I am running a coherence XML from the gpt in cluster environment. I am getting the following error. My gpt.vmoptions are as follows in HPC:
Enter one VM parameter per line
For example, to adjust the maximum memory usage to 512 MB, uncomment the following line:
-Xmx512m
To include another file, uncomment the following line:
-include-options [path to other .vmoption file]
-Xmx36G
-Xms30G
-XX:+AggressiveOpts
-Xverify:none
-Dnetbeans.mainclass=org.esa.snap.main.Main
-Dsun.java2d.noddraw=true
-Dsun.awt.nopixfmt=true
-Dsun.java2d.dpiaware=false
saiiitb@clogin72:~/vvsk/SNAP_output/Coherence/Bottom> gpt -x -q 30 Btm_Coh20180105_20180821.xml
INFO: org.esa.snap.core.gpf.operators.tooladapter.ToolAdapterIO: Initializing external tool adapters
SEVERE: org.esa.s2tbx.dataio.gdal.activator.GDALDistributionInstaller: The environment variable LD_LIBRARY_PATH does not contain the current folder ‘.’. Its value is ‘/usr/lib64/mpi/gcc/openmpi/lib64’.
Executing processing graph
INFO: org.hsqldb.persist.Logger: dataFileCache open start
Master: 05Jan2018
Slave: 05Jan2018 prep baseline: 0.0 temp baseline: 0.0
Slave: 21Aug2018 prep baseline: -16.92045 temp baseline: -228.00008
======
Master: 21Aug2018
Slave: 05Jan2018 prep baseline: 16.91745 temp baseline: 228.00008
Slave: 21Aug2018 prep baseline: 0.0 temp baseline: 0.0
IFG: isTOPSARBurstProduct = true
Master: 05Jan2018
Slave: 05Jan2018 prep baseline: 0.0 temp baseline: 0.0
Slave: 21Aug2018 prep baseline: -17.328152 temp baseline: -228.00008
======
Master: 21Aug2018
Slave: 05Jan2018 prep baseline: 17.324049 temp baseline: 228.00008
Slave: 21Aug2018 prep baseline: 0.0 temp baseline: 0.0
IFG: isTOPSARBurstProduct = true
Master: 05Jan2018
Slave: 05Jan2018 prep baseline: 0.0 temp baseline: 0.0
Slave: 21Aug2018 prep baseline: -17.872156 temp baseline: -228.00008
======
Master: 21Aug2018
Slave: 05Jan2018 prep baseline: 17.866983 temp baseline: 228.00008
Slave: 21Aug2018 prep baseline: 0.0 temp baseline: 0.0
IFG: isTOPSARBurstProduct = true
…10%GC overhead limit exceeded
GC overhead limit exceeded
java.lang.NullPointerException
java.lang.NullPointerException
java.lang.NullPointerException
java.lang.NullPointerException
java.lang.NullPointerException
at com.sun.media.jai.util.SunCachedTile.(SunCachedTile.java:80)
at com.sun.media.jai.util.SunTileCache.add(SunTileCache.java:257)
at javax.media.jai.OpImage.addTileToCache(OpImage.java:1087)
at javax.media.jai.OpImage.getTile(OpImage.java:1142)
at javax.media.jai.PlanarImage.cobbleFloat(PlanarImage.java:3254)
at javax.media.jai.PlanarImage.getData(PlanarImage.java:2181)
at com.bc.ceres.glevel.MultiLevelImage.getData(MultiLevelImage.java:64)
at org.esa.snap.core.gpf.internal.OperatorContext.getSourceTile(OperatorContext.java:407)
at org.esa.snap.core.gpf.internal.OperatorContext.getSourceTile(OperatorContext.java:393)
at org.esa.snap.core.gpf.Operator.getSourceTile(Operator.java:461)
at org.esa.s1tbx.sentinel1.gpf.TOPSARMergeOp.computeTileInOneSwathFloat(TOPSARMergeOp.java:745)
at org.esa.s1tbx.sentinel1.gpf.TOPSARMergeOp.computeTileStack(TOPSARMergeOp.java:662)
at org.esa.snap.core.gpf.internal.OperatorImageTileStack.computeRect(OperatorImageTileStack.java:116)
at org.esa.snap.core.gpf.internal.OperatorImageTileStack.computeTile(OperatorImageTileStack.java:85)
at com.sun.media.jai.util.SunTileScheduler.scheduleTile(SunTileScheduler.java:904)
at javax.media.jai.OpImage.getTile(OpImage.java:1129)
at javax.media.jai.PlanarImage.getData(PlanarImage.java:2085)
at com.bc.ceres.glevel.MultiLevelImage.getData(MultiLevelImage.java:64)
at org.esa.snap.core.gpf.internal.OperatorContext.getSourceTile(OperatorContext.java:407)
at org.esa.snap.core.gpf.internal.OperatorContext.getSourceTile(OperatorContext.java:393)
at org.esa.snap.core.gpf.internal.OperatorImage.computeRect(OperatorImage.java:73)
at javax.media.jai.SourcelessOpImage.computeTile(SourcelessOpImage.java:137)
at com.sun.media.jai.util.SunTileScheduler.scheduleTile(SunTileScheduler.java:904)
at javax.media.jai.OpImage.getTile(OpImage.java:1129)
at com.sun.media.jai.util.RequestJob.compute(SunTileScheduler.java:247)
at com.sun.media.jai.util.WorkerThread.run(SunTileScheduler.java:468)
java.lang.RuntimeException: Waiting thread received a null tile.
