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From: SourceForge.net <no...@so...> - 2007-03-12 09:14:42
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Support Requests item #1678553, was opened at 2007-03-11 22:29 Message generated for change (Comment added) made by chfl You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744812&aid=1678553&group_id=139893 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Install Problem (example) Group: None Status: Open Priority: 5 Private: Yes Submitted By: Tarraco (tarraco) Assigned to: Nobody/Anonymous (nobody) Summary: link to libsbml Initial Comment: Hello, I cannot install SBMLode as configure gets stuck,complaining about linking problems. Would you have any suggestions? Thanks, regards ER ----------------------------------------- :~/Desktop/SBML_odeSolver-1.6.0>configure checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for gawk... gawk checking whether make sets $(MAKE)... yes checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking for g++... g++ checking for C++ compiler default output file name... a.out checking whether the C++ compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking for style of include used by make... GNU checking dependency style of g++... gcc3 checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed checking dependency style of gcc... gcc3 checking how to run the C preprocessor... gcc -E checking for ranlib... ranlib checking for a BSD-compatible install... /usr/bin/install -c checking whether make sets $(MAKE)... (cached) yes checking for autoconf... /usr/bin/autoconf checking for aclocal... /usr/bin/aclocal checking for make... /usr/bin/make checking for ar... /usr/bin/ar checking for swig... /usr/bin/swig checking for perl... /usr/bin/perl checking for SBML Library headers... yes checking for SBML Library... yes configure: found SBML Library Version 2.3.4 checking correct functioning of SBML... no: CFLAGS=-g -O2 -I/usr/local/include -I/usr/local/include/sbml LDFLAGS= -Wl,-rpath,/usr/local/lib -L/usr/local/lib LIBS= -lxerces-c -lsbml configure: error: Can not link to SBML Library: Please, make sure to use libSBML version >= 2.3.2 ---------------------------------------------------------------------- >Comment By: Christoph Flamm (chfl) Date: 2007-03-12 10:14 Message: Logged In: YES user_id=1113720 Originator: NO hi tarraco, the Tokyo release (v 1.6.0) of SBML_ODE_solver has a known bug in the configure scripts concerning the dispach between libxerces-c and libexpat. this bug is fixed in the CVS repository. if you have automake/autoconf installed on you system, than the easiest fix for your problem would be to checkout the current CVS version of SBML_ODE_solver then run the autogen.sh script to generate the configure script from the m4 files, followed by ./configure --with-expat=/PATH_TO_EXPAST_INSTALL_DIR. i tested building SBML_ODE_solver with libexpat on a fresh CVS checkout and it works fine. in addition to the configure script bug a couple of other bugs have been fixed in the CVS version. (the CVS version currently links to the older sundials suite v2.1.1). we plan to make a new release of the SBML_ODE_solver around May which will use the latest version of the sundials suite v2.3.0. if you need any further help please do not hesitate to contact us. =;) xtof ---------------------------------------------------------------------- Comment By: Tarraco (tarraco) Date: 2007-03-11 22:30 Message: Logged In: YES user_id=1741056 Originator: YES Maybe I sould add that my libsbml works with expat ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744812&aid=1678553&group_id=139893 |
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From: SourceForge.net <no...@so...> - 2007-03-11 21:30:54
|
Support Requests item #1678553, was opened at 2007-03-11 21:29 Message generated for change (Comment added) made by tarraco You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744812&aid=1678553&group_id=139893 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Install Problem (example) Group: None Status: Open Priority: 5 Private: Yes Submitted By: Tarraco (tarraco) Assigned to: Nobody/Anonymous (nobody) Summary: link to libsbml Initial Comment: Hello, I cannot install SBMLode as configure gets stuck,complaining about linking problems. Would you have any suggestions? Thanks, regards ER ----------------------------------------- :~/Desktop/SBML_odeSolver-1.6.0>configure checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for gawk... gawk checking whether make sets $(MAKE)... yes checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking for g++... g++ checking for C++ compiler default output file name... a.out checking whether the C++ compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking for style of include used by make... GNU checking dependency style of g++... gcc3 checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed checking dependency style of gcc... gcc3 checking how to run the C preprocessor... gcc -E checking for ranlib... ranlib checking for a BSD-compatible install... /usr/bin/install -c checking whether make sets $(MAKE)... (cached) yes checking for autoconf... /usr/bin/autoconf checking for aclocal... /usr/bin/aclocal checking for make... /usr/bin/make checking for ar... /usr/bin/ar checking for swig... /usr/bin/swig checking for perl... /usr/bin/perl checking for SBML Library headers... yes checking for SBML Library... yes configure: found SBML Library Version 2.3.4 checking correct functioning of SBML... no: CFLAGS=-g -O2 -I/usr/local/include -I/usr/local/include/sbml LDFLAGS= -Wl,-rpath,/usr/local/lib -L/usr/local/lib LIBS= -lxerces-c -lsbml configure: error: Can not link to SBML Library: Please, make sure to use libSBML version >= 2.3.2 ---------------------------------------------------------------------- >Comment By: Tarraco (tarraco) Date: 2007-03-11 21:30 Message: Logged In: YES user_id=1741056 Originator: YES Maybe I sould add that my libsbml works with expat ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744812&aid=1678553&group_id=139893 |
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From: SourceForge.net <no...@so...> - 2007-03-11 21:29:17
|
Support Requests item #1678553, was opened at 2007-03-11 21:29 Message generated for change (Tracker Item Submitted) made by Item Submitter You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744812&aid=1678553&group_id=139893 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: Install Problem (example) Group: None Status: Open Priority: 5 Private: Yes Submitted By: Tarraco (tarraco) Assigned to: Nobody/Anonymous (nobody) Summary: link to libsbml Initial Comment: Hello, I cannot install SBMLode as configure gets stuck,complaining about linking problems. Would you have any suggestions? Thanks, regards ER ----------------------------------------- :~/Desktop/SBML_odeSolver-1.6.0>configure checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for gawk... gawk checking whether make sets $(MAKE)... yes checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking for g++... g++ checking for C++ compiler default output file name... a.out checking whether the C++ compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking for style of include used by make... GNU checking dependency style of g++... gcc3 checking for gcc... gcc checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed checking dependency style of gcc... gcc3 checking how to run the C preprocessor... gcc -E checking for ranlib... ranlib checking for a BSD-compatible install... /usr/bin/install -c checking whether make sets $(MAKE)... (cached) yes checking for autoconf... /usr/bin/autoconf checking for aclocal... /usr/bin/aclocal checking for make... /usr/bin/make checking for ar... /usr/bin/ar checking for swig... /usr/bin/swig checking for perl... /usr/bin/perl checking for SBML Library headers... yes checking for SBML Library... yes configure: found SBML Library Version 2.3.4 checking correct functioning of SBML... no: CFLAGS=-g -O2 -I/usr/local/include -I/usr/local/include/sbml LDFLAGS= -Wl,-rpath,/usr/local/lib -L/usr/local/lib LIBS= -lxerces-c -lsbml configure: error: Can not link to SBML Library: Please, make sure to use libSBML version >= 2.3.2 ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744812&aid=1678553&group_id=139893 |
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From: Eric F. <efe...@ph...> - 2007-02-27 15:31:20
