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sbmlsolver-discuss
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From: Takeshi A. <ta...@fi...> - 2011-04-26 07:54:16
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Hi all, I would like to use SBML_odeSolver with the latest version of SUNDIALS i.e. 2.4.0: https://computation.llnl.gov/casc/sundials/ At a glance some changes to odeSolver's code will be necessary for that. Please tell me if you have any plan or consideration for the upgrade. Cheers, -- Takeshi Abe |
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From: Takeshi A. <ta...@fi...> - 2011-05-06 06:31:01
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Hi all, So here is a proposed patch for upgrading to SUNDIALS 2.4.0. Note that it is still rough but compiles successfully with CVS trunk. During making changes I found a few points to be checked carefully: * many API functions and typedefs of CVODE/CVODES are renamed. * the `cvadj_mem' field is no longer needed for adjoint case; instead, we must pass `cvode_mem' and `which' to the related functions. * new wrappers, like CVodeGetB/CVodeGetQuadB/CVodeGetSens, answer the next time of the integration as an output parameter. I think we can use it to replace the original code to compute the next time, but still undone. Any comments and/or suggestions would be appreciated. Cheers, -- Takeshi Abe On Tue, 26 Apr 2011 16:54:03 +0900 (JST), Takeshi Abe <ta...@fi...> wrote: > Hi all, > > I would like to use SBML_odeSolver with the latest version of SUNDIALS > i.e. 2.4.0: https://computation.llnl.gov/casc/sundials/ > At a glance some changes to odeSolver's code will be necessary for that. > Please tell me if you have any plan or consideration for the upgrade. |
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From: Rainer M. <ra...@tb...> - 2011-05-06 12:46:38
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Hi Takeshi, great work! Christoph and me will probably move the current source to github next week, and I will test your patch here then. If all is OK, you could directly submit yourself to github, OK? Rainer On 05/06/2011 08:30 AM, Takeshi Abe wrote: > Hi all, > > So here is a proposed patch for upgrading to SUNDIALS 2.4.0. > Note that it is still rough but compiles successfully with CVS trunk. > > During making changes I found a few points to be checked carefully: > * many API functions and typedefs of CVODE/CVODES are renamed. > * the `cvadj_mem' field is no longer needed for adjoint case; instead, > we must pass `cvode_mem' and `which' to the related functions. > * new wrappers, like CVodeGetB/CVodeGetQuadB/CVodeGetSens, answer the > next time of the integration as an output parameter. I think we can > use it to replace the original code to compute the next time, but > still undone. > > Any comments and/or suggestions would be appreciated. > > Cheers, > -- Takeshi Abe > > On Tue, 26 Apr 2011 16:54:03 +0900 (JST), Takeshi Abe <ta...@fi...> wrote: >> Hi all, >> >> I would like to use SBML_odeSolver with the latest version of SUNDIALS >> i.e. 2.4.0: https://computation.llnl.gov/casc/sundials/ >> At a glance some changes to odeSolver's code will be necessary for that. >> Please tell me if you have any plan or consideration for the upgrade. >> >> >> ------------------------------------------------------------------------------ >> WhatsUp Gold - Download Free Network Management Software >> The most intuitive, comprehensive, and cost-effective network >> management toolset available today. Delivers lowest initial >> acquisition cost and overall TCO of any competing solution. >> http://p.sf.net/sfu/whatsupgold-sd >> >> >> _______________________________________________ >> sbmlsolver-discuss mailing list >> sbm...@li... >> https://lists.sourceforge.net/lists/listinfo/sbmlsolver-discuss |
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From: Takeshi A. <ta...@fi...> - 2011-05-09 01:00:08
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Hi Rainer, Thanks for your reply! On Fri, 06 May 2011 14:46:22 +0200, Rainer Machne <ra...@tb...> wrote: > great work! Christoph and me will probably move the current source to > github next week, and I will test your patch here then. If all is OK, > you could directly submit yourself to github, OK? Yes, no problem. Cheers, -- Takeshi Abe |
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From: Takeshi A. <ta...@fi...> - 2011-06-01 00:47:35
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Hi all, On Mon, 09 May 2011 09:59:59 +0900 (JST), Takeshi Abe <ta...@fi...> wrote: > Thanks for your reply! > > On Fri, 06 May 2011 14:46:22 +0200, Rainer Machne <ra...@tb...> wrote: >> great work! Christoph and me will probably move the current source to >> github next week, and I will test your patch here then. If all is OK, >> you could directly submit yourself to github, OK? > Yes, no problem. Sorry for my impatience, but feel free to ask me if you have some problems. Cheers, -- Takeshi Abe |
