Closed 7yl4r closed 1 year ago
Dan has reprocessed the files and flipped the latitude. The dataset is still showing as failed in the status.html, but I don't see any big errors in the DasDds output.
Based on this maybe it has something to do with permissions? The files are publicly readable on the hypervisor:
[tylar@dune ~]$ ls -lah /mnt/sdb/moda_oc_7d_gom/MODA_2005134_2005140_7D_GOM_OC.nc
-rw-r--r--. 1 dotis imars-common 141M Mar 10 17:17 /mnt/sdb/moda_oc_7d_gom/MODA_2005134_2005140_7D_GOM_OC.nc
I just followed these instructions to resolve possible SELINUX issues.
The files appear readable in the container:
[tylar@dune ~]$ docker exec -it erddap bash -c "ls -lah /mnt/sdb/moda_oc_7d_gom/MODA_2005134_2005140_7D_GOM_OC.nc"
-rw-r--r--. 1 4509 4504 141M Mar 10 22:17 /mnt/sdb/moda_oc_7d_gom/MODA_2005134_2005140_7D_GOM_OC.nc
I don't see anything helpful from the erddap logs in docker:
[tylar@dune ~]$ docker logs erddap 2>&1 | grep -Ev "IllegalArgument|Http11Processor|at org.|at java.|Note:"
ERDDAP configured with:
ERDDAP_MEMORY=64G
ERDDAP_adminAddress=123 Irrelevant St.
ERDDAP_adminCity=Nowhere
ERDDAP_adminCountry=USA
ERDDAP_adminEmail=nobody@example.com
ERDDAP_adminIndividualName=Axiom Docker Install
ERDDAP_adminInstitution=Axiom Docker Install
ERDDAP_adminInstitutionUrl=https://github.com/axiom-data-science/docker-erddap
ERDDAP_adminPhone=555-555-5555
ERDDAP_adminPosition=Software Engineer
ERDDAP_adminPostalCode=99504
ERDDAP_adminStateOrProvince=AK
ERDDAP_baseHttpsUrl=https://localhost:8443
ERDDAP_bigParentDirectory=/erddapData
ERDDAP_emailDailyReportsTo=nobody@example.com
ERDDAP_emailEverythingTo=nobody@example.com
ERDDAP_emailFromAddress=nothing@example.com
ERDDAP_emailPassword=
ERDDAP_emailProperties=
ERDDAP_emailSmtpHost=
ERDDAP_emailSmtpPort=
ERDDAP_emailUserName=
ERDDAP_flagKeyKey=73976bb0-9cd4-11e3-a5e2-0800200c9a66
ERDDAP Running with: -server -Xms64G -Xmx64G -XX:+HeapDumpOnOutOfMemoryError -Djava.awt.headless=true -XX:+UseConcMarkSweepGC -XX:+CMSClassUnloadingEnabled -DerddapContentDirectory=/usr/local/tomcat/content/erddap/ -Djna.tmpdir=/tmp/ -Djava.security.egd=file:/dev/./urandom
13-Jan-2023 16:41:07.070 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version name: Apache Tomcat
13-Jan-2023 16:41:07.073 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server built: Jan 17 2022 22:07:47 UTC
13-Jan-2023 16:41:07.073 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Server version number: 8.5.75.0
13-Jan-2023 16:41:07.073 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Name: Linux
13-Jan-2023 16:41:07.073 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log OS Version: 4.18.0-408.el8.x86_64
13-Jan-2023 16:41:07.073 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Architecture: amd64
13-Jan-2023 16:41:07.074 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Java Home: /usr/local/openjdk-8/jre
13-Jan-2023 16:41:07.074 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Version: 1.8.0_322-b06
13-Jan-2023 16:41:07.074 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log JVM Vendor: Oracle Corporation
13-Jan-2023 16:41:07.074 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_BASE: /usr/local/tomcat
13-Jan-2023 16:41:07.074 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log CATALINA_HOME: /usr/local/tomcat
13-Jan-2023 16:41:07.075 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.config.file=/usr/local/tomcat/conf/logging.properties
13-Jan-2023 16:41:07.075 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager
13-Jan-2023 16:41:07.075 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xms64G
