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IDR / deployment

Deployment infrastructure for the Image Data Resource
https://idr.openmicroscopy.org/about/deployment.html
BSD 2-Clause "Simplified" License
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Support OpenJDK 11.0.11 #331

Closed sbesson closed 3 years ago

sbesson commented 3 years ago

Follow-up of #329, this PR:

sbesson commented 3 years ago

After deployment, this seems to be sufficient to restore import

[sbesson@prod97-omeroreadwrite ~]$ java -version
openjdk version "11.0.11" 2021-04-20 LTS
OpenJDK Runtime Environment 18.9 (build 11.0.11+9-LTS)
OpenJDK 64-Bit Server VM 18.9 (build 11.0.11+9-LTS, mixed mode, sharing)
[sbesson@prod97-omeroreadwrite ~]$ /opt/omero/server/OMERO.server/bin/omero import test.fake
Using session for demo@localhost:4064. Idle timeout: 10 min. Current group: Public
2021-05-07 14:48:04,955 362        [      main] INFO          ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.5.8
2021-05-07 14:48:04,971 378        [      main] INFO          ome.formats.importer.ImportConfig - Bioformats version: 0.6.6 revision: 55bcf78bf629ab5dfc5f3e4f677043f11cbc4a57 date: 5 March 2021
2021-05-07 14:48:05,030 437        [      main] INFO   formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO
2021-05-07 14:48:05,374 781        [      main] INFO      ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM
2021-05-07 14:48:05,423 830        [      main] INFO      ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 45ms. (48ms total) [0 unknowns]
2021-05-07 14:48:05,462 869        [      main] INFO       ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:4064
2021-05-07 14:48:05,923 1330       [      main] INFO       ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back
2021-05-07 14:48:06,204 1611       [      main] INFO       ome.formats.OMEROMetadataStoreClient - Pinging session every 300s.
2021-05-07 14:48:06,212 1619       [      main] INFO       ome.formats.OMEROMetadataStoreClient - Server: 5.6.0
2021-05-07 14:48:06,212 1619       [      main] INFO       ome.formats.OMEROMetadataStoreClient - Client: 5.5.8
2021-05-07 14:48:06,212 1619       [      main] INFO       ome.formats.OMEROMetadataStoreClient - Java Version: 11.0.11
2021-05-07 14:48:06,212 1619       [      main] INFO       ome.formats.OMEROMetadataStoreClient - OS Name: Linux
2021-05-07 14:48:06,212 1619       [      main] INFO       ome.formats.OMEROMetadataStoreClient - OS Arch: amd64
2021-05-07 14:48:06,212 1619       [      main] INFO       ome.formats.OMEROMetadataStoreClient - OS Version: 3.10.0-1160.25.1.el7.x86_64
2021-05-07 14:48:06,497 1904       [      main] WARN                    ome.system.UpgradeCheck - UPGRADE AVAILABLE:Please upgrade to 5.6.1. See http://downloads.openmicroscopy.org/latest/omero for the latest version.
2021-05-07 14:48:06,506 1913       [2-thread-1] INFO   ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION
2021-05-07 14:48:10,033 5440       [2-thread-1] INFO   ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START
2021-05-07 14:48:10,048 5455       [3-thread-1] INFO   ts.importer.transfers.UploadFileTransfer - Transferring /home/sbesson/test.fake...
2021-05-07 14:48:10,078 5485       [3-thread-1] INFO   ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/sbesson/test.fake
2021-05-07 14:48:10,116 5523       [3-thread-1] INFO   ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/sbesson/test.fake
2021-05-07 14:48:10,195 5602       [2-thread-1] INFO   ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END
2021-05-07 14:48:10,274 5681       [2-thread-1] INFO   ormats.importer.cli.LoggingImportMonitor - IMPORT_STARTED Logfile: 39806723
2021-05-07 14:48:10,753 6160       [l.Client-0] INFO   ormats.importer.cli.LoggingImportMonitor - METADATA_IMPORTED Step: 1 of 5  Logfile: 39806723
2021-05-07 14:48:11,029 6436       [l.Client-1] INFO   ormats.importer.cli.LoggingImportMonitor - PIXELDATA_PROCESSED Step: 2 of 5  Logfile: 39806723
2021-05-07 14:48:11,500 6907       [l.Client-0] INFO   ormats.importer.cli.LoggingImportMonitor - THUMBNAILS_GENERATED Step: 3 of 5  Logfile: 39806723
2021-05-07 14:48:11,527 6934       [l.Client-1] INFO   ormats.importer.cli.LoggingImportMonitor - METADATA_PROCESSED Step: 4 of 5  Logfile: 39806723
2021-05-07 14:48:11,547 6954       [l.Client-0] INFO   ormats.importer.cli.LoggingImportMonitor - OBJECTS_RETURNED Step: 5 of 5  Logfile: 39806723
2021-05-07 14:48:11,652 7059       [l.Client-1] INFO   ormats.importer.cli.LoggingImportMonitor - IMPORT_DONE Imported file: /home/sbesson/test.fake
Image:12922352
Other imported objects:
Fileset:4782652

