Sorry for the silence but I don't have access to a Mac to help beyond
this. What I would have done to try to debug is to play around with
the LD_LIBRARY_PATH and LD_PRELOAD variables (or their Mac
equivalents), and also build debug versions of Open Babel and run the
Java from gdb or valgrind to find the exact point of failure in our
code, or take a look at the core dump mentioned in your email. Also it
can be worth trying the Oracle supplied Java instead of the Mac one
(if there is a difference).
- Noel
On 6 October 2016 at 18:52, Jason Ott <jott...@ucr.edu> wrote:
> Here is the simple code I wrote to test loading the library:
>
> public static void runOpenBabel() {
> logger.info(System.getProperty("java.library.path"));
> try {
>
> //System.load("~/Applications/openbabel/lib/libopenbabel_java.jnilib");
> System.loadLibrary("openbabel_java");
> logger.debug("Successfully loaded the openbabel lib");
> } catch(UnsatisfiedLinkError e) {
> logger.fatal("cannot load jni lib");
> }
> }
>
> The path ends up being: ~Applications/openbabel/lib
>
> What I do is I add to the java.library.path variable:
> -Djava.library.path=/path/to/openbabel/lib/ => which translates to above
>
> And the above code will throw the following error:
>
> #
> # A fatal error has been detected by the Java Runtime Environment:
> #
> # SIGSEGV (0xb) at pc=0x0000000110c55761, pid=64236, tid=7171
> #
> # JRE version: Java(TM) SE Runtime Environment (8.0_60-b27) (build
> 1.8.0_60-b27)
> # Java VM: Java HotSpot(TM) 64-Bit Server VM (25.60-b23 mixed mode bsd-amd64
> compressed oops)
> # Problematic frame:
> # C [libawt_lwawt.dylib+0x44761] JNI_OnLoad+0x91
> #
> # Failed to write core dump. Core dumps have been disabled. To enable core
> dumping, try "ulimit -c unlimited" before starting Java again
> #
> # An error report file with more information is saved as:
> # /Users/jason/Projects/IntelliJ/ChemTrails/hs_err_pid64236.log
> #
> # If you would like to submit a bug report, please visit:
> # http://bugreport.java.com/bugreport/crash.jsp
> # The crash happened outside the Java Virtual Machine in native code.
> # See problematic frame for where to report the bug.
> #
>
> Process finished with exit code 134
>
> Upon running CMake, make, make install for openbabel there were no reported
> errors.
>
>
>
>
> On Thu, Oct 6, 2016 at 10:06 AM, Jason Ott <jott...@ucr.edu> wrote:
>>
>> MacOS Sierra 10.12 (16A323) with 2.4.0 of OpenBabel and Java 1.8.0_60
>>
>> On Wed, Oct 5, 2016 at 11:30 PM, Noel O'Boyle <baoille...@gmail.com>
>> wrote:
>>>
>>> What exact OS and version are you using?
>>>
>>>
>>> On 5 Oct 2016 10:47 p.m., "Jason Ott" <jott...@ucr.edu> wrote:
>>>>
>>>> The bindings get built just fine. I the both the jar and jnilib files
>>>> are created. The problem that arises is when I try to run openbabel within
>>>> my java application. I implement the tutorial and I get:
>>>> # A fatal error has been detected by the Java Runtime Environment:
>>>> #
>>>> # SIGSEGV (0xb) at pc=0x000000011e879761, pid=62346, tid=6915
>>>> ...
>>>> Process finished with exit code 134
>>>>
>>>> The jar is in the classpath and the jni is loaded using: either
>>>> System.load("/path/to/jnilib"); or System.loadLibrary("openbabel_java");
>>>> where I add the jnilib to the class.path environment variable. I assume
>>>> I'm
>>>> doing this part correctly. But I could be mistaken.
>>>>
>>>> Thanks,
>>>> Jason
>>>>
>>>> On Wed, Oct 5, 2016 at 1:07 PM, Noel O'Boyle <baoille...@gmail.com>
>>>> wrote:
>>>>>
>>>>> Sorry - missed that. It's best to ignore that README as you shouldn't
>>>>> need to run g++ yourself. The bindings are built when you run "make &&
>>>>> make install". Just make sure that CMake finds Eigen at the configure
>>>>> step.
>>>>>
>>>>> If it still doesn't work please provide your CMakeCache.txt, and the
>>>>> output of "VERBOSE=1 make", and maybe we can see where things are
>>>>> going wrong.
