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Using the mingW api I get an exception (could not load dependent
libraries)...
The model compiles well with opencell so i suppose it's an environment
issue...
I would try the ccgs way following the test given by Alan.

Thanks, Paolo

On Tue, Dec 20, 2011 at 11:10 AM, <
cellml-tools-developers-request at cellml.org> wrote:

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> Today's Topics:
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> 1. simulating model programmatically (Paolo Pannarale)
> 2. Re: simulating model programmatically (Alan Garny)
> 3. Re: simulating model programmatically (Andrew Miller)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 20 Dec 2011 10:30:01 +0100
> From: Paolo Pannarale <p.pannarale at gmail.com>
> Subject: [cellml-dev] simulating model programmatically
> To: cellml-tools-developers at cellml.org
> Message-ID:
> <CAB5pjwbMfDw70pgtH+zMzzmXtyg7srUVDkcCqeiag9vZB+SYzQ at
> mail.gmail.com
> >
> Content-Type: text/plain; charset="windows-1252"
>
> Dear Cellml Developers, I'm a PhD student in Bari and I'm developing a Java
> application based on the cellmlapi (cellml-sdk-1.10-Win32-MSVC10.
> exe, MingW didn't worked, generating a could not load dependent libaries
> exception). I need to programmatically solve a model and I got some clue
> about how to do it inspecting the opencell source code. I get an exception
> (Unexpected exception generating code) when calling
> cis.compileModelODE(model) and I guess this is because the api need a c
> compiler to compile the code. I tried to adding the following env variables
> but this didn't work. Can you pls help me?
> BR, thanks, Paolo
>
> CELLML_HOME C:\Program Files (x86)\cellml-sdk-1.10_msvc
> PATH C:\Program Files (x86)\OpenCell\gcc\bin;C:\Program Files
> (x86)\OpenCell\gcc\libexec\gcc\mingw32\3.4.2;%CELLML_HOME%\lib
> LIBRARY_PATH C:\Program Files
> (x86)\OpenCell\gcc\lib\gcc\mingw32\3.4.2;C:\Program Files
> (x86)\OpenCell\gcc\lib
>
> the code i use is the following (the model is loaded properly, i can do a
> getcmetaid(), I use fully instantiate imports, i can simulate the model in
> opencell correctly)
>
> System.loadLibrary("java_cis");
> cis = cellml_bootstrap.CISBootstrap.createIntegrationService();
> Model model = (new ModelLoader(modelfile)).getModel();
> ODESolverCompiledModel oscm = cis.compileModelODE(model); >>
> Exception (Unexpected exception generating code)
> ODESolverRun osr = cis.createODEIntegrationRun(oscm);
> osr.setStepType(ODEIntegrationStepType.BDF_IMPLICIT_1_5_SOLVE);
> osr.setProgressObserver(this);
> double epsAbs=1E-6, epsRel=1E-6, scalVar=1, scalRate=0, maxstep=1,
> tabstepsize=0.01, startBvar=0, stopBvar=10, maxDensity=1000;
> boolean tabstrict = false;
> osr.setStepSizeControl(epsAbs, epsRel, scalVar, scalRate, maxstep);
> osr.setTabulationStepControl(tabstepsize, tabstrict);
> osr.setResultRange(startBvar, stopBvar, maxDensity);
> osr.start();
>
>
> --
> ?[M]y work, which I?ve done for a long time, was not pursued in order to
> gain the praise I now enjoy, but chiefly from a craving after knowledge,
> which I notice resides in me more than in most other men. And
> wherewithal, whenever I found out anything remarkable, I have thought it my
> duty to put down my discovery on paper, so that all ingenious people might
> be informed thereof.?
> (van Leeuwenhoek, Letter to the Royal Society, June 12 1716)
>
> ?Make it as simple as possible. But not simpler?.
> (Albert Einstein)
>
> "The best way to predict the future is to invent it".
> (Alan Kay)
>
> ___________________________________
>
> Questo documento ? indirizzato esclusivamente al destinatario.
> Tutte le informazioni ivi contenute, compresi eventuali allegati,
> sono soggette a riservatezza secondo i termini del D.Lgs. 196/2003
> in materia di "privacy" e ne ? proibito l'utilizzo da parte di
> altri soggetti. Se avesse ricevuto per errore questo messaggio,
> La preghiamo cortesemente di contattare il mittente al pi? presto
> e di cancellare il messaggio subito dopo. Grazie.
> ----
> This document is exclusively intended for the stated addressee.
> All information therein, including any attachment, are reserved
> as per Italian D.Lgs. 196/2003 about privacy, and cannot be used
> by third parties. In case you received this message by mistake,
> please inform the sender and delete the message afterward.
> Thank you.
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>
> ------------------------------
>
> Message: 2
> Date: Tue, 20 Dec 2011 11:07:27 +0100
> From: "Alan Garny" <alan.garny at dpag.ox.ac.uk>
> Subject: Re: [cellml-dev] simulating model programmatically
> To: "'A list for the developers of CellML tools'"
> <cellml-tools-developers at cellml.org>
> Message-ID: <003601ccbeff$2e4e8ee0$8aebaca0$@dpag.ox.ac.uk>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Paolo,
>
>
>