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Dear Rainer, Thanks for your answer. I have now been able to sort out the compilation of libsbml-2.3.4 on AIX and use its API. I have already the patches on that list, but I'll send them to you as diffs. Note that these patches are more suitable to compile using xlc_r on AIX. Using gcc, libsbml compiles with only very minor changes in configure. So I guess the changes are compiler-specific and will interest only a very small number of users... Kind regards, Eric -----Original Message----- From: Rainer Machne [mailto:ra...@tb...] Sent: 25 February 2007 20:37 To: Eric Fernandez Cc: sbm...@li... Subject: Re: [SOSlib-discuss] compilation issues on AIX[Scanned] Hi Eric, sorry for the late reply, we have been at our institute's yearly seminar week. I've noticed that you have also emailed to the libSBML list about libSBML version 3 issues. Was the problem you describe below solved by using libSBML 2.3.4? A lot of changes are expected with libSBML 3.0.0 and we plan an update some time after it has been officially released. It would be great if you could propose the patches for compiling on AIX! Just email them to this list or to me personally. Rainer On Thu, 22 Feb 2007, Eric Fernandez wrote: > Hi, > > I am trying to compile SOSlib on an AIX 5.3 /IBM POWERPC environment > (using IBM compilers xlc_r and xlC_r) and had some issues. Some of them > I could fix, and I would be glad to propose some patches to the project. > However, I still have a problem compiling it: > > source='drawGraph.c' object='drawGraph.o' libtool=no DEPDIR=.deps > depmode=aix /bin/sh ../config/depcomp xlc_r -DHAVE_CONFIG_H -I. -I. > -I../src/sbmlsolver -I/hpc/work/fernandz/local32/include > -I/hpc/work/fernandz/local32/include > -I/hpc/work/fernandz/local32/include/sbml > -I/hpc/work/fernandz/local32/include > -I/hpc/work/fernandz/local32/include/sbml/sbml -I. -c drawGraph.c > > "drawGraph.c", line 853.3: 1506-045 (S) Undeclared identifier > ModifierSpeciesReference_t > > SBML headers are in the correct location : > /hpc/work/fernandz/local32/include/sbml > What am I doing wrong? > > Eric > > > ------------------------------------------------------------------------ - > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDE V > _______________________________________________ > sbmlsolver-discuss mailing list > sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbmlsolver-discuss > ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV _______________________________________________ sbmlsolver-discuss mailing list sbm...@li... https://lists.sourceforge.net/lists/listinfo/sbmlsolver-discuss |
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From: Rainer M. <ra...@tb...> - 2007-02-25 20:37:45
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Hi Eric, sorry for the late reply, we have been at our institute's yearly seminar week. I've noticed that you have also emailed to the libSBML list about libSBML version 3 issues. Was the problem you describe below solved by using libSBML 2.3.4? A lot of changes are expected with libSBML 3.0.0 and we plan an update some time after it has been officially released. It would be great if you could propose the patches for compiling on AIX! Just email them to this list or to me personally. Rainer On Thu, 22 Feb 2007, Eric Fernandez wrote: > Hi, > > I am trying to compile SOSlib on an AIX 5.3 /IBM POWERPC environment > (using IBM compilers xlc_r and xlC_r) and had some issues. Some of them > I could fix, and I would be glad to propose some patches to the project. > However, I still have a problem compiling it: > > source='drawGraph.c' object='drawGraph.o' libtool=no DEPDIR=.deps > depmode=aix /bin/sh ../config/depcomp xlc_r -DHAVE_CONFIG_H -I. -I. > -I../src/sbmlsolver -I/hpc/work/fernandz/local32/include > -I/hpc/work/fernandz/local32/include > -I/hpc/work/fernandz/local32/include/sbml > -I/hpc/work/fernandz/local32/include > -I/hpc/work/fernandz/local32/include/sbml/sbml -I. -c drawGraph.c > > "drawGraph.c", line 853.3: 1506-045 (S) Undeclared identifier > ModifierSpeciesReference_t > > SBML headers are in the correct location : > /hpc/work/fernandz/local32/include/sbml > What am I doing wrong? > > Eric > > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > sbmlsolver-discuss mailing list > sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbmlsolver-discuss > ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV _______________________________________________ sbmlsolver-discuss mailing list sbm...@li... https://lists.sourceforge.net/lists/listinfo/sbmlsolver-discuss |
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From: Eric F. <efe...@ph...> - 2007-02-22 13:34:36
|
Hi, I am trying to compile SOSlib on an AIX 5.3 /IBM POWERPC environment (using IBM compilers xlc_r and xlC_r) and had some issues. Some of them I could fix, and I would be glad to propose some patches to the project. However, I still have a problem compiling it: source='drawGraph.c' object='drawGraph.o' libtool=no DEPDIR=.deps depmode=aix /bin/sh ../config/depcomp xlc_r -DHAVE_CONFIG_H -I. -I. -I../src/sbmlsolver -I/hpc/work/fernandz/local32/include -I/hpc/work/fernandz/local32/include -I/hpc/work/fernandz/local32/include/sbml -I/hpc/work/fernandz/local32/include -I/hpc/work/fernandz/local32/include/sbml/sbml -I. -c drawGraph.c "drawGraph.c", line 853.3: 1506-045 (S) Undeclared identifier ModifierSpeciesReference_t SBML headers are in the correct location : /hpc/work/fernandz/local32/include/sbml What am I doing wrong? Eric ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys-and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV _______________________________________________ sbmlsolver-discuss mailing list sbm...@li... https://lists.sourceforge.net/lists/listinfo/sbmlsolver-discuss |
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From: Rainer M. <ra...@tb...> - 2007-02-02 14:09:40
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Eryk updating is generally a good idea :-) we should however really try to locate that bug, it's very strange. Rainer W Eryk Wolski wrote: > Rainer... > > The integration results are definitely the same... The difference is in > the sensitivities > > Yes I have updated the code after the error was removed .... a checkout > from beginning of octorber .. (I remember that the error report on > sourceforege was made after we have found the error) and I am using the > same checkout on both machines ... > > I will try to switch to the latest version of SBML ode solver .... as > soon as time permits... > > Eryk > > > > > On 2/2/07, *Rainer Machne* <ra...@tb... > <mailto:ra...@tb...>> wrote: > > Hi Eryk, > > No, we don't know of any such differences currently. Could you send the > model or the code? > > Have you updated SOSlib, after the sensitivity bug that you had reported > was fixed? This bug was fixed in 2006-10-13 02:49 as documented at > sourceforge. > > We did a wrong initialization of CVODES sensitivities in version 1.6.0, > and it worked for normal use but not for iterative use of the same > solver structure. > However, also for the first run, the correct initialization (to 0) > depended on the compiler. Some compilers might do this wrongly. So if > you use SOSlib code from before the bugfix, the described bug and > differences with compilers is easily possible. > > Rainer > > W Eryk Wolski wrote: > > Hi, > > > > Was developing some code based on the SBML ode Solver cvodes etc. > using > > gcc (GCC) 4.0.3 (Ubuntu 4.0.3-1ubuntu5) > > > > moved now to a platform > > with > > gcc (GCC) 3.4.6 20060404 (Red Hat 3.4.6-3) > > > > Do hi have to any reasons to expect differences ? .... > > I am asking because to my surprise I am getting different > sensitivities > > with precisely the same code... > > > > Eryk > > > > > > > ------------------------------------------------------------------------ > > > > > ------------------------------------------------------------------------- > > Using Tomcat but need to do more? Need to support web services, > security? > > Get stuff done quickly with pre-integrated technology to make > your job easier. > > Download IBM WebSphere Application Server v.1.0.1 based on Apache > Geronimo > > > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > <http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642> > > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > sbmlsolver-devel mailing list > > sbm...@li... > <mailto:sbm...@li...> > > https://lists.sourceforge.net/lists/listinfo/sbmlsolver-devel > > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job easier. > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > > > ------------------------------------------------------------------------ > > _______________________________________________ > sbmlsolver-devel mailing list > sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbmlsolver-devel |
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From: W E. W. <wew...@gm...> - 2007-02-02 13:44:54
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Rainer... The integration results are definitely the same... The difference is in the sensitivities Yes I have updated the code after the error was removed .... a checkout from beginning of octorber .. (I remember that the error report on sourceforege was made after we have found the error) and I am using the same checkout on both machines ... I will try to switch to the latest version of SBML ode solver .... as soon as time permits... Eryk On 2/2/07, Rainer Machne <ra...@tb...> wrote: > > Hi Eryk, > > No, we don't know of any such differences currently. Could you send the > model or the code? > > Have you updated SOSlib, after the sensitivity bug that you had reported > was fixed? This bug was fixed in 2006-10-13 02:49 as documented at > sourceforge. > > We did a wrong initialization of CVODES sensitivities in version 1.6.0, > and it worked for normal use but not for iterative use of the same > solver structure. > However, also for the first run, the correct initialization (to 0) > depended on the compiler. Some compilers might do this wrongly. So if > you use SOSlib code from before the bugfix, the described bug and > differences with compilers is easily possible. > > Rainer > > W Eryk Wolski wrote: > > Hi, > > > > Was developing some code based on the SBML ode Solver cvodes etc. using > > gcc (GCC) 4.0.3 (Ubuntu 4.0.3-1ubuntu5) > > > > moved now to a platform > > with > > gcc (GCC) 3.4.6 20060404 (Red Hat 3.4.6-3) > > > > Do hi have to any reasons to expect differences ? .... > > I am asking because to my surprise I am getting different sensitivities > > with precisely the same code... > > > > Eryk > > > > > > ------------------------------------------------------------------------ > > > > > ------------------------------------------------------------------------- > > Using Tomcat but need to do more? Need to support web services, > security? > > Get stuff done quickly with pre-integrated technology to make your job > easier. > > Download IBM WebSphere Application Server v.1.0.1 based on Apache > Geronimo > > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > sbmlsolver-devel mailing list > > sbm...@li... > > https://lists.sourceforge.net/lists/listinfo/sbmlsolver-devel > > |