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From: Rainer M. <ra...@tb...> - 2011-06-16 14:42:08
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Hi, Finally I have time to start moving to github. I am following the instructions here, since it seems to keep the full CVS history: http://ghantoos.org/2010/11/11/migrating-sourceforge-cvs-source-repository-to-github/ Is that a good idea? Any better instructions? Currently, I am stuck at the third series of steps already. My git says: git cvsimport -p x -v -d /home/mescalin/raim/programs/sbmlsolver/ sbmlsolver git: 'cvsimport' is not a git command. See 'git --help'. Any ideas? Rainer On 06/01/2011 02:47 AM, Takeshi Abe wrote: > Hi all, > > On Mon, 09 May 2011 09:59:59 +0900 (JST), Takeshi Abe <ta...@fi...> wrote: >> Thanks for your reply! >> >> On Fri, 06 May 2011 14:46:22 +0200, Rainer Machne <ra...@tb...> wrote: >>> great work! Christoph and me will probably move the current source to >>> github next week, and I will test your patch here then. If all is OK, >>> you could directly submit yourself to github, OK? >> Yes, no problem. > Sorry for my impatience, but feel free to ask me if you have some problems. > > Cheers, > -- Takeshi Abe > > ------------------------------------------------------------------------------ > Simplify data backup and recovery for your virtual environment with vRanger. > Installation's a snap, and flexible recovery options mean your data is safe, > secure and there when you need it. Data protection magic? > Nope - It's vRanger. Get your free trial download today. > http://p.sf.net/sfu/quest-sfdev2dev > _______________________________________________ > sbmlsolver-discuss mailing list > sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbmlsolver-discuss > |
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From: Takeshi A. <ta...@fi...> - 2011-06-17 01:38:05
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Hi Rainer, On Thu, 16 Jun 2011 16:05:56 +0200, Rainer Machne <ra...@tb...> wrote: > Finally I have time to start moving to github. > > I am following the instructions here, since it seems to keep the full > CVS history: > http://ghantoos.org/2010/11/11/migrating-sourceforge-cvs-source-repository-to-github/ > > Is that a good idea? Any better instructions? I think it is a good way to go. > > Currently, I am stuck at the third series of steps already. My git says: > git cvsimport -p x -v -d /home/mescalin/raim/programs/sbmlsolver/ sbmlsolver > > git: 'cvsimport' is not a git command. See 'git --help'. The message suggests that your git does not have the cvsimport module, which is separate from git-core. Presuming that your system is a Linux distribution, in case of Fedora, the meta package "git-all" provides it: https://admin.fedoraproject.org/pkgdb/acls/name/git If you use Debian or Ubuntu, just install git-cvs: http://packages.debian.org/git-cvs HTH. Cheers, -- Takeshi Abe |
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From: Rainer M. <ra...@tb...> - 2011-06-17 14:14:40
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If that was it already, it was really simple. Now, I guess I have to learn how to work with github too :) https://github.com/raim/SBML_odeSolver Thanks for your help, Takeshi! Now, should we move to Sundials 2.4.0 already? cheers, Rainer On 06/17/2011 03:37 AM, Takeshi Abe wrote: > Hi Rainer, > > On Thu, 16 Jun 2011 16:05:56 +0200, Rainer Machne <ra...@tb...> wrote: >> Finally I have time to start moving to github. >> >> I am following the instructions here, since it seems to keep the full >> CVS history: >> http://ghantoos.org/2010/11/11/migrating-sourceforge-cvs-source-repository-to-github/ >> >> Is that a good idea? Any better instructions? > I think it is a good way to go. > >> >> Currently, I am stuck at the third series of steps already. My git says: >> git cvsimport -p x -v -d /home/mescalin/raim/programs/sbmlsolver/ sbmlsolver >> >> git: 'cvsimport' is not a git command. See 'git --help'. > The message suggests that your git does not have the cvsimport module, which is > separate from git-core. > Presuming that your system is a Linux distribution, in case of Fedora, the meta > package "git-all" provides it: > https://admin.fedoraproject.org/pkgdb/acls/name/git > If you use Debian or Ubuntu, just install git-cvs: > http://packages.debian.org/git-cvs > HTH. > > Cheers, > -- Takeshi Abe > |
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From: Takeshi A. <ta...@fi...> - 2011-06-17 15:29:13
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Hi Rainer, On Fri, 17 Jun 2011 16:14:28 +0200, Rainer Machne <ra...@tb...> wrote: > > If that was it already, it was really simple. Now, I guess I have to > learn how to work with github too :) > > https://github.com/raim/SBML_odeSolver Great! Thanks for your work. > > Thanks for your help, Takeshi! Now, should we move to Sundials 2.4.0 > already? We can, and there seems some options to do that; pushing the patch into the master branch is simple but may break its stability, or is it reasonable to prepare a dedicated branch for SUNDIALS 2.4.0? Cheers, -- Takeshi Abe |
