[Solved] RDKit broken after update

Community Extensions
1

Hello all,

 

I have just updated the RDKit collection and I get the "Could not load native RDKit Library" warning in a workflow that was working minutes before the update.

 

The machine on which the workflow is running is a 64 bit Windows. I read a few posts about an issue with x64 architecture. Did the wrong version of the library get installed? How do I revert back to the one that was working?

 

Cheers,

Fred

2

Dear Fred,

 

I would like to try to reproduce your issue. What KNIME version are you running? Also, could you please check what Java version is used by KNIME? Just enter the following in a command shell and replace %KNIME% with your install directory to find out the Java version:

C:\%KNIME%\jre\bin\java.exe -version
 

Thanks.

 

Kind regards,

Manuel

3

Dear Fred,

 

I just tested with KNIME 2.6.3 and KNIME 2.7.2 on my Window 7 64-bit machine with the latest RDKit Nodes from the KNIME Community Release update site: http://tech.knime.org/update/community-contributions/release

 

The RDKit versions I have installed are shown in dialog Help => About KNIME => Installation Details:

Tab Installed Software (Feature):

RDKit KNIME Integration 2.1.0.210302211506.

Tab Plugins:

RDKit Chemistry Type Definition Plugin 2.1.0.201302041554

RDKit Nodes for Knime 2.1.0.201302211506

RDKit binaries for 64-bit Windows 2.1.0.201302061056

 

Please check your versions - I have the feeling that you may still have gotten an older version. There is a chance that the Community update site was not fully updated yet when I posted my announcement.

 

Kind regards,

Manuel

4

Hello Manuel,

 

Thanks a lot for looking into this.

The version of KNIME I'm using is 2.6.3 and the RDKit info is

  • RDKit KNIME integration 2.1.0.201302211506
  • RDKit Chemistry Type Definition Plugin 2.1.0.201302041554
  • RDKit Nodes for Knime 2.1.0.201302211506
  • RDKit binaries for 64-bit Windows 2.1.0.201302061056

So, exactly the same as yours, except the 2.1.0.2013 of the RDKit KNIME, which may be a typo.

 

Good news, though, everything is working now, without me doing anything but opening another workflow...

 

Cheers,

Fred

5

Hi Fred,

 

good to hear. You are right with the typo, you have the correct versions.

Just curious: Did you restart Eclipse after you updated the RDKit Nodes before running the failing workflow? As native DLLs are involved in the RDKit nodes this is crucial.

 

Kind regards,

Manuel

6

Hello Manuel,

 

I am not sure what you mean by "Did you restart Eclipse". What is it I have to do to restart Eclipse?

Sorry I've not had time to answer earlier than now... and thanks again for your help!

 

Cheers,

Fred

7

Just realised I forgot to include the Java version I'm on:

java version "1.6.0_22"
Java(TM) SE Runtime Environment (build 1.6.0_22-b04)
Java HotSpot(TM) 64-Bit Server VM (build 17.1-b03, mixed mode)

8

With "restart" I mean closing the Eclipse application and starting it again. Usually, it would ask you to do this anyway when you install a new plugin or update an existing one.

As it works now I do not think we need to pursue this any further.

 

Kind regards,

Manuel

9

Hello Manuel,

 

Thanks for your reply. Unfortunately, it does not work. I was under the impression that it was working as the nodes were displaying a green traffic-light icon. However, trying to run the workflow yields the same error. Sorry for the confusion.

 

If by closing the Eclipse application you mean restarting KNIME, then yes, I restarted it.

 

Can you think of anything else I could try? It is a shame: thanks to the RDKit nodes, I was close to implementing an error-free solution and now, because of the update I performed, I cannot use this solution anymore.

 

Please, let me know what can be done to fix this,

Fred

10

Oh no.

I have just moved to a 64bit Mac, and my favourite nodes dont work now. The RDKit nodes simply fail with the error;

 

ERROR RDKit Could not load native RDKit library

WARN  Molecule to RDKit Could not load native RDKit library

 

I am on KNIME 2.7.2, and the latest nightly build of RDKit. Mac is 64bit Retina Macbook Pro with the OS X 10.8.2. RDkit versions below;

  RDKit KNIME integration 2.1.0.201302211506 org.rdkit.knime.feature.feature.group NIBR

  RDKit KNIME Wizards 2.1.0.201212031505 org.rdkit.knime.wizards.feature.feature.group NIBR

 

Simon.

11

Welcome - cutting edge sux sometimes.

RDKit KNIME integration 2.1.0.201302211506 and

RDKit KNIME Wizards 2.1.0.201212031505,

but OS X 10.6.8.

All seems OK here for RDKit (not so for ImageBee).

Do you have both Java 1.6 and 1.7 installed? Or just one of them?

(the other) Simon

12

Hi,

I am on just Java 1.7.0_17-b02. Do I need Java 1.6 also, and if so how do I get this ? I've been to the Java site but only 1.7 is available for OS X.

Simon.

13

Hello,

 

I'm on Java 1.6, on Windows. Could it be an x64-related issue?

 

Does anybody else have an issue with the latest RDKit nodes under x64 architecture?

 

 

Fred

14

Hi Simon,

This could be a java 1.7 problem. The nodes were definitely built for java 1.6 and I personally haven't tested them with 1.7.

I don't have a Mac with 1.7, so I can't test this out to see what's going on, but I should be able to do some testing later in the week when a colleague with a more up-to-date Mac gets back from vacation.

-greg

 

15

It's definitely not purely x64. We use the nodes on 64bit machines all the time.

Manuel, who regularly works with knime on x64 windows, will hopefully be able to expand on this a bit more.

-greg

 

16

Try installing Java 1.6 from here (it will co-exist with 1.7):

http://support.apple.com/kb/DL1572

But check your Java Pref panel first to see if it's not already installed. The pref panel will let you change the preferred order too.

 

(the other) Simon

17

Thanks for the link to Java 1.6, I installed this and restarted the machine, but no joy.

Still encountering the same issues.

Simon.

18

Dear Fred, dear Simon,

 

sorry that the issue is still not resolved. I am unable to reproduce it on Windows and have no Mac. Could you please send me more information in an email (with attachments)? Send it to manuel.schwarze(at)novartis.com.

  1. Please send me your configuration: Open KNIME and select from the menu Help - About KNIME. Click the Configuration tab and copy and paste everything into a text file config.txt and send this to me.
  2. Please prepare a knime.log file: Close KNIME. Go into your workspace folder and there remove the file .metadata/knime/knime.log. Then restart KNIME and try to use the RDKit nodes as you did before. Close down KNIME again after the failure and send me the new created file .metadata/knime/knime.log from your workspace.

Thanks!

 

Kind regards,

Manuel

 

19

Hi,

I am experiencing the same problem with the update.

"Could not load native RDKit Library"

Attached to this post you will find the error stack trace (logs) + snapshot with the plugins installed in a _fresh_ KNIME 2.7.2 installation. Hope it helps to solve to problem.

Thanks in advance.

Oscar

 

20

Hi Oscar,

Is this issue on MAC OSX, if so there is an immediate solution.

Unfortunately there was an error in the KNIME MAC build which results in RDKit not working when this extension is installed. This was rectified last night, and deleting your KNIME install and downloading afresh from KNIME.org will solve the problem with the RDKit native library errors. Thanks to Aaron for this quick fix.

Simon.