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From: Rainer M. <ra...@tb...> - 2007-02-02 12:39:14
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Hi Eryk, No, we don't know of any such differences currently. Could you send the model or the code? Have you updated SOSlib, after the sensitivity bug that you had reported was fixed? This bug was fixed in 2006-10-13 02:49 as documented at sourceforge. We did a wrong initialization of CVODES sensitivities in version 1.6.0, and it worked for normal use but not for iterative use of the same solver structure. However, also for the first run, the correct initialization (to 0) depended on the compiler. Some compilers might do this wrongly. So if you use SOSlib code from before the bugfix, the described bug and differences with compilers is easily possible. Rainer W Eryk Wolski wrote: > Hi, > > Was developing some code based on the SBML ode Solver cvodes etc. using > gcc (GCC) 4.0.3 (Ubuntu 4.0.3-1ubuntu5) > > moved now to a platform > with > gcc (GCC) 3.4.6 20060404 (Red Hat 3.4.6-3) > > Do hi have to any reasons to expect differences ? .... > I am asking because to my surprise I am getting different sensitivities > with precisely the same code... > > Eryk > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job easier. > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > > > ------------------------------------------------------------------------ > > _______________________________________________ > sbmlsolver-devel mailing list > sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbmlsolver-devel |
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From: W E. W. <wew...@gm...> - 2007-02-02 12:09:14
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Hi, Was developing some code based on the SBML ode Solver cvodes etc. using gcc (GCC) 4.0.3 (Ubuntu 4.0.3-1ubuntu5) moved now to a platform with gcc (GCC) 3.4.6 20060404 (Red Hat 3.4.6-3) Do hi have to any reasons to expect differences ? .... I am asking because to my surprise I am getting different sensitivities with precisely the same code... Eryk |
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From: Rainer M. <ra...@tb...> - 2007-02-01 18:46:01
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Hi Eryk, I took a quick look and - wow - that looks very nice! As we are currently not in an active development phase, it may take some time until we can fully review and test everything. I try my best below, and stronlgy hope that I am not misinterpreting. One first question about your structure Variable_t: In its definition, it says double value; /**< two dimensional array with the design points */ but actually is not an array but a simple double. Should it become one? Or do I understand it wrongly? If yes, we could then have a batch solver function, that loops through the designpoints and returns an array of cvodeResults or SBMLResults, right? In the following some questions, regarding possible integration and fusion of your function with existing functions. This is based on my above interpreation that double value should be an array. If this is not the case, then please just forget my alternative proposal in the following: W Eryk Wolski wrote: > The changes I would be going to make are going to include: > editing src/Makefile.am > adding src/varySettings.c > adding src/sbmlsolver/varySettings.h > > editing Makefile.am <http://makefile.am/> in directory example. > and adding > examples/Sensitivitytest.c > examples/DesignPointExample.c From my first peek it looks as if you do not need to change any existing files (except for Makefiles). Is this correct? > > I kept all the functions which I would like to have added to SBML_Solver > in varySettings.c and varySettings.h. However, I do patch many of the > existing structures in the lib e.g. > > SBML_ODESOLVER_API Variable_t * OdeModel_getVariable( odeModel_t * > odemodel , double value, char * parameterStr , char * reactionStr ); > SBML_ODESOLVER_API Variable_t * VariableIndex_getVariable( > variableIndex_t * vi, double value, char *parameterStr , char *reactionStr); > SBML_ODESOLVER_API void Variable_free( Variable_t *variable ); One problematic thing is the potential confusion of having to different structures with very similar names: Variable_t and VariableIndex_t. I would like to propose an alternative (hoping that I understood your code correctly): First, handling of local reaction/kinetic law parameters: We could introduce a function like variableIndex_t *ODEModel_getRxnVariableIndex(odeModel_t *odemodel, char *parameterStr, char *reactionStr) which would retrieve the existing variableIndex_t only if the calling application has done globalizeParameter(model, parameterStr, reactionStr) before constructing the odeModel_t (it would just return NULL if the variable called "r_rid_id" is not available). This would actually be a nice service offered by SOSlib! Internally we could add the field "rid" to variableIndex and use the fused version "r_rid_id" in the equations only. This way we would be fit to change the internal concatenation in case this becomes necessary for future SBML versions (who knows :) ). Second, to set the DesignPoint structure, we could fuse v4 = OdeModel_getVariable(odemodel,.1,"V2","J1"); DesignPoint_addDimension(dp,v4,3); into vi = ODEModel_getRxnVariableIndex(odemodel, "V2","J1"); DesignPoint_addDimension(dp, vi, 3, .1), This would include moving the "value" array (if it should be one) from Variable_t to the DesignPoint_t, replacing the Variable_t field in DesignPoint_t by the existing variableIndex_t and changing the function DesignPoint_addDimension to also take the value. Did I get something wrong? > SBML_ODESOLVER_API int > IntegratorInstance_setDesignPoint(integratorInstance_t * > integratorInstance, DesignPoint_t * designpoint); This is just a wrapper around IntegratorInstance_setVariableValue to be called after IntegratorInstance_reset, right? In case that "value" should be an array, this function would need to be passed an additional index, to indicate to which values to set the model to, right? > SBML_ODESOLVER_API Variable_t * Variable_create( double value, char > *parameterStr , char *reactionStr); > SBML_ODESOLVER_API int Model_change(Model_t *model, /*SBML level 2! See > example*/ > DesignPoint_t *dp); This is just like IntegratorInstance_setDesignPoint but on the level of the SBML structure Model_t, right? By having the additional "rid" field in VariableIndex_t above suggestions should also work on this level. > SBML_ODESOLVER_API cvodeResults_t * Model_solve(Model_t * model , > cvodeSettings_t *settings); Is this different from the existing function Model_odeSolver((Model_t *m, cvodeSettings_t *set) ? > the only new struct I introduced is DesignPoint (ParameterSet migth be a > better name). I also like DesignPoint, but I guess you are right, and ParameterSet is easier to understand. On the other hand, the same function could also be used to vary initial conditions, and thus ODE variables, right? > > I remember adding varySettings.h and varySettings.c 2006 only to find > this files deleted a few weeks later... Sorry for that. It didn't use SOSlib's internal memory and error management, which were very fresh back then. And I wanted to fuse it into the existing code, but as you might remember, I miserably failed :-( back then. And sorry if I misunderstood your code and above suggestions won't work. Currently the next release is planned for March or April and I definitely hope that we can take DesignPoint/ParameterSet and batch solver wrapper functions into this release. Thanks for the contribution! Rainer it might be better if a few > people review the code first so that a more persistent change if wished > can be made. > I attach the files... > > cheers > Eryk > > > > On 11/23/06, *Rainer Machne* <ra...@tb... > <mailto:ra...@tb...>> wrote: > > Hi Friends, > > here a rough todo list for the next release ... at least some of the > stuff below should be done before the next release. If you have > preferences/opions or want to add things feel free: > > Functionality: > General: > * odeSolverBatch (use Eryk's code) > * assignment rule ordering (also consider DAE systems/IDA solver > extension) > * variable compartments, ODEs in amounts > * online compilation > * exact event detection > -> Rainer and Xtof > > Text-based input files for: > ** reaction network: Vienna Reaction library > ** ODE system: xppaut format > -> Xtof > > Sens. Analysis output: > * Direct Lyapunov Exponent analysis > * Fisher Information Matrix > -> James and Stefan :-) ??? > > Dependencies: > * libSBML 3 > * Sundials 2.3.0 > -> Rainer and Xtof > > Pending: > * Test suite ?? > ** Functionality > ** Performance > > Configure: > * malloc.h > * -R/-rpath switch > * general refactoring!! > -> Rainer and Xtof > > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to > share your > opinions on IT & business topics through brief surveys - and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > <http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV> > _______________________________________________ > sbmlsolver-devel mailing list > sbm...