search

raim / SBML_odeSolver

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)
http://www.tbi.univie.ac.at/~raim/odeSolver/
GNU Lesser General Public License v2.1
21 stars 9 forks source link

configure issues with recent libsbml and sundials versions #5

Open smoretti opened 5 years ago

smoretti commented 5 years ago

Hi

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

raim commented 5 years ago

Thanks for reporting. The current SOSlib works only with Sundials 2.4.0 and libSBML 3.4.1. You could install those locally and use --with-sundials and --with-libsbml flags for configure. The lib64 is actually searched in the configure scripts, and should be found, if libs with extensions .so, .sl or .dylib are present (see file config/sbml.m4. Perhaps try the --with flags?

smoretti commented 5 years ago

Thanks for your feedback. Do you plan to update SOSlib to sundials 3 and libSBML 5?