my installation journey

[zwep]

Hi,

I have installed (and uninstalled) JEMRIS quite some time now. This time I faced a couple of problems that I just figured out. I want to summarize them here for anyone else that is going to try and install this in the future.

After installing the dependencies, I use the following commands to build JEMRIS

cd jemris

mkdir build

cd build

cmake ..

make

sudo make install

However, running cmake .. gave me some errors. Initially I had problems with not being able to find my hdf5 install:

Make Error at /usr/share/cmake-3.16/Modules/FindPackageHandleStandardArgs.cmake:146 (message):
  Could NOT find HDF5 (missing: HDF5_LIBRARIES HDF5_INCLUDE_DIRS C CXX)
  (found version "")
Call Stack (most recent call first):
  /usr/share/cmake-3.16/Modules/FindPackageHandleStandardArgs.cmake:393 (_FPHSA_FAILURE_MESSAGE)
  /usr/share/cmake-3.16/Modules/FindHDF5.cmake:929 (find_package_handle_standard_args)
  CMakeLists.txt:106 (find_package)

-- Configuring incomplete, errors occurred!

After installing `sudo apt-get install libhdf5-dev`, everything worked fine.

Then GiNaC gave issues when running `cmake ..`:

~/Downloads/jemris/src/ginac_functions.h: In function ‘void compile_ex(const GiNaC::ex&, const GiNaC::symbol&, const GiNaC::symbol&, const GiNaC::symbol&, const GiNaC::symbol&, double (*&)(double, double, double, double), std::string)’:
~/Downloads/jemris/src/ginac_functions.h:393:70: error: no matching function for call to ‘GiNaC::container<std::__cxx11::list>::container(const GiNaC::relational, const GiNaC::relational, const GiNaC::relational, const GiNaC::relational)’
  393 |  ex expr_with_xyzg = expr.subs(lst(sym1==x, sym2==y, sym3==z, sym4==g));
      |                                                                      ^
In file included from /usr/local/include/ginac/lst.h:26,
                 from /usr/local/include/ginac/normal.h:29,
                 from /usr/local/include/ginac/ginac.h:31,
                 from ~/Downloads/jemris/src/Attribute.h:46,
                 from ~/Downloads/jemris/src/Attribute.cpp:31:

This was, by surprised, solved by replacing
    ex expr_with_xyzg = expr.subs(lst(sym1==x, sym2==y, sym3==z, sym4==g));
To
    ex expr_with_xyzg = expr.subs(lst());

In the file `~/jemris/src/ginac_functions.h`

Then, after running `cmake ..` again, a known error occured:

~/Downloads/jemris/src/Bloch_McConnell_CV_Model.cpp:274:39: error: ‘CV_FUNCTIONAL’ was not declared in this scope
  274 |    m_cvode_mem = CVodeCreate(CV_ADAMS,CV_FUNCTIONAL);

This was fixed by replacing

    m_cvode_mem = CVodeCreate (CV_ADAMS, CV_FUNCTIONAL);

to

    m_cvode_mem = CVodeCreate (CV_ADAMS);

in the files

    ~/jemris/src/Bloch_CV_Model.cpp

    ~/jemris/src/Bloch_McConnell_CV_Model.cpp

I hope this might help someone (or maybe myself) in the future. If the creators have any comments on my change I am glad to hear them

Greetings

[zwep]

haha okay the make/make install worked.

But I just tried a simple simulation on the command line and got

[CVODE ERROR]  cvNlsInit
  Setting linear solver solve function failed


[CVODE ERROR]  cvInitialSetup
  The nonlinear solver's init routine failed.

so..... need to fix that later