Cannot open saved KNIME table on another KNIME installation

KNIME Extensions
1

I have saved the resulting table of an image processing workflow to a .table file using the table writer node.
The table contains 16 rows but a couple of images and weight 2Gb in total.

Opening the table file on my KNIME installation using a table reader node works on my installation, but on other installation/machines, the table reader turns green but the table view keep showing “Loading port content” forever.
It’s not an issue of memory, the machine on which I tested have plenty of RAM, storage and CPU.

The table file can be downloaded here

2

As a workaround I will save the table and images separately as images and csv.
So that I am also not bound to KNIME to visualize the results.

1 Like
3

Hi @l.thomas,

Are you running the same version of KNIME Analytics Platform on both machines? We have changed the format of how KNIME tables are stored at some point in the past, which could lead to the issues.

Also, is there more information in the knime.log after trying to open the table on the second machine?

Best,
Stefan

4

Hi Stefan, thanks for the answer,

Both installation (mine that can open and the non functioning) are 3.7.2.

The log does not contain any error message (see below). Or do you spot anything suspect ?
I was wondering if it could be a limitation on the file size ?

But in the end I prefer saving separatly images and table as csv. I am not bound to KNIME to quickly check the data, it’s possibly safer for long term storage and I can further copy/move a fraction of the data rather than having a monolithic 2Gb table :stuck_out_tongue:

