ERROR RDKit Could not load native RDKit library

Community Extensions
1

Hi all,

i tried to use the new RDKit-Nodes yesterday but i always get the following error when i try to configure one of the nodes: " ERROR     RDKit     Could not load native RDKit library "

I installed the nodes without any difficulty from http://tech.knime.org/update/community-contributions/nightly .

I'm running KNIME 2.3 on a Windows 7 - 64bit system.

Any idea what i'm doing wrong or where my KNIME could find his lost RDKit library ? ;)  

Thanks in advance!

janosch

2

The problem is that at the moment there are no RDKit binaries for 64bit windows. I will take a look over the next few days and see if I can get a good 64bit build. If that works I'll update the community site.

-greg

3

Hallo Greg

I have experienced the same problem even running KNIME 2.3.0 32bit on a Windows 7 (64bit).

I am not convinced is a problem of RDKit binaries for 64bit windows.

Best

-andrea

4

Hi Andrea,

As for Win64 there are simply not binaries yet, so it cannot work at the moment. As for Win32 it should work if you have also installed the feature containing binaries. If not, could you send the corresponding lines in the log file?

Thorsten

5

Hallo Thorsten

ok. I got the point. Here the latest lines of log.

As you see there are also other errors, which I still cannot understand.

2010-12-14 12:29:33,810 INFO  main NodeLogger : #############################################################
2010-12-14 12:29:33,811 INFO  main NodeLogger : #                                                           #
2010-12-14 12:29:33,811 INFO  main NodeLogger : # Welcome to KNIME v2.3.0.0027960 (Build November 25, 2009)      #
2010-12-14 12:29:33,811 INFO  main NodeLogger : # the Konstanz Information Miner                            #
2010-12-14 12:29:33,811 INFO  main NodeLogger : # Based on Eclipse, www.eclipse.org                         #
2010-12-14 12:29:33,811 INFO  main NodeLogger : # Uses: Java, GEF, Log4J                                    #
2010-12-14 12:29:33,812 INFO  main NodeLogger : #                                                           #
2010-12-14 12:29:33,812 INFO  main NodeLogger : #############################################################
2010-12-14 12:29:33,812 INFO  main NodeLogger : #                                                           #
2010-12-14 12:29:33,812 INFO  main NodeLogger : # Copyright, 2003 - 2010                                    #
2010-12-14 12:29:33,812 INFO  main NodeLogger : # University of Konstanz, Germany.                          #
2010-12-14 12:29:33,812 INFO  main NodeLogger : # Chair for Bioinformatics and Information Mining           #
2010-12-14 12:29:33,813 INFO  main NodeLogger : # Prof. Dr. Michael R. Berthold                             #
2010-12-14 12:29:33,813 INFO  main NodeLogger : # and KNIME GmbH, Konstanz, Germany                         #
2010-12-14 12:29:33,813 INFO  main NodeLogger : # website: http://www.knime.org                             #
2010-12-14 12:29:33,813 INFO  main NodeLogger : # email: contact@knime.org                                  #
2010-12-14 12:29:33,813 INFO  main NodeLogger : #                                                           #
2010-12-14 12:29:33,813 INFO  main NodeLogger : #############################################################
2010-12-14 12:29:33,814 INFO  main NodeLogger : # For more details see the KNIME log file:                  #
2010-12-14 12:29:33,814 INFO  main NodeLogger : # C:\Users\andrea\knime_2.2.2\workspace\.metadata\knime\knime.log
2010-12-14 12:29:33,814 INFO  main NodeLogger : #-----------------------------------------------------------#
2010-12-14 12:29:33,814 INFO  main NodeLogger : # logging date=Tue Dec 14 12:29:33 CET 2010
2010-12-14 12:29:33,814 INFO  main NodeLogger : # java.version=1.6.0_22
2010-12-14 12:29:33,815 INFO  main NodeLogger : # java.vm.version=17.1-b03
2010-12-14 12:29:33,815 INFO  main NodeLogger : # java.vendor=Sun Microsystems Inc.
2010-12-14 12:29:33,815 INFO  main NodeLogger : # os.name=Windows 7
2010-12-14 12:29:33,815 INFO  main NodeLogger : # number of CPUs=2
2010-12-14 12:29:33,815 INFO  main NodeLogger : # assertions=off
2010-12-14 12:29:33,819 INFO  main NodeLogger : # host=mypad
2010-12-14 12:29:33,819 INFO  main NodeLogger : # max mem=2730MB
2010-12-14 12:29:33,819 INFO  main NodeLogger : #############################################################
2010-12-14 12:29:33,873 DEBUG main KNIMECorePlugin : Setting KNIME max thread count to 4
2010-12-14 12:29:33,873 DEBUG main KNIMECorePlugin : Setting KNIME temp dir to "C:\Users\andrea\AppData\Local\Temp"
2010-12-14 12:29:33,874 INFO  main NodeLogger : Changing logging level to ERROR
2010-12-14 12:29:36,968 ERROR main RepositoryManager : Node de.mpicbg.tds.knime.hcstools.screenmining.doseresponse.DoseResponseFactory' from plugin 'de.mpicbg.tds.knime.hcstools' could not be created.
2010-12-14 12:29:37,215 ERROR main RepositoryManager : Node de.mpicbg.tds.knime.scripting.scripting.GroovyScriptNodeFactory' from plugin 'de.mpicbg.tds.knime.scripting.groovy' could not be created. The corresponding plugin bundle could not be activated!
2010-12-14 12:29:37,217 ERROR main RepositoryManager : Node de.mpicbg.tds.knime.scripting.r.RSnippetNodeFactory' from plugin 'de.mpicbg.tds.knime.scripting.r' could not be created.
2010-12-14 12:29:37,219 ERROR main RepositoryManager : Node de.mpicbg.tds.knime.scripting.r.RSnippetNodeFactory21' from plugin 'de.mpicbg.tds.knime.scripting.r' could not be created.
2010-12-14 12:29:37,221 ERROR main RepositoryManager : Node de.mpicbg.tds.knime.scripting.r.OpenInRNodeFactory' from plugin 'de.mpicbg.tds.knime.scripting.r' could not be created.
2010-12-14 12:29:37,223 ERROR main RepositoryManager : Node de.mpicbg.tds.knime.scripting.r.RPlotNodeFactory' from plugin 'de.mpicbg.tds.knime.scripting.r' could not be created.
2010-12-14 12:29:37,225 ERROR main RepositoryManager : Node de.mpicbg.tds.knime.scripting.r.genericr.GenericRSnippetFactory' from plugin 'de.mpicbg.tds.knime.scripting.r' could not be created.
2010-12-14 12:29:37,226 ERROR main RepositoryManager : Node de.mpicbg.tds.knime.scripting.r.genericr.GenericRSnippetSourceFactory' from plugin 'de.mpicbg.tds.knime.scripting.r' could not be created.
2010-12-14 12:29:37,228 ERROR main RepositoryManager : Node de.mpicbg.tds.knime.scripting.r.genericr.GenericOpenInRNodeFactory' from plugin 'de.mpicbg.tds.knime.scripting.r' could not be created.
2010-12-14 12:29:37,246 ERROR main RepositoryManager : Node de.mpicbg.tds.knime.scripting.r.genericr.GenericRPlotFactory' from plugin 'de.mpicbg.tds.knime.scripting.r' could not be created.
2010-12-14 12:33:46,847 ERROR main RDKit : Could not load native RDKit library
 