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From: Rainer M. <ra...@tb...> - 2011-06-17 15:33:50
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On 06/17/2011 05:29 PM, Takeshi Abe wrote: > Hi Rainer, > > On Fri, 17 Jun 2011 16:14:28 +0200, Rainer Machne <ra...@tb...> wrote: >> >> If that was it already, it was really simple. Now, I guess I have to >> learn how to work with github too :) >> >> https://github.com/raim/SBML_odeSolver > Great! Thanks for your work. > >> >> Thanks for your help, Takeshi! Now, should we move to Sundials 2.4.0 >> already? > We can, and there seems some options to do that; pushing the patch into > the master branch is simple but may break its stability, or is it > reasonable to prepare a dedicated branch for SUNDIALS 2.4.0? It should be simple to fuse it back into the master, right? I guess, starting a branch would also be a good exercise for me (and others) to learn how this works? I already added you as a collaborator. So if possible, please go ahead and start a Sundials 2.4.0 branch. Or I can do that next week. Rainer |
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From: Takeshi A. <ta...@fi...> - 2011-06-17 15:54:37
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On Fri, 17 Jun 2011 17:33:41 +0200, Rainer Machne <ra...@tb...> wrote: >> We can, and there seems some options to do that; pushing the patch into >> the master branch is simple but may break its stability, or is it >> reasonable to prepare a dedicated branch for SUNDIALS 2.4.0? > > It should be simple to fuse it back into the master, right? I guess, > starting a branch would also be a good exercise for me (and others) to > learn how this works? Yes, branching and merging back turns easy in case of git. > > I already added you as a collaborator. So if possible, please go ahead > and start a Sundials 2.4.0 branch. Or I can do that next week. Done, we now have the sundials-2.4.0 branch extended by the patch. Cheers, -- Takeshi Abe |
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From: Lukas E. <lu...@eb...> - 2011-06-16 19:30:19
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Hi Rainer Hurray - soslib is alive and kicking! Did you install git-cvsimport? On ubunutu I had to install the git-cvs and cvsps packages to make git understand. Oh - and I will hopefully come to the TBI tomorrow - are you around noonish? All the best Lukas On 16/06/11 15:05, Rainer Machne wrote: > Hi, > > Finally I have time to start moving to github. > > I am following the instructions here, since it seems to keep the full > CVS history: > http://ghantoos.org/2010/11/11/migrating-sourceforge-cvs-source-repository-to-github/ > > Is that a good idea? Any better instructions? > > > Currently, I am stuck at the third series of steps already. My git says: > git cvsimport -p x -v -d /home/mescalin/raim/programs/sbmlsolver/ sbmlsolver > > git: 'cvsimport' is not a git command. See 'git --help'. > > Any ideas? > > Rainer > > On 06/01/2011 02:47 AM, Takeshi Abe wrote: >> Hi all, >> >> On Mon, 09 May 2011 09:59:59 +0900 (JST), Takeshi Abe<ta...@fi...> wrote: >>> Thanks for your reply! >>> >>> On Fri, 06 May 2011 14:46:22 +0200, Rainer Machne<ra...@tb...> wrote: >>>> great work! Christoph and me will probably move the current source to >>>> github next week, and I will test your patch here then. If all is OK, >>>> you could directly submit yourself to github, OK? >>> Yes, no problem. >> Sorry for my impatience, but feel free to ask me if you have some problems. >> >> Cheers, >> -- Takeshi Abe >> >> ------------------------------------------------------------------------------ >> Simplify data backup and recovery for your virtual environment with vRanger. >> Installation's a snap, and flexible recovery options mean your data is safe, >> secure and there when you need it. Data protection magic? >> Nope - It's vRanger. Get your free trial download today. >> http://p.sf.net/sfu/quest-sfdev2dev >> _______________________________________________ >> sbmlsolver-discuss mailing list >> sbm...@li... >> https://lists.sourceforge.net/lists/listinfo/sbmlsolver-discuss >> > > > ------------------------------------------------------------------------------ > EditLive Enterprise is the world's most technically advanced content > authoring tool. Experience the power of Track Changes, Inline Image > Editing and ensure content is compliant with Accessibility Checking. > http://p.sf.net/sfu/ephox-dev2dev > _______________________________________________ > sbmlsolver-discuss mailing list > sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbmlsolver-discuss -- Lukas Endler Comp. Neurobiol. Group EMBL/EBI (http://www.ebi.ac.uk/) email: lu...@eb... mobile: +447500547176 skype: lukasendler |
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