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From: SourceForge.net <no...@so...> - 2007-10-03 19:01:11
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Support Requests item #1807116, was opened at 2007-10-03 15:01 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=1807116&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: No Submitted By: Eva (eva_1983) Assigned to: Nobody/Anonymous (nobody) Summary: Installing on Mac OSX 10.4.10 Initial Comment: Hi all, I am trying to install SBML_odeSolver-1.6.0 on a Mac OSX 10.4.10. I already installed the libraries: Sundials 2.1.1 in: /Users/eva/Desktop/Code/sundials/lib and libSBML 2.3.5 in: /Users/eva/Desktop/LibSBML I tried to configure the SBML ODE Solver by: ./configure --with-libsbml="/Users/eva/Desktop/LibSBML" --with-sundials="/Users/eva/Desktop/Code/sundials/lib" But it does not find my SBML Library. Here is the output: checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking whether make sets $(MAKE)... yes checking build system type... powerpc-apple-darwin8.10.0 checking host system type... powerpc-apple-darwin8.10.0 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... swig checking for perl... /usr/bin/perl checking for SBML Library Version... expr: syntax error expr: syntax error expr: syntax error ./configure: line 4175: test: -eq: unary operator expected configure: found SBML Library Version checking correct functioning of SBML... no: CFLAGS=-g -O2 -I/Users/eva/Desktop/LibSBML/include -I/Users/eva/Desktop/LibSBML/include/sbml LDFLAGS= -L/Users/eva/Desktop/LibSBML/lib LIBS= -lxerces-c -lsbml configure: error: Can not link to SBML Library: Please, make sure to use libSBML version >= 2.3.2 Someone can please help me? Thanks, Eva. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744812&aid=1807116&group_id=139893 |
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From: SourceForge.net <no...@so...> - 2007-10-03 18:57:24
|
Bugs item #1807109, was opened at 2007-10-03 14:50 Message generated for change (Settings changed) made by eva_1983 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744811&aid=1807109&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: None Group: None Status: Open Resolution: None >Priority: 9 Private: No Submitted By: Eva (eva_1983) Assigned to: Nobody/Anonymous (nobody) Summary: Prolem Installing SBML Ode Solver on Mac Initial Comment: Hi all, I am trying to install SBML_odeSolver-1.6.0 on a Mac OSX 10.4.10. I already installed the libraries: Sundials 2.1.1 in: /Users/eva/Desktop/Code/sundials/lib and libSBML 2.3.5 in: /Users/eva/Desktop/LibSBML I tried to configure the SBML ODE Solver by: ./configure --with-libsbml="/Users/eva/Desktop/LibSBML" --with-sundials="/Users/eva/Desktop/Code/sundials/lib" But it does not find my SBML Library. Here is the output: checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking whether make sets $(MAKE)... yes checking build system type... powerpc-apple-darwin8.10.0 checking host system type... powerpc-apple-darwin8.10.0 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... swig checking for perl... /usr/bin/perl checking for SBML Library Version... expr: syntax error expr: syntax error expr: syntax error ./configure: line 4175: test: -eq: unary operator expected configure: found SBML Library Version checking correct functioning of SBML... no: CFLAGS=-g -O2 -I/Users/eva/Desktop/LibSBML/include -I/Users/eva/Desktop/LibSBML/include/sbml LDFLAGS= -L/Users/eva/Desktop/LibSBML/lib LIBS= -lxerces-c -lsbml configure: error: Can not link to SBML Library: Please, make sure to use libSBML version >= 2.3.2 Someone can please help me? Thanks, Eva. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744811&aid=1807109&group_id=139893 |
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From: SourceForge.net <no...@so...> - 2007-10-03 18:56:23
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Bugs item #1807109, was opened at 2007-10-03 14:50 Message generated for change (Settings changed) made by eva_1983 You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744811&aid=1807109&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: None Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Eva (eva_1983) Assigned to: Nobody/Anonymous (nobody) >Summary: Prolem Installing SBML Ode Solver on Mac Initial Comment: Hi all, I am trying to install SBML_odeSolver-1.6.0 on a Mac OSX 10.4.10. I already installed the libraries: Sundials 2.1.1 in: /Users/eva/Desktop/Code/sundials/lib and libSBML 2.3.5 in: /Users/eva/Desktop/LibSBML I tried to configure the SBML ODE Solver by: ./configure --with-libsbml="/Users/eva/Desktop/LibSBML" --with-sundials="/Users/eva/Desktop/Code/sundials/lib" But it does not find my SBML Library. Here is the output: checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking whether make sets $(MAKE)... yes checking build system type... powerpc-apple-darwin8.10.0 checking host system type... powerpc-apple-darwin8.10.0 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... swig checking for perl... /usr/bin/perl checking for SBML Library Version... expr: syntax error expr: syntax error expr: syntax error ./configure: line 4175: test: -eq: unary operator expected configure: found SBML Library Version checking correct functioning of SBML... no: CFLAGS=-g -O2 -I/Users/eva/Desktop/LibSBML/include -I/Users/eva/Desktop/LibSBML/include/sbml LDFLAGS= -L/Users/eva/Desktop/LibSBML/lib LIBS= -lxerces-c -lsbml configure: error: Can not link to SBML Library: Please, make sure to use libSBML version >= 2.3.2 Someone can please help me? Thanks, Eva. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744811&aid=1807109&group_id=139893 |
