ERDDAP setup problem

[Flora Karathanasi]

Hello everyone,

I'm trying to set up my own ERDDAP for the first time on my laptop in order to start playing and experimenting before setting it up on a server for the needs of a project at my work.

I'm a new linux user and running ubuntu 18.04. For the moment, I managed to have the latest version of java/tomcat working (http://localhost:8080/ is on), but I get an HTTP status 500 - internal server error. I followed the instructions for the initial setup (https://coastwatch.pfeg.noaa.gov/erddap/download/setup.html#initialSetup), apart from step 5 (ProxyPass), along with some posts from the google group, but apparently I have missed something. 

From the catalina.out file (shown below), I can't figure out what is wrongly configured and I would appreciate it if someone can provide any hints.

////**** ERD Low Level Startup

localTime=2021-06-07T21:38:54+03:00

erddapVersion=2.12

Java 11.0.11 (64 bit, AdoptOpenJDK) on Linux (5.4.0-74-generic).

MemoryInUse=   465 MB (highWaterMark=   465 MB) (Xmx ~= 1500 MB)

SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".

SLF4J: Defaulting to no-operation (NOP) logger implementation

SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.

logLevel=info: verbose=true reallyVerbose=false

ERROR in File2.deleteIfOld: dir=/usr/local/tomcat/content/erddap/dataset/_FileVisitor/ isn't a directory.

bigParentDirectory=/usr/local/tomcat/content/erddap/

webInfParentDirectory=/usr/local/tomcat/webapps/erddap/

java.awt.HeadlessException

 at gov.noaa.pfel.coastwatch.sgt.SgtUtil.isBufferedImageAccelerated(SgtUtil.java:368)

 at gov.noaa.pfel.erddap.util.EDStatic.<clinit>(EDStatic.java:1628)

 at gov.noaa.pfel.erddap.Erddap.<init>(Erddap.java:223)

bufferedImage isAccelerated=[unknown]

  copying images/ file: erddapStart2.css

Custom messages.xml not found at /usr/local/tomcat/content/erddap/messages.xml

Using default messages.xml from  /usr/local/tomcat/webapps/erddap/WEB-INF/classes/gov/noaa/pfel/erddap/util/messages.xml

CfToFromGcmd static loading /usr/local/tomcat/webapps/erddap/WEB-INF/classes/gov/noaa/pfel/erddap/util/CfToGcmd.txt

*** ERD Low Level Startup finished successfully.

Please let me know if more information is needed.

Thanks,

Flora

[Frederic Leclercq]

Hi Flora,

You might need to use java 8 (1.8)?  

And not really sure, but I think it's a better practice to set the 'bigParentDirectory' path to outside your tomcat files? I think you currently point to the dataset.xml file (instead of your locally stored data files)

Best regards,

Fred.

[Bob Simons]

As Fred says, use Java 8 (1.8).   That alone is sufficient to explain trouble.

I don't see any other problems in the info you provided. 

As Fred says, bigParentDirectory should be outside the tomcat directory, so that later, when you update tomcat, bigParentDirectory is unaffected.

In general, if ERDDAP isn't starting up, look in [bigParentDirectory]/logs/log.txt. If log.txt doesn't show any errors, see catalina.out.

ERDDAP only sends messages to log.txt when a buffer is full. You can flush the buffer by visiting the status.html page. 

If ERDDAP isn't starting up, it is possible that the error message is getting written to the buffer but then isn't getting written to log.txt. I'll try to improve that. 

I hope that helps.

[Flora Karathanasi]

Dear Frederic and Bob,

thank you very much for your suggestions. 

I switched to java 8 version and put bigParentDirectory outside the tomcat directory, and ERDAPP is finally running! 

@Frederic: I'm pointing to the default datasets.xml file, just to test if ERDDAP is working.

Now that is on, there are still a lot of things to customize and manage... 

Best regards,

Flora

[MarieDejean]

Hi,

I had quite the same problem except that I have jave8 running.
I copy/paste my last lines in catalina.out (see below).