@li... > <mailto:sbm...@li...> > https://lists.sourceforge.net/lists/listinfo/sbmlsolver-devel > > > > ------------------------------------------------------------------------ > > /* > Last changed Time-stamp: <2006-04-19 16:23:17 raim> > $Id: varySettings.c,v 1.1 2006/05/08 13:40:53 witek96 Exp $ > */ > /* > * > * This library is free software; you can redistribute it and/or modify it > * under the terms of the GNU Lesser General Public License as published > * by the Free Software Foundation; either version 2.1 of the License, or > * any later version. > * > * This library is distributed in the hope that it will be useful, but > * WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF > * MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and > * documentation provided hereunder is on an "as is" basis, and the > * authors have no obligations to provide maintenance, support, > * updates, enhancements or modifications. In no event shall the > * authors be liable to any party for direct, indirect, special, > * incidental or consequential damages, including lost profits, arising > * out of the use of this software and its documentation, even if the > * authors have been advised of the possibility of such damage. See > * the GNU Lesser General Public License for more details. > * > * You should have received a copy of the GNU Lesser General Public License > * along with this library; if not, write to the Free Software Foundation, > * Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA. > * > * The original code contained here was initially developed by: > * > * Witold Wolski > * > * Contributor(s): > * > */ > > #include "sbmlsolver/varySettings.h" > > > /**Allocate storage for DesignPoint_t of dimensions*/ > > SBML_ODESOLVER_API DesignPoint_t* DesignPoint_create(int dimensions) > { > DesignPoint_t * dp; > ASSIGN_NEW_MEMORY(dp, struct DesignPoint, NULL); > dp->dimensions = dimensions; > dp->variables = (Variable_t ** ) calloc(dimensions, sizeof(Variable_t)); > return(dp); > } > > SBML_ODESOLVER_API DesignPoint_t * DesignPoint_clone(DesignPoint_t * designpoint) > { > DesignPoint_t * dp; > ASSIGN_NEW_MEMORY(dp, struct DesignPoint, NULL); > dp->dimensions = designpoint->dimensions; > dp->variables = (Variable_t ** ) calloc(designpoint->dimensions , sizeof(Variable_t)); > > return(dp); > } > > > SBML_ODESOLVER_API void DesignPoint_free(DesignPoint_t* designpoint) > { > int i; > for(i=0;i < designpoint->dimensions; i++) > { > Variable_free(designpoint->variables[i]); > } > free(designpoint->variables); > free(designpoint); > } > > SBML_ODESOLVER_API void DesignPoint_dumpXML(DesignPoint_t * dp, FILE * pFile) > { > int i; > variableIndex_t * vi; > fprintf(pFile,"<DesignPoint dimensions=\"%i\">\n",dp->dimensions); > for(i =0; i < dp->dimensions; i++) > { > if(dp->variables[i] != NULL) > { > fprintf(pFile," <variable id=\"%s\" ",dp->variables[i]->id); > fprintf(pFile," rid=\"%s\" ",dp->variables[i]->rid); > fprintf(pFile," value=\"%f\" ",dp->variables[i]->value); > if(dp->variables[i]->variableindex != NULL) > { > vi = dp->variables[i]->variableindex; > if(vi->type == CONSTANT) > fprintf( pFile , " typeIndex=\"%i\" " , vi->type_index); > fprintf( pFile , " index=\"%i\"/>\n" , vi->index); > } > } > } > fprintf(pFile, "</DesignPoint>\n" ); > > } > > > > SBML_ODESOLVER_API void DesignPoint_print(DesignPoint_t * dp) > { > int i; > variableIndex_t * vi; > printf("dimensions %i\n",dp->dimensions); > for(i =0; i < dp->dimensions; i++) > { > if(dp->variables[i] != NULL) > { > printf("id %s\n",dp->variables[i]->id); > printf("rid %s\n",dp->variables[i]->rid); > printf("value %f\n",dp->variables[i]->value); > if(dp->variables[i]->variableindex != NULL) > { > vi = dp->variables[i]->variableindex; > if(vi->type == CONSTANT) > printf("CONSTANT\n"); > printf("typeIndex %i\n",vi->type_index); > printf("index %i\n",vi->index); > } > } > printf("==============\n"); > } > } > > /**Add variable to Design point > \param dp DesignPoint_t > \param variable > \param dimension \< dp-> dimension */ > > SBML_ODESOLVER_API void DesignPoint_addDimension( DesignPoint_t * dp, Variable_t * variable, int dimension) > { > if( dimension >= 0 && dimension < dp->dimensions) > { > if((dp->variables[dimension]) != NULL) > { > Variable_free(dp->variables[dimension]); > } > dp->variables[dimension] = variable; > } > } > > /**Update all parameter values in the design point > * \param dp DesignPoint_t > * \param values new parameter values in logarithmic > */ > > SBML_ODESOLVER_API int DesignPoint_update(DesignPoint_t * dp, double * log_values) > { > int i; > for(i = 0; i< dp->dimensions; i++) > { > dp->variables[i]->value = exp(log_values[i]); > } > } > > /** Get all parameter values of a design point > * \param dp DesignPoint_t > * \return an array of doubles with the parameter values > */ > > SBML_ODESOLVER_API double * DesignPoint_getValues(DesignPoint_t * dp) > { > int i; > double *res = calloc(dp->dimensions, sizeof(double)); > for(i = 0; i < dp->dimensions; i++) > { > res[i] = dp->variables[i]->value; > } > return(res); > } > > > /** creates a variable > \param model SBML odeModel_t > \param value paramter value > \param char parameterStr Identifier > \param cahr reactionsStr Identifier > */ > > SBML_ODESOLVER_API Variable_t * OdeModel_getVariable( odeModel_t * odemodel > , double value, char * parameterStr , char * reactionStr ) > { > char * local_param; > variableIndex_t * variableindex; > Variable_t * variable; > int i; > if(odemodel != NULL) > { > if ( (reactionStr != NULL && strlen(reactionStr) > 0) ) > { > ASSIGN_NEW_MEMORY_BLOCK(local_param, > strlen(parameterStr) + strlen(reactionStr) + 4, > char , 0); > sprintf( local_param, "r_%s_%s", reactionStr , parameterStr ); > variableindex = ODEModel_getVariableIndex( odemodel, local_param ); > free( local_param ); > } > else > { > variableindex = ODEModel_getVariableIndex(odemodel, parameterStr); > } > if(variableindex !=NULL) > { > variable = VariableIndex_getVariable( variableindex , value , parameterStr , reactionStr ); > } > else > { > return(NULL); /*alternatively ? > return(Variable_create(value, parameterStr , reactionStr)); > */ > } > } > else > { > return(NULL); > } > return(variable); > } > > /**creates a variable from index*/ > SBML_ODESOLVER_API Variable_t * VariableIndex_getVariable( variableIndex_t * vi, double value, char *parameterStr , char *reactionStr) > { > Variable_t * variable; > char * local_param; > ASSIGN_NEW_MEMORY(variable, struct Variable, NULL); > ASSIGN_NEW_MEMORY(variable->variableindex, variableIndex_t, NULL); > > variable->variableindex->type = vi->type; > variable->variableindex->type_index = vi->type_index; > variable->variableindex->index = vi->index; > > if(reactionStr != NULL && strlen(reactionStr) > 0 ) > { > ASSIGN_NEW_MEMORY_BLOCK(variable->rid, strlen(reactionStr)+1, char, 0); > sprintf(variable->rid, "%s", reactionStr); > } > else > variable->rid = NULL; > if( parameterStr != NULL && strlen(parameterStr) > 0 ) > { > ASSIGN_NEW_MEMORY_BLOCK(variable->id, strlen(parameterStr)+1, char, 0); > sprintf(variable->id, "%s", parameterStr); > } > else > variable->id = NULL; > > variable->value = value; > return(variable); > } > > /** Remove struct Variable_t from memory*/ > > SBML_ODESOLVER_API void Variable_free( Variable_t *variable ) > { > if(variable != NULL) > { > if(variable->id != NULL) > free(variable->id); > if(variable->rid != NULL) > free(variable->rid); > if(variable->variableindex != NULL) > VariableIndex_free(variable->variableindex); > free(variable); > } > } > > SBML_ODESOLVER_API Variable_t * Variable_clone( Variable_t * variable_old ) > { > Variable_t * variable; > char * local_param; > > ASSIGN_NEW_MEMORY(variable, struct Variable, NULL); > variable->variableindex = variable_old->variableindex; > > if(variable_old->rid != NULL && strlen(variable_old->rid) > 0 ) > { > ASSIGN_NEW_MEMORY_BLOCK(variable->rid, strlen(variable_old->rid)+1, char, 0); > sprintf(variable->rid, "%s", variable_old->rid); > } > else > variable->rid = NULL; > if( variable_old->id != NULL && strlen(variable_old->id) > 0 ) > { > ASSIGN_NEW_MEMORY_BLOCK(variable->id, strlen(variable_old->id)+1, char, 0); > sprintf(variable->id, "%s", variable_old->id); > } > else > variable->id = NULL; > variable->value = variable_old->value; > return(variable); > } > > > SBML_ODESOLVER_API int IntegratorInstance_setDesignPoint(integratorInstance_t * integratorInstance, DesignPoint_t * designpoint) > { > int i = 0; > for(i = 0; i < designpoint->dimensions;i++) > { > if(designpoint->variables[i]->variableindex != NULL) > { > IntegratorInstance_setVariableValue(integratorInstance > , designpoint->variables[i]->variableindex > , designpoint->variables[i]->value); > } > else > { > return(-1); > } > } > return(1); > } > > > /** old style parameter scan -- working*/ > > /**Create a variable - Simple version, works only with old style parameter scan functions: Model_change and Model_solve*/ > SBML_ODESOLVER_API