6

Andrea,

Could it be that you are running a 64bit version of KNIME? The maximum memory of 2730MB suggests so since on 32bit it cannot be more than ~1500MB. You cannot load 32bit libraries (such as the ones for RDKit) in a 64bit process.

Thorsten

7

Hi Thorsten,

thanks for taking care. No, I am running 32bit Knime on 64bit Windows7.

This is what I have on my knime2.3.0 help>aboutknime>installationdetails>configuration:

*** Platform Details:

*** System properties:
awt.toolkit=sun.awt.windows.WToolkit
eclipse.application=org.knime.product.KNIME_APPLICATION
eclipse.commands=-os
win32
-ws
win32
-arch
x86_64
-showsplash
-launcher
C:\Users\andrea\knime_2.3.0\knime.exe
-name
Knime
--launcher.library
C:\Users\andrea\knime_2.3.0\plugins/org.eclipse.equinox.launcher.win32.win32.x86_64_1.1.1.R36x_v20100810\eclipse_1309.dll
-startup
C:\Users\andrea\knime_2.3.0\plugins/org.eclipse.equinox.launcher_1.1.0.v20100507.jar
-clean
-vm

....etc

Thx again

-andrea

 

8

Well, this one

-arch
x86_64

says you are running 64bit ;-)

9

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