>>>>>
>>>>> - Noel
>>>>>
>>>>> On 5 October 2016 at 19:01, Jason Ott <jott...@ucr.edu> wrote:
>>>>> > I have eigen3 installed. If you look at my gcc install command. I
>>>>> > had to
>>>>> > add a path for it. It's there and functional.
>>>>> >
>>>>> >
>>>>> > On Oct 5, 2016 10:55, "Noel O'Boyle" <baoille...@gmail.com> wrote:
>>>>> >>
>>>>> >> This part is covered in the docs at least. You are missing eigen.
>>>>> >>
>>>>> >>
>>>>> >> On 5 Oct 2016 6:02 p.m., "Jason Ott" <jott...@ucr.edu> wrote:
>>>>> >>>
>>>>> >>> That worked like a charm! Thanks. So now I have been trying to
>>>>> >>> include
>>>>> >>> said java bindings in my project...
>>>>> >>>
>>>>> >>> I added the openbabel.jar file to my classpath. So I can import
>>>>> >>> and all
>>>>> >>> classes are resolved and looking good! However, when I try running
>>>>> >>> the
>>>>> >>> basic program from the tutorial my
>>>>> >>> System.loadLibrary("openbabel_java")
>>>>> >>> throws a segfault from native up to my java.
>>>>> >>>
>>>>> >>> I tried to follow the readme in the /scripts/java/ directory, but I
>>>>> >>> cannot get the very first compilation step to work. But I noticed
>>>>> >>> that
>>>>> >>> under [install_path]/lib/ there is both the openbabel.jar and
>>>>> >>> libopenbabel_java.jnilib, which should be enough to get the thing
>>>>> >>> working.
>>>>> >>>
>>>>> >>> When I follow that readme in /scripts/java/ I get the following
>>>>> >>> error:
>>>>> >>>
>>>>> >>> openbabel-java.cpp:9941:25: error: no member named 'DiverseConfGen'
>>>>> >>> in
>>>>> >>> 'OpenBabel::OBForceField'
>>>>> >>>
>>>>> >>> result = (int)(arg1)->DiverseConfGen(arg2,arg3,arg4,arg5);
>>>>> >>> jresult =
>>>>> >>> (jint)result; return jresult; }
>>>>> >>>
>>>>> >>> ~~~~~~ ^
>>>>> >>>
>>>>> >>> openbabel-java.cpp:9946:25: error: no member named 'DiverseConfGen'
>>>>> >>> in
>>>>> >>> 'OpenBabel::OBForceField'
>>>>> >>>
>>>>> >>> result = (int)(arg1)->DiverseConfGen(arg2,arg3,arg4); jresult =
>>>>> >>> (jint)result; return jresult; }
>>>>> >>>
>>>>> >>> ~~~~~~ ^
>>>>> >>>
>>>>> >>> openbabel-java.cpp:9950:54: error: no member named 'DiverseConfGen'
>>>>> >>> in
>>>>> >>> 'OpenBabel::OBForceField'
>>>>> >>>
>>>>> >>> arg3 = (unsigned int)jarg3; result =
>>>>> >>> (int)(arg1)->DiverseConfGen(arg2,arg3); jresult = (jint)result;
>>>>> >>> return
>>>>> >>> jresult; }
>>>>> >>>
>>>>> >>> ~~~~~~ ^
>>>>> >>>
>>>>> >>> openbabel-java.cpp:9954:25: error: no member named 'DiverseConfGen'
>>>>> >>> in
>>>>> >>> 'OpenBabel::OBForceField'
>>>>> >>>
>>>>> >>> result = (int)(arg1)->DiverseConfGen(arg2); jresult =
>>>>> >>> (jint)result;
>>>>> >>> return jresult; }
>>>>> >>>
>>>>> >>> ~~~~~~ ^
>>>>> >>>
>>>>> >>> 4 errors generated.
>>>>> >>>
>>>>> >>>
>>>>> >>> I compile with the following command: g++ -c -fpic
>>>>> >>> openbabel-java.cpp -I
>>>>> >>> ../../include/ -I
>>>>> >>>
>>>>> >>> /Library/Java/JavaVirtualMachines/jdk1.8.0_60.jdk/Contents/Home/include/
>>>>> >>> -I
>>>>> >>>
>>>>> >>> /Library/Java/JavaVirtualMachines/jdk1.8.0_60.jdk/Contents/Home/include/darwin/
>>>>> >>> -I /opt/local/include/eigen3/
>>>>> >>>
>>>>> >>>
>>>>> >>> Any support would be appreciated. Thanks.