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From: SourceForge.net <no...@so...> - 2007-10-03 18:50:29
|
Bugs item #1807109, was opened at 2007-10-03 14:50 Message generated for change (Tracker Item Submitted) made by Item Submitter You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744811&aid=1807109&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: None Group: None Status: Open Resolution: None Priority: 5 Private: No Submitted By: Eva (eva_1983) Assigned to: Nobody/Anonymous (nobody) Summary: Prolem Installing on Mac Initial Comment: Hi all, I am trying to install SBML_odeSolver-1.6.0 on a Mac OSX 10.4.10. I already installed the libraries: Sundials 2.1.1 in: /Users/eva/Desktop/Code/sundials/lib and libSBML 2.3.5 in: /Users/eva/Desktop/LibSBML I tried to configure the SBML ODE Solver by: ./configure --with-libsbml="/Users/eva/Desktop/LibSBML" --with-sundials="/Users/eva/Desktop/Code/sundials/lib" But it does not find my SBML Library. Here is the output: checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for gawk... no checking for mawk... no checking for nawk... no checking for awk... awk checking whether make sets $(MAKE)... yes checking build system type... powerpc-apple-darwin8.10.0 checking host system type... powerpc-apple-darwin8.10.0 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... swig checking for perl... /usr/bin/perl checking for SBML Library Version... expr: syntax error expr: syntax error expr: syntax error ./configure: line 4175: test: -eq: unary operator expected configure: found SBML Library Version checking correct functioning of SBML... no: CFLAGS=-g -O2 -I/Users/eva/Desktop/LibSBML/include -I/Users/eva/Desktop/LibSBML/include/sbml LDFLAGS= -L/Users/eva/Desktop/LibSBML/lib LIBS= -lxerces-c -lsbml configure: error: Can not link to SBML Library: Please, make sure to use libSBML version >= 2.3.2 Someone can please help me? Thanks, Eva. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744811&aid=1807109&group_id=139893 |
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From: SourceForge.net <no...@so...> - 2007-06-13 12:33:07
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Feature Requests item #1736446, was opened at 2007-06-13 05:33 Message generated for change (Tracker Item Submitted) made by Item Submitter You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744814&aid=1736446&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: None Group: Next Release (example) Status: Open Priority: 5 Private: No Submitted By: Nobody/Anonymous (nobody) Assigned to: Nobody/Anonymous (nobody) Summary: The SBML events Initial Comment: Dear Sir/Madam, First of all, thank you very much for providing this fantastic world-class library to us. It really helped our research a lot. Secondly, our research group has tried to simulate a SBML model with SBML events by using SOSlib. Unfortunately, it seems that the current version (SBML_odeSolver-1.6.0) doesn’t support SBML events. I’ve gone through your website and known that your next version (Version 1.7 The Linz Release) will include the SBML events. May I ask what the estimated releasing date for The Linz Release? Since our research group is keen to use the SBML events function, is any possible that our group can get the pre-release version? Thank you very much and best regards, Xuan Liu ----------------------------------------------------------- Xuan Liu Bioinformatics Research Centre A416, Davidson Building University of Glasgow G12 8QQ, Scotland, UK email: xl...@dc... Tel: +44 (0) 141 330 8752 Fax: +44 (0) 141 330 3690 ----------------------------------------------------------- ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744814&aid=1736446&group_id=139893 |
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From: Rainer M. <ra...@tb...> - 2007-06-11 11:06:11
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Hi All, James and Christoph have changed the SUNDIALS interface to use the latest version of SUNDIALS. We will commit that to CVS within the next 3 days! So please, update/commit today if you want to keep using the old sundials for a while. Rainer |
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From: SourceForge.net <no...@so...> - 2007-06-11 08:11:16
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Feature Requests item #1732300, was opened at 2007-06-06 21:03 Message generated for change (Comment added) made by raimc You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744814&aid=1732300&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: None Group: None Status: Open Priority: 5 Private: No Submitted By: Nobody/Anonymous (nobody) Assigned to: Nobody/Anonymous (nobody) Summary: libsbml 3 Initial Comment: Do you have any plans to use libsbml3 any time soon? Our sbml involves constructs from level2, version2 that requires libsbml3, but tools we have written for parameter optimization, etc, use SOSLib. ---------------------------------------------------------------------- >Comment By: Rainer Machne (raimc) Date: 2007-06-11 10:11 Message: Logged In: YES user_id=1124477 Originator: NO Yes, we are currently (around sbml hackathon) estimating the effort to switch to libsbml3, then decide if we want to support only version 3 or also older versions, and - depending on required effort - create and submit the new code will to the CVS project soon - maybe even within the next few days, and within the official next release during summer or fall this year. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744814&aid=1732300&group_id=139893 |