Variable_t * Variable_create( double value, char *parameterStr , char *reactionStr) > { > Variable_t * variable; > ASSIGN_NEW_MEMORY(variable, struct Variable, NULL); > > if(reactionStr != NULL && strlen(reactionStr) > 0 ) > { > ASSIGN_NEW_MEMORY_BLOCK(variable->rid, strlen(reactionStr)+1, char, 0); > sprintf(variable->rid, "%s", reactionStr); > } > else > variable->rid = NULL; > if( parameterStr != NULL && strlen(parameterStr) > 0 ) > { > ASSIGN_NEW_MEMORY_BLOCK(variable->id, strlen(parameterStr)+1, char, 0); > sprintf(variable->id, "%s", parameterStr); > } > else > variable->id = NULL; > > variable->value = value; > return(variable); > } > > > /** changes parameters in the Model_t representation */ > SBML_ODESOLVER_API int Model_change(Model_t *model, /*SBML level 2! See example*/ > DesignPoint_t *dp > ) > { > int i; > SBMLResults_t * results; > for(i=0;i < dp->dimensions; i++) > { > if ( ! Model_setValue(model, dp->variables[i]->id , dp->variables[i]->rid, dp->variables[i]->value)) > { > printf("Parameter %s \n", dp->variables[i]->id); > Warn(stderr, "Parameter for variation not found in the model.", dp->variables[i]->id); > return(0); > } > } > return(1); > } > > > SBML_ODESOLVER_API cvodeResults_t * Model_solve(Model_t * model, cvodeSettings_t *settings) > { > cvodeResults_t * results; > odeModel_t * odemodel = ODEModel_create(model); > integratorInstance_t * integratorInstance; > RETURN_ON_FATALS_WITH(NULL); > > /** > Second, an integratorInstance is created from the odeModel > and the passed cvodeSettings. If that worked out ... > */ > > integratorInstance = IntegratorInstance_create(odemodel, settings); > RETURN_ON_FATALS_WITH(NULL); > > /** .... the integrator loop can be started, > that invoking CVODE to move one time step and store. > The function will also handle events and > check for steady states. > */ > > while(!IntegratorInstance_timeCourseCompleted(integratorInstance)) > { > IntegratorInstance_integrateOneStep(integratorInstance); > RETURN_ON_ERRORS_WITH(NULL); > } > > results = IntegratorInstance_createResults(integratorInstance); > > /* free integration data */ > IntegratorInstance_free(integratorInstance); > /* free odeModel */ > ODEModel_free(odemodel); > /* ... well done. */ > return(results); > } > > > > /* test */ > > > > > ------------------------------------------------------------------------ > > /* > Last changed Time-stamp: <2006-04-19 16:23:17 raim> > $Id: doxygenComments.c,v 1.00 2006/04/11 13:10:45 afinney Exp $ > */ > /* > * > * This library is free software; you can redistribute it and/or modify it > * under the terms of the GNU Lesser General Public License as published > * by the Free Software Foundation; either version 2.1 of the License, or > * any later version. > * > * This library is distributed in the hope that it will be useful, but > * WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF > * MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and > * documentation provided hereunder is on an "as is" basis, and the > * authors have no obligations to provide maintenance, support, > * updates, enhancements or modifications. In no event shall the > * authors be liable to any party for direct, indirect, special, > * incidental or consequential damages, including lost profits, arising > * out of the use of this software and its documentation, even if the > * authors have been advised of the possibility of such damage. See > * the GNU Lesser General Public License for more details. > * > * You should have received a copy of the GNU Lesser General Public License > * along with this library; if not, write to the Free Software Foundation, > * Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA. > * > * The original code contained here was initially developed by: > * > * Witold Wolski > * > * Contributor(s): > * > */ > > #ifndef _VARYSETTINGS_H_ > #define _VARYSETTINGS_H_ > > > > #include <stdio.h> > #include <stdlib.h> > #include <string.h> > #include <string.h> > #include <time.h> > #include <math.h> > > #include <sbmlsolver/odeSolver.h> > #include <sbmlsolver/sbml.h> > #include <sbmlsolver/solverError.h> > #include <sbmlsolver/variableIndex.h> > #include <sbmlsolver/odeModel.h> > #include <sbml/SBMLTypes.h> > > #ifdef __cplusplus > extern "C" { > #endif > > typedef struct Variable Variable_t; > /** Structure of parameter value for parameter scan */ > struct Variable > { > char *id; /**< SBML ID of the species, compartment or parameter to be varied */ > char *rid; /**< SBML Reaction ID, if a local parameter is to be varied */ > variableIndex_t * variableindex; > double value; /**< two dimensional array with the design points */ > }; > > typedef struct DesignPoint DesignPoint_t; > > struct DesignPoint > { > Variable_t ** variables; /**< array of variables */ > int dimensions; /**< length of variable array*/ > }; > > SBML_ODESOLVER_API DesignPoint_t* DesignPoint_create(int dimensions); > SBML_ODESOLVER_API DesignPoint_t * DesignPoint_clone(DesignPoint_t * designpoint); > > SBML_ODESOLVER_API double * DesignPoint_getValues(DesignPoint_t * dp); > SBML_ODESOLVER_API void DesignPoint_free(DesignPoint_t* designpoint); > SBML_ODESOLVER_API void DesignPoint_addDimension( DesignPoint_t * dp, Variable_t * variable, int dimension); > SBML_ODESOLVER_API int DesignPoint_update(DesignPoint_t * dp, double * log_values); > SBML_ODESOLVER_API void DesignPoint_dumpXML(DesignPoint_t * dp, FILE *pFile); > > SBML_ODESOLVER_API Variable_t * OdeModel_getVariable( odeModel_t * odemodel , double value, char * parameterStr , char * reactionStr ); > SBML_ODESOLVER_API Variable_t * VariableIndex_getVariable( variableIndex_t * vi, double value, char *parameterStr , char *reactionStr); > SBML_ODESOLVER_API void Variable_free( Variable_t *variable ); > SBML_ODESOLVER_API int IntegratorInstance_setDesignPoint(integratorInstance_t * integratorInstance, DesignPoint_t * designpoint); > SBML_ODESOLVER_API Variable_t * Variable_create( double value, char *parameterStr , char *reactionStr); > SBML_ODESOLVER_API int Model_change(Model_t *model, /*SBML level 2! See example*/ > DesignPoint_t *dp); > SBML_ODESOLVER_API cvodeResults_t * Model_solve(Model_t * model , cvodeSettings_t *settings); > > #ifdef __cplusplus > } > #endif > > #endif // _VARYSETTINGS_H_ > > > ------------------------------------------------------------------------ > > /* > Last changed Time-stamp: <2005-12-16 16:28:40 raim> > $Id: Sense.c,v 1.2 2005/12/16 15:29:18 raimc Exp $ > */ > /* > * > * This library is free software; you can redistribute it and/or modify it > * under the terms of the GNU Lesser General Public License as published > * by the Free Software Foundation; either version 2.1 of the License, or > * any later version. > * > * This library is distributed in the hope that it will be useful, but > * WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF > * MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and > * documentation provided hereunder is on an "as is" basis, and the > * authors have no obligations to provide maintenance, support, > * updates, enhancements or modifications. In no event shall the > * authors be liable to any party for direct, indirect, special, > * incidental or consequential damages, including lost profits, arising > * out of the use of this software and its documentation, even if the > * authors have been advised of the possibility of such damage. See > * the GNU Lesser General Public License for more details. > * > * You should have received a copy of the GNU Lesser General Public License > * along with this library; if not, write to the Free Software Foundation, > * Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA. > * > * The original code contained here was initially developed by: > * > * Witold Wolski > * > * Contributor(s): > */ > > #include <stdio.h> > #include <malloc.h> > #include <math.h> > #include <stdlib.h> > #include <ctype.h> > #include <string.h> > > #include "sbmlsolver/integratorInstance.h" > #include "sbmlsolver/solverError.h" > #include "sbmlsolver/varySettings.h" > #include <sbml/SBMLTypes.h> > > > int testVariable() > { > Variable_t * variable; > printf("in testVariable\n"); > variable = Variable_create(2.0,"V1",NULL); > Variable_free(variable); > } > > int testDesignPoint() > { > Variable_t * variable; > DesignPoint_t * designpoint; > printf("in testDesignPoint\n"); > variable = Variable_create(2.0,"V1",NULL); > designpoint = DesignPoint_create(5); > DesignPoint_addDimension(designpoint,variable,0); > DesignPoint_free(designpoint); > } > > /**Example with fast version of parameter change*/ > int doit3() > { > Variable_t *v1,*v2,*v3,*v4,*v5; > variableIndex_t *y1; > integratorInstance_t * integratorInstance; > DesignPoint_t * dp; > cvodeSettings_t * cs; > cvodeResults_t * cvoderesults; > odeModel_t * odemodel; > char * modelStr = "MAPK.xml"; > SBMLDocument_t * d2, * document = readSBML( modelStr ); > Model_t * model; > int i=0, j=0, k=0; > > /* char *model; */ > if ( SBMLDocument_getLevel(document) == 1 ) > { > d2 = convertModel(document); > model = SBMLDocument_getModel(d2); > } > else > { > model = SBMLDocument_getModel(document); > } > > /*first do globalise the paramters*/ > > globalizeParameter(model,"V2","J1"); > globalizeParameter(model,"KK2","J1"); > odemodel = ODEModel_create(model); > > dp = DesignPoint_create(5); /*create design point with 5 dimensions*/ > v1 = OdeModel_getVariable(odemodel, 2.0, "V1", NULL); > DesignPoint_addDimension(dp,v1,0); > v2 = OdeModel_getVariable(odemodel, 8.0, "Ki", NULL); > DesignPoint_addDimension(dp,v2,1); > v3 = OdeModel_getVariable(odemodel,10.0,"K1",NULL); > DesignPoint_addDimension(dp,v3,2); > v4 = OdeModel_getVariable(odemodel,.1,"V2","J1"); > DesignPoint_addDimension(dp,v4,3); > v5 = OdeModel_getVariable(odemodel, 2.0,"KK2","J1"); > DesignPoint_addDimension(dp,v5,4); > DesignPoint_print(dp); > printf("\n\n"); > > y1 = ODEModel_getVariableIndex(odemodel,"MKK_P"); > > /*DesignPoint_print(dp);*/ > cs = CvodeSettings_create(); > CvodeSettings_setTime(cs, 300, 10); > CvodeSettings_setErrors(cs, 1e-9, 1e-4, 1000); > CvodeSettings_setStoreResults(cs, 1); > CvodeSettings_setSensitivity(cs,1); > > /*res = Model_odeSolverDesing(model,cs,dp); > printf("num sens %d\n",SBMLResults_getNumSens(res));*/ > > RETURN_ON_FATALS_WITH(1); > integratorInstance = IntegratorInstance_create(odemodel,cs); > IntegratorInstance_setDesignPoint(integratorInstance,dp); > > IntegratorInstance_dumpNames(integratorInstance); > > printf("nsens %d \n", integratorInstance->data->nsens); > printf("neq %d \n", integratorInstance->data->neq); > printf("nvalues %d \n", integratorInstance->data->nvalues); > > while (!IntegratorInstance_timeCourseCompleted(integratorInstance)) > { > IntegratorInstance_integrateOneStep(integratorInstance); > > /* > IntegratorInstance_dumpPSensitivities(integratorInstance,v1->variableindex); > IntegratorInstance_dumpYSensitivities(integratorInstance,y1); > */ > > for(i = 0; i < integratorInstance->data->neq; i++) > { > for(j=0; j < integratorInstance->data-> nsens; j++) > { > printf("%f \t",integratorInstance->data->sensitivity[i][j]); > } > printf("\n"); > } > printf("\n\n\n"); > /* > IntegratorInstance_dumpPSensitivities(integratorInstance,v2->variableindex); > IntegratorInstance_dumpYSensitivities(integratorInstance,y2); > /* > IntegratorInstance_dumpPSensitivities(integratorInstance,v3->variableindex); > IntegratorInstance_dumpPSensitivities(integratorInstance,v4->variableindex); > IntegratorInstance_dumpPSensitivities(integratorInstance,v5->variableindex); > */ > RETURN_ON_ERRORS_WITH(1); > } > > cvoderesults = IntegratorInstance_createResults(integratorInstance); > printf("Printing cvoderesults\n==============================\n"); > > for(k = 0; k <= cvoderesults->nout; k++) > { > for(i = 0; i < cvoderesults->neq; i++) > { > for(j=0; j < cvoderesults->nsens; j++) > { > printf("%f \t",cvoderesults->sensitivity[i][j][k]); > } > printf("\n"); > } > printf("\n\n\n"); > } > IntegratorInstance_free(integratorInstance); > DesignPoint_free(dp); > ODEModel_free(odemodel); > SBMLDocument_free(d2); > SBMLDocument_free(document); > return(1); > } > > > int main(int argc, char *argv[]) > { > int result = testVariable(); > result = testDesignPoint(); > result = doit3(); > printf("done3\n"); > return( result ); > } > > > > ------------------------------------------------------------------------ > > /* > Last changed Time-stamp: <2005-12-16 16:28:40 raim> > $Id: Sense.c,v 1.2 2005/12/16 15:29:18 raimc Exp $ > */ > /* > * > * This library is free software; you can redistribute it and/or modify it > * under the terms of the GNU Lesser General Public License as published > * by the Free Software Foundation; either version 2.1 of the License, or > * any later version. > * > * This library is distributed in the hope that it will be useful, but > * WITHOUT ANY WARRANTY, WITHOUT EVEN THE IMPLIED WARRANTY OF > * MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. The software and > * documentation provided hereunder is on an "as is" basis, and the > * authors have no obligations to provide maintenance, support, > * updates, enhancements or modifications. In no event shall the > * authors be liable to any party for direct, indirect, special, > * incidental or consequential damages, including lost profits, arising > * out of the use of this software and its documentation, even if the > * authors have been advised of the possibility of such damage. See > * the GNU Lesser General Public License for more details. > * > * You should have received a copy of the GNU Lesser General Public License > * along with this library; if not, write to the Free Software Foundation, > * Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA. > * > * The original code contained here was initially developed by: > * > * Witold Wolski > * > * Contributor(s): > */ > > #include <stdio.h> > #include <malloc.h> > #include <math.h> > #include <stdlib.h> > #include <ctype.h> > #include <string.h> > > #include "sbmlsolver/integratorInstance.h" > #include "sbmlsolver/solverError.h" > #include "sbmlsolver/varySettings.h" > #include <sbml/SBMLTypes.h> > > > > > void myODEModel_dumpNames(odeModel_t *om) > { > int i; > printf("myODEModel_dumpNames\n"); > for ( i=(om->neq+om->nass+1); i<(om->neq+om->nass+om->nconst+om->nalg); i++ ) > printf("%s ", om->names[i]); > printf("\n"); > } > > /**Example with fast version of parameter change*/ > > int doit3() > { > Variable_t *v1,*v2,*v3,*v4,*v5; > variableIndex_t *y1; > integratorInstance_t * integratorInstance; > DesignPoint_t * dp; > cvodeSettings_t * cs; > cvodeResults_t * cvoderesults; > odeModel_t * odemodel; > char * modelStr = "MAPK.xml"; > SBMLDocument_t * d2, * document = readSBML( modelStr ); > Model_t * model; > int i=0, j=0, k=0; > > /* char *model; */ > if ( SBMLDocument_getLevel(document) == 1 ) > { > d2 = convertModel(document); > model = SBMLDocument_getModel(d2); > } > else > { > model = SBMLDocument_getModel(document); > } > > /*first do globalise the paramters*/ > > globalizeParameter(model,"V2","J1"); > globalizeParameter(model,"KK2","J1"); > odemodel = ODEModel_create(model); > > dp = DesignPoint_create(5); /*create design point with 5 dimensions*/ > v1 = OdeModel_getVariable(odemodel, 2.0, "V1", NULL); > DesignPoint_addDimension(dp,v1,0); > v2 = OdeModel_getVariable(odemodel, 8.0, "Ki", NULL); > DesignPoint_addDimension(dp,v2,1); > v3 = OdeModel_getVariable(odemodel,10.0,"K1",NULL); > DesignPoint_addDimension(dp,v3,2); > v4 = OdeModel_getVariable(odemodel,.1,"V2","J1"); > DesignPoint_addDimension(dp,v4,3); > v5 = OdeModel_getVariable(odemodel, 2.0,"KK2","J1"); > DesignPoint_addDimension(dp,v5,4); > DesignPoint_print(dp); > printf("\n\n"); > > y1 = ODEModel_getVariableIndex(odemodel,"MKK_P"); > > /*DesignPoint_print(dp);*/ > cs = CvodeSettings_create(); > CvodeSettings_setTime(cs, 300, 10); > CvodeSettings_setErrors(cs, 1e-9, 1e-4, 1000); > CvodeSettings_setStoreResults(cs, 1); > CvodeSettings_setSensitivity(cs,1); > > /*res = Model_odeSolverDesing(model,cs,dp); > printf("num sens %d\n",SBMLResults_getNumSens(res));*/ > > RETURN_ON_FATALS_WITH(1); > integratorInstance = IntegratorInstance_create(odemodel,cs); > IntegratorInstance_setDesignPoint(integratorInstance,dp); > > printf("5 Global parameters\n"); > myODEModel_dumpNames(integratorInstance->om); > > printf("nsens (sensitivities) %d \n", integratorInstance->data->nsens); > printf("neq (equations) %d \n", integratorInstance->data->neq); > printf("nvalues %d \n", integratorInstance->data->nvalues); > > while (!IntegratorInstance_timeCourseCompleted(integratorInstance)) > { > IntegratorInstance_integrateOneStep(integratorInstance); > > /* > for(i = 0; i < integratorInstance->data->neq; i++) > { > for(j = 1; j < integratorInstance->data-> nsens; j++) > { > printf("%f \t",integratorInstance->data->sensitivity[i][j]); > } > printf("\n"); > } > printf("\n\n\n"); > */ > > /* > IntegratorInstance_dumpPSensitivities(integratorInstance,v1->variableindex); > IntegratorInstance_dumpYSensitivities(integratorInstance,y1); > IntegratorInstance_dumpPSensitivities(integratorInstance,v2->variableindex); > IntegratorInstance_dumpYSensitivities(integratorInstance,y2); > IntegratorInstance_dumpPSensitivities(integratorInstance,v3->variableindex); > IntegratorInstance_dumpPSensitivities(integratorInstance,v4->variableindex); > IntegratorInstance_dumpPSensitivities(integratorInstance,v5->variableindex); > */ > > RETURN_ON_ERRORS_WITH(1); > } > > cvoderesults = IntegratorInstance_createResults(integratorInstance); > printf("Printing cvoderesults\n==============================\n"); > > for(k = 1; k <= cvoderesults->nout; k++) > { > for(i = 0; i < cvoderesults->neq; i++) > { > for(j=1; j < cvoderesults->nsens; j++) > { > printf("%f \t",cvoderesults->sensitivity[i][j][k]); > } > printf("\n"); > } > printf("\n\n\n"); > } > > IntegratorInstance_free(integratorInstance); > DesignPoint_free(dp); > ODEModel_free(odemodel); > SBMLDocument_free(d2); > SBMLDocument_free(document); > return(1); > } > > int main(int argc, char *argv[]) > { > int result; > result = doit3(); > printf("done3\n"); > return( result ); > } > > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job easier. > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > > > ------------------------------------------------------------------------ > > _______________________________________________ > sbmlsolver-devel mailing list > sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbmlsolver-devel |
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From: W E. W. <wew...@gm...> - 2007-02-01 16:03:23