> I don?t use the Java binding version of the CellML API, but could it be
> that
> your using the MSVC version of the API might cause problems with CIS trying
> to compile the model using gcc? (For what is worth, I personally use the
> MinGW version of the CellML API and I got CIS to compile my models fine, on
> Windows at least.) Otherwise, have you tried to use CCGS to generate some C
> code, and then try to compile that code manually? (You might, for this,
> want
> to check the CCGS test called CellML2C;
>
> http://cellml-api.hg.sourceforge.net/hgweb/cellml-api/cellml-api/raw-file/c2
> b71f1a915d/CCGS/tests/CellML2C.cpp) The idea would be to establish that it
> can at least be done. If that?s the case, then it would mean that the issue
> is indeed related to CIS or, rather, to your environment not being suitable
> for CIS use.
>
>
>
> Alan
>
>
>
> From: cellml-tools-developers-bounces at cellml.org
> [mailto:cellml-tools-developers-bounces at cellml.org] On Behalf Of Paolo
> Pannarale
> Sent: 20 December 2011 10:30
> To: cellml-tools-developers at cellml.org
> Subject: [cellml-dev] simulating model programmatically
>
>
>
> Dear Cellml Developers, I'm a PhD student in Bari and I'm developing a Java
> application based on the cellmlapi (cellml-sdk-1.10-Win32-MSVC10.
>
> exe, MingW didn't worked, generating a could not load dependent libaries
> exception). I need to programmatically solve a model and I got some clue
> about how to do it inspecting the opencell source code. I get an exception
> (Unexpected exception generating code) when calling
> cis.compileModelODE(model) and I guess this is because the api need a c
> compiler to compile the code. I tried to adding the following env variables
> but this didn't work. Can you pls help me?
> BR, thanks, Paolo
>
> CELLML_HOME C:\Program Files (x86)\cellml-sdk-1.10_msvc
> PATH C:\Program Files (x86)\OpenCell\gcc\bin;C:\Program Files
> (x86)\OpenCell\gcc\libexec\gcc\mingw32\3.4.2;%CELLML_HOME%\lib
> LIBRARY_PATH C:\Program Files
> (x86)\OpenCell\gcc\lib\gcc\mingw32\3.4.2;C:\Program Files
> (x86)\OpenCell\gcc\lib
>
> the code i use is the following (the model is loaded properly, i can do a
> getcmetaid(), I use fully instantiate imports, i can simulate the model in
> opencell correctly)
>
> System.loadLibrary("java_cis");
> cis = cellml_bootstrap.CISBootstrap.createIntegrationService();
> Model model = (new ModelLoader(modelfile)).getModel();
> ODESolverCompiledModel oscm = cis.compileModelODE(model); >>
> Exception (Unexpected exception generating code)
> ODESolverRun osr = cis.createODEIntegrationRun(oscm);
> osr.setStepType(ODEIntegrationStepType.BDF_IMPLICIT_1_5_SOLVE);
> osr.setProgressObserver(this);
> double epsAbs=1E-6, epsRel=1E-6, scalVar=1, scalRate=0, maxstep=1,
> tabstepsize=0.01, startBvar=0, stopBvar=10, maxDensity=1000;
> boolean tabstrict = false;
> osr.setStepSizeControl(epsAbs, epsRel, scalVar, scalRate, maxstep);
> osr.setTabulationStepControl(tabstepsize, tabstrict);
> osr.setResultRange(startBvar, stopBvar, maxDensity);
> osr.start();
>
>
>
> --
> ?[M]y work, which I?ve done for a long time, was not pursued in order to
> gain the praise I now enjoy, but chiefly from a craving after knowledge,
> which I notice resides in me more than in most other men. And
> wherewithal, whenever I found out anything remarkable, I have thought it my
> duty to put down my discovery on paper, so that all ingenious people might
> be informed thereof.?
> (van Leeuwenhoek, Letter to the Royal Society, June 12 1716)
>
> ?Make it as simple as possible. But not simpler?.
> (Albert Einstein)
>
> "The best way to predict the future is to invent it".
> (Alan Kay)
>
> ___________________________________
>
> Questo documento ? indirizzato esclusivamente al destinatario.
> Tutte le informazioni ivi contenute, compresi eventuali allegati,
> sono soggette a riservatezza secondo i termini del D.Lgs. 196/2003
> in materia di "privacy" e ne ? proibito l'utilizzo da parte di
> altri soggetti. Se avesse ricevuto per errore questo messaggio,
> La preghiamo cortesemente di contattare il mittente al pi? presto
> e di cancellare il messaggio subito dopo. Grazie.
> ----
> This document is exclusively intended for the stated addressee.
> All information therein, including any attachment, are reserved
> as per Italian D.Lgs. 196/2003 about privacy, and cannot be used
> by third parties. In case you received this message by mistake,
> please inform the sender and delete the message afterward.
> Thank you.
>
> -------------- next part --------------
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>
> ------------------------------
>
> Message: 3
> Date: Tue, 20 Dec 2011 23:10:09 +1300
> From: Andrew Miller <ak.miller at auckland.ac.nz>
> Subject: Re: [cellml-dev] simulating model programmatically
> To: A list for the developers of CellML tools
> <cellml-tools-developers at cellml.org>