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From: SourceForge.net <no...@so...> - 2007-06-06 19:03:14
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Feature Requests item #1732300, was opened at 2007-06-06 12:03 Message generated for change (Tracker Item Submitted) made by Item Submitter You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744814&aid=1732300&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: None Group: None Status: Open Priority: 5 Private: No Submitted By: Nobody/Anonymous (nobody) Assigned to: Nobody/Anonymous (nobody) Summary: libsbml 3 Initial Comment: Do you have any plans to use libsbml3 any time soon? Our sbml involves constructs from level2, version2 that requires libsbml3, but tools we have written for parameter optimization, etc, use SOSLib. ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=744814&aid=1732300&group_id=139893 |
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From: Rainer M. <ra...@tb...> - 2007-05-15 19:04:17
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Hi, now also the forward sensitivity function can be compiled. In CVS now. Performance for forward sensitivity calculation is roughly 8-fold! However, there is a problem with using multiple code instances in TCC - they can be used but cause a segmentation fault when the second instance is freed. We need two code instances because sensitivity function can change between subsequent solver runs, but the ODE and Jacobi stay the same. So until I get a response by the TCC people, whether this will be solved soon or whether anyone has a patch, I will leave it like this to avoid unnecessary TCC allocations/compilations. If TCC can't be patched soon, we can either a) have an additional sensitivity compilation option, so the leak can be avoided but still compilation for ODE/Jacobi functions used or b) also re-compile the ODE/Jacobi function for each new sensitivity run So please watch out: there are memory leaks because currently, the sensitivity code is not freed after usage! Rainer Rainer Machne wrote: > Hi Everyone, > > Great news: > > as recently several people started to use SOSlib on supercomputing > clusters, we were motivated to go into the code again and optimize. > > Christoph and me went through Andrew Finney's old code for online > compilation of the right-hand side functions passed to CVODES (including > command-line calls etc.). > > So I just managed to get the same code running under Linux using the > Tiny C Compiler as a library and the very cool TCC online compilation: > > tcc_compile_string(TCCState *s, char *sourceCode); > > > So far it works only for the one bottle-neck function that evaluates > ODEs (and not e.g. for jacobi evaluation or sensitivity stuff). > > But that already brings significant performance gains! E.g. for the > example model MAPK.xml, integrating to time 100000 in 1000 steps: > > without compilation: 2.13 seconds > with tcc compilation: 0.53 seconds > > A strange effect is that at higher error tolerances and long integration > times the results start to differ. We need to check where the different > round-offs etc. are made. At lower tolerances the results are exactly > the same. > > > The new code is in CVS now. Linking to TCC is optional, so everything > else should still work as before. > > Caveat: TCC so far only works on 32-bit architecture, and thus all > libraries (sundials, xerces/expat, libsbml and soslib) must also be > compiled and run on 32-bit machines. > > So we can only hope that TCC will soon be available for x86_64, > otherwise we could still implement command-line calls, like for the > Windows version (where back then tcc didn't work as a library). > (TCC can be run on 64-bit but only with -m32 options and asfaik it's not > possible to have a mixed architecture code in on tool). > > > TCC is available from http://fabrice.bellard.free.fr/tcc/ > > However, I used Robert Landley's fork because I couldn't compile the > original, and he seems to be the only one still working on it: > > http://landley.net/code/tinycc > > It should work with both ... in principle. > > > So if that all works (with all rhs functions), I think there are not > much more possibilities to get faster, i.e. to make better use of > SUNDIALS from arbitrary ODE models. > > We can only include the usual reaction network analysis, i.e. mass > conservation analysis, to get rid of unnecessary ODEs etc. However, I > guess, that won't bring very much gain, because the lost equation is > similar to a still existing one which still needs to be solved by > CVODES. Maybe "fast reaction analysis" would have some potential? > > So, I think we are close to becoming as fast as possible. > > Well, there'd probably still be possibilities with model-specific > "preconditioning" and such stuff about which I don't know much. Feel > free to propose your ideas :) > > Rainer > > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by DB2 Express > Download DB2 Express C - the FREE version of DB2 express and take > control of your XML. No limits. Just data. Click to get it now. > http://sourceforge.net/powerbar/db2/ > _______________________________________________ > sbmlsolver-discuss mailing list > sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbmlsolver-discuss |
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From: Rainer M. <ra...@tb...> - 2007-05-10 21:55:47