at com.sun.media.jai.util.SunTileScheduler.scheduleTile(SunTileScheduler.java:963)
at javax.media.jai.OpImage.getTile(OpImage.java:1129)
at javax.media.jai.PlanarImage.cobbleFloat(PlanarImage.java:3254)
at javax.media.jai.PlanarImage.getData(PlanarImage.java:2181)
at com.bc.ceres.glevel.MultiLevelImage.getData(MultiLevelImage.java:64)
at org.esa.snap.core.gpf.internal.OperatorContext.getSourceTile(OperatorContext.java:407)
at org.esa.snap.core.gpf.internal.OperatorContext.getSourceTile(OperatorContext.java:393)
at org.esa.snap.core.gpf.Operator.getSourceTile(Operator.java:461)
at org.esa.s1tbx.sentinel1.gpf.TOPSARMergeOp.computeTileInOneSwathFloat(TOPSARMergeOp.java:745)
at org.esa.s1tbx.sentinel1.gpf.TOPSARMergeOp.computeTileStack(TOPSARMergeOp.java:662)
at org.esa.snap.core.gpf.internal.OperatorImageTileStack.computeRect(OperatorImageTileStack.java:116)
at org.esa.snap.core.gpf.internal.OperatorImageTileStack.computeTile(OperatorImageTileStack.java:85)
at com.sun.media.jai.util.SunTileScheduler.scheduleTile(SunTileScheduler.java:904)
at javax.media.jai.OpImage.getTile(OpImage.java:1129)
at javax.media.jai.PlanarImage.getData(PlanarImage.java:2085)
at com.bc.ceres.glevel.MultiLevelImage.getData(MultiLevelImage.java:64)
at org.esa.snap.core.gpf.internal.OperatorContext.getSourceTile(OperatorContext.java:407)
at org.esa.snap.core.gpf.internal.OperatorContext.getSourceTile(OperatorContext.java:393)
at org.esa.snap.core.gpf.internal.OperatorImage.computeRect(OperatorImage.java:73)
at javax.media.jai.SourcelessOpImage.computeTile(SourcelessOpImage.java:137)
at com.sun.media.jai.util.SunTileScheduler.scheduleTile(SunTileScheduler.java:904)
at javax.media.jai.OpImage.getTile(OpImage.java:1129)
at com.sun.media.jai.util.RequestJob.compute(SunTileScheduler.java:247)
at com.sun.media.jai.util.WorkerThread.run(SunTileScheduler.java:468)
90% done.
org.esa.snap.core.gpf.OperatorException: GC overhead limit exceeded
at org.esa.snap.core.gpf.graph.GraphProcessor$GPFImagingListener.errorOccurred(GraphProcessor.java:363)
at com.sun.media.jai.util.SunTileScheduler.sendExceptionToListener(SunTileScheduler.java:1646)
at com.sun.media.jai.util.SunTileScheduler.scheduleTile(SunTileScheduler.java:921)
at javax.media.jai.OpImage.getTile(OpImage.java:1129)
at javax.media.jai.PlanarImage.cobbleFloat(PlanarImage.java:3254)
at javax.media.jai.PlanarImage.getData(PlanarImage.java:2181)
at com.bc.ceres.glevel.MultiLevelImage.getData(MultiLevelImage.java:64)
at javax.media.jai.PlanarImage.getExtendedData(PlanarImage.java:2440)
at org.esa.snap.core.gpf.internal.OperatorContext.getSourceTile(OperatorContext.java:405)
at org.esa.snap.core.gpf.Operator.getSourceTile(Operator.java:481)
at org.esa.s1tbx.insar.gpf.InterferogramOp.computePartialTile(InterferogramOp.java:1387)
at org.esa.s1tbx.insar.gpf.InterferogramOp.computeTileStackForTOPSARProduct(InterferogramOp.java:1258)
at org.esa.s1tbx.insar.gpf.InterferogramOp.computeTileStack(InterferogramOp.java:853)
at org.esa.snap.core.gpf.internal.OperatorImageTileStack.computeRect(OperatorImageTileStack.java:116)
at org.esa.snap.core.gpf.internal.OperatorImageTileStack.computeTile(OperatorImageTileStack.java:85)
at com.sun.media.jai.util.SunTileScheduler.scheduleTile(SunTileScheduler.java:904)
at javax.media.jai.OpImage.getTile(OpImage.java:1129)
