[Solved] RDKit broken after update

omora · March 19, 2013, 11:58am

Hi Simon,

many thanks for your message, but I am experiencing this problem on windows 7 x64.

What is more odd for me is that I have the following two scenarios:

Machine A: KNIME 2.7.2 + RDKIT -> Works fine
Machine B: KNIME 2.7.2 + RDKIT -> "Could not load native RDKit Library"

Applying the _same_ "installation protocol":

1.- Download a fresh installation of KNIME (Windows 64) 2.7.2

2.- Install KNIME Base Chemistry Types & Nodes from

KNIME Update Site - http://www.knime.org/update/2.7/

3.- Install RDkit KNIME Integration from

COM - http://tech.knime.org/update/community-contributions/2.7

I am trying to compare base/machine configurations of both computes but I am not able to find out any difference. Anybody has a clue of what I have to check or compare ?

Thanks in advance!

Oscar

omora · March 19, 2013, 1:44pm

Hi,

I think that my problem is that I have not installed the following library in the computers where the RDkit does not work:

http://www.microsoft.com/en-us/download/details.aspx?id=14632

Does it make sense ? Is there any recommendation about this (maybe is better to install other c++ lib)?

Thanks

Oscar

manuelschwarze · March 19, 2013, 11:18pm

Dear Oscar,

thanks for the log information. Could you please also make the following available:

1. Open the non-working KNIME and select from the menu Help - About KNIME. Press the "Installation Details" button. Click the Configuration tab and copy and paste everything into a text file config.txt and make it available.

2. Could you please check what files and folders are physically available under the folder C:\Users\User\Documents\KNIME\knime_2.7.2\plugins\org.rdkit.knime.bin.win32.x86_64_2.1.0.201302061056\ on your machine? Does it exist at all?

Did you try out to install that C++ DLL as you suggested in your last post? Did it make a difference?

Kind regards,

Manuel

omora · March 21, 2013, 10:24pm

Manuel,

thanks for your message. The installation of the Microsoft Visual C++ 2010 Redistributable Package (x64) has solved all my problems. If your are insterested I have attached to this post the file config.txt (with the info that you asked me in your last post of a non working KNIME ).

And this is the structure and contents o the folder

C:\Users\User\Documents\KNIME\knime_2.7.2\plugins\org.rdkit.knime.bin.win32.x86_64_2.1.0.201302061056\
C:.
├───META-INF
│       MANIFEST.MF
│
└───os
    └───win32
        └───x86_64
                boost_regex-vc100-mt-1_51.dll
                boost_system-vc100-mt-1_51.dll
                GraphMolWrap.dll

Let me insist that I have no longer problems with the rdkit plugin, but I thought that maybe this information is useful for us.

Oscar

config.txt

manuelschwarze · March 22, 2013, 7:08pm

Thanks, Oscar. This information about the C++ library is very useful and may help others.

-Manuel

Ellert_van_Koperen · March 27, 2013, 3:48pm

We have similar problems, but on Mac machines.

Is there an archive of the update site somewhere? I would think that if the version in http://tech.knime.org/update/community-contributions/2.7/CommunityContributions_US_201303070826.zip is now broken, removing it and reinstalling from an older version might help for the moment.

richards99 · March 27, 2013, 4:08pm

The issue on the Mac machines is related to a faulty KNIME build of 2.7.2, which only manifests as a problem when you come to install the RDKit nodes.

Have you tried redownloading KNIME from the KNIME.org website and then putting RDKit back onto this.

Simon.

Ellert_van_Koperen · March 27, 2013, 5:18pm

Just reinstalled knime on one machine and it indeed makes the problem go away.

Unfortunately the installation of knime with all the node-libraries and licenses that my coworkers use takes quite a bit of clicking and time, that is why i was looking for another way to solve this, but no luck.

Frederic_Dedieu · April 16, 2013, 11:48am

Hello,

I tried installing KNIME 6.3 on the same Windows 2008 R2 (SP1) server. I still get the "Could not load native RDKit library" error.

I also realised that I have the same error on my Windows XP PC, with KNIME 2.7.2.

One of my colleagues has the exact same issue on Windows 7 with KNIME 2.6.3.

We are using different workflows.