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Hi Everyone, Great news: as recently several people started to use SOSlib on supercomputing clusters, we were motivated to go into the code again and optimize. Christoph and me went through Andrew Finney's old code for online compilation of the right-hand side functions passed to CVODES (including command-line calls etc.). So I just managed to get the same code running under Linux using the Tiny C Compiler as a library and the very cool TCC online compilation: tcc_compile_string(TCCState *s, char *sourceCode); So far it works only for the one bottle-neck function that evaluates ODEs (and not e.g. for jacobi evaluation or sensitivity stuff). But that already brings significant performance gains! E.g. for the example model MAPK.xml, integrating to time 100000 in 1000 steps: without compilation: 2.13 seconds with tcc compilation: 0.53 seconds A strange effect is that at higher error tolerances and long integration times the results start to differ. We need to check where the different round-offs etc. are made. At lower tolerances the results are exactly the same. The new code is in CVS now. Linking to TCC is optional, so everything else should still work as before. Caveat: TCC so far only works on 32-bit architecture, and thus all libraries (sundials, xerces/expat, libsbml and soslib) must also be compiled and run on 32-bit machines. So we can only hope that TCC will soon be available for x86_64, otherwise we could still implement command-line calls, like for the Windows version (where back then tcc didn't work as a library). (TCC can be run on 64-bit but only with -m32 options and asfaik it's not possible to have a mixed architecture code in on tool). TCC is available from http://fabrice.bellard.free.fr/tcc/ However, I used Robert Landley's fork because I couldn't compile the original, and he seems to be the only one still working on it: http://landley.net/code/tinycc It should work with both ... in principle. So if that all works (with all rhs functions), I think there are not much more possibilities to get faster, i.e. to make better use of SUNDIALS from arbitrary ODE models. We can only include the usual reaction network analysis, i.e. mass conservation analysis, to get rid of unnecessary ODEs etc. However, I guess, that won't bring very much gain, because the lost equation is similar to a still existing one which still needs to be solved by CVODES. Maybe "fast reaction analysis" would have some potential? So, I think we are close to becoming as fast as possible. Well, there'd probably still be possibilities with model-specific "preconditioning" and such stuff about which I don't know much. Feel free to propose your ideas :) Rainer |
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From: Rainer M. <ra...@tb...> - 2007-05-09 15:49:22
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Hi Everyone, A related problem to the one from the previous email (species in substance units): Currently SOSlib can not handle variable compartments (just as e.g. copasi and MathSBML). For this case ALL ODEs need to be formulated in substance rather than substance/volume units, and species in concentration units will need additional assignment rules to map their values from the ODE variables, and this will probably involve significant changes to the code. To have ODEs in substance units we only need to leave out the division by the compartment, as the kinetic laws in SBML are already in substance/time units. Instead of (current) ODEs: 1) for X in substance units: dX/dt = stoichiometry * kineticLaw(X) 2) for X in substance/volume: dX/dt = stoichiometry * kineticLaw(X) / volume we will have: 1) for X in substance units, as above: dX/dt = stoichiometry * kineticLaw(X) 2) for X in substance/volume: dX_amount /dt = stoichiometry * kineticLaw(X) X = X_amount / volume where X_amount is an internal variable we need to define and X is defined by a new internal assignment rule. Does anyone see any problems with above approach? Rainer |
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From: Rainer M. <ra...@tb...> - 2007-05-09 15:46:31
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Hi Everyone, SOSlib code starts to live again a bit. We have just recently found out that we didn't account for species that are defined with HasOnlySubstanceUnits == true, or which live in a compartment with SpatialDimension == 0. In both cases, the units of the species in all equations of the model are in substance instead of concentration (substance/volume) units. ODEs for such species change from: dX/dt = stoichiometry * kineticLaw(X) / volume to: dX/dt = stoichiometry * kineticLaw(X) While I have never seen such a model, it is possible in SBML. It should work now with SOSlib but I couldn't test it, because I don't know any model which has such species. If anyone knows about such models (doesn't have to be in SBML), please send me a link or reference, so I can test it. We still solve 100 out of 113 semantic test suite models correctly, so nothing should have changed for usual models. The new code is at sourceforge CVS now. Rainer |
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From: Christoph F. <xt...@tb...> - 2007-04-27 10:22:15
