Compilation problem

[lopezmarinn]

I am installing tumorcode on ubuntu 18.10. cmake worked fine, after some minor corrections on the version of the ubuntu in CMakeLists.txt. But with the make part I obtained this error:

vdd@vdd:~/nelia/tumorcode-master/build$ make [ 16%] Built target mwlib [ 48%] Built target common [ 55%] Built target vesselgenlib [ 71%] Built target krebs [ 75%] Built target detailedo2 [ 77%] Linking CXX executable test_cluster_stackoverflow /usr/bin/ld: ../../common/lib/libcommon.a(hdfio.cpp.o): undefined reference to symbol '_ZN3MPI8Datatype4FreeEv' /usr/bin/ld: //usr/lib/x86_64-linux-gnu/libmpi_cxx.so.40: error adding symbols: DSO missing from command line collect2: error: ld returned 1 exit status make[2]: [src/tests/H5/CMakeFiles/test_cluster_stackoverflow.dir/build.make:184: src/tests/H5/test_cluster_stackoverflow] Error 1 make[1]: [CMakeFiles/Makefile2:362: src/tests/H5/CMakeFiles/test_cluster_stackoverflow.dir/all] Error 2 make: *** [Makefile:130: all] Error 2

I got the same error on debian 9.8 (strech) During the make part I modified the hdfio.cpp do to the error:

/home/vdd/nelia/original/tumorcode-master/src/common/hdfio.cpp: At global scope: /home/vdd/nelia/original/tumorcode-master/src/common/hdfio.cpp:1158:19: error: template-id ‘readAttrFromH5’ for ‘void readAttrFromH5(H5::H5Object&, const string&, float&)’ does not match any template declaration template void readAttrFromH5(H5::H5Object &g, const string &name, T &output_buffer);

In this case I modified line 1158: void readAttrFromH5’ for ‘void readAttrFromH5(const H5::H5Object&, const string&, float&)’ and everything compiled, but I do not know what to do. Any help?

[thierry3000]

Dear lopezmarinn, thank you for considering "Tumorcode" as option!!!! Your first error (undefined reference to symbol '_ZN3MPI8Datatype4FreeEv') indicates that you did not use the MPI compiler wrapper for compilation (mpicc). In Ubuntu 18, the provided default Trilinos is compiled with mpi, therefore you also need it for Tumorcode.

Try the following:

• delete your build directory
• set mpiwrapper as compiler (export CC=mpicc and export CXX=mpicxx)
• run cmake again

I successfully use the dev_fredrich branch on a default Ubuntu 18.04 system, but I never tried 18.10. I the above does not work out, do not hesitate to contact me.

Cheers, Thierry

[thierry3000]

Sorry for closing, that was a mistake. Maybe you also installed a parallel version of libhdf? That would also require the mpi wrapper. Best Thierry

[lopezmarinn]

Hi Thierry, Thank you for your quick response. With the suggested corrections everything compile. Best Regards Nelia