm/java-11-openjdk-amd64/bin/java
-Djava.util.logging.config.file=/var/lib/tomcat9/conf/logging.proper
28660 tomcat 20 0 4011M 112M 32844 R 101. 2.9 8:32.93
/usr/lib/jvm/java-11-openjdk-amd64/bin/java
-Djava.util.logging.config.file=/var/lib/tomcat9/conf/logging.proper
28679 tomcat 20 0 4011M 112M 32844 S 7.5 2.9 0:40.84
/usr/lib/jvm/java-11-openjdk-amd64/bin/java
-Djava.util.logging.config.file=/var/lib/tomcat9/conf/logging.proper
28701 tomcat 20 0 4011M 112M 32844 S 0.6 2.9 0:03.08
/usr/lib/jvm/java-11-openjdk-amd64/bin/java
-Djava.util.logging.config.file=/var/lib/tomcat9/conf/logging.proper
28760 tomcat 20 0 4011M 112M 32844 S 0.0 2.9 0:02.59
/usr/lib/jvm/java-11-openjdk-amd64/bin/java
-Djava.util.logging.config.file=/var/lib/tomcat9/conf/logging.proper
28695 tomcat 20 0 4011M 112M 32844 S 0.0 2.9 0:17.27
/usr/lib/jvm/java-11-openjdk-amd64/bin/java
-Djava.util.logging.config.file=/var/lib/tomcat9/conf/logging.proper
28696 tomcat 20 0 4011M 112M 32844 S 0.0 2.9 0:14.38
/usr/lib/jvm/java-11-openjdk-amd64/bin/java
-Djava.util.logging.config.file=/var/lib/tomcat9/conf/logging.proper
28665 tomcat 20 0 4011M 112M 32844 S 0.0 2.9 0:00.50
/usr/lib/jvm/java-11-openjdk-amd64/bin/java
-Djava.util.logging.config.file=/var/lib/tomcat9/conf/logging.proper
28746 tomcat 20 0 4011M 112M 32844 S 0.0 2.9 0:00.44
/usr/lib/jvm/java-11-openjdk-amd64/bin/java
-Djava.util.logging.config.file=/var/lib/tomcat9/conf/logging.proper
28700 tomcat 20 0 4011M 112M 32844 S 0.0 2.9 0:00.01
/usr/lib/jvm/java-11-openjdk-amd64/bin/java
-Djava.util.logging.config.file=/var/lib/tomcat9/conf/logging.proper
28702 tomcat 20 0 4011M 112M 32844 S 0.0 2.9 0:00.16
/usr/lib/jvm/java-11-openjdk-amd64/bin/java
-Djava.util.logging.config.file=/var/lib/tomcat9/conf/logging.proper
28669 tomcat 20 0 4011M 112M 32844 S 0.0 2.9 0:00.11
/usr/lib/jvm/java-11-openjdk-amd64/bin/java
-Djava.util.logging.config.file=/var/lib/tomcat9/conf/logging.proper
28691 tomcat 20 0 4011M 112M 32844 S 0.0 2.9 0:00.01
/usr/lib/jvm/java-11-openjdk-amd64/bin/java
-Djava.util.logging.config.file=/var/lib/tomcat9/conf/logging.proper
28668 tomcat 20 0 4011M 112M 32844 S 0.0 2.9 0:00.15
/usr/lib/jvm/java-11-openjdk-amd64/bin/java
-Djava.util.logging.config.file=/var/lib/tomcat9/conf/logging.proper
28716 tomcat 20 0 4011M 112M 32844 S 0.0 2.9 0:00.40
/usr/lib/jvm/java-11-openjdk-amd64/bin/java
-Djava.util.logging.config.file=/var/lib/tomcat9/conf/logging.proper
28666 tomcat 20 0 4011M 112M 32844 S 0.0 2.9 0:00.08
/usr/lib/jvm/java-11-openjdk-amd64/bin/java
-Djava.util.logging.config.file=/var/lib/tomcat9/conf/logging.proper
28667 tomcat 20 0 4011M 112M 32844 S 0.0 2.9 0:00.00
/usr/lib/jvm/java-11-openjdk-amd64/bin/java
-Djava.util.logging.config.file=/var/lib/tomcat9/conf/logging.proper
28689 tomcat 20 0 4011M 112M 32844 S 0.0 2.9 0:00.00
/usr/lib/jvm/java-11-openjdk-amd64/bin/java
-Djava.util.logging.config.file=/var/lib/tomcat9/conf/logging.proper
28693 tomcat 20 0 4011M 112M 32844 S 0.0 2.9 0:00.00
/usr/lib/jvm/java-11-openjdk-amd64/bin/java
-Djava.util.logging.config.file=/var/lib/tomcat9/conf/logging.proper
28694 tomcat 20 0 4011M 112M 32844 S 0.0 2.9 0:00.00
/usr/lib/jvm/java-11-openjdk-amd64/bin/java
-Djava.util.logging.config.file=/var/lib/tomcat9/conf/logging.proper
28697 tomcat 20 0 4011M 112M 32844 S 0.0 2.9 0:00.00
/usr/lib/jvm/java-11-openjdk-amd64/bin/java
-Djava.util.logging.config.file=/var/lib/tomcat9/conf/logging.proper
28747 tomcat 20 0 4011M 112M 32844 S 0.0 2.9 0:00.00
/usr/lib/jvm/java-11-openjdk-amd64/bin/java
-Djava.util.logging.config.file=/var/lib/tomcat9/conf/logging.proper
28758 tomcat 20 0 4011M 112M 32844 S 0.0 2.9 0:00.00
/usr/lib/jvm/java-11-openjdk-amd64/bin/java
-Djava.util.logging.config.file=/var/lib/tomcat9/conf/logging.proper
Sure looks like 100% CPU usage. I wonder what is happening.
-chris
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