Biotissue Build Information

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This page contains any information on the build for the biotissue project.


This section lists all the pieces of the biotissue build in three sections. The first is third-party software (this section could also include MPI but that's sort of a given). The second section lists software that is not directly associated with the biotissue project but is developed and maintained at SCOREC. The third lists all the biotissue specific software pieces.

The order of the software pieces also represent a viable ordering for building.


  • Boost 
    Only some boost header files are used, so boost does not need to be built, only included. (Currently we use version 1.44.0)
  • Simmetrix 
    Simmetrix's SimModeler is used to define the models, boundary conditions, and meshes, so simmetrix functions are used to load these files. This is the only proprietary piece of the biotissue code.
  • Petsc 
    Petsc (Scorec wiki) solvers are used for the main finite element matrix solve on the macroscale. (Currently we use version 3.2-p7)
    The following is the configure command used to start building petsc on the Q:
   ./configure --download-superlu_dist=1 --download-parmetis=~/barn-shared/ParMetis-3.2.0-p1.tar.gz --download-f-blas-lapack=~/barn-shared/fblaslapack-3.1.1.tar.gz \ 
   --with-cc=mpicc --with-fc=mpif90 --with-debugging=0 --with-shared-libraries=0 COPTFLAGS="-O3 -march=p4 -mtune=p4" FOPTFLAGS="-O3 -qarch=p4"


  • PCU 
    Parallel Control Utility (PCU) is used for parallel communication. It is primarily used in AMSI and APF and not biotissue directly, but must be initialized in main.
  • AMSI 
    AMSI is primarily used for communication of multiscale data between the scales. AMSI is dependent on Boost and the AMSI_PCU version is also dependent on PCU.
  • APF 
    Adaptive Parallel Field (APF) is used for storage and manipulation of field data. It is dependent on PCU. It is replacing the role of MCTK in this project: Biotissue MCTK to APF Refactor.
  • APF-SIM 
    APF-SIM provides an interface between APF and Simmetrix's meshSim. It is dependent on APF and Simmetrix.


CMake is used to build each of the following pieces. Build scripts are provided in the biotissue repository for each of the following pieces. These should work for either the scorec system or the Q. The build scripts essentially just call cmake while setting cmake variables. The scripts are all named something like, for example, except for the final compile of main which is called An environmental variable can be set in order to compile using optimization flags.

  • dep/las 
  • dep/scorecutil 
  • dep/sparskit 
  • dep/sparskit/dep/sparskit-scorec 
  • dep/femanalysis 
  • micro_fo 
    Fiber only RVE calculations
  • macro 
    Macroscale finite element analysis
  • macro/test/SourceMain 
    Compile of and linking of all libraries

Q Build

This section lists specifics for building on the Q.

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