> Message-ID: <4EF05F01.30900 at auckland.ac.nz>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> On 20/12/11 22:30, Paolo Pannarale wrote:
> > Dear Cellml Developers, I'm a PhD student in Bari and I'm developing a
> > Java application based on the cellmlapi (cellml-sdk-1.10-Win32-MSVC10.
> > exe, MingW didn't worked, generating a could not load dependent libaries
> > exception). I need to programmatically solve a model and I got some clue
> > about how to do it inspecting the opencell source code. I get an
> > exception (Unexpected exception generating code) when calling
> > cis.compileModelODE(model) and I guess this is because the api need a c
> > compiler to compile the code. I tried to adding the following env
> > variables but this didn't work. Can you pls help me?
>
> Hi Paolo,
>
> You do need a C compiler for CIS to work, but the error you are getting
> indicates that something is going wrong earlier than that; it is likely
> that the model you are testing with is invalid, under or
> overconstrained, or beyond the solving capabilities of CIS.
>
> Look at the interface defined in CCGS.idl to see how to interface with
> the code generator - running it through the code generator, even with
> default options, will give you a more detailed error about what is wrong
> with the model. You can also use the VACSS service to do in depth
> validation of a CellML model against the CellML specification (with
> additional warnings about certain problems).
>
> Best wishes,
> Andrew
>
> > BR, thanks, Paolo
> >
> > CELLML_HOME C:\Program Files (x86)\cellml-sdk-1.10_msvc
> > PATH C:\Program Files (x86)\OpenCell\gcc\bin;C:\Program Files
> > (x86)\OpenCell\gcc\libexec\gcc\mingw32\3.4.2;%CELLML_HOME%\lib
> > LIBRARY_PATH C:\Program Files
> > (x86)\OpenCell\gcc\lib\gcc\mingw32\3.4.2;C:\Program Files
> > (x86)\OpenCell\gcc\lib
> >
> > the code i use is the following (the model is loaded properly, i can do
> > a getcmetaid(), I use fully instantiate imports, i can simulate the
> > model in opencell correctly)
> >
> > System.loadLibrary("java_cis");
> > cis = cellml_bootstrap.CISBootstrap.createIntegrationService();
> > Model model = (new ModelLoader(modelfile)).getModel();
> > ODESolverCompiledModel oscm = cis.compileModelODE(model); >>
> > Exception (Unexpected exception generating code)
> > ODESolverRun osr = cis.createODEIntegrationRun(oscm);
> > osr.setStepType(ODEIntegrationStepType.BDF_IMPLICIT_1_5_SOLVE);
> > osr.setProgressObserver(this);
> > double epsAbs=1E-6, epsRel=1E-6, scalVar=1, scalRate=0,
> > maxstep=1, tabstepsize=0.01, startBvar=0, stopBvar=10, maxDensity=1000;
> > boolean tabstrict = false;
> > osr.setStepSizeControl(epsAbs, epsRel, scalVar, scalRate,
> maxstep);
> > osr.setTabulationStepControl(tabstepsize, tabstrict);
> > osr.setResultRange(startBvar, stopBvar, maxDensity);
> > osr.start();
> >
> >
> > --
> > ?[M]y work, which I?ve done for a long time, was not pursued in order
> > to gain the praise I now enjoy, but chiefly from a craving after
> > knowledge, which I notice resides in me more than in most other
> > men. And wherewithal, whenever I found out anything remarkable, I have
> > thought it my duty to put down my discovery on paper, so that all
> > ingenious people might be informed thereof.?
> > (van Leeuwenhoek, Letter to the Royal Society, June 12 1716)
> >
> > ?Make it as simple as possible. But not simpler?.
> > (Albert Einstein)
> >
> > "The best way to predict the future is to invent it".
> > (Alan Kay)
> >
> > ___________________________________
> >
> > Questo documento ? indirizzato esclusivamente al destinatario.
> > Tutte le informazioni ivi contenute, compresi eventuali allegati,
> > sono soggette a riservatezza secondo i termini del D.Lgs. 196/2003
> > in materia di "privacy" e ne ? proibito l'utilizzo da parte di
> > altri soggetti. Se avesse ricevuto per errore questo messaggio,
> > La preghiamo cortesemente di contattare il mittente al pi? presto
> > e di cancellare il messaggio subito dopo. Grazie.
> > ----
> > This document is exclusively intended for the stated addressee.
> > All information therein, including any attachment, are reserved
> > as per Italian D.Lgs. 196/2003 about privacy, and cannot be used
> > by third parties. In case you received this message by mistake,
> > please inform the sender and delete the message afterward.
> > Thank you.
> >
> >
> > _______________________________________________
> > cellml-tools-developers mailing list
> > cellml-tools-developers at cellml.org
> > http://lists.cellml.org/mailman/listinfo/cellml-tools-developers
>
>
>
> ------------------------------
>
> _______________________________________________
> cellml-tools-developers mailing list
> cellml-tools-developers at cellml.org
> http://lists.cellml.org/mailman/listinfo/cellml-tools-developers
>
>
> End of cellml-tools-developers Digest, Vol 46, Issue 4
> ******************************************************
>



