dear,
When i run a groupby calculation i receive runtime error and crash , i'm processing 10k smile structure. Seems not a problem of swap memory.
thanks
Can you be a bit more specific about the error you get?
Dear ,
I tried to split 10% of the dataset and rerun but i find
ERROR GroupBy Execute failed: ("NullPointerException"): null
Row Sampling 0:820:127 failed to apply settings: unable to create new native thread
I checked for null value and there was no one, and after knime crash or send me this error
Execute failed: unable to create new native thread
what could be the problem?
Please send also the full stack trace from the knime.log. It could be that you are running out of Java memory, you may try to increase the -Xmx value in the knime.ini.
from log file i found this
2012-11-09 12:11:44,925 DEBUG KNIME-Worker-0 GroupBy : Execute failed: ("NullPointerException"): null
java.lang.NullPointerException
at org.knime.core.data.DataType$1.compareDataValues(DataType.java:235)
at org.knime.core.data.DataValueComparator.compare(DataValueComparator.java:123)
at org.knime.core.data.sort.TableSorter$RowComparator.compare(TableSorter.java:766)
at org.knime.core.data.sort.TableSorter$RowComparator.compare(TableSorter.java:1)
at java.util.Arrays.mergeSort(Unknown Source)
at java.util.Arrays.mergeSort(Unknown Source)
at java.util.Arrays.mergeSort(Unknown Source)
at java.util.Arrays.mergeSort(Unknown Source)
at java.util.Arrays.mergeSort(Unknown Source)
at java.util.Arrays.mergeSort(Unknown Source)
at java.util.Arrays.mergeSort(Unknown Source)
at java.util.Arrays.mergeSort(Unknown Source)
at java.util.Arrays.mergeSort(Unknown Source)
at java.util.Arrays.mergeSort(Unknown Source)
at java.util.Arrays.mergeSort(Unknown Source)
at java.util.Arrays.sort(Unknown Source)
at java.util.Collections.sort(Unknown Source)
at org.knime.core.data.sort.TableSorter.sortOnDisk(TableSorter.java:504)
at org.knime.core.data.sort.TableSorter.sortInternal(TableSorter.java:338)
at org.knime.core.data.sort.BufferedDataTableSorter.sort(BufferedDataTableSorter.java:145)
at org.knime.base.data.sort.SortedTable.<init>(SortedTable.java:206)
at org.knime.base.data.sort.SortedTable.<init>(SortedTable.java:173)
at org.knime.base.node.preproc.groupby.GroupByTable.sortTable(GroupByTable.java:387)
at org.knime.base.node.preproc.groupby.BigGroupByTable.createGroupByTable(BigGroupByTable.java:183)
at org.knime.base.node.preproc.groupby.GroupByTable.<init>(GroupByTable.java:239)
at org.knime.base.node.preproc.groupby.BigGroupByTable.<init>(BigGroupByTable.java:157)
at org.knime.base.node.preproc.groupby.GroupByNodeModel.createGroupByTable(GroupByNodeModel.java:682)
at org.knime.base.node.preproc.groupby.GroupByNodeModel.createGroupByTable(GroupByNodeModel.java:638)
at org.knime.base.node.preproc.groupby.GroupByNodeModel.createGroupByTable(GroupByNodeModel.java:616)
at org.knime.base.node.preproc.groupby.GroupByNodeModel.execute(GroupByNodeModel.java:597)
at org.knime.core.node.NodeModel.executeModel(NodeModel.java:536)
at org.knime.core.node.Node.invokeNodeModelExecute(Node.java:995)
at org.knime.core.node.Node.execute(Node.java:889)
at org.knime.core.node.workflow.SingleNodeContainer.performExecuteNode(SingleNodeContainer.java:894)
at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:100)
at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:166)
at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:124)
at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:239)
2012-11-09 12:11:44,972 DEBUG KNIME-Worker-0 WorkflowManager : GroupBy 0:820:121 doBeforePostExecution
2012-11-09 12:11:44,972 DEBUG KNIME-Worker-0 NodeContainer : GroupBy 0:820:121 has new state: POSTEXECUTE
2012-11-09 12:11:44,972 DEBUG KNIME-Worker-0 NodeContainer : MetaNode 0:820 has new state: EXECUTING
2012-11-09 12:11:44,972 DEBUG KNIME-Worker-0 KnimeResourceNavigator : Node message changed: ERROR: Error in sub flow.
2012-11-09 12:11:44,972 DEBUG KNIME-Worker-0 NodeContainer : Lead Optz Drug Rules 0 has new state: EXECUTING
2012-11-09 12:11:44,972 DEBUG KNIME-Worker-0 WorkflowManager : GroupBy 0:820:121 doAfterExecute - failure
2012-11-09 12:11:44,972 DEBUG KNIME-Worker-0 GroupBy : reset
2012-11-09 12:11:44,972 DEBUG KNIME-Worker-0 GroupBy : clean output ports.
2012-11-09 12:11:44,972 DEBUG KNIME-Worker-0 WorkflowFileStoreHandlerRepository : Removing handler b0478ac8-9d41-4e51-a023-035d4499d485 (GroupBy 0:820:121: <no directory>) - 0 remaining
2012-11-09 12:11:44,972 DEBUG KNIME-Worker-0 NodeContainer : GroupBy 0:820:121 has new state: IDLE
2012-11-09 12:11:44,972 DEBUG KNIME-Worker-0 GroupBy : Configure succeeded. (GroupBy)
2012-11-09 12:11:44,972 DEBUG KNIME-Worker-0 NodeContainer : GroupBy 0:820:121 has new state: CONFIGURED
2012-11-09 12:11:44,972 DEBUG KNIME-Worker-0 KnimeResourceNavigator : state changed to IDLE
2012-11-09 12:11:44,972 DEBUG KNIME-Worker-0 NodeContainer : MetaNode 0:820 has new state: IDLE
2012-11-09 12:11:44,972 DEBUG KNIME-Worker-0 KnimeResourceNavigator : state changed to IDLE
2012-11-09 12:11:44,972 DEBUG KNIME-Worker-0 NodeContainer : Lead Optz Drug Rules 0 has new state: IDLE
2012-11-09 12:11:44,972 DEBUG KNIME-Worker-0 NodeContainer : Lead Optz Drug Rules 0 has new state: IDLE
2012-11-09 12:11:44,972 DEBUG KNIME-WFM-Parent-Notifier NodeContainer : Workflow Manager has new state: IDLE
2012-11-09 12:11:44,972 DEBUG KNIME-Worker-0 NodeContainer : MetaNode 0:820 has new state: IDLE
Hello Fab,
I'm sorry for these inconveniences. It seems to be a problem with the sorting of the input table based on the selected groupby columns. Could you please tell me the data types (e.g. double, string, smiles, etc.) of the selected group columns (the columns you included in the group tab).
As a workaround you could try to skip the sorting of the input table by selecting the "Process in memory" option on the options tab. However this settings might consume a lot of memory depending on the number of groups and the selected aggregation method.
Thanks a lot for your help,
Tobias