Scripts within HemoCell

hemocell/examples/makefile

Multiple helper commands are accessable through make:

  • make cmakefiles

    replace <case>/CmakeLists.txt with ./CmakeLists_template.txt if you want to update the build process for all cases.

  • make executables

    compile every case

  • make all

    synonym for make executables

  • make clean

    remove all build directories, CMakeLists.txt and executables

hemocell/patch/patchPLB.sh

Patch Palabos to add some features that HemoCell needs but are by default not available.

hemocell/scripts/batchPostProcess.sh

This scripts uses the *XMF.py files to generate all necessary xmf-files so that the output of a job can be read into ParaView and others. This script should be run within the hemocell/examples/<case> or hemocell/examples/<case>/tmp directory. like so:

cd hemocell/examples/<case>
../../scripts/batchPostProcess.sh

hemocell/scripts/cartesius[_intel]_env.sh

These files contain the corresponding build dependencies on the cartesius system of SurfSara. They should be sourced instead of executed:

. ./scripts/cartesius_env.sh

hemocell/scripts/CellInfoMergeCSV.sh

This script merges the CSV output from multiple processors into a single one in the current directory. Use it in the tmp directory like this:

cd hemocell/examples/<case>/tmp/
. ./scripts/CellInfoMergeCSV.sh