2019-06-11 16:30:53,205 : DEBUG : main : NodeContainer : Table Reader : 0:1 : Table Reader 0:1 has new state: IDLE
2019-06-11 16:30:53,208 : DEBUG : main : Node : Table Reader : 0:1 : Configure succeeded. (Table Reader)
2019-06-11 16:30:53,208 : DEBUG : main : NodeContainer : Table Reader : 0:1 : Table Reader 0:1 has new state: CONFIGURED
2019-06-11 16:30:53,208 : DEBUG : main : NodeContainer : Table Reader : 0:1 : KNIME_project 0 has new state: CONFIGURED
2019-06-11 16:30:54,609 : DEBUG : main : ExecuteAction :  :  : Creating execution job for 1 node(s)...
2019-06-11 16:30:54,610 : DEBUG : main : NodeContainer :  :  : Table Reader 0:1 has new state: CONFIGURED_MARKEDFOREXEC
2019-06-11 16:30:54,610 : DEBUG : main : NodeContainer :  :  : Table Reader 0:1 has new state: CONFIGURED_QUEUED
2019-06-11 16:30:54,610 : DEBUG : main : NodeContainer :  :  : KNIME_project 0 has new state: EXECUTING
2019-06-11 16:30:54,610 : DEBUG : KNIME-WFM-Parent-Notifier : NodeContainer :  :  : ROOT  has new state: EXECUTING
2019-06-11 16:30:54,610 : DEBUG : KNIME-Worker-6 : WorkflowManager : Table Reader : 0:1 : Table Reader 0:1 doBeforePreExecution
2019-06-11 16:30:54,610 : DEBUG : KNIME-Worker-6 : NodeContainer : Table Reader : 0:1 : Table Reader 0:1 has new state: PREEXECUTE
2019-06-11 16:30:54,610 : DEBUG : KNIME-Worker-6 : WorkflowManager : Table Reader : 0:1 : Table Reader 0:1 doBeforeExecution
2019-06-11 16:30:54,611 : DEBUG : KNIME-Worker-6 : NodeContainer : Table Reader : 0:1 : Table Reader 0:1 has new state: EXECUTING
2019-06-11 16:30:54,611 : DEBUG : KNIME-Worker-6 : WorkflowDataRepository : Table Reader : 0:1 : Adding handler 62a8d990-859e-4427-8b08-fad4da6508c0 (Table Reader 0:1: <no directory>) - 1 in total
2019-06-11 16:30:54,611 : DEBUG : KNIME-Worker-6 : LocalNodeExecutionJob : Table Reader : 0:1 : Table Reader 0:1 Start execute
2019-06-11 16:31:11,712 : DEBUG : KNIME-Worker-6 : Buffer : Table Reader : 0:1 : Opening input stream on file "C:\Users\User1\AppData\Local\Temp\4\knime_KNIME_project26203\knime_container_20190611_3385345473703860701.tmp", 0 open streams
2019-06-11 16:31:11,716 : DEBUG : KNIME-Worker-6 : Buffer : Table Reader : 0:1 : Using table format org.knime.core.data.container.DefaultTableStoreFormat
2019-06-11 16:31:11,730 : DEBUG : KNIME-TableIO-1 : Buffer : Table Reader : 0:1 : Forcing buffer to disc as it contains file store cells that need special handling
2019-06-11 16:31:11,731 : DEBUG : KNIME-TableIO-1 : WriteFileStoreHandler : Table Reader : 0:1 : Duplicating file store objects - file store handler id 06b04691-195c-4d8e-a9ae-1556c71f7480 is unknown to org.knime.core.node.workflow.WorkflowDataRepository
2019-06-11 16:31:11,731 : DEBUG : KNIME-TableIO-1 : WriteFileStoreHandler : Table Reader : 0:1 : Dump of valid file store handlers follows, omitting further log output
2019-06-11 16:31:11,731 : DEBUG : KNIME-TableIO-1 : WorkflowDataRepository : Table Reader : 0:1 : Valid file store handlers are:
2019-06-11 16:31:11,731 : DEBUG : KNIME-TableIO-1 : WorkflowDataRepository : Table Reader : 0:1 : --------- Start --------------
2019-06-11 16:31:11,731 : DEBUG : KNIME-TableIO-1 : WorkflowDataRepository : Table Reader : 0:1 :   62a8d990-859e-4427-8b08-fad4da6508c0 (Table Reader 0:1: <no directory>)
2019-06-11 16:31:11,731 : DEBUG : KNIME-TableIO-1 : WorkflowDataRepository : Table Reader : 0:1 : --------- End ----------------
2019-06-11 16:31:11,732 : DEBUG : KNIME-TableIO-1 : WriteFileStoreHandler : Table Reader : 0:1 : Assigning temp directory to file store "62a8d990-859e-4427-8b08-fad4da6508c0 (Table Reader 0:1: C:\Users\User1\AppData\Local\Temp\4\knime_KNIME_project26203\fs-Table_0-1-26207)"
2019-06-11 16:31:12,567 : DEBUG : KNIME-Worker-6 : Buffer : Table Reader : 0:1 : Buffer file (C:\Users\User1\AppData\Local\Temp\4\knime_KNIME_project26203\knime_container_20190611_9189562762371696835.bin.gz) is 0.065MB in size
2019-06-11 16:31:12,567 : INFO  : KNIME-Worker-6 : LocalNodeExecutionJob : Table Reader : 0:1 : Table Reader 0:1 End execute (17 secs)
2019-06-11 16:31:12,567 : DEBUG : KNIME-Worker-6 : WorkflowManager : Table Reader : 0:1 : Table Reader 0:1 doBeforePostExecution