at javax.media.jai.PlanarImage.cobbleFloat(PlanarImage.java:3254)
at javax.media.jai.PlanarImage.getData(PlanarImage.java:2181)
at com.bc.ceres.glevel.MultiLevelImage.getData(MultiLevelImage.java:64)
at org.esa.snap.core.gpf.internal.OperatorContext.getSourceTile(OperatorContext.java:407)
at org.esa.snap.core.gpf.internal.OperatorContext.getSourceTile(OperatorContext.java:393)
at org.esa.snap.core.gpf.Operator.getSourceTile(Operator.java:461)
at org.esa.s1tbx.sentinel1.gpf.TOPSARDeburstOp.computeTileInOneSwathFloat(TOPSARDeburstOp.java:895)
at org.esa.s1tbx.sentinel1.gpf.TOPSARDeburstOp.computeTileStack(TOPSARDeburstOp.java:802)
at org.esa.snap.core.gpf.internal.OperatorImageTileStack.computeRect(OperatorImageTileStack.java:116)
at org.esa.snap.core.gpf.internal.OperatorImageTileStack.computeTile(OperatorImageTileStack.java:85)
at com.sun.media.jai.util.SunTileScheduler.scheduleTile(SunTileScheduler.java:904)
at javax.media.jai.OpImage.getTile(OpImage.java:1129)
at javax.media.jai.PlanarImage.cobbleFloat(PlanarImage.java:3254)
at javax.media.jai.PlanarImage.getData(PlanarImage.java:2181)
at com.bc.ceres.glevel.MultiLevelImage.getData(MultiLevelImage.java:64)
at org.esa.snap.core.gpf.internal.OperatorContext.getSourceTile(OperatorContext.java:407)
at org.esa.snap.core.gpf.internal.OperatorContext.getSourceTile(OperatorContext.java:393)
at org.esa.snap.core.gpf.Operator.getSourceTile(Operator.java:461)
at org.esa.s1tbx.sentinel1.gpf.TOPSARMergeOp.computeTileInOneSwathFloat(TOPSARMergeOp.java:745)
at org.esa.s1tbx.sentinel1.gpf.TOPSARMergeOp.computeTileStack(TOPSARMergeOp.java:662)
at org.esa.snap.core.gpf.internal.OperatorImageTileStack.computeRect(OperatorImageTileStack.java:116)
at org.esa.snap.core.gpf.internal.OperatorImageTileStack.computeTile(OperatorImageTileStack.java:85)
at com.sun.media.jai.util.SunTileScheduler.scheduleTile(SunTileScheduler.java:904)
at javax.media.jai.OpImage.getTile(OpImage.java:1129)
at javax.media.jai.PlanarImage.getData(PlanarImage.java:2085)
at com.bc.ceres.glevel.MultiLevelImage.getData(MultiLevelImage.java:64)
at org.esa.snap.core.gpf.internal.OperatorContext.getSourceTile(OperatorContext.java:407)
at org.esa.snap.core.gpf.internal.OperatorContext.getSourceTile(OperatorContext.java:393)
at org.esa.snap.core.gpf.internal.OperatorImage.computeRect(OperatorImage.java:73)
at javax.media.jai.SourcelessOpImage.computeTile(SourcelessOpImage.java:137)
at com.sun.media.jai.util.SunTileScheduler.scheduleTile(SunTileScheduler.java:904)
at javax.media.jai.OpImage.getTile(OpImage.java:1129)
at com.sun.media.jai.util.RequestJob.compute(SunTileScheduler.java:247)
at com.sun.media.jai.util.WorkerThread.run(SunTileScheduler.java:468)
Caused by: org.esa.snap.core.gpf.OperatorException: GC overhead limit exceeded
at org.esa.snap.engine_utilities.gpf.OperatorUtils.catchOperatorException(OperatorUtils.java:432)
at org.esa.s1tbx.sentinel1.gpf.BackGeocodingOp.computeTileStack(BackGeocodingOp.java:493)
at org.esa.snap.core.gpf.internal.OperatorImageTileStack.computeRect(OperatorImageTileStack.java:116)
at org.esa.snap.core.gpf.internal.OperatorImageTileStack.computeTile(OperatorImageTileStack.java:85)
at com.sun.media.jai.util.SunTileScheduler.scheduleTile(SunTileScheduler.java:904)
… 48 more
Caused by: org.esa.snap.core.gpf.OperatorException: GC overhead limit exceeded