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hi john, the Perl bindings of SOSlib are not functional at the moment. the idea for the bindings is to generate them in a semi automatic fashion using Swig (http://www.swig.org/), which allows to generate bindings for many different languages like Java, Python, Perl, ... with one interface file. (libsbml is a very good example which follows this strategy) the problem with Swig is that it does not support all the features equally well for the various languages. While Java and Python are equally well supported by Swig, this is not the case for Perl. another basic question is if only the high level API of SOSlib should be accessible via the bindings, or if every function which is in the SOSlib should have be bindings. our time frame to fix the Perl bindings is around June to July, and we will definitely use Swig for that. so if you want to develop Java bindings I would suggest to use Swig for that purpose. it would be also very kind if you could contribute the Java bindings to SOSlib or parts of them once you have developed them. if you need any help concerning binding generation using Swig, please don't hesitate to contact me. =;) xtof -- Christoph Flamm Institut fuer Theoretische Chemie | email: xt...@tb... Universitaet Wien | phone: ++43-1-4277-527-39 Waehringerstrasse 17/3/308 | fax: ++43-1-4277-527-93 A-1090 Wien, Austria | www: http://www.tbi.univie.ac.at/~xtof John Legato writes: > Hi, > > We would like to leverage the capabilities of SOSlib from a Java > application we are developing called QBT (Quantitative Biology Tool). > Do Java bindings for SOSlib exist? How were the Perl bindings generated? > Would it be reasonable for us to take a similar approach using Java? > > Thanks > > John |
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From: Rainer M. <ra...@tb...> - 2007-04-16 17:42:37
|
Hi there,
as no one of you has subscribed to the official discuss list, I am
forced to bug you here: can anyone remember the configure bug reported
below?
Somehow I remember that I also once had this error, but can't remember
how it was solved.
Akira suggested (on the other list) that old version of some programs
(expr and test) are the cause.
Any other ideas? Christoph, do you know which lines to delete from
configure to avoid the libSBML version test to avoid this problem, in
case Phillip doesn't find new version of expr and test for his platform
(btw, what is Falcon??)
Rainer
-------- Original Message --------
Subject: [SOSlib-discuss] Difficulty compiling
Date: Mon, 16 Apr 2007 09:15:52 -0400
From: Phillip Tabor <pt...@gm...>
To: sbm...@li...
Hello,
while attempting to compile the sbml ode solver library on our machines,
the following error crops up:
Jim, Phil,
This is the error message I'm getting when building SBML ODE on Falcon.
I rebuilt everything with the GNU compilers just to be sure we were on
the same footing with everything:
checking for SBML Library Version... expr: syntax error
expr: syntax error
expr: syntax error
./configure: line 4175: test: -eq: unary operator expected
configure: found SBML Library Version
checking correct functioning of SBML... no:
CFLAGS=-g -O2 -I/app/moes/platform/opteron.hp/include
-I/app/moes/platform/opteron.hp/include/sbml
LDFLAGS= -Wl,-rpath,/app/moes/platform/opteron.hp/lib
-L/app/moes/platform/opteron.hp/lib
LIBS= -lxerces-c -lsbml
configure: error: Can not link to SBML Library:
Please, make sure to use libSBML version >= 2.3.2
I've already sent the config.log. I'm pretty certain it's a configure
file issue, but I haven't been able to track it down just yet.
Has anyone encountered anything similar? Is this perhaps user error (our
tech guy is working on it for me)?
|
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From: Rainer M. <ra...@tb...> - 2007-04-12 09:53:18
|
Hi, Some tiny bit of life starts at the public SOSlib discussion email list. (However, it's still less then the SPAM level there.) Some time ago, I have removed everyone who is also on the SOSlib-devel (this) list from SOSlib-discuss and instead forwarded all emails to here. However, this is painful, because I always have to accept these forwarded messages at the SOSlib-devel web interface. For both reasons, I have just removed SOSlib-devel from the SOSlib-discuss subscriber list. It would be great if you people here (developers) could also subscribe to SOSlib-discuss yourself, and take part in this public list, maybe help users solve there problems or start discussions about further development and requirements. PLEASE, subscribe here: https://lists.sourceforge.net/lists/listinfo/sbmlsolver-discuss THANKS, Rainer |
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From: <sbm...@li...> - 2007-04-12 09:41:21
|
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From: Rainer M. <ra...@tb...> - 2007-04-12 09:39:32
|
Hi Roy and Phillip, You might even get better performance, if you use the integration routines at a finer level via the odeModel and integratorInstance interface functions. At this level, you can create both the internal odeModel (derived from the SBML input) and the SUNDIALS integrator instance only once, and run as many integrations as you like. The function IntegratorInstance_setVariableValue allows you to set any parameters or variables in between (also during) the integration runs. This level would save you a lot of memory allocation and general performance. You can use Andrew Finney's ParameterScanner.c program in the example folder of the SOSlib distribution as a template for your own program, or just use it as a commandline tool if you are happy with its output. It's usage is described at http://www.tbi.univie.ac.at/~raim/odeSolver/doc/app.html#param If you are interested, I can help you changing the output of ParameterScanner.c to your requirements. Currently it only gives the results of the chosen variable at some specified end-time of integration, and that in gnuplot format. Would you need the whole time-courses? Also, if you want to analyze local parameters of kinetic laws, you will need to "globalize" these parameters before calling any SOSlib functions, because