If you can have a look and tell me what I missed.
Thanks a lot 
Marie

----

////**** ERD Low Level Startup

localTime=2021-12-15T12:12:58+01:00
erddapVersion=2.14
Java 1.8.0_292 (64 bit, Private Build) on Linux (5.11.0-41-generic).
MemoryInUse=    17 MB (highWaterMark=    17 MB) (Xmx ~= 910 MB)

SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
logLevel=info: verbose=true reallyVerbose=false

ERROR in File2.deleteIfOld: dir=/opt/tomcat/content/erddap/dataset/_FileVisitor/ isn't a directory.
bigParentDirectory=/opt/tomcat/content/erddap/
webInfParentDirectory=/opt/tomcat/webapps/erddap/

java.awt.HeadlessException
 at gov.noaa.pfel.coastwatch.sgt.SgtUtil.isBufferedImageAccelerated(SgtUtil.java:368)
 at gov.noaa.pfel.erddap.util.EDStatic.<clinit>(EDStatic.java:1628)
 at gov.noaa.pfel.erddap.Erddap.<init>(Erddap.java:223)


bufferedImage isAccelerated=[unknown]
  copying images/ file: erddapStart2.css

Custom messages.xml not found at /opt/tomcat/content/erddap/messages.xml
Using default messages.xml from  /opt/tomcat/webapps/erddap/WEB-INF/classes/gov/noaa/pfel/erddap/util/messages.xml
CfToFromGcmd static loading /opt/tomcat/webapps/erddap/WEB-INF/classes/gov/noaa/pfel/erddap/util/CfToGcmd.txt

*** ERD Low Level Startup finished successfully.

[Roy Mendelssohn - NOAA Federal]

Hi Marie:

Where is the new Tomcat located, I assume there is sill a system Tomcat on your machine, what does you setenv.sh look like, and how did you do the start?

Thanks,

-Roy

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**********************
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**********************
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Supervisory Operations Research Analyst
NOAA/NMFS
Environmental Research Division
Southwest Fisheries Science Center
***Note new street address***
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Phone: (831)-420-3666
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[Bob Simons]

ERDDAP startup has 3 phases:

1) Tomcat. Log information from Tomcat is put in a [tomcat]/logs/ log file (catalina.log?) So low level error messages are there.

2) Low level ERDDAP. Log information from ERDDAP is written to the terminal window. That's what you show above. It " finished successfully."  Yea!

3) High level ERDDAP. Log information is put in [bigParentDirectory]/logs/log.txt. So you need to look in that file for error messages. I'm pretty sure you'll find the problem there.

I hope that helps. 

If you can't understand the error message when you find it, post it here or email it to me.

Best wishes.

[Bob Simons]

The problem was solved.

The problem that Marie had was caused by using Tomcat 10. When she switched to Tomcat 9 (as recommended in the installation instructions), ERDDAP worked.

[Xuning Tan - NOAA Federal]

Hello,

Just noticed that my base docker image erddap has the same errors, but we're using Java 1.8.0_322, Tomcat 9. My problem is other erddap container uses this docker image cann't start tomcat properly. Thanks for any hints you may have. Following is from the two catalina.out respectively:

----------------------------------------

02-Feb-2022 16:56:19.212 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version name:   Apache Tomcat/9.0.56

.

.

02-Feb-2022 16:56:30.352 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in [10853] milliseconds

////**** ERD Low Level Startup

localTime=2022-02-02T16:57:59+00:00
erddapVersion=2.14
Java 1.8.0_322 (64 bit, Red Hat, Inc.) on Linux (3.10.0-1160.53.1.el7.x86_64).
MemoryInUse=    38 MB (highWaterMark=    38 MB) (Xmx ~= 1437 MB)

SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
logLevel=info: verbose=true reallyVerbose=false

