Here are a few things I've noticed as I followed the installation tutorial on the GliomaWebsite.
1.the install script in GliomaSolver/INSTALL makes the HYPRE library, which requires by default an mpi implementation, an mpi implementation is being installed only during the install_inferenceTools script. The workaround was just running the install_inferenceTools first, but maybe making the mpi could be moved in the 'install' script
The installation of mpich required a fortran compiler by default, and the workaround of installing mpich with flag --disable-fortran does not work, as the torc library contains some fortran code. So perhaps a fortran compiler should be specified as prerequisite
Small typos in installation scripts:
--in install_inferenceTools_on-linux-64-bit.sh, line 38: make isntall
--in install_inferenceTools_on-linux-64-bit.sh, line 46: rm -r rm ${mpich_src}, double remove
--in install_inferenceTools_on-linux-64-bit.sh, line 59, perhaps missing flag -r
--script required to run the inference eventually generated in GliomaSolver/Simulations/PatientInference/Inference: run_inference.sh, reads: mpirun -np $M ./tmcmc_glioma.par. I think it should be mpirun -np $M ./engine_tmcmc
I've had compilation and linking issues with the default versions (default as in the version installed when running sudo apt-get install gcc gfortran g++) of gcc compilers and binutils shipping with kubuntu 19, ubuntu 18. I didn't manage to find any straightforward way to get the required versions in these OS versions, but I had luck with Ubuntu 16.04 . The tested versions that work are ld 2.26.1 and gcc 5.4.0.
The easiest way to get access to this toolchain for me was making a docker image of ubuntu 16 and installing everything required there, hence people would be able to run everything in a container. I could share the dockerfile if you would like : the only caveat being that there is a preprocessing script requiring matlab, and people would have to modify the dockerfile in order to install matlab and license it themselves.
Edit: 5. I also had to manually add ..../gsl-install/lib to LD_LIBRARY_PATH, maybe it could be added with the others during the install script
Edit: 6. extractInferenceOutput.sh does not find binary brain256 (when placed as per tutorial). placing brain256 in the root directoy /GliomaSolver/ fixes it
Hi Jana,
Here are a few things I've noticed as I followed the installation tutorial on the GliomaWebsite.
1.the install script in GliomaSolver/INSTALL makes the HYPRE library, which requires by default an mpi implementation, an mpi implementation is being installed only during the install_inferenceTools script. The workaround was just running the install_inferenceTools first, but maybe making the mpi could be moved in the 'install' script
The installation of mpich required a fortran compiler by default, and the workaround of installing mpich with flag --disable-fortran does not work, as the torc library contains some fortran code. So perhaps a fortran compiler should be specified as prerequisite
Small typos in installation scripts: --in install_inferenceTools_on-linux-64-bit.sh, line 38: make isntall --in install_inferenceTools_on-linux-64-bit.sh, line 46: rm -r rm ${mpich_src}, double remove --in install_inferenceTools_on-linux-64-bit.sh, line 59, perhaps missing flag -r --script required to run the inference eventually generated in GliomaSolver/Simulations/PatientInference/Inference: run_inference.sh, reads: mpirun -np $M ./tmcmc_glioma.par. I think it should be mpirun -np $M ./engine_tmcmc
I've had compilation and linking issues with the default versions (default as in the version installed when running sudo apt-get install gcc gfortran g++) of gcc compilers and binutils shipping with kubuntu 19, ubuntu 18. I didn't manage to find any straightforward way to get the required versions in these OS versions, but I had luck with Ubuntu 16.04 . The tested versions that work are ld 2.26.1 and gcc 5.4.0. The easiest way to get access to this toolchain for me was making a docker image of ubuntu 16 and installing everything required there, hence people would be able to run everything in a container. I could share the dockerfile if you would like : the only caveat being that there is a preprocessing script requiring matlab, and people would have to modify the dockerfile in order to install matlab and license it themselves.
Edit: 5. I also had to manually add ..../gsl-install/lib to LD_LIBRARY_PATH, maybe it could be added with the others during the install script
Edit: 6. extractInferenceOutput.sh does not find binary brain256 (when placed as per tutorial). placing brain256 in the root directoy /GliomaSolver/ fixes it
Tudor