SOSlib only treats global parameters as constants of the ODE model, while locals are replaced during ODE construction. However, we also have such a globalizeParemter function, internally in release 1.6.0, but that can easily be "externalized" so you can use it in your application (or just copy/paste it :) ). For the next release we plan much better support for such parameter scans also for the main commandline tool, as we realize that this is the most widely used application for SOSlib. Rainer Roy Wollman wrote: > Hi Phillip, > > Did you consider using it as a library instead of using the command line > utility? > An example of a library usage that changes a parameter can be found: > > http://www.csc.fi/english/research/sciences/bioscience/programs/sysbio/parameterChange.c > > It will be almost the exact thing to change initial conditions, without > parsing the xml file. > > Roy > > > Phillip Tabor wrote: >> Hello, >> >> I am attempting to use the odeSolver commandline tool and I'd like to >> know if there is a way to input the initial rate constants as an >> array. In other words, does the program have to parse the .xml file at >> every iteration, or is there a way to override this and simply pass it >> an array of numbers to be assigned as rates to the odes? >> >> I am attempting to use the software to fit kinetic rate constants with >> an evolutionary algorithm. This requires many executions of the >> program, and having to parse the .xml file on each run will add a >> considerable amount of overhead to the execution time. >> >> >> ------------------------------------------------------------------------ >> >> ------------------------------------------------------------------------- >> 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 ------------------------------------------------------------------------- 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: Roy W. <rwo...@uc...> - 2007-04-11 21:09:24
|
Hi Phillip, Did you consider using it as a library instead of using the command line utility? An example of a library usage that changes a parameter can be found: http://www.csc.fi/english/research/sciences/bioscience/programs/sysbio/parameterChange.c It will be almost the exact thing to change initial conditions, without parsing the xml file. Roy Phillip Tabor wrote: > Hello, > > I am attempting to use the odeSolver commandline tool and I'd like to > know if there is a way to input the initial rate constants as an > array. In other words, does the program have to parse the .xml file at > every iteration, or is there a way to override this and simply pass it > an array of numbers to be assigned as rates to the odes? > > I am attempting to use the software to fit kinetic rate constants with > an evolutionary algorithm. This requires many executions of the > program, and having to parse the .xml file on each run will add a > considerable amount of overhead to the execution time. > > > ------------------------------------------------------------------------ > > ------------------------------------------------------------------------- > 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: Phillip T. <pt...@gm...> - 2007-04-11 19:52:19
|
------------------------------------------------------------------------- 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...> - 2007-03-29 10:08:20
|
Will Norman wrote: > Rainer Machne wrote: >> Dear Will, >> >> I guess, you referring to program Sense (Sense.exe in Windows) in the >> example folder. >> >> In that case: yes, you are right. >> >> In the "p" mode you can choose one parameter and will get >> sensitivities to this parameter for one or more chosen variables. >> In the "v" mode you can choose one variable (as above) and will get >> sensitivities of this variable to one ore more chosen parameter.s > > Just to clarify when you say parameter here do you mean the SBML type > Parameter, or in an abstract sense where parameter is just what is > passed to the program (and could be an SBML Parameter or Species). I mean the latter, parameters, or constants, of the derived ODE system, which can be SBML Parameters or Species or Compartments. This is always confusing and it's good that you ask. Maybe we should start to speak of "constants" rather then "parameters" in our tutorials and programs to avoid this confusion: SBML Species, Parameters, Compartments <-> ODE Variables, Constants. Rainer > Thanks once again for the help! > > >> Variables are >> >> * species, if their concentration is defined by reactions or SBML rate >> rules (and not if set set constant or defined by an assignment rule), or >> >> * parameters if defined by a rate rule (and not if constant or defined >> by an assigment rule). >> >> Please note that currently variable compartments are not handled >> correctly!! Thus I left them out in above description. >> >> Ok? >> >> Also note, that it would be very easy to just create your own little C >> program, specific to your requirements. >> >> Using the current CVS version will also improve sensitivity analysis >> significantly! In 1.6.0 sensitivities are calculated w.r.t. all >> constants of the model, while in current CVS version sensitivities are >> calculated only for the chosen constants. However, I haven't adapted >> the example/Sense program to that improvement yet. >> Furthermore current CVS version allows to calculate sensitivities >> w.r.t. to initial conditions of variables. >> >> regards, >> Rainer >> >> >> >> >> >> >> >> >> Will Norman wrote: >>> I am building a web-app that uses the SBML Solver library, and was >>> wondering what the acceptable parameters are for the two modes of >>> sensitivity analysis. >>> >>> Here is what I am thinking, is this correct? >>> >>> For Parameter: >>> >>> Takes in a single parameter (either variable or constant) >>> >>> and one or more variable Species, Parameters or Compartments >>> >>> For Variable: >>> >>> Takes in a single variable Species, Parameter, or Compartment >>> >>> and one or more variable or constant Parameters >>> >>> Thanks for the clarification. >>> >>> >>> >>> >>> ------------------------------------------------------------------------- >>> >>> 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 >> > > > ------------------------------------------------------------------------- > 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: Will N. <jw...@cl...> - 2007-03-29 00:18:04