ERROR in File2.deleteIfOld: dir=/bigparentdir/dataset/_FileVisitor/ isn't a directory.
bigParentDirectory=/bigparentdir/

webInfParentDirectory=/usr/local/tomcat/webapps/erddap/
java.awt.HeadlessException
 at gov.noaa.pfel.coastwatch.sgt.SgtUtil.isBufferedImageAccelerated(SgtUtil.java:368)
 at gov.noaa.pfel.erddap.util.EDStatic.<clinit>(EDStatic.java:1628)
 at gov.noaa.pfel.erddap.Erddap.<init>(Erddap.java:223)

bufferedImage isAccelerated=[unknown]

Custom messages.xml not found at /usr/local/tomcat/content/erddap/messages.xml
Using default messages.xml from  /usr/local/tomcat/webapps/erddap/WEB-INF/classes/gov/noaa/pfel/erddap/util/messages.xml
CfToFromGcmd static loading /usr/local/tomcat/webapps/erddap/WEB-INF/classes/gov/noaa/pfel/erddap/util/CfToGcmd.txt
*** ERD Low Level Startup finished successfully.

----------------------------------------

The other container using above never finished the ERD Low Level Startup. Both have WARNING on digester "No rules found":

========================

02-Feb-2022 17:48:11.287 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [/usr/local/tomcat/webapps/host-manager]
02-Feb-2022 17:48:11.289 WARNING [main] org.apache.tomcat.util.digester.Digester.endElement No rules found matching [Context/role]
02-Feb-2022 17:48:11.289 WARNING [main] org.apache.tomcat.util.digester.Digester.endElement No rules found matching [Context/user]
02-Feb-2022 17:48:11.305 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [/usr/local/tomcat/webapps/host-manager] has finished in [18] ms
02-Feb-2022 17:48:11.305 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [/usr/local/tomcat/webapps/manager]
02-Feb-2022 17:48:11.307 WARNING [main] org.apache.tomcat.util.digester.Digester.endElement No rules found matching [Context/role]
02-Feb-2022 17:48:11.307 WARNING [main] org.apache.tomcat.util.digester.Digester.endElement No rules found matching [Context/user]
02-Feb-2022 17:48:11.320 INFO [main] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [/usr/local/tomcat/webapps/manager] has finished in [14] ms
02-Feb-2022 17:48:11.323 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler ["http-nio-4093"]
02-Feb-2022 17:48:11.331 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in [10892] milliseconds

[Bob Simons]

For the first catalina.out: There doesn't appear to be anything wrong with the low level startup. So if there is trouble with that ERDDAP, you need to look in log.txt for error messages that ERDDAP has written.

For the second catalina.out: I have no idea. I've never seen warnings related to Digester. I note that they are warnings (usually not fatal), not errors (which are fatal). So I'm surprised ERDDAP didn't begin its "ERD Low Level Startup" (Did it? Is that further down in the catalina log?). I would search the web for information about the Digester warning (if there aren't any actual "Error"s).

Sorry that probably isn't much help. But it is odd that there aren't actual error messages from ERDDAP or Tomcat.

And I don't use Docker, so I'm no help diagnosing problems related to it.

Best wishes.

[Xuning Tan - NOAA Federal]

First catalina.out has the Digester warning too, but ERDDAP runs fine. My report on this thread says using Java 1.8.0_322, Tomcat 9 would get rid of these SLF4J errors seem not work for us.

Second one, ERDDAP didn't begin its  "ERD Low Level Startup"

Thanks always!

[Bob Simons]

The SLF4J (which is a logging system used by netcdf-java) lines are log lines reporting SLF4J's runtime setup. They aren't fatal errors for SLF4J or ERDDAP. 

If ERDDAP doesn't begin it's Low Level Startup, there should be an error message related to the problem in one of the Tomcat log files. There is the (remote?) possibility that Tomcat never tried to start ERDDAP because ERDDAP is not set up properly in Tomcat or no one ever sent a request to that ERDDAP.  You can test that partly with: Did Tomcat unpack the erddap.war file into an erddap directory with subfolders and files?

And I think this is in Docker. I don't know how ERDDAP is deployed by Docker or how to diagnose Docker-related problems. Some Docker+ERDDAP user needs to help you.

One thing you can always do: go back to the installation instructions and double check that everything was done correctly.

Good luck.