raim / sbml_odesolver Goto Github PK

a C library for symbolic and numerical analysis of a system of ordinary differential equations (ODEs) derived from a chemical reaction network encoded in the Systems Biology Markup Language (SBML)

Home Page: http://www.tbi.univie.ac.at/~raim/odeSolver/

License: GNU Lesser General Public License v2.1

Perl 0.36% C++ 1.36% C 87.11% Shell 7.35% Makefile 2.08% Fortran 1.05% Awk 0.01% M4 0.70%

sbml_odesolver's Issues

Unable to build

Hi,
I tried to build SBML_odeSolver under Debian and was running into the same error as it was reported on the sundials list:

In file included from sbmlsolver/processAST.h:44:0,
from arithmeticCompiler.c:46:
./sbmlsolver/odeModel.h:171:3: error: unknown type name ‘CVDenseJacFn’
CVDenseJacFn compiledCVODEJacobianFunction;
^~~~~~~~~~~~
In file included from sbmlsolver/processAST.h:44:0,
from compiler.c:44:
./sbmlsolver/odeModel.h:171:3: error: unknown type name ‘CVDenseJacFn’
CVDenseJacFn compiledCVODEJacobianFunction;
^~~~~~~~~~~~
./sbmlsolver/odeModel.h:185:3: error: unknown type name ‘CVDenseJacFnB’
CVDenseJacFnB compiledCVODEAdjointJacobianFunction;
^~~~~~~~~~~~~
./sbmlsolver/odeModel.h:187:3: error: unknown type name ‘CVDenseJacFnB’
CVDenseJacFnB current_AdjJAC;
^~~~~~~~~~~~~

Any clue how to solve this?
Kind regards, Andreas.

Please add release tags

Hi,
I would consider maintaining this project as Debian package. However, I have no sensible clue what version number to use and I also have no good way to realise new versions that are intended for user consumption. It would be nice if you could add tags to specify releases which would fix this.
Kind regards, Andreas.

configure issues with recent libsbml and sundials versions

I try to install SBML_odeSolver but have issues at the configure step with recent versions of libsbml (5.17.0) and sundials (3.2.0).

About sundials, I managed to pass the configure step by tweaking the configure script a bit. Then the make command fails with this error message:

In file included from ./sbmlsolver/cvodeData.h:51:0,
                 from sbmlsolver/arithmeticCompiler.h:51,
                 from arithmeticCompiler.c:43:
./sbmlsolver/odeModel.h:49:33: fatal error: cvodes/cvodes_dense.h: No such file or directory
 #include <cvodes/cvodes_dense.h>

It looks cvodes/cvodes_dense.h is no longer available in sundials 3.2.0.

About libsbml, headers and libraries are found but the code run to test libsbml is maybe out-dated and does not work with libsbml 5.17.0

checking for SBML Library headers... yes
checking for SBML Library... yes
checking for correct functioning of SBML... no:
                   CPPFLAGS=-I/usr/include 
                   LDFLAGS=-Wl,-rpath,/usr/lib64 -L/usr/lib64 
                   LIBS=-lsbml -lxml2 -ldl

Also I have a general problem with most of my libraries being in /usr/lib64, not in /usr/lib.
The configure step try to guess the library path sometimes wrongly.

Thanks

Nix

With a lot of help, I managed to get this to build using nix: https://nixos.org. It built for me on macOS using

nix-build --pure sundialsTest.nix -I nixpkgs=https://github.com/nixos/nixpkgs-channels/archive/nixos-unstable-small.tar.gz

I hope to get round to making it part of nixpkgs but just in case I don't, I am leaving the derivation here:

{ pkgs ? import <nixpkgs>
  { overlays = [(self: super: {



sundials = super.sundials.overrideAttrs (o: rec {

    configureFlags = "--enable-shared";
    version = "2.7.0";

    # override sundials version because SBML_odeSolver is unhappy with
    # > 2.7.0
    src = pkgs.fetchurl {
      url = "https://computation.llnl.gov/projects/${o.pname}/download/${o.pname}-${version}.tar.gz";
      sha256 = "01513g0j7nr3rh7hqjld6mw0mcx5j9z9y87bwjc16w2x2z3wm7yk";
    };
});


