[Geoserver-users] Large NetCDF file errors

GeoServer GeoServer User
1

Hi all,

I'm trying to use Geoserver with large NetCDF files and have been encountering some issues.

When working with large rasters, indexing takes a long time and causes the front end and REST api to become unresponsive. Some of the climate data I work with is ~500*1000*55000*32bit*3variables (150 years of downscaled daily data) = ~330GB per file. After ~3 hours of indexing however, it stops processing and errors out:

20 Jul 15:38:16 WARN [netcdf.NetCDFFormat] - Unable to connect
org.geotools.data.DataSourceException: Unable to connect
Caused by: org.geotools.data.DataSourceException: java.io.IOException: Error occured on rollback
Caused by: java.lang.RuntimeException: java.io.IOException: Error occured on rollback
Caused by: java.io.IOException: Error occured on rollback
Caused by: org.h2.jdbc.JdbcSQLException: IO Exception: java.io.IOException: Negative seek offset; /var/lib/tomcat7/webapps-available/geoserver2711/geoserver_data/climate-data/.pr+tasmax+tasmin_day_BCCAQ+ANUSPLIN300+ACCESS1-0_historical+rcp45_r1i1p1_19500101-21001231_57daab961b0813f95a47bf4e3312d0f79cde766b/pr+tasmax+tasmin_day_BCCAQ+ANUSPLIN300+ACCESS1-0_historical+rcp45_r1i1p1_19500101-21001231.7212500018817963839.temp.db; SQL statement:
ROLLBACK [90031-119]
Caused by: java.io.IOException: Negative seek offset

20 Jul 15:38:16 INFO [geoserver.web] - Getting list of coverages for saved store /var/lib/tomcat7/webapps-available/geoserver2711/geoserver_data/climate-data/pr+tasmax+tasmin_day_BCCAQ+ANUSPLIN300+ACCESS1-0_historical+rcp45_r1i1p1_19500101-21001231.nc
java.lang.RuntimeException: Could not list layers for this store, an error occurred retrieving them: Failed to create reader from /var/lib/tomcat7/webapps-available/geoserver2711/geoserver_data/climate-data/pr+tasmax+tasmin_day_BCCAQ+ANUSPLIN300+ACCESS1-0_historical+rcp45_r1i1p1_19500101-21001231.nc and hints null
Caused by: java.io.IOException: Failed to create reader from /var/lib/tomcat7/webapps-available/geoserver2711/geoserver_data/climate-data/pr+tasmax+tasmin_day_BCCAQ+ANUSPLIN300+ACCESS1-0_historical+rcp45_r1i1p1_19500101-21001231.nc and hints null

At that point it had created 78 <fname>.<fnum>.log.db files at 33MB each, with the last one (fnum=78) being 26MB, and a single ~2.3GB *.temp.db file.

I have measured read speeds on this source and they run ~350MB/s. We should be able to read (and index) the entire file in at most 15 minutes single threaded.

Does anyone else have experience using Geoserver with large NetCDF files?

Geoserver 2.7.1.1
Tomcat 7.0.42
Java 1.7.0_65-b32

NetCDF plugin from:
http://ares.opengeo.org/geoserver/2.7.x/community-latest/

Thanks,
Basil

--
Basil Veerman
Web Application Developer
Pacific Climate Impacts Consortium
http://www.pacificclimate.org/
Tel: (250) 721-6395

2

Dear Basil,
with the work we are doing as we speak we can move the internal index
in PostGIS rather than using H2, this could help.

Can you provide offline one of these files for us to play with?

Regards,
Simone Giannecchini

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@simogeo
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On Wed, Jul 22, 2015 at 8:28 PM, Basil Veerman <bveerman@anonymised.com> wrote:

Hi all,

I'm trying to use Geoserver with large NetCDF files and have been
encountering some issues.

When working with large rasters, indexing takes a long time and causes
the front end and REST api to become unresponsive. Some of the climate
data I work with is ~500*1000*55000*32bit*3variables (150 years of
downscaled daily data) = ~330GB per file. After ~3 hours of indexing
however, it stops processing and errors out:

20 Jul 15:38:16 WARN [netcdf.NetCDFFormat] - Unable to connect
org.geotools.data.DataSourceException: Unable to connect
Caused by: org.geotools.data.DataSourceException: java.io.IOException:
Error occured on rollback
Caused by: java.lang.RuntimeException: java.io.IOException: Error
occured on rollback
Caused by: java.io.IOException: Error occured on rollback
Caused by: org.h2.jdbc.JdbcSQLException: IO Exception:
java.io.IOException: Negative seek offset;
/var/lib/tomcat7/webapps-available/geoserver2711/geoserver_data/climate-data/.pr+tasmax+tasmin_day_BCCAQ+ANUSPLIN300+ACCESS1-0_historical+rcp45_r1i1p1_19500101-21001231_57daab961b0813f95a47bf4e3312d0f79cde766b/pr+tasmax+tasmin_day_BCCAQ+ANUSPLIN300+ACCESS1-0_historical+rcp45_r1i1p1_19500101-21001231.7212500018817963839.temp.db;
SQL statement:
ROLLBACK [90031-119]
Caused by: java.io.IOException: Negative seek offset

20 Jul 15:38:16 INFO [geoserver.web] - Getting list of coverages for
saved store
/var/lib/tomcat7/webapps-available/geoserver2711/geoserver_data/climate-data/pr+tasmax+tasmin_day_BCCAQ+ANUSPLIN300+ACCESS1-0_historical+rcp45_r1i1p1_19500101-21001231.nc
java.lang.RuntimeException: Could not list layers for this store, an
error occurred retrieving them: Failed to create reader from
/var/lib/tomcat7/webapps-available/geoserver2711/geoserver_data/climate-data/pr+tasmax+tasmin_day_BCCAQ+ANUSPLIN300+ACCESS1-0_historical+rcp45_r1i1p1_19500101-21001231.nc
and hints null
Caused by: java.io.IOException: Failed to create reader from
/var/lib/tomcat7/webapps-available/geoserver2711/geoserver_data/climate-data/pr+tasmax+tasmin_day_BCCAQ+ANUSPLIN300+ACCESS1-0_historical+rcp45_r1i1p1_19500101-21001231.nc
and hints null

At that point it had created 78 <fname>.<fnum>.log.db files at 33MB
each, with the last one (fnum=78) being 26MB, and a single ~2.3GB
*.temp.db file.

I have measured read speeds on this source and they run ~350MB/s. We
should be able to read (and index) the entire file in at most 15 minutes
single threaded.

Does anyone else have experience using Geoserver with large NetCDF files?

Geoserver 2.7.1.1
Tomcat 7.0.42
Java 1.7.0_65-b32

NetCDF plugin from:
http://ares.opengeo.org/geoserver/2.7.x/community-latest/

Thanks,
Basil

--
Basil Veerman
Web Application Developer
Pacific Climate Impacts Consortium
http://www.pacificclimate.org/
Tel: (250) 721-6395

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