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Hi Rainer , all... Add 1 Currently I went further and have introduced two "classes" CB_SimulatorInterface and CB_Solver which encapsulate the integrator instance - allow for an easy update of parameters and return a structure CB_SimulatorOutput and CB_SimulatoroutputSet ... which are part of an CaliBayes API which we are developing here in Newcastle in the programming language C. Both those classes CB_SimulatorInterface and CB_Solver depend on a patched version of the SBML ode Solver API .. it would be a huge help if this patch could be integrated into the standard development tree of the SBML ode Solver API ... The changes I would be going to make are going to include: editing src/Makefile.am adding src/varySettings.c adding src/sbmlsolver/varySettings.h editing Makefile.am <http://makefile.am/> in directory example. and adding examples/Sensitivitytest.c examples/DesignPointExample.c I kept all the functions which I would like to have added to SBML_Solver in varySettings.c and varySettings.h. However, I do patch many of the existing structures in the lib e.g. SBML_ODESOLVER_API Variable_t * OdeModel_getVariable( odeModel_t * odemodel , double value, char * parameterStr , char * reactionStr ); SBML_ODESOLVER_API Variable_t * VariableIndex_getVariable( variableIndex_t * vi, double value, char *parameterStr , char *reactionStr); SBML_ODESOLVER_API void Variable_free( Variable_t *variable ); SBML_ODESOLVER_API int IntegratorInstance_setDesignPoint(integratorInstance_t * integratorInstance, DesignPoint_t * designpoint); SBML_ODESOLVER_API Variable_t * Variable_create( double value, char *parameterStr , char *reactionStr); SBML_ODESOLVER_API int Model_change(Model_t *model, /*SBML level 2! See example*/ DesignPoint_t *dp); SBML_ODESOLVER_API cvodeResults_t * Model_solve(Model_t * model , cvodeSettings_t *settings); the only new struct I introduced is DesignPoint (ParameterSet migth be a better name). I remember adding varySettings.h and varySettings.c 2006 only to find this files deleted a few weeks later... it might be better if a few people review the code first so that a more persistent change if wished can be made. I attach the files... cheers Eryk On 11/23/06, Rainer Machne <ra...@tb...> wrote: > > Hi Friends, > > here a rough todo list for the next release ... at least some of the > stuff below should be done before the next release. If you have > preferences/opions or want to add things feel free: > > Functionality: > General: > * odeSolverBatch (use Eryk's code) > * assignment rule ordering (also consider DAE systems/IDA solver > extension) > * variable compartments, ODEs in amounts > * online compilation > * exact event detection > -> Rainer and Xtof > > Text-based input files for: > ** reaction network: Vienna Reaction library > ** ODE system: xppaut format > -> Xtof > > Sens. Analysis output: > * Direct Lyapunov Exponent analysis > * Fisher Information Matrix > -> James and Stefan :-) ??? > > Dependencies: > * libSBML 3 > * Sundials 2.3.0 > -> Rainer and Xtof > > Pending: > * Test suite ?? > ** Functionality > ** Performance > > Configure: > * malloc.h > * -R/-rpath switch > * general refactoring!! > -> Rainer and Xtof > > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share > your > opinions on IT & business topics through brief surveys - and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > sbmlsolver-devel mailing list > sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbmlsolver-devel > |
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From: Rainer M. <ra...@tb...> - 2007-01-30 15:22:00
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Hi, to adapt function naming, the function CvodeSettings_setSteadyState has been renamed to CvodeSettings_setHaltOnSteadyState Also the function IntegratorInstance_checkSteadyState will NOT issue a warning message upon detection anymore (only if called iternally with above option set to true, i.e. when the integrator will stop upon detection). Thus this function can be called by any application to check for steady state during integration. The threshold for steady state detection can be set via CvodeSettings_setSteadyStateThreshold since recently upon user request. Rainer ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV _______________________________________________ sbmlsolver-discuss mailing list sbm...@li... https://lists.sourceforge.net/lists/listinfo/sbmlsolver-discuss |
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From: Rainer M. <ra...@tb...> - 2007-01-29 19:34:40
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Dear Liu Zhicong, First I must say that unfortunately Andrew, our only Windows developer, is currently occupied in other projects. Personally I can not interpret your error messages. I will try to contact Andrew about it and hope that he has some idea. In the meantime I will try my best to help you out: Could you give some details on which functions of SOSlib you are using? (Maybe you could also try to use the sourceforge CVS version of SOSlib and see whether your error still occurs - some bugs have been fixed there, see bug list at sourceforge). However, due to above situation, the windows directories are probably be up-to-date, in case you use this.) In principle it is quite easy to run multiple integrations based on the same input model. You can create as many integrator instance as your system can manage, based on one ode model structure. SOSlib will actually handle memory errors and report according errors via its error management system and just return NULL instead of a new integrator Instance if the system is out of memory. See the examples directory e.g. the file ChangingIntegratorInstance.c (executable changeIntInst if you use the Makefile in this directory, don't know how that works on Windows) to learn about usage of SOSlib at the level of odeModel_t and integratorInstance_t. Using several integratorInstance_t instances created from one odeModel_t should be no problem and work without any memory loss. Did this help you? I am very sorry that we currently have no good support for Windows users. We would appreciate any contributions from this side. In general it would be great to get some feedback on problems and experiences you had with using SOSlib under Windows! Rainer liu zhicong wrote: > I use sbmlsovler library in mutil-thread application(this is a parameter scan > application).I use mutil-thread to scan difference parameter range and then i > get an exception (siginfo: ExceptionCode=0xc0000005, reading address > 0x0bbd4000). > SBML_odeSolver.dll is load at: > 0x0b660000 - 0x0b679000 D:\WINDOWS\SBML_odeSolver.dll > > Registers: > EAX=0x0bbcd090, EBX=0x0b0d0da0, ECX=0x0bbb4378, EDX=0x00003f91 > ESP=0x0b6ffb04, EBP=0x0b6ffb38, ESI=0x0b6ffb30, EDI=0x00000000 > EIP=0x1000142b, EFLAGS=0x00010246 > > Top of Stack: (sp=0x0b6ffb04) > 0x0b6ffb04: 00c810fb 0b0d0e60 0b6ffb4c 0bbcd090 > 0x0b6ffb14: 00000000 00003f91 0bbcd090 02af2aa0 > 0x0b6ffb24: 00000000 0bbcd090 00b2e720 00000001 > 0x0b6ffb34: 038d37b8 0b6ffbc8 00ccf3a4 00003f91 > 0x0b6ffb44: 0bbcd090 00000000 038d37b8 0b6ffbb4 > 0x0b6ffb54: 6d7ace4f 6d8065e8 6d6eaf79 0b6ffbc0 > 0x0b6ffb64: 0b6ffbc4 6d71a0bf 0b0d0da0 00000006 > 0x0b6ffb74: 00000008 00b345c0 02afb9e8 02afb9e8 > > My OS info: > > OS: Windows XP Build 2600 Service Pack 2 > > CPU:total 1 family 47, cmov, cx8, fxsr, mmx, sse, sse2 > > Memory: 4k page, physical 2096624k(1210096k free), swap 2988112k(2303676k > free) > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveys - and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > > > ------------------------------------------------------------------------ > > _______________________________________________ > sbmlsolver-discuss mailing list > sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbmlsolver-discuss > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveys - and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > > > ------------------------------------------------------------------------ > > _______________________________________________ > sbmlsolver-devel mailing list > sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbmlsolver-devel |
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From: Rainer M. <ra...@tb...> - 2007-01-29 16:33:44
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Hi Eryk, W Eryk Wolski wrote: > Hi... > > It might be that I have asked this question a few months ago on this > list but can not recall the answer... > > My question is with regard to: > > integratorInstance->data ->nsens > integratorInstance->data->neq > integratorInstance->data->sensitivity > where data is cvodeData. > > The model I have 5 global parameters > and 8 (outputs) equations, than: > > neq == 8 True > nsens == 5 False nsens is 6.... what the 6 th sensitivity stands for? The 6th sensitivity is probably the compartment, which is treated as a constant parameter in the odeModel. Have you noticed that you can now set the parameters for sensitivity analysis? Use CvodeSettings_setSensParams(cvodeSettings_t *, char **sensIDs, int nsens); to pass a list to cvodeSettings_t, where sensIDs is an array of strings containing the SBML IDs of the parameters to which you want to calculate sensitivities and nsens is the size of this array. Unfortunately, there is no other way to avoid calculating sensitivities for compartments. This is always included in the default sens.analysis, as on the ODE level we do not distinguish between compartments and other model parameters anymore. > and the dimension of > integratorInstance->data->sensitivity > is neq x nsens > > and are the rows 2-6 or the 1-5 are those i am looking for? On the level of the integratorInstance you can get the name of the parameter via char* IntegratorInstance_getSensVariableName(integratorInstance_t *engine, int i) where 0 <= i < nsens. On the level of SBMLResults you can use char *SBMLResults_getSensParam(SBMLResults_t *res, int i) where again 0 <= i < nsens. You can get nsens with SBMLResults_getNumSens(SBMLResults_t *res) ODEModel_getNsens(odeModel_t *); For the default case nsens = nconst. For the non-default case the application has set nsens itself via above function. I just realized that above functions are named differently and that CvodeSettings and IntegratorInstance are missing the Nsens function. These should be added to the API! For now I have added a general comment on refactoring, coordinating and streamlining API functions for all our structures (odeModel, integratorInstance, cvodeSettings) to the list at http://www.tbi.univie.ac.at/wiki/index.php/SOSlibDevel#API_reorganization Rainer > > > Eryk > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveys - and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > > > ------------------------------------------------------------------------ > > _______________________________________________ > sbmlsolver-devel mailing list > sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbmlsolver-devel |