at org.esa.snap.engine_utilities.gpf.OperatorUtils.catchOperatorException(OperatorUtils.java:432)
at org.esa.s1tbx.sentinel1.gpf.BackGeocodingOp.computeSlavePixPos(BackGeocodingOp.java:948)
at org.esa.s1tbx.sentinel1.gpf.BackGeocodingOp.computePartialTile(BackGeocodingOp.java:750)
at org.esa.s1tbx.sentinel1.gpf.BackGeocodingOp.computeTileStack(BackGeocodingOp.java:487)
… 51 more
Caused by: java.lang.OutOfMemoryError: GC overhead limit exceeded
at org.esa.snap.core.dataop.resamp.BilinearInterpolationResampling.resample(BilinearInterpolationResampling.java:78)
at org.esa.snap.core.dataop.dem.BaseElevationModel.getElevation(BaseElevationModel.java:99)
at org.esa.s1tbx.sentinel1.gpf.BackGeocodingOp.computeSlavePixPos(BackGeocodingOp.java:927)
at org.esa.s1tbx.sentinel1.gpf.BackGeocodingOp.computePartialTile(BackGeocodingOp.java:750)
at org.esa.s1tbx.sentinel1.gpf.BackGeocodingOp.computeTileStack(BackGeocodingOp.java:487)
at org.esa.snap.core.gpf.internal.OperatorImageTileStack.computeRect(OperatorImageTileStack.java:116)
at org.esa.snap.core.gpf.internal.OperatorImageTileStack.computeTile(OperatorImageTileStack.java:85)
at com.sun.media.jai.util.SunTileScheduler.scheduleTile(SunTileScheduler.java:904)
at javax.media.jai.OpImage.getTile(OpImage.java:1129)
at javax.media.jai.PlanarImage.cobbleFloat(PlanarImage.java:3254)
at javax.media.jai.PlanarImage.getData(PlanarImage.java:2181)
at com.bc.ceres.glevel.MultiLevelImage.getData(MultiLevelImage.java:64)
at javax.media.jai.PlanarImage.getExtendedData(PlanarImage.java:2440)
at org.esa.snap.core.gpf.internal.OperatorContext.getSourceTile(OperatorContext.java:405)
at org.esa.snap.core.gpf.Operator.getSourceTile(Operator.java:481)
at org.esa.s1tbx.insar.gpf.InterferogramOp.computePartialTile(InterferogramOp.java:1387)
at org.esa.s1tbx.insar.gpf.InterferogramOp.computeTileStackForTOPSARProduct(InterferogramOp.java:1258)
at org.esa.s1tbx.insar.gpf.InterferogramOp.computeTileStack(InterferogramOp.java:853)
at org.esa.snap.core.gpf.internal.OperatorImageTileStack.computeRect(OperatorImageTileStack.java:116)
at org.esa.snap.core.gpf.internal.OperatorImageTileStack.computeTile(OperatorImageTileStack.java:85)
at com.sun.media.jai.util.SunTileScheduler.scheduleTile(SunTileScheduler.java:904)
at javax.media.jai.OpImage.getTile(OpImage.java:1129)
at javax.media.jai.PlanarImage.cobbleFloat(PlanarImage.java:3254)
at javax.media.jai.PlanarImage.getData(PlanarImage.java:2181)
at com.bc.ceres.glevel.MultiLevelImage.getData(MultiLevelImage.java:64)
at org.esa.snap.core.gpf.internal.OperatorContext.getSourceTile(OperatorContext.java:407)
at org.esa.snap.core.gpf.internal.OperatorContext.getSourceTile(OperatorContext.java:393)
at org.esa.snap.core.gpf.Operator.getSourceTile(Operator.java:461)
at org.esa.s1tbx.sentinel1.gpf.TOPSARDeburstOp.computeTileInOneSwathFloat(TOPSARDeburstOp.java:895)
at org.esa.s1tbx.sentinel1.gpf.TOPSARDeburstOp.computeTileStack(TOPSARDeburstOp.java:802)
at org.esa.snap.core.gpf.internal.OperatorImageTileStack.computeRect(OperatorImageTileStack.java:116)
at org.esa.snap.core.gpf.internal.OperatorImageTileStack.computeTile(OperatorImageTileStack.java:85)
Error: GC overhead limit exceeded
– org.jblas INFO Deleting /tmp/jblas6448387189809509375/libjblas.so
– org.jblas INFO Deleting /tmp/jblas6448387189809509375/libjblas_arch_flavor.so
– org.jblas INFO Deleting /tmp/jblas6448387189809509375