--
?[M]y work, which I?ve done for a long time, was not pursued in order to
gain the praise I now enjoy, but chiefly from a craving after knowledge,
which I notice resides in me more than in most other men. And
wherewithal, whenever I found out anything remarkable, I have thought it my
duty to put down my discovery on paper, so that all ingenious people might
be informed thereof.?
(van Leeuwenhoek, Letter to the Royal Society, June 12 1716)

?Make it as simple as possible. But not simpler?.
(Albert Einstein)

"The best way to predict the future is to invent it".
(Alan Kay)

___________________________________

Questo documento ? indirizzato esclusivamente al destinatario.
Tutte le informazioni ivi contenute, compresi eventuali allegati,
sono soggette a riservatezza secondo i termini del D.Lgs. 196/2003
in materia di "privacy" e ne ? proibito l'utilizzo da parte di
altri soggetti. Se avesse ricevuto per errore questo messaggio,
La preghiamo cortesemente di contattare il mittente al pi? presto
e di cancellare il messaggio subito dopo. Grazie.
----
This document is exclusively intended for the stated addressee.
All information therein, including any attachment, are reserved
as per Italian D.Lgs. 196/2003 about privacy, and cannot be used
by third parties. In case you received this message by mistake,
please inform the sender and delete the message afterward.
Thank you.
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• [cellml-dev] cellml-tools-developers Digest, Vol 46, Issue 4, Paolo Pannarale, 12/21/2011

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