[Ala-portal] Problems loading huge DwC Archive

Marie Elise Lecoq melecoq at gbif.fr
Wed Jun 1 18:43:26 CEST 2016


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-ccda64ce6c2d.zip
.

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 at 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-ccda64ce6c2d.zip
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-ccda64ce6c2d.zip

On Wed, Jun 1, 2016 at 12:21 AM, Tim Robertson <trobertson at 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
> [2]
> https://github.com/AtlasOfLivingAustralia/biocache-store/blob/master/src/ma
> in/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
>
> On 01/06/16 05:05, "Ala-portal on behalf of melecoq"
> <ala-portal-bounces at lists.gbif.org on behalf of melecoq at 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 at lists.gbif.org
> >http://lists.gbif.org/mailman/listinfo/ala-portal
>
>


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