13-Jan-2023 16:41:07.075 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Xmx64G
13-Jan-2023 16:41:07.075 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+HeapDumpOnOutOfMemoryError
13-Jan-2023 16:41:07.075 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.awt.headless=true
13-Jan-2023 16:41:07.079 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+UseConcMarkSweepGC
13-Jan-2023 16:41:07.079 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -XX:+CMSClassUnloadingEnabled
13-Jan-2023 16:41:07.079 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -DerddapContentDirectory=/usr/local/tomcat/content/erddap/
13-Jan-2023 16:41:07.079 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djna.tmpdir=/tmp/
13-Jan-2023 16:41:07.079 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.security.egd=file:/dev/./urandom
13-Jan-2023 16:41:07.079 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djdk.tls.ephemeralDHKeySize=2048
13-Jan-2023 16:41:07.080 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.protocol.handler.pkgs=org.apache.catalina.webresources
13-Jan-2023 16:41:07.080 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dorg.apache.catalina.security.SecurityListener.UMASK=0027
13-Jan-2023 16:41:07.080 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dignore.endorsed.dirs=
13-Jan-2023 16:41:07.080 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.base=/usr/local/tomcat
13-Jan-2023 16:41:07.080 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Dcatalina.home=/usr/local/tomcat
13-Jan-2023 16:41:07.080 INFO [main] org.apache.catalina.startup.VersionLoggerListener.log Command line argument: -Djava.io.tmpdir=/usr/local/tomcat/temp
13-Jan-2023 16:41:07.081 INFO [main] org.apache.catalina.core.AprLifecycleListener.lifecycleEvent Loaded Apache Tomcat Native library [1.2.31] using APR version [1.7.0].
13-Jan-2023 16:41:07.081 INFO [main] org.apache.catalina.core.AprLifecycleListener.lifecycleEvent APR capabilities: IPv6 [true], sendfile [true], accept filters [false], random [true], UDS [{4}].
13-Jan-2023 16:41:07.081 INFO [main] org.apache.catalina.core.AprLifecycleListener.lifecycleEvent APR/OpenSSL configuration: useAprConnector [false], useOpenSSL [true]
13-Jan-2023 16:41:07.084 INFO [main] org.apache.catalina.core.AprLifecycleListener.initializeSSL OpenSSL successfully initialized [OpenSSL 1.1.1k 25 Mar 2021]
13-Jan-2023 16:41:07.161 INFO [main] org.apache.coyote.AbstractProtocol.init Initializing ProtocolHandler ["http-nio-8080"]
13-Jan-2023 16:41:07.175 INFO [main] org.apache.tomcat.util.net.NioSelectorPool.getSharedSelector Using a shared selector for servlet write/read
13-Jan-2023 16:41:07.192 INFO [main] org.apache.catalina.startup.Catalina.load Initialization processed in 699 ms
13-Jan-2023 16:41:07.225 INFO [main] org.apache.catalina.core.StandardService.startInternal Starting service [Catalina]
13-Jan-2023 16:41:07.226 INFO [main] org.apache.catalina.core.StandardEngine.startInternal Starting Servlet engine: [Apache Tomcat]
13-Jan-2023 16:41:07.234 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deploying web application directory [/usr/local/tomcat/webapps/erddap]
13-Jan-2023 16:41:14.199 INFO [localhost-startStop-1] org.apache.jasper.servlet.TldScanner.scanJars At least one JAR was scanned for TLDs yet contained no TLDs. Enable debug logging for this logger for a complete list of JARs that were scanned but no TLDs were found in them. Skipping unneeded JARs during scanning can improve startup time and JSP compilation time.