})]; }}:

with pkgs;

let

  libSBML = stdenv.mkDerivation rec {
  src = pkgs.fetchurl {
    url = https://sourceforge.net/projects/sbml/files/libsbml/5.17.0/stable/libSBML-5.17.0-core-src.tar.gz;
    sha256 = "153l67jb1q888y91kb439bwy6d3vsz4aqgpbcqhskmg842bx4axb";
  };
  version = "5.17.0";
  name = "libSBML-${version}";
  buildInputs = [ libxml2 ];
  NIX_CFLAGS_COMPILE = "-I${libxml2.dev}/include/libxml2";

  # these files are refering to /bin/pwd which does not exist in a nix
  # context
  patchPhase = ''
    sed -i 's/\/bin\/pwd/pwd/' config/makefile-common-vars.mk.in
    sed -i 's/\/bin\/pwd/pwd/' src/bindings/matlab/Makefile.in
    sed -i 's/\/bin\/pwd/pwd/' src/bindings/matlab/test/Makefile.in
  '';
};

in

{
  SBML_odeSolver = stdenv.mkDerivation rec {
    src = pkgs.fetchgit {
      url = git://github.com/raim/SBML_odeSolver;
      rev = "0a1aa2becadceb95b2d61a9fdafa9c3cc620748f";
      sha256 = "0mp7nik6hxifxkic8c6pi6kqnnd5vv9s2h06n1z0f8prg6cfg1ly";
    };
    version = "1.9.0.1";
    name = "SBML_odeSolver-${version}";
    buildInputs = [ sundials libSBML pkgconfig autoreconfHook libxml2 ];

    configureFlags = ["--with-libsbml=${libSBML}"
                      "--with-sundials=${sundials}"];
    doCheck = false;

    # fprintf takes a const char * as first argument, or a format
    # string
    patchPhase = ''
      sed -i 's/fprintf(stderr, errors);/fprintf(stderr, "%s", errors);/' examples/ChangingParameterIntegrator.c
      '';

  };
}

CVODES error with -t flag on sundials-2.4.0 branch

I'm interested in using SBML_odeSolver to compute sensitivities to help with optimisation and parameter searching. I've managed to get sundials and SBML_odeSolver compiled (which was a bit of a challenge on Scientific Linux 7), but now have the following error:

odeSolver tutorial/Goodwin_SomoS.xml -t

[CVODES ERROR]  CVode
  No integration tolerances for sensitivity variables have been specified.

      Error -22 ???
    Warning 120000  Integration not successful. Results are not complete.
#t dx1/ddefault dx1/ddummy2 dx1/ddummy3 dx1/ddummy1 dx1/dsa3_degraded dx1/dsa2_degraded dx1/dsa1_degraded dx1/dsa13_degraded dx1/dFGF8 dx1/dsa15_degraded dx1/dgene_fgf8 dx1/dp dx1/dk1 dx1/dk2 dx1/dk3 dx1/dk4 dx1/dk9 dx1/dk5 dx1/dk6 dx1/dk7 dx1/dk8 dx1/dk10 dx1/ddfgf8 dx1/dmama dX3/ddefault dX3/ddummy2 dX3/ddummy3 dX3/ddummy1 dX3/dsa3_degraded dX3/dsa2_degraded dX3/dsa1_degraded dX3/dsa13_degraded dX3/dFGF8 dX3/dsa15_degraded dX3/dgene_fgf8 dX3/dp dX3/dk1 dX3/dk2 dX3/dk3 dX3/dk4 dX3/dk9 dX3/dk5 dX3/dk6 dX3/dk7 dX3/dk8 dX3/dk10 dX3/ddfgf8 dX3/dmama dX2/ddefault dX2/ddummy2 dX2/ddummy3 dX2/ddummy1 dX2/dsa3_degraded dX2/dsa2_degraded dX2/dsa1_degraded dX2/dsa13_degraded dX2/dFGF8 dX2/dsa15_degraded dX2/dgene_fgf8 dX2/dp dX2/dk1 dX2/dk2 dX2/dk3 dX2/dk4 dX2/dk9 dX2/dk5 dX2/dk6 dX2/dk7 dX2/dk8 dX2/dk10 dX2/ddfgf8 dX2/dmama dX2bis/ddefault dX2bis/ddummy2 dX2bis/ddummy3 dX2bis/ddummy1 dX2bis/dsa3_degraded dX2bis/dsa2_degraded dX2bis/dsa1_degraded dX2bis/dsa13_degraded dX2bis/dFGF8 dX2bis/dsa15_degraded dX2bis/dgene_fgf8 dX2bis/dp dX2bis/dk1 dX2bis/dk2 dX2bis/dk3 dX2bis/dk4 dX2bis/dk9 dX2bis/dk5 dX2bis/dk6 dX2bis/dk7 dX2bis/dk8 dX2bis/dk10 dX2bis/ddfgf8 dX2bis/dmama dfgf8/ddefault dfgf8/ddummy2 dfgf8/ddummy3 dfgf8/ddummy1 dfgf8/dsa3_degraded dfgf8/dsa2_degraded dfgf8/dsa1_degraded dfgf8/dsa13_degraded dfgf8/dFGF8 dfgf8/dsa15_degraded dfgf8/dgene_fgf8 dfgf8/dp dfgf8/dk1 dfgf8/dk2 dfgf8/dk3 dfgf8/dk4 dfgf8/dk9 dfgf8/dk5 dfgf8/dk6 dfgf8/dk7 dfgf8/dk8 dfgf8/dk10 dfgf8/ddfgf8 dfgf8/dmama 
##SENSITIVITIES
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 