2019-06-11 16:31:12,567 : DEBUG : KNIME-Worker-6 : NodeContainer : Table Reader : 0:1 : Table Reader 0:1 has new state: POSTEXECUTE
2019-06-11 16:31:12,567 : DEBUG : KNIME-Worker-6 : WorkflowManager : Table Reader : 0:1 : Table Reader 0:1 doAfterExecute - success
2019-06-11 16:31:12,567 : DEBUG : KNIME-Worker-6 : NodeContainer : Table Reader : 0:1 : Table Reader 0:1 has new state: EXECUTED
2019-06-11 16:31:12,568 : DEBUG : KNIME-Worker-6 : NodeContainer : Table Reader : 0:1 : KNIME_project 0 has new state: EXECUTED
2019-06-11 16:31:12,568 : DEBUG : KNIME-WFM-Parent-Notifier : NodeContainer :  :  : ROOT  has new state: IDLE
2019-06-11 16:31:16,682 : DEBUG : main : OpenPortViewAction :  :  : Open Port View Table Reader (#1)
2019-06-11 16:31:16,706 : DEBUG : AWT-EventQueue-0 : Buffer : Table Reader : 0:1 : Opening input stream on file "C:\Users\User1\AppData\Local\Temp\4\knime_KNIME_project26203\knime_container_20190611_9189562762371696835.bin.gz", 0 open streams
2019-06-11 16:31:31,124 : DEBUG : KNIME-Node-Usage-Writer : NodeTimer$GlobalNodeStats :  :  : Successfully wrote node usage stats to file: D:\KNIME\Olafs_workspace\.metadata\knime\nodeusage_3.0.json
2019-06-11 16:31:31,125 : DEBUG : KNIME-Node-Usage-Sender : NodeTimer$GlobalNodeStats :  :  : Sending of usage stats disabled.
2019-06-11 16:31:32,739 : DEBUG : main : WorkflowRootEditPart :  :  : WorkflowRootEditPart deactivated
2019-06-11 16:31:32,743 : DEBUG : main : WorkflowEditor :  :  : Disposing editor...
2019-06-11 16:31:32,744 : DEBUG : main : ProjectWorkflowMap :  :  : unregistering org.knime.workbench.editor2.WorkflowEditor@956cf3d from file:/D:/KNIME/Olafs_workspace/KNIME_project/. 0 left.
2019-06-11 16:31:32,744 : DEBUG : main : ProjectWorkflowMap : KNIME_project : 0 : Removing "file:/D:/KNIME/Olafs_workspace/KNIME_project/" from project map (0 remaining)
2019-06-11 16:31:32,744 : DEBUG : main : WorkflowManager : KNIME_project : 0 : Removing project "KNIME_project 0"
2019-06-11 16:31:32,746 : DEBUG : main : WorkflowDataRepository : Table Reader : 0:1 : Removing handler 62a8d990-859e-4427-8b08-fad4da6508c0 (Table Reader 0:1: C:\Users\User1\AppData\Local\Temp\4\knime_KNIME_project26203\fs-Table_0-1-26207) - 0 remaining
2019-06-11 16:31:32,794 : WARN  : main : WriteFileStoreHandler : Table Reader : 0:1 : Disposing file store "62a8d990-859e-4427-8b08-fad4da6508c0 (Table Reader 0:1: C:\Users\User1\AppData\Local\Temp\4\knime_KNIME_project26203\fs-Table_0-1-26207)" - folder not or only partially deleted
2019-06-11 16:31:32,794 : DEBUG : main : ReadTableNodeModel : Table Reader : 0:1 : Removing all (0) views from model.
2019-06-11 16:31:32,794 : DEBUG : main : Node : Table Reader : 0:1 : clean output ports.
2019-06-11 16:31:32,795 : DEBUG : main : Buffer : Table Reader : 0:1 : Closing input stream on "C:\Users\User1\AppData\Local\Temp\4\knime_KNIME_project26203\knime_container_20190611_9189562762371696835.bin.gz", 0 remaining
2019-06-11 16:31:32,795 : DEBUG : KNIME-Temp-File-Deleter : Buffer :  :  : Deleted temporary file "C:\Users\User1\AppData\Local\Temp\4\knime_KNIME_project26203\knime_container_20190611_9189562762371696835.bin.gz"
2019-06-11 16:31:32,797 : DEBUG : main : WorkflowManager : KNIME_project : 0 : Project "KNIME_project 0" removed (1 remaining)
2019-06-11 16:31:33,228 : INFO  : KNIME-Worker-7 : WorkflowManager : KNIME_project : 0 : Could not delete temporary directory for workflow KNIME_project at C:\Users\User1\AppData\Local\Temp\4\knime_KNIME_project26203
5

That makes perfect sense :wink:

Could you also please check, which version of KNIME Image Processing you are running on both machines (Help > About KNIME Analytics Platform > Installation Details and the version for KNIME Image Processing on the first tab)? Thanks!

3 Likes
6

I think you spotted it !
With the previous version of KNIME image processing 1.7.0.201904290603 it works,
updating to the last version 1.7.0.201906080526 I have the issue :wink:

5 Likes
7

We have improved some things with respect to how images get serialized. LUTs in particular would blow up the table size prior to the fix. The downside: Reading/Writing tables with versions before and after won’t work… Sorry about the hassle!

2 Likes