|
Rainer Machne wrote: > Dear Will, > > I guess, you referring to program Sense (Sense.exe in Windows) in the > example folder. > > In that case: yes, you are right. > > In the "p" mode you can choose one parameter and will get > sensitivities to this parameter for one or more chosen variables. > In the "v" mode you can choose one variable (as above) and will get > sensitivities of this variable to one ore more chosen parameter.s Just to clarify when you say parameter here do you mean the SBML type Parameter, or in an abstract sense where parameter is just what is passed to the program (and could be an SBML Parameter or Species). Thanks once again for the help! > > Variables are > > * species, if their concentration is defined by reactions or SBML rate > rules (and not if set set constant or defined by an assignment rule), or > > * parameters if defined by a rate rule (and not if constant or defined > by an assigment rule). > > Please note that currently variable compartments are not handled > correctly!! Thus I left them out in above description. > > Ok? > > Also note, that it would be very easy to just create your own little C > program, specific to your requirements. > > Using the current CVS version will also improve sensitivity analysis > significantly! In 1.6.0 sensitivities are calculated w.r.t. all > constants of the model, while in current CVS version sensitivities are > calculated only for the chosen constants. However, I haven't adapted > the example/Sense program to that improvement yet. > Furthermore current CVS version allows to calculate sensitivities > w.r.t. to initial conditions of variables. > > regards, > Rainer > > > > > > > > > Will Norman wrote: >> I am building a web-app that uses the SBML Solver library, and was >> wondering what the acceptable parameters are for the two modes of >> sensitivity analysis. >> >> Here is what I am thinking, is this correct? >> >> For Parameter: >> >> Takes in a single parameter (either variable or constant) >> >> and one or more variable Species, Parameters or Compartments >> >> For Variable: >> >> Takes in a single variable Species, Parameter, or Compartment >> >> and one or more variable or constant Parameters >> >> Thanks for the clarification. >> >> >> >> >> ------------------------------------------------------------------------- >> >> 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 > > ------------------------------------------------------------------------- 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...> - 2007-03-28 15:46:09
|
Dear Will, I guess, you referring to program Sense (Sense.exe in Windows) in the example folder. In that case: yes, you are right. In the "p" mode you can choose one parameter and will get sensitivities to this parameter for one or more chosen variables. In the "v" mode you can choose one variable (as above) and will get sensitivities of this variable to one ore more chosen parameter.s Variables are * species, if their concentration is defined by reactions or SBML rate rules (and not if set set constant or defined by an assignment rule), or * parameters if defined by a rate rule (and not if constant or defined by an assigment rule). Please note that currently variable compartments are not handled correctly!! Thus I left them out in above description. Ok? Also note, that it would be very easy to just create your own little C program, specific to your requirements. Using the current CVS version will also improve sensitivity analysis significantly! In 1.6.0 sensitivities are calculated w.r.t. all constants of the model, while in current CVS version sensitivities are calculated only for the chosen constants. However, I haven't adapted the example/Sense program to that improvement yet. Furthermore current CVS version allows to calculate sensitivities w.r.t. to initial conditions of variables. regards, Rainer Will Norman wrote: > I am building a web-app that uses the SBML Solver library, and was > wondering what the acceptable parameters are for the two modes of > sensitivity analysis. > > Here is what I am thinking, is this correct? > > For Parameter: > > Takes in a single parameter (either variable or constant) > > and one or more variable Species, Parameters or Compartments > > For Variable: > > Takes in a single variable Species, Parameter, or Compartment > > and one or more variable or constant Parameters > > Thanks for the clarification. > > > > > ------------------------------------------------------------------------- > 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 ------------------------------------------------------------------------- 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: Will N. <jw...@cl...> - 2007-03-27 21:22:42
|
