Compilation error for /src/ginac_functions.h

[maxime-z]

Trying to build and install the latest commit from jemris master branch (also v2.8.3) on ubuntu 20.04 x86_64, with GiNaC of release 1.8.1. And I encountered an error when building /src/Attribute.cpp and /src/ginac_functions.h with error info as following:

It seems to be caused by the update of GiNaC interface.

Thanks in advance.

[ 1%] Building CXX object src/CMakeFiles/core.dir/Attribute.cpp.o
In file included from /home/mri/jemris/src/Attribute.cpp:34:
/home/mri/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)':
/home/mri/jemris/src/ginac_functions.h:393:70: error: no matching function for call to 'GiNaC::containerstd::__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 /home/mri/jemris/src/Attribute.h:46,
from /home/mri/jemris/src/Attribute.cpp:31:
/usr/local/include/ginac/container.h:108:2: note: candidate: 'GiNaC::container< >::container(std::initializer_listGiNaC::ex) [with C = std::__cxx11::list]'
108 | container(std::initializer_list il)
| ^~~~~~~~~
/usr/local/include/ginac/container.h:108:2: note: candidate expects 1 argument, 4 provided
/usr/local/include/ginac/container.h:102:2: note: candidate: 'GiNaC::container< >::container(std::vectorGiNaC::ex::const_iterator, std::vectorGiNaC::ex::const_iterator) [with C = std::__cxx11::list; std::vectorGiNaC::ex::const_iterator = __gnu_cxx::__normal_iterator<const GiNaC::ex, std::vectorGiNaC::ex >]'
102 | container(exvector::const_iterator b, exvector::const_iterator e)
| ^~~~~~~~~
/usr/local/include/ginac/container.h:102:2: note: candidate expects 2 arguments, 4 provided
/usr/local/include/ginac/container.h:96:11: note: candidate: 'GiNaC::container< >::container(GiNaC::container< >::STLT&&) [with C = std::__cxx11::list; GiNaC::container< >::STLT = std::__cxx11::list<GiNaC::ex, std::allocatorGiNaC::ex >]'
96 | explicit container(STLT && v)
| ^~~~~~~~~
/usr/local/include/ginac/container.h:96:11: note: candidate expects 1 argument, 4 provided
/usr/local/include/ginac/container.h:90:2: note: candidate: 'GiNaC::container< >::container(const STLT&) [with C = std::__cxx11::list; GiNaC::container< >::STLT = std::__cxx11::list<GiNaC::ex, std::allocatorGiNaC::ex >]'
90 | container(STLT const & s)
| ^~~~~~~~~
/usr/local/include/ginac/container.h:90:2: note: candidate expects 1 argument, 4 provided
/usr/local/include/ginac/container.h:254:1: note: candidate: 'GiNaC::container< >::container() [with C = std::__cxx11::list]'
254 | container::container()
| ^~~~~~~~~~~~
/usr/local/include/ginac/container.h:254:1: note: candidate expects 0 arguments, 4 provided
/usr/local/include/ginac/container.h:73:7: note: candidate: 'GiNaC::containerstd::__cxx11::list::container(const GiNaC::containerstd::__cxx11::list&)'
73 | class container : public basic, public container_storage {
| ^~~~~~~~~
/usr/local/include/ginac/container.h:73:7: note: candidate expects 1 argument, 4 provided
/usr/local/include/ginac/container.h:73:7: note: candidate: 'GiNaC::containerstd::__cxx11::list::container(GiNaC::containerstd::__cxx11::list&&)'
/usr/local/include/ginac/container.h:73:7: note: candidate expects 1 argument, 4 provided
make[2]: *** [src/CMakeFiles/core.dir/build.make:128: src/CMakeFiles/core.dir/Attribute.cpp.o] Error 1
make[1]: *** [CMakeFiles/Makefile2:202: src/CMakeFiles/core.dir/all] Error 2
make: *** [Makefile:163: all] Error 2

[pkhateri]

I got the same problem.
Were you able to solve it?
Or is there anybody here to help on that? I would really appreciate it.
Thanks.

[cncastillo]

This problem has been fixed by #13. Thanks, @pkhateri!

Having said that, I had other problems installing it on Ubuntu 21.10. I detailed them below with my solutions:

1) CVODE

My version of CVODE (Sundials) gave an error as CV_FUNCTIONAL was not being found. The reason is a breaking change made in CVODE 4.0, removing that variable completely. In the JEMRIS' Google group they suggest removing that variable in the code before compiling, but this made my simulations to be incorrect. To fix it, I just removed libsundials-dev and compiled sundials-2.7.0. After installing that version of sundials I could compile JEMRIS with no problems.

2) CONDA (for the new BART Recon)

For some reason, my conda environment was not being detected by MATLAB. I had to add this to my startup.m:

% update PATH
[~,path]=system('echo -n $PATH');
[~,user]=system('echo -n $USER');
setenv('PATH',path+":/home/"+user+"/miniconda3/bin") %Conda environment
clear result user

3) LD_LIBRARY_PATH

As I use ZSH, both JEMRIS_sim.m and JEMRIS_seq.m were not working as expected. Had to change the LD_LIBRARY_PATH on those files to:

'LD_LIBRARY_PATH="/usr/local/lib"; '

4) Docker

Last but not least, as docker is being run without sudo this can generate an error in Linux:

docker: Got permission denied while trying to connect to the Docker daemon socket at unix:///var/run/docker.sock: Post http://%2Fvar%2Frun%2Fdocker.sock/v1.24/containers/create: dial unix /var/run/docker.sock: connect: permission denied.
See 'docker run --help'.

To fix it I had to follow the instructions in the Docker website. Regardless, this was not permanent. So I just use

sudo chmod 666 /var/run/docker.sock

before using the JEMRIS reconstruction.

Hope this is helpful to someone, Cheers! 😄