13-Jan-2023 16:41:14.248 INFO [localhost-startStop-1] org.apache.catalina.startup.HostConfig.deployDirectory Deployment of web application directory [/usr/local/tomcat/webapps/erddap] has finished in [7,013] ms
13-Jan-2023 16:41:14.251 INFO [main] org.apache.coyote.AbstractProtocol.start Starting ProtocolHandler ["http-nio-8080"]
13-Jan-2023 16:41:14.261 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in 7069 ms
////**** EDStatic Low Level Startup
localTime=2023-01-13T16:41:37+00:00
erddapVersion=2.18
Java 1.8.0_322 (64 bit, Oracle Corporation) on Linux (4.18.0-408.el8.x86_64).
MemoryInUse= 845 MB (highWaterMark= 845 MB) (Xmx ~= 65303 MB)
logLevel=info: verbose=true reallyVerbose=false
got bigParentDirectory from ERDDAP_bigParentDirectory
got emailFromAddress from ERDDAP_emailFromAddress
got emailEverythingTo from ERDDAP_emailEverythingTo
ERROR in File2.deleteIfOld: dir=/erddapData/dataset/_FileVisitor/ isn't a directory.
bigParentDirectory=/erddapData/
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:1830)
at gov.noaa.pfel.erddap.Erddap.<init>(Erddap.java:223)
bufferedImage isAccelerated=[unknown]
got baseHttpsUrl from ERDDAP_baseHttpsUrl
got adminInstitution from ERDDAP_adminInstitution
got adminInstitutionUrl from ERDDAP_adminInstitutionUrl
got adminIndividualName from ERDDAP_adminIndividualName
got adminPosition from ERDDAP_adminPosition
got adminPhone from ERDDAP_adminPhone
got adminAddress from ERDDAP_adminAddress
got adminCity from ERDDAP_adminCity
got adminStateOrProvince from ERDDAP_adminStateOrProvince
got adminPostalCode from ERDDAP_adminPostalCode
got adminCountry from ERDDAP_adminCountry
got adminEmail from ERDDAP_adminEmail
got flagKeyKey from ERDDAP_flagKeyKey
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
*** EDStatic Low Level Startup finished successfully.
06-Mar-2023 12:07:22.181 INFO [http-nio-8080-exec-16] org.apache.coyote.AbstractProcessor.parseHost The host [www.$$$$$] is not valid
I don't know the importance of ERROR in File2.deleteIfOld: dir=/erddapData/dataset/_FileVisitor/ isn't a directory.
but this looks to be a global issue, not one specific to this dataset.
This issue seems to be similar to this unresolved issue with an older dataset.
Note that NFS is no longer a factor here, because these files are on a local drive (/mnt/sdb
).
Hmm. I don't think I can help much with this.
From: Tylar @.> Sent: Tuesday, March 14, 2023 11:32 AM To: USF-IMARS/erddap-config @.> Cc: dotis @.>; Mention @.> Subject: Re: [USF-IMARS/erddap-config] moda_oc_7d_gom failing (Issue #35)
This issue seems to be similar to this unresolved issue with an older datasethttps://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fmarinebon%2Fmbon-dashboard-server%2Fissues%2F36&data=05%7C01%7Cdotis%40usf.edu%7C15c5a5e02fe445351ba808db24a15741%7C741bf7dee2e546df8d6782607df9deaa%7C0%7C0%7C638144047593163430%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=eV94X8xzNq9rWxA7BDLjsczibfSPTGfFxm%2B9BRQjW%2Bg%3D&reserved=0.
Note that NFS is no longer a factor here, because these files are on a local drive (/mnt/sdb).