Any ideas?

Cheers,

Fred

manuelschwarze · April 17, 2013, 11:35am

Dear Fred,

have you tried already the solution that Oscar found (alias omora)? He posted in this thread about installing a missing Microsoft C++ Library, which solved his issue on Win 7 64-bit system: http://www.microsoft.com/en-us/download/details.aspx?id=14632

Sorry, I have no other idea in the moment.

Kind regards,

Manuel

Frederic_Dedieu · April 19, 2013, 9:40am

Hello Manuel,

I installed the x64 on the Windows 2008 R2 (SP1) server and x86 on my XP PC and this now works.

Thank you all for your help,

Fred

James_Davidson · May 13, 2013, 1:56pm

Hi Manuel and Greg,

I know this thread is marked as 'solved', but I had been having the same issue and just now managed to solve it - but in a different fashion. I am running KNIME 2.7.4 on Win 7 (64 bit), and already have the 64-bit C++ redistributable installed.

My RDKit installation details are:

RDKit KNIME integration 2.1.0.201305030649 org.rdkit.knime.feature.feature.group NIBR

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

One line from the log file stood out for me, and made me think it might be a java issue, but actually it appears that boost_regex-vc100-mt-1_51.dll has gone awol(!):

Caused by: java.lang.UnsatisfiedLinkError: no boost_regex-vc100-mt-1_51 in java.library.path

Examining my RDKit plugin path compared to that on our KNIME Server (which is successfully running an earlier version of RDKit nodes on 2.7.4) and there is a difference - boost_regex-vc100-mt-1_51.dll is indeed missing from my local system... I just copied the version from the server over, and restarted KNIME locally, and now the RDKit nodes are working again!

Kind regards

James

manuelschwarze · May 14, 2013, 10:15am

Hi James,

thanks for letting us know. This is a bug we need to solve asap. I will take a look today.

Kind regards,

Manuel

manuelschwarze · May 15, 2013, 11:14am

Hi James,

the fix is available in the latest nightly build. I just tried it out, and it works now for me (while it failed before updating with the error you reported).

Kind regards,

Manuel

mkrom · February 21, 2014, 11:16am

Hello, I still have this problem on two computers with latest (yesterday's) KNIME with RDKit nodes. See error messages below.

Any suggestions will be appreciated.

Thanks,

Michal

WARN RDKitTypesPluginActivator Library file GraphMolWrap.dll found: C:\Temp\knime_2.9.1\plugins\org.rdkit.knime.bin.win32.x86_2.4.0.201402061135\os\win32\x86\GraphMolWrap.dll

ERROR RDKitTypesPluginActivator Loading of library GraphMolWrap.dll failed (possibly a subsequent error): C:\Temp\knime_2.9.1\configuration\org.eclipse.osgi\bundles\libtemp\224_0\GraphMolWrap.dll: Can't find dependent libraries

ERROR RDKitTypesPluginActivator The library GraphMolWrap.dll has dependency issues. Please run a dependency walker on this file to find out what is missing.

ERROR RDKitTypesPluginActivator Suggestion for fix: Please correct your system libraries based on the outcome of the dependency walker.

WARN RDKit From Molecule Could not load native RDKit library: C:\Temp\knime_2.9.1\plugins\org.rdkit.knime.bin.win32.x86_2.4.0.201402061135\os\win32\x86\boost_system-vc100-mt-1_51.dll: Can't find dependent libraries

thor · February 21, 2014, 11:29am

Does your Windows have all recent updates installed? We saw a similar issue on a fresh Windows 7 installation, but it resolved itself after we installed all pending Windows updates.

mkrom · February 21, 2014, 11:36am

I don't think that we have all recent updates - and this can't be solved easily (central management of updates by sys admins). Anyway, KNIME/RDKit worked in our hands for months on the very same computers and suddenly stopped.

By the way - we're using Windows 7 32 bit with 32-bit version of Knime.

mkrom · February 21, 2014, 2:09pm

Solved: Copied msvcp100.dll to KNIME\jre\bin

So it seems that this library had mysteriously disappeared from the computer.

system · April 21, 2023, 9:11pm

This topic was automatically closed 90 days after the last reply. New replies are no longer allowed.