>>>>> >>>
>>>>> >>>
>>>>> >>> On Wed, Oct 5, 2016 at 6:48 AM, Noel O'Boyle <baoille...@gmail.com>
>>>>> >>> wrote:
>>>>> >>>>
>>>>> >>>> Ah -- looks like we missed something in the release. The Swig
>>>>> >>>> bindings
>>>>> >>>> should have been included. As it is, you will need to install
>>>>> >>>> swig,
>>>>> >>>> and specify -DSWIG_EXECUTABLE=whatever.
>>>>> >>>>
>>>>> >>>> - Noel
>>>>> >>>>
>>>>> >>>> On 5 October 2016 at 01:10, Jason Ott <jott...@ucr.edu> wrote:
>>>>> >>>> > Hello all!
>>>>> >>>> >
>>>>> >>>> > I have been trying all day to build the java bindings for open
>>>>> >>>> > babel.
>>>>> >>>> > I
>>>>> >>>> > have:
>>>>> >>>> >
>>>>> >>>> > installed through mac ports,
>>>>> >>>> > downloaded source and compiled using the following flags:
>>>>> >>>> >
>>>>> >>>> > -DCMAKE_INSTALL_PREFIX=~/Applications/openbabel
>>>>> >>>> > -DJAVA_BINDINGS=ON
>>>>> >>>> > -DBUILD_GUI=OFF
>>>>> >>>> >
>>>>> >>>> > I am running MacOS Sierra. No special configs or anything. The
>>>>> >>>> > java
>>>>> >>>> > bindings are never generated in the
>>>>> >>>> > openbabel-openbabel-2.4.0/scripts/java/
>>>>> >>>> > folder or anywhere in the installation location.
>>>>> >>>> >
>>>>> >>>> > When I do the "cmake ./
>>>>> >>>> > -DCMAKE_INSTALL_PREFIX=~/Applications/openbabel
>>>>> >>>> > -DJAVA_BINDINGS=ON -DBUILD_GUI=OFF" I get the following output:
>>>>> >>>> >
>>>>> >>>> > -- Using included inchi library.
>>>>> >>>> > -- Could NOT find wxWidgets (missing: wxWidgets_LIBRARIES
>>>>> >>>> > wxWidgets_INCLUDE_DIRS)
>>>>> >>>> > -- Checking available shared pointer...
>>>>> >>>> > -- Use std::shared_ptr in memory
>>>>> >>>> > -- Cairo found. PNG output will be supported.
>>>>> >>>> > -- GUI will not be built
>>>>> >>>> > -- Could NOT find SWIG (missing: SWIG_EXECUTABLE SWIG_DIR)
>>>>> >>>> > -- Could NOT find SWIG (missing: SWIG_EXECUTABLE SWIG_DIR)
>>>>> >>>> > (Required
>>>>> >>>> > is at
>>>>> >>>> > least version "2.0")
>>>>> >>>> > -- SWIG 2.0 NOT found
>>>>> >>>> > -- Configuring done
>>>>> >>>> > -- Generating done
>>>>> >>>> > -- Build files have been written to:
>>>>> >>>> > /Users/jason/Desktop/openbabel-openbabel-2-4-0
>>>>> >>>> >
>>>>> >>>> > So that tells me that that java AND python bindings should exist
>>>>> >>>> > *somewhere*
>>>>> >>>> > but they don't.
>>>>> >>>> >
>>>>> >>>> > Thanks,
>>>>> >>>> >
>>>>> >>>> > Jason
>>>>> >>>> >
>>>>> >>>> >
>>>>> >>>> >
>>>>> >>>> > ------------------------------------------------------------------------------
>>>>> >>>> > Check out the vibrant tech community on one of the world's most
>>>>> >>>> > engaging tech sites, SlashDot.org! http://sdm.link/slashdot
>>>>> >>>> > _______________________________________________
>>>>> >>>> > OpenBabel-discuss mailing list
>>>>> >>>> > OpenBabel-discuss@lists.sourceforge.net
>>>>> >>>> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>>>>> >>>> >
>>>>> >>>
>>>>> >>>
>>>>> >
>>>>
>>>>
>>
>
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