for whatever reason your environment does not seem to be correctly set up ... from the screenshot i assume you use a recent SUSE linux, correct? Could you tell me what shell you are using?
right now I'm not quite sure how to resolve the issue for all linux distros. So i would recommend to start the modules like this:
Hi Frank, and thanks for the quick response. I'm trying it right now at home (on openSUSE 11.0, versus 10.3 at work). I get pretty same error after following your instructions. As this output from pstree shows, the broker and roadRunner are running happily (and I'm using bash, the only shell I really know my way around):
Since there's no real indication of what the error is (or at least not one that makes sense to me), I've played around with loading SBML models with the different tools. Loading models into AutoLayout works. JacobianViewer on the other hand just says "The model could not be loaded. The error message given was: A model needs to be loaded before one can use this method". The most useful information was printed a few times to stderr by something (I'm not sure what):
An exception was thrown by the type initializer for libsbml.libsbmlPINVOKE
at SBW.RPCOutCall.waitForReply (Int32 moduleId) [0x00000]
at SBW.SBWRPC.call (Int32 moduleTo, Int32 service, Int32 method, SBW.DataBlockWriter args) [0x00000]
Is there some way I can enable logging/debugging or otherwise get to see the details of the exception that's mentioned? And is it straightforward to build SBW from source for someone who's never been exposed to mono before?
Maybe I should also try installing the 32-bit version of the whole OS just to see if that has anything to do with the problem... what distributions/versions have you tested the Linux version of SBW with?
Cheers,
//Carl
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
again I'm sorry for your trouble I have to admit I use mainly OS X and Windows and thus only test different Linux distributions whenever i hear about a problem. Personally I prefer Ubuntu (newer varieties), that is why the last release did have more glitches on other distributions. In the meantime i have SBW working on openSuse 11, centos 4.6 and some older fedora.
I could offer to sent you new versions of the compiled binaries for whatever distro you use.
the exception you are seeing:
An exception was thrown by the type initializer for
libsbml.libsbmlPINVOKE
basically means that the new libsbml - C# bindins can't be found. There should be a libsbmlcs.so
in the <SBW-dir>/CSharp (or your LD_LIBRARY_PATH. Perhaps you could run a ldd on it and make sure that you have libbz2, libz, libxml2 and libsbml in your path.
please let me know what you find ... oh and sorry for the delay
best
Frank
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Opening SBML files always fails
Killing the broker and restarting it, manually setting SBW_HOME and PATH had some effect. The error message is now different.
$ SBW_HOME=/home/carl/SBW-2.7.8 PATH=$PATH:/home/carl/SBW-2.7.8/bin Broker
Then from SBW Inspector Module -> start edu.kgi.roadRunner.sim Simulation Service -> open any model ->
Exception : An exception was thrown by the type initializer for libsbml.libsbmlPINVOKE
Detailed Exception :
sorry to hear about the trouble,
for whatever reason your environment does not seem to be correctly set up ... from the screenshot i assume you use a recent SUSE linux, correct? Could you tell me what shell you are using?
right now I'm not quite sure how to resolve the issue for all linux distros. So i would recommend to start the modules like this:
(bash)
export SBW_HOME=/home/carl/SBW-2.7.8
export PATH=$PATH:$SBW_HOME/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$SBW_HOME/CSharp:$SBW_HOME/lib
Broker &
cd $SBW_HOME/CSharp
mono roadRunner.exe &
now it should work as expected with:
mono SimDriver.exe
again sorry for the trouble
best
Frank
Hi Frank, and thanks for the quick response. I'm trying it right now at home (on openSUSE 11.0, versus 10.3 at work). I get pretty same error after following your instructions. As this output from pstree shows, the broker and roadRunner are running happily (and I'm using bash, the only shell I really know my way around):
│ └─bash,3877
│ ├─Broker,21716
│ │ ├─NOMModule,21778 -sbwmodule -unique
│ │ │ ├─{NOMModule},21780
│ │ │ └─{NOMModule},21782
│ │ ├─(SBW_STRUCTURAL,21818)
│ │ ├─SBW_STRUCTURAL,21823 -sbwmodule
│ │ │ ├─{SBW_STRUCTURAL},21826
│ │ │ └─{SBW_STRUCTURAL},21827
│ │ ├─(sh,21767)
│ │ ├─(sh,21783)
│ │ ├─(sh,21800)
│ │ ├─(sh,21809)
│ │ ├─{Broker},21719
│ │ ├─{Broker},21720
│ │ ├─{Broker},21728
│ │ ├─{Broker},21733
│ │ ├─{Broker},21736
│ │ ├─{Broker},21737
│ │ ├─{Broker},21774
│ │ ├─{Broker},21775
│ │ ├─{Broker},21779
│ │ ├─{Broker},21787
│ │ ├─{Broker},21815
│ │ └─{Broker},21824
│ ├─mono,21723 roadRunner.exe
│ │ ├─{mono},21726
│ │ ├─{mono},21727
│ │ ├─{mono},21729
│ │ └─{mono},21735
│ └─mono,21730 SimDriverNET.exe
│ ├─{mono},21731
│ ├─{mono},21732
│ ├─{mono},21734
│ └─{mono},21772
Since there's no real indication of what the error is (or at least not one that makes sense to me), I've played around with loading SBML models with the different tools. Loading models into AutoLayout works. JacobianViewer on the other hand just says "The model could not be loaded. The error message given was: A model needs to be loaded before one can use this method". The most useful information was printed a few times to stderr by something (I'm not sure what):
An exception was thrown by the type initializer for libsbml.libsbmlPINVOKE
at SBW.RPCOutCall.waitForReply (Int32 moduleId) [0x00000]
at SBW.SBWRPC.call (Int32 moduleTo, Int32 service, Int32 method, SBW.DataBlockWriter args) [0x00000]
Is there some way I can enable logging/debugging or otherwise get to see the details of the exception that's mentioned? And is it straightforward to build SBW from source for someone who's never been exposed to mono before?
Maybe I should also try installing the 32-bit version of the whole OS just to see if that has anything to do with the problem... what distributions/versions have you tested the Linux version of SBW with?
Cheers,
//Carl
Hello carl,
again I'm sorry for your trouble I have to admit I use mainly OS X and Windows and thus only test different Linux distributions whenever i hear about a problem. Personally I prefer Ubuntu (newer varieties), that is why the last release did have more glitches on other distributions. In the meantime i have SBW working on openSuse 11, centos 4.6 and some older fedora.
I could offer to sent you new versions of the compiled binaries for whatever distro you use.
the exception you are seeing:
An exception was thrown by the type initializer for
libsbml.libsbmlPINVOKE
basically means that the new libsbml - C# bindins can't be found. There should be a libsbmlcs.so
in the <SBW-dir>/CSharp (or your LD_LIBRARY_PATH. Perhaps you could run a ldd on it and make sure that you have libbz2, libz, libxml2 and libsbml in your path.
please let me know what you find ... oh and sorry for the delay
best
Frank