Re: [Open Babel] Java API: Can't use OB anymore due to UnsatisfiedLinkError
Found the issue: I recently installed Avogadro which ships with a different version of openbabel-2.dll. Because Avogadro adds PATH information to System variables in contrast to OpenBabel which uses user variables for PATH, the openbabel-2.dll in Avogadro is picked up first. My solution is to manually add the path to the openbabel installation to System PATH BEFORE Avogadro. -- View this message in context: http://forums.openbabel.org/Java-API-Can-t-use-OB-anymore-due-to-UnsatisfiedLinkError-tp4657311p4657313.html Sent from the General discussion mailing list archive at Nabble.com. -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
[Open Babel] Java API: Can't use OB anymore due to UnsatisfiedLinkError
I'm constantly getting an UnsatisfiedLinkError: C:\Program Files\OpenBabel-2.3.2\openbabel_java.dll: The specified procedure could not be found exception when calling System.loadLibrary(openbabel_java); This used to work previously on the same laptop. Now it has been couple of weeks since I last used the Java API so I have no clue what change might have affected this. PATH is set correctly. I also tried System.load with abolsute path to dll and the result is the same exception. I also re-installed openbabel (and restarted) but to no avail. Does anyone here have an idea what could be causing this? A dependency loaded by openbabel_java.dll (or openbable-2.dll)? -- View this message in context: http://forums.openbabel.org/Java-API-Can-t-use-OB-anymore-due-to-UnsatisfiedLinkError-tp4657311.html Sent from the General discussion mailing list archive at Nabble.com. -- Learn Graph Databases - Download FREE O'Reilly Book Graph Databases is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/13534_NeoTech ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Java API: Can't use OB anymore due to UnsatisfiedLinkError
I just realized that the python extensions fails with the same error:
import pybel
Traceback (most recent call last):
File stdin, line 1, in module
File C:\Python27\lib\site-packages\pybel.py, line 52, in module
import openbabel as ob
File C:\Python27\lib\site-packages\openbabel.py, line 37, in module
_openbabel = swig_import_helper()
File C:\Python27\lib\site-packages\openbabel.py, line 33, in
swig_import_helper
_mod = imp.load_module('_openbabel', fp, pathname, description)
*ImportError: DLL load failed: The specified procedure could not be found.*
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Re: [Open Babel] Java API: setting OBConformerScore will crash application
Hi Noel, Here a link to a zip file containing the compiled jar, mols.smi and windows cmd file: https://drive.google.com/file/d/0B1KuZlTEmhZNV2l5clhoVlZ5blk/edit?usp=sharing This application fails on 2 different Windows 7 PCs (one 32, the other 64 bit but both run java and OB 32-bit). I now realized that in some cases I actually get an error log file generated: https://drive.google.com/file/d/0B1KuZlTEmhZNeTVWdU9hemQ0U2c/edit?usp=sharing Hope that helps. -- View this message in context: http://forums.openbabel.org/Java-API-setting-OBConformerScore-will-crash-application-tp4656958p4657029.html Sent from the General discussion mailing list archive at Nabble.com. -- Sponsored by Intel(R) XDK Develop, test and display web and hybrid apps with a single code base. Download it for free now! http://pubads.g.doubleclick.net/gampad/clk?id=111408631iu=/4140/ostg.clktrk ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Java API: setting OBConformerScore will crash application
It seems not possible to create a simple application were this issue happens. As a context I'm reading in molecules, generating 3D coordinates and then generate the Spectrophore. In a simple script-like snippet this works. In the complete application the results are written to an output file, there are cli-options but fundamentally it does not do anything different and the code for conformer searching is the same. But here it always fails with a java error. And commenting conformerSearch.SetScore(score); reproducibly fixes the issue. I will investigate further to try to find a simple example to demonstrate this. -- View this message in context: http://forums.openbabel.org/Java-API-setting-OBConformerScore-will-crash-application-tp4656958p4656960.html Sent from the General discussion mailing list archive at Nabble.com. -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Java API: setting OBConformerScore will crash application
Geoff Hutchison wrote When you say does not allow any options to be set, do you mean the OBConformerScore isn't set? No I meant that the options are not exposed as cli parameters and hence it runs with default parameters (eg. nr of conformers, nr of children, mutability,...) -- View this message in context: http://forums.openbabel.org/Java-API-setting-OBConformerScore-will-crash-application-tp4656958p4656968.html Sent from the General discussion mailing list archive at Nabble.com. -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Open Babel] Java API: setting OBConformerScore will crash application
This is confusing. This issue is some weird memory issue. At the end of this
post is the most simple code I could come up with that reproduces the
problem for me.
I can make the code work by removing or commenting just any of the following
lines (only one of them is enough):
- conformerSearch.SetScore(score); // will then use default
OBRMSDConformerScore
- String str = StringUtils.join(strArray, ',');
For the StringUtils part, the length of the array matters. 5000 still works,
8000 does not. However in my original application I completely removed that
and it still has the issue. This tells me it is some weird memory problem
that can be caused by generating long strings (but not limited to this).
This issue then breaks OBEnergyConformerScore but not the default
OBRMSDConformerScore.
The error code from event viewer according to my google search means heap
corruption.
See below the mentioned code. It has a dependency on
org.apache.commons.lang3.
code
package conformergenerator;
import org.apache.commons.lang3.StringUtils;
import org.openbabel.OBBuilder;
import org.openbabel.OBConformerScore;
import org.openbabel.OBConformerSearch;
import org.openbabel.OBConversion;
import org.openbabel.OBEnergyConformerScore;
import org.openbabel.OBMol;
public class App {
public static void main(String[] args) {
System.loadLibrary(openbabel_java);
System.out.println(Create OBMol from smiles);
OBConversion conv = new OBConversion();
OBMol mol = new OBMol();
conv.SetInFormat(smi);
boolean hasNext = conv.ReadFile(mol, mols.smi);
String[] strArray = buildArray(1);
while (hasNext) {
System.out.println(Adding Hydrogens);
mol.AddHydrogens();
System.out.println(Generate 3D coordinates);
OBBuilder builder = new OBBuilder();
builder.Build(mol);
System.out.println(Generate Conformers);
OBConformerSearch conformerSearch = new OBConformerSearch();
OBConformerScore score = new OBEnergyConformerScore();
conformerSearch.SetScore(score);
if (!conformerSearch.Setup(mol)) {
String message = Generating conformers failed.;
throw new IllegalArgumentException(message);
}
conformerSearch.Search();
conformerSearch.GetConformers(mol);
String str = StringUtils.join(strArray, ',');
// the idea would be to add this as property to mol
// but not required for the code to fail
hasNext = conv.Read(mol);
}
System.out.println(Success!!!);
}
private static String[] buildArray(int numElements) {
String[] a = new String[numElements];
for (int i = 0; i numElements; i++) {
a[i] = a;
}
return a;
}
}
/code
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[Open Babel] Java API: setting OBConformerScore will crash application
Just using codeOBConformerSearch conformerSearch = new OBConformerSearch();/code works. However I want to use different scoring than RMSD, which seems to be the default (not really documented). If I do this code OBConformerSearch conformerSearch = new OBConformerSearch(); OBConformerScore score = new OBEnergyConformerScore(); conformerSearch.SetScore(score); /code The application will always crash. Any ideas how I can solve this issue? (Windows 7) -- View this message in context: http://forums.openbabel.org/Java-API-setting-OBConformerScore-will-crash-application-tp4656958.html Sent from the General discussion mailing list archive at Nabble.com. -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