==> Summary
1 file uploaded, 1 fileset created, 1 image imported, 0 errors in 0:00:05.160
[sbesson@prod97-omeroreadwrite ~]$ /opt/omero/server/OMERO.server/bin/omero admin diagnostics
/opt/omero/server/OMERO.server/etc/grid/config.xml read-only

================================================================================
OMERO Diagnostics (admin) 5.9.0
================================================================================

Commands:   java -version                  11.0.11   (/usr/bin/java)
Commands:   python -V                      3.6.8     (/opt/omero/server/venv3/bin/python -- 2 others)
Commands:   icegridnode --version          3.6.5     (/usr/bin/icegridnode)
Commands:   icegridadmin --version         3.6.5     (/usr/bin/icegridadmin)
Commands:   psql --version                 11.11     (/usr/bin/psql)
Commands:   openssl version                1.0.2     (/usr/bin/openssl)

Server:     icegridnode                    running
Server:     Blitz-0                        active (pid = 31358, enabled)
Server:     OMERO.Glacier2                 active (pid = 31379, enabled)
Server:     Tables-0                       active (pid = 31377, enabled)

Log dir:    /opt/omero/server/OMERO.server/var/log exists
Log files:  Blitz-0.log                    14.4 MB       errors=4    warnings=174 
Log files:  DropBox.log                    n/a
Log files:  FileServer.log                 n/a
Log files:  Indexer-0.log                  n/a
Log files:  MonitorServer.log              n/a
Log files:  Processor-0.log                n/a
Log files:  Tables-0.log                   10.3 KB       errors=1    warnings=8   
Log files:  TestDropBox.log                n/a
Log files:  master.err                     81.7 KB       errors=0    warnings=3   
Log files:  master.out                     empty
Log files:  Total size                     14.49 MB

Environment:OMERO_HOME=(unset)             
Environment:OMERODIR=/opt/omero/server/OMERO.server 
Environment:OMERO_NODE=(unset)             
Environment:OMERO_MASTER=(unset)           
Environment:OMERO_USERDIR=(unset)          
Environment:OMERO_TMPDIR=(unset)           
Environment:PATH=/opt/omero/server/venv3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/sbesson/.local/bin:/home/sbesson/bin 
Environment:PYTHONPATH=(unset)             
Environment:ICE_HOME=(unset)               
Environment:LD_LIBRARY_PATH=(unset)        
Environment:DYLD_LIBRARY_PATH=(unset)      

OMERO SSL port:4064                           
OMERO TCP port:4063                           
OMERO data dir:'/data/OMERO'                  Exists? True  Is writable? False
OMERO temp dir:'/home/sbesson/omero/tmp'      Exists? True  Is writable? True   (Size: 0)

JVM settings: Blitz-${index}                -Xmx24G -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Indexer-${index}              -Xmx4800m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: PixelData-${index}            -Xmx7200m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Repository-${index}           -Xmx4800m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions

Jar:        lib/server/formats-api.jar     Bio-Formats API  0.6.6   5 March 2021    55bcf78bf629ab5dfc5f3e4f677043f11cbc4a57
Jar:        lib/server/formats-bsd.jar     BSD Bio-Formats readers and writers  0.6.6   5 March 2021    55bcf78bf629ab5dfc5f3e4f677043f11cbc4a57
Jar:        lib/server/formats-gpl.jar     Bio-Formats library  0.6.6   5 March 2021    55bcf78bf629ab5dfc5f3e4f677043f11cbc4a57
Jar:        lib/server/ome-codecs.jar      OME Codecs   0.2.5   13 August 2019  1a8b147d5673b975e14f33d78a2be886fbaf0e20
Jar:        lib/server/ome-common.jar      OME Common Java  6.0.4   21 October 2019 650939cfa026e33d2f38c1f56c74715dfb44b974
Jar:        lib/server/ome-jai.jar         OME JAI  0.1.0   28 June 2017    96ed34bf59f5ba3b51e3d60e342f30962a46c292
Jar:        lib/server/ome-mdbtools.jar    MDB Tools (Java port)    5.3.2   7 August 2018   68ffca2a95750cbb96f0d11785851aa4a554c0a4
Jar:        lib/server/ome-poi.jar         OME POI  5.3.3   6 August 2018   3887f4b2b21e195fa76ec4378858f6278aed5dcd
Jar:        lib/server/ome-xml.jar         OME XML library  6.0.1   9 May 2019  4d5b2e68d178de967d53100a1726b447726282cd
Jar:        lib/server/omero-blitz.jar     jar  5.5.5       
Jar:        lib/server/omero-common.jar    jar  5.5.3       
Jar:        lib/server/omero-gateway.jar   jar  5.6.2       
Jar:        lib/server/omero-model.jar     jar  5.5.3       
Jar:        lib/server/omero-renderer.jar  jar  5.5.3       
Jar:        lib/server/omero-romio.jar     jar  5.5.3       
Jar:        lib/server/omero-server.jar    jar  5.5.5
sbesson commented 3 years ago

@dominikl I'll leave you to confirm the imports running on prod97 are successful before merging this.

dominikl commented 3 years ago

👍 Looks good. Didn't notice any issues when importing into prod97.