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From: W E. W. <wew...@gm...> - 2007-01-29 16:09:57
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Hi... It might be that I have asked this question a few months ago on this list but can not recall the answer... My question is with regard to: integratorInstance->data ->nsens integratorInstance->data->neq integratorInstance->data->sensitivity where data is cvodeData. The model I have 5 global parameters and 8 (outputs) equations, than: neq == 8 True nsens == 5 False nsens is 6.... what the 6 th sensitivity stands for? and the dimension of integratorInstance->data->sensitivity is neq x nsens and are the rows 2-6 or the 1-5 are those i am looking for? Eryk |
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From: Rainer M. <ra...@tb...> - 2007-01-29 15:14:59
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W Eryk Wolski wrote: > Hi, > > If I change a parameter value using : > IntegratorInstance_setVariable > > does > IntegratorInstance_reset > restores the originial parameter values? Currently yes. You should call IntegratorInstance_reset FIRST and THEN do the IntegratorInstance_setVariableValue Rainer > cheers > Eryk > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveys - and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > > > ------------------------------------------------------------------------ > > _______________________________________________ > sbmlsolver-devel mailing list > sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbmlsolver-devel |
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From: W E. W. <wew...@gm...> - 2007-01-29 11:43:46
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Hi, If I change a parameter value using : IntegratorInstance_setVariable does IntegratorInstance_reset restores the originial parameter values? cheers Eryk |
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From: liu z. <wat...@gm...> - 2007-01-29 04:44:52
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------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV |
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From: Rainer M. <ra...@tb...> - 2007-01-26 11:38:46
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Hi, Thorsten Lenser has found a small memory leak. It was due to the code made during the SBML forum meeting (SBML-independent use of the solver starting from ODEs, via ODEModel_createFromODEs) and should now be fixed. In CVS. Please update. Rainer ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV _______________________________________________ sbmlsolver-discuss mailing list sbm...@li... https://lists.sourceforge.net/lists/listinfo/sbmlsolver-discuss |
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From: Rainer M. <ra...@tb...> - 2007-01-25 16:32:12
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I wrote: > It uses functions defined in the rootFinder.c file in the src directory. The KINSOL interface file in source directory is called nullSolver.c, not rootFinder.c R ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV _______________________________________________ sbmlsolver-discuss mailing list sbm...@li... https://lists.sourceforge.net/lists/listinfo/sbmlsolver-discuss |
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From: Rainer M. <ra...@tb...> - 2007-01-25 12:39:34
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Thorsten Lenser wrote: > Unfortunately, steady state > detection is quite provisional in the odeSolver, especially since one cannot > specify the threshold at which a steady state is reached. This one was easy and I just commited the new option to CVS. From a C program: CvodeSettings_setSteadyStateTreshold(set, 1e-6); Command-line: odeSolver model.xml --time 1e4 -s --threshold 1e-6 Note that the threshold is used to compare with the current mean value + standard deviation of all ODEs, between all "printsteps". Rainer ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV _______________________________________________ sbmlsolver-discuss mailing list sbm...@li... https://lists.sourceforge.net/lists/listinfo/sbmlsolver-discuss |
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From: Rainer M. <ra...@tb...> - 2007-01-25 11:55:33
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Hi Thorsten, Thorsten Lenser wrote: > Hello everyone, > > I am using the odeSolver in an evolutionary algorithm that evolves SBML > models. Many of the tasks that I want my networks to perform rely on some > forms of switching between steady-states. Unfortunately, steady state > detection is quite provisional in the odeSolver, especially since one cannot > specify the threshold at which a steady state is reached. Are there any plans > to improve this for the next release? It would be easy to provide an optional threshold for steady state detection! Thanks for the suggestion, I will definitely include this option and will let you know as soon as it is in the CVS. (BTW, I would currently suggest using the CVS version. It is quite stable and has a lot of improvements and bug fixes and might even be a bit faster). We keep looking for a general and global solver that could calculate all steady states but have no concrete plans, currently. There exists some test code interfacing SUNDIALS KINSOL, which could detect local steady states, close to the initial conditions. It actually works but not very well. If you are interested in that, you could check out latest version from sourceforge CVS and take a look at the file findRoot.c in the examples folder. You could manually include this example program in the Makefile.am (before running configure) or compile it by hand. Only use it with SBML level 2 (otherwise it segfaults as it doesn't do the internal conversion). It uses functions defined in the rootFinder.c file in the src directory. Maybe a better usage of KINSOL could provide a better functionality to detect steady states without integrating or during integrating. The provisional way of detecting steady states during integration might however still be faster and really find the steady state of an integration (and not a close steady state that can't be reached with the set initial conditions). But I have never gone into the details of KINSOL. > Apart from that, thanks for providing this great tool! Very welcome. Thanks for using it and for the compliments :-) Rainer ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV _______________________________________________ sbmlsolver-discuss mailing list sbm...@li... https://lists.sourceforge.net/lists/listinfo/sbmlsolver-discuss |
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From: Thorsten L. <thl...@mi...> - 2007-01-25 11:34:21
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Hello everyone, I am using the odeSolver in an evolutionary algorithm that evolves SBML models. Many of the tasks that I want my networks to perform rely on some forms of switching between steady-states. Unfortunately, steady state detection is quite provisional in the odeSolver, especially since one cannot specify the threshold at which a steady state is reached. Are there any plans to improve this for the next release? Apart from that, thanks for providing this great tool! Kind regards, Thorsten -- Thorsten Lenser Bio Systems Analysis Group Institute of Computer Science Friedrich-Schiller-University Jena 07743 Jena, Germany Office: Ernst-Abbe-Platz 2, Room 3422 Phone: +49 (0)3641-9-46463 Fax: +49 (0)3641-9-46302 ------------------------------------------------------------------------- Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT & business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV _______________________________________________ sbmlsolver-discuss mailing list sbm...@li... https://lists.sourceforge.net/lists/listinfo/sbmlsolver-discuss |
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From: Rainer M. <ra...@tb...> - 2006-11-24 14:00:02
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Hi, sorry, we had commited malfunctional configure scripts yesterday. should be OK now. if you had updated yesterday, please update now again. Thanks Rainer |
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