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found the error in /erddapData/logs/log.txt
:
Emailing "86861bdaf3af ERDDAP: ERROR while saving dirTable, fileTable, or badFiles for moda_oc_7d_gom" to
datasets.xml error on line #717
While trying to load datasetID=moda_oc_7d_gom (after 17 ms)
java.lang.RuntimeException: datasets.xml error on or before line #717: FileNotFoundException: /erddapData/dataset/om/moda_oc_7d_gom/dirTable.nc93412081725963838 (Permission denied)
at gov.noaa.pfel.erddap.dataset.EDD.fromXml(EDD.java:471)
at gov.noaa.pfel.erddap.LoadDatasets.run(LoadDatasets.java:359)
Caused by: java.io.FileNotFoundException: /erddapData/dataset/om/moda_oc_7d_gom/dirTable.nc93412081725963838 (Permission denied)
at ucar.unidata.io.RandomAccessFile.<init>(RandomAccessFile.java:322)
at ucar.unidata.io.RandomAccessFile.<init>(RandomAccessFile.java:301)
at ucar.nc2.internal.iosp.netcdf3.N3iospWriter.create(N3iospWriter.java:84)
at ucar.nc2.write.NetcdfFormatWriter.<init>(NetcdfFormatWriter.java:321)
at ucar.nc2.write.NetcdfFormatWriter.<init>(NetcdfFormatWriter.java:42)
at ucar.nc2.write.NetcdfFormatWriter$Builder.build(NetcdfFormatWriter.java:251)
at gov.noaa.pfel.coastwatch.pointdata.Table.saveAsFlatNc(Table.java:28685)
at gov.noaa.pfel.coastwatch.pointdata.Table.saveAsEnhancedFlatNc(Table.java:6081)
at gov.noaa.pfel.erddap.dataset.EDD.saveDirTableFileTableBadFiles(EDD.java:10603)
at gov.noaa.pfel.erddap.dataset.EDDGridFromFiles.<init>(EDDGridFromFiles.java:1125)
at gov.noaa.pfel.erddap.dataset.EDDGridFromNcLow.<init>(EDDGridFromNcLow.java:96)
at gov.noaa.pfel.erddap.dataset.EDDGridFromNcFiles.<init>(EDDGridFromNcFiles.java:102)
at gov.noaa.pfel.erddap.dataset.EDDGridFromFiles.fromXml(EDDGridFromFiles.java:299)
at gov.noaa.pfel.erddap.dataset.EDD.fromXml(EDD.java:430)
... 1 more
This could be a larger issue with the setup (or lack of setup) of the /erddapData
directory in the docker-compose.yml file. I am going to attempt a fix, docker-compose down --rmi all --volumes && docker-compose up -d
, then check back in at least an hour.
Yep, that fixed it.
http://131.247.136.200:8080/erddap/griddap/moda_oc_7d_gom.graph
Upside down! I knew it. I will re-orient. I take it the lat was not the issue.
From: Tylar @.> Sent: Tuesday, March 14, 2023 1:22 PM To: USF-IMARS/erddap-config @.> Cc: dotis @.>; Mention @.> Subject: Re: [USF-IMARS/erddap-config] moda_oc_7d_gom failing (Issue #35)
Yep, that fixed it.
http://131.247.136.200:8080/erddap/griddap/moda_oc_7d_gom.graphhttps://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2F131.247.136.200%3A8080%2Ferddap%2Fgriddap%2Fmoda_oc_7d_gom.graph&data=05%7C01%7Cdotis%40usf.edu%7C197854ee262f4e7d90ae08db24b0c1db%7C741bf7dee2e546df8d6782607df9deaa%7C0%7C0%7C638144113824006482%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=uGLknt0QqnRCe8ioLKT5SVne%2BAoFE%2BJeRffyP7yK9v0%3D&reserved=0
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Apparently not.
I don't know why we were getting that error. The error did go away after you reoriented, but the way it is now is obviously worse.
Ok. None of the other roi are done that way, so I will change these back and re-populate the ERDDAP and re-test. Thanks.
From: Tylar @.> Sent: Tuesday, March 14, 2023 1:30 PM To: USF-IMARS/erddap-config @.> Cc: dotis @.>; Mention @.> Subject: Re: [USF-IMARS/erddap-config] moda_oc_7d_gom failing (Issue #35)
Apparently not.
I don't know why we were getting that error. The error did go away after you reoriented, but the way it is now is obviously worse.
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Dataset is failing according to status.html.
DasDds output:
Possible issues from the DasDds output:
java.awt.HeadlessException
This is expected and not related
time variable spacing
DasDds is complaining about the spacing of the time variable being uneven, but this is common and should not be breaking the dataset.
latitude needs to be in ascending order
I think this is the issue. The latitude variable needs to be flipped around.
@dotis: Can we try that and see if the updated files work with ERDDAP?