Hi all,
If it can help, you can find attached the error that I got in the collectory.
Cheers, Marie
On Wed, Jun 1, 2016 at 9:43 AM, Marie Elise Lecoq melecoq@gbif.fr wrote:
Hi Tim, all,
Unfortunately, the error occurs before the beginning of the loading. You can find below the logging track when I executed "biocache load -dr179" command. The error comes from the upload, I got the same error when I tried to access this URL : http://metadonnee.gbif.fr/upload/1464722424642/75956ee6-1a2b-4fa3-b3e8-ccda6... .
The VM that hosts the collectory modules, used to have 4Go of RAM. I asked if it was possible to increase it (for a limited time) and I have got 32 Go, now. Even with this increase of memory, we still got the error.
Thanks for your answer, Cheers, Marie
root@vm-6:/home/ubuntu# biocache load dr179 SLF4J: Class path contains multiple SLF4J bindings. SLF4J: Found binding in [jar:file:/usr/lib/biocache/lib/slf4j-log4j12-1.7.5.jar!/org/slf4j/impl/StaticLoggerBinder.class] SLF4J: Found binding in [jar:file:/usr/lib/biocache/lib/logback-classic-1.1.3.jar!/org/slf4j/impl/StaticLoggerBinder.class] SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation. SLF4J: Actual binding is of type [org.slf4j.impl.Log4jLoggerFactory] 2016-06-01 15:57:04,029 INFO : [ConfigModule] - Using config file: /data/biocache/config/biocache-config.properties 2016-06-01 15:57:04,036 DEBUG: [ConfigModule] - Loading configuration from /data/biocache/config/biocache-config.properties 2016-06-01 15:57:04,203 DEBUG: [ConfigModule] - Initialising DAO 2016-06-01 15:57:04,210 DEBUG: [ConfigModule] - Initialising SOLR 2016-06-01 15:57:04,212 DEBUG: [ConfigModule] - Initialising name matching indexes 2016-06-01 15:57:04,212 DEBUG: [ConfigModule] - Loading name index from /data/lucene/namematching 2016-06-01 15:57:04,796 DEBUG: [ConfigModule] - Initialising persistence manager 2016-06-01 15:57:04,798 DEBUG: [ConfigModule] - Configure complete 2016-06-01 15:57:05,064 DEBUG: [CassandraPersistenceManager] - Initialising cassandra connection pool with pool name: biocache-store-pool 2016-06-01 15:57:05,065 DEBUG: [CassandraPersistenceManager] - Initialising cassandra connection pool with hosts: 192.168.0.19 2016-06-01 15:57:05,065 DEBUG: [CassandraPersistenceManager] - Initialising cassandra connection pool with port: 9160 2016-06-01 15:57:05,065 DEBUG: [CassandraPersistenceManager] - Initialising cassandra connection pool with max connections: -1 2016-06-01 15:57:05,065 DEBUG: [CassandraPersistenceManager] - Initialising cassandra connection pool with max retries: 6 2016-06-01 15:57:05,065 DEBUG: [CassandraPersistenceManager] - Initialising cassandra connection pool with operation timeout: 80000 2016-06-01 15:57:05,361 DEBUG: [Config] - Using local media store 2016-06-01 15:57:05,419 INFO : [Config] - Using the default set of blacklisted media URLs 2016-06-01 15:57:05,763 INFO : [Loader] - Starting to load resource: dr179 2016-06-01 15:57:06,748 INFO : [DataLoader] - Darwin core archive loading 2016-06-01 15:57:06,952 INFO : [DataLoader] - Downloading zip file from http://metadonnee.gbif.fr/upload/1464722424642/75956ee6-1a2b-4fa3-b3e8-ccda6... 2016-06-01 15:57:09,235 INFO : [DataLoader] - Content-Disposition: attachment;filename=75956ee6-1a2b-4fa3-b3e8-ccda64ce6c2d.zip 2016-06-01 15:57:09,236 ERROR: [DataLoader] - Server returned HTTP response code: 500 for URL: http://metadonnee.gbif.fr/upload/1464722424642/75956ee6-1a2b-4fa3-b3e8-ccda6...
On Wed, Jun 1, 2016 at 12:21 AM, Tim Robertson trobertson@gbif.org wrote:
Hi Marie
Do you see any output at all? E.g. Are there log lines like: 1000 >> last key : 123, UUID: Š records per sec: 4567 2000 >> last key : 423, UUID: Š records per sec: 4568
As far as I can tell, the code [1] is using the usual GBIF DwC-A Reader which is just an iterator and should not use significant memory for that.
I notice it appears to be batching [2]. I am not familiar with that code but I¹d expect to find config for a batch size, and perhaps if it is not set it might default to unlimited?
The DwC-A reader also handles pre-deflated zips (i.e. A directory, not a zip file). You could try unzipping it using standard tools and then rather than using a URL, reference a local directory so that it calls the loadLocal [3] instead of downloading, unzipping and then loading which is what a URL will invoke.
I¹m sorry I have not loaded a large file myself, but I know it should be possible.
I hope this helps provide some ideas at least.
Many thanks, Tim
[1]
https://github.com/AtlasOfLivingAustralia/biocache-store/blob/master/src/ma in/scala/au/org/ala/biocache/load/DwCALoader.scala#L159 https://github.com/AtlasOfLivingAustralia/biocache-store/blob/master/src/main/scala/au/org/ala/biocache/load/DwCALoader.scala#L159 [2]
https://github.com/AtlasOfLivingAustralia/biocache-store/blob/master/src/ma in/scala/au/org/ala/biocache/load/DwCALoader.scala#L325 https://github.com/AtlasOfLivingAustralia/biocache-store/blob/master/src/main/scala/au/org/ala/biocache/load/DwCALoader.scala#L325 [3]
https://github.com/AtlasOfLivingAustralia/biocache-store/blob/master/src/ma in/scala/au/org/ala/biocache/load/DwCALoader.scala#L130 https://github.com/AtlasOfLivingAustralia/biocache-store/blob/master/src/main/scala/au/org/ala/biocache/load/DwCALoader.scala#L130
On 01/06/16 05:05, "Ala-portal on behalf of melecoq" <ala-portal-bounces@lists.gbif.org on behalf of melecoq@gbif.fr> wrote:
Dear all, I'm still hold with my dataset with more than 20 millions occurrences.
I understood that the issue was due to the large size of the Zipfile. It's too big for the ZipFile Java Api. I did a little trick and I was able to create the data resource. I integrate the DwC Archive with occurrence and verbatim files with just 15 occurrences, then I changed those files with the real ones and it seems to work.
Now, the problem is when I try to load the Zip File into the Cassandra using load function from the biocache, I got a Java out of memory heap error because the code use the RAM to download, unzip and read the file. Unfortunately, 4 Go (zip file) and 23 Go (unzip file) is too big for it.
Do you know if there is another way to do it ? Can I unzip the file and run the loading after it ? Or can I "manually" integrate data into the Cassandra ?
Thanks in advance for your help. Cheers, Marie _______________________________________________ Ala-portal mailing list Ala-portal@lists.gbif.org http://lists.gbif.org/mailman/listinfo/ala-portal
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