I am building a web-app that uses the SBML Solver library, and was wondering what the acceptable parameters are for the two modes of sensitivity analysis. Here is what I am thinking, is this correct? For Parameter: Takes in a single parameter (either variable or constant) and one or more variable Species, Parameters or Compartments For Variable: Takes in a single variable Species, Parameter, or Compartment and one or more variable or constant Parameters Thanks for the clarification. ------------------------------------------------------------------------- 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...> - 2007-03-21 17:28:02
|
Dear Eric, I have forwarded your email to the developer email list, as others might be interested or have ideas on your remaining AIX problems. > very strangely, static int memoryExhaustion = 0; in solverError.c is not > initialized on AIX (on Linux it works fine), mhm... strange. Can you (or anyone else) think of a workaround to initialize this global variable to 0? We don't get any warning about this, so it seems to be ISO-C90/ANSI-C compatible. > Also, I found that only the serial versions of Sundials libraries are > used. My aim is now to convert cvodeSolver.c and odeModel.c to use > nvector_parallel.h I also haven't looked at the details of the parallel solvers in SUNDIALS. However, when looking at the examples given by SUNDIALS I remember that I had the impression that it might require to somehow parallelize the ODE system itself! This might be very difficult with our approach of arbitraty ODE models. But maybe I am wrong. It would be great if you could have a look at that! Generally, the SUNDIALS email list is very responsive and helpful. But we should try to find out what we can before contacting them. >if > that is successful, I'll happily share the adaptation with you. That would of course be a great contribution! BTW, we also need to fully implement the online TCC-based compilation of all right-hand-side functions. Andrew had implemented that on Windows and it didn't work out-of-the-box on our Linux systems here. We never had a look at it, but I think it will be probably be rather easy to implement it generally, based on optional SOSlib compilation linking to the TCC library. Rainer Rainer Machne wrote: > > -------- Original Message -------- > Subject: SOSlib progress on AIX / parallel support? > Date: Wed, 21 Mar 2007 16:28:11 -0000 > From: Eric Fernandez <efe...@ph...> > To: Rainer Machne <ra...@tb...> > > Dear Rainer, > > I hope you are well and that you enjoyed your holidays. > > I contacted you a couple of weeks ago about SOSlib that I wanted to > install on an AIX server. I finally managed to do it, thanks to a > debugging session. For some reason, the conversion of models from Level > 1 to Level 2 does not work, because of some issue with libsbml. Also, > very strangely, static int memoryExhaustion = 0; in solverError.c is not > initialized on AIX (on Linux it works fine), although compiled with gcc > 3.3.2, and of course leaded to the software stopping. Maybe a bug in > gcc-3.3.2 ? I had to deactivate the memory checks (I know, it's bad) > meanwhile. > > Also, I found that only the serial versions of Sundials libraries are > used. My aim is now to convert cvodeSolver.c and odeModel.c to use > nvector_parallel.h instead (and doing the adjustments for parallel > processing). I was wondering, have you already done this ? According to > my understanding of SOSlib, this should be possible and should not > interfere with events, as events are tested and triggered after each ODE > solving time step. However I admit I walk in the dark there. Anyway, if > that is successful, I'll happily share the adaptation with you. > > Kind regards, > > Dr Eric Fernandez > Senior Simulation Scientist > Physiomics plc > The Magdalen Centre > The Oxford Science Park > Oxford > OX4 4GA > UK > Tel: +44(0)1865 784986 > > > ------------------------------------------------------------------------- > 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...> - 2007-03-21 17:16:02
|
-------- Original Message -------- Subject: SOSlib progress on AIX / parallel support? Date: Wed, 21 Mar 2007 16:28:11 -0000 From: Eric Fernandez <efe...@ph...> To: Rainer Machne <ra...@tb...> Dear Rainer, I hope you are well and that you enjoyed your holidays. I contacted you a couple of weeks ago about SOSlib that I wanted to install on an AIX server. I finally managed to do it, thanks to a debugging session. For some reason, the conversion of models from Level 1 to Level 2 does not work, because of some issue with libsbml. Also, very strangely, static int memoryExhaustion = 0; in solverError.c is not initialized on AIX (on Linux it works fine), although compiled with gcc 3.3.2, and of course leaded to the software stopping. Maybe a bug in gcc-3.3.2 ? I had to deactivate the memory checks (I know, it's bad) meanwhile. Also, I found that only the serial versions of Sundials libraries are used. My aim is now to convert cvodeSolver.c and odeModel.c to use nvector_parallel.h instead (and doing the adjustments for parallel processing). I was wondering, have you already done this ? According to my understanding of SOSlib, this should be possible and should not interfere with events, as events are tested and triggered after each ODE solving time step. However I admit I walk in the dark there. Anyway, if that is successful, I'll happily share the adaptation with you. Kind regards, Dr Eric Fernandez Senior Simulation Scientist Physiomics plc The Magdalen Centre The Oxford Science Park Oxford OX4 4GA UK Tel: +44(0)1865 784986 |
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