##SENSITIVITIES
#t dx1/ddefault dx1/ddummy2 dx1/ddummy3 dx1/ddummy1 dx1/dsa3_degraded dx1/dsa2_degraded dx1/dsa1_degraded dx1/dsa13_degraded dx1/dFGF8 dx1/dsa15_degraded dx1/dgene_fgf8 dx1/dp dx1/dk1 dx1/dk2 dx1/dk3 dx1/dk4 dx1/dk9 dx1/dk5 dx1/dk6 dx1/dk7 dx1/dk8 dx1/dk10 dx1/ddfgf8 dx1/dmama dX3/ddefault dX3/ddummy2 dX3/ddummy3 dX3/ddummy1 dX3/dsa3_degraded dX3/dsa2_degraded dX3/dsa1_degraded dX3/dsa13_degraded dX3/dFGF8 dX3/dsa15_degraded dX3/dgene_fgf8 dX3/dp dX3/dk1 dX3/dk2 dX3/dk3 dX3/dk4 dX3/dk9 dX3/dk5 dX3/dk6 dX3/dk7 dX3/dk8 dX3/dk10 dX3/ddfgf8 dX3/dmama dX2/ddefault dX2/ddummy2 dX2/ddummy3 dX2/ddummy1 dX2/dsa3_degraded dX2/dsa2_degraded dX2/dsa1_degraded dX2/dsa13_degraded dX2/dFGF8 dX2/dsa15_degraded dX2/dgene_fgf8 dX2/dp dX2/dk1 dX2/dk2 dX2/dk3 dX2/dk4 dX2/dk9 dX2/dk5 dX2/dk6 dX2/dk7 dX2/dk8 dX2/dk10 dX2/ddfgf8 dX2/dmama dX2bis/ddefault dX2bis/ddummy2 dX2bis/ddummy3 dX2bis/ddummy1 dX2bis/dsa3_degraded dX2bis/dsa2_degraded dX2bis/dsa1_degraded dX2bis/dsa13_degraded dX2bis/dFGF8 dX2bis/dsa15_degraded dX2bis/dgene_fgf8 dX2bis/dp dX2bis/dk1 dX2bis/dk2 dX2bis/dk3 dX2bis/dk4 dX2bis/dk9 dX2bis/dk5 dX2bis/dk6 dX2bis/dk7 dX2bis/dk8 dX2bis/dk10 dX2bis/ddfgf8 dX2bis/dmama dfgf8/ddefault dfgf8/ddummy2 dfgf8/ddummy3 dfgf8/ddummy1 dfgf8/dsa3_degraded dfgf8/dsa2_degraded dfgf8/dsa1_degraded dfgf8/dsa13_degraded dfgf8/dFGF8 dfgf8/dsa15_degraded dfgf8/dgene_fgf8 dfgf8/dp dfgf8/dk1 dfgf8/dk2 dfgf8/dk3 dfgf8/dk4 dfgf8/dk9 dfgf8/dk5 dfgf8/dk6 dfgf8/dk7 dfgf8/dk8 dfgf8/dk10 dfgf8/ddfgf8 dfgf8/dmama

raim / sbml_odesolver Goto Github PK

sbml_odesolver's Issues

Unable to build

Please add release tags

configure issues with recent libsbml and sundials versions

Nix

CVODES error with -t flag on sundials-2.4.0 branch

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