Work Description

Installation Instructions

These instructions explain how to build CRIMSON Flowsolver on openSUSE Leap 15.1 (Linux). They have been tested on a completely fresh install of the OS. You will need to adjust them accordingly for other flavours of Linux.

1. Install the dependencies using the system pacakge manager
   • sudo zypper install kernel-default-devel git scons openmpi openmpi-devel gcc-c++ gcc-fortran python-devel cblas-devel blas-devel lapack-devel cmake libboost_headers1_66_0-devel libboost_thread1_66_0-devel libboost_filesystem1_66_0-devel python2-numpy python2-scipy
2. Setup paths
   • Add the mpi compilers bin folder to your system path (in this case, export PATH=$PATH:/usr/lib64/mpi/gcc/openmpi/bin - but this will almost certainly differ on your system if it is not opensuse Leap 15.1) and their runtime libraries to the LD_LIBRARY_PATH (in the opensuse case: export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/lib64/mpi/gcc/openmpi/lib64 - but check for your system where the mpi runtime libraries are located)
   • You probably want to put these exports in your ~/.bashrc file and then open a fresh terminal in order to activate it.
3. Install PetSc
   • Get petsc-3.2-p7 from the PetSc website. Untar it in some folder and compile it, but note that the values for the lib locations may vary on your system, and use a PETSC_ARCH according to your gcc version (although this is just for your own records): ./configure PETSC_ARCH=gcc_7.4.1-opt --with-memalign=64 --with-debugging=0 COPTFLAGS=-O2 -fp-model precise FOPTFLAGS=-O2 -fp-model source --with-x=0 CXXOPTFLAGS=-O2 --with-blas-lib=/usr/lib64/libblas.so --with-lapack-lib=/usr/lib64/liblapack.so --with-mpi-dir=/usr/lib64/mpi/gcc/openmpi/
   • After configuring is complete, follow the instructions in the console for compiling PetSc
   • After compilation, follow the instructions in the console for testing PetSc. Note that the fortran compiler may issue some warnings, which the petsc test system will report as failures - but if the only actual error output are the warnings, it is most likely fine
4. Install VTK version 5.8.0
   • Get vtk version 5.8.0 - it is available with CRIMSON modifications here
   • Run the following configuration command, but make sure you set /some/install/path to be where you want vtk to be installed - and remember it for later setting up of CRIMSON cmake -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx -DVTK_USE_RENDERING=OFF -DCMAKE_INSTALL_PREFIX=/some/install/path -DCMAKE_CXX_FLAGS=-Wno-error=narrowing
   • make && make install
5. Configure CRIMSON Flowsolver
   • Copy buildoptions.py.example from the CRIMSON root to buildoptions.py.
   • Edit buildoptions.py, setting the #setme fields. Not all of these will be required, particularly if some of the libraries are in the system lib64 folder. As a minimum, you'll need to set PETSC_TOP (to point at the petsc root folder) PETSC_BUILD (to be the value you set in PETSC_ARCH during the petsc configure call), VTK_TOP (to be whatever CMAKE_INSTALL_PREFIX you set during the vtk cmake step). Be careful to note how the paths are assembled in this script: relative paths and special characters such as ~ are not supported.
6. Compile CRIMSON Flowsolver
   • In the CRIMSON root, run scons -jN test=1 debug=0 to compile using N processes
   • After a successful build, go into the testbin subfolder, and run ./mytest N, to test on N processes. Allow the test suite to finish.
7. Use the CRIMSON Flowsolver on your own simulations
   • To run CRIMSON Flowsolver, use the script in the bin folder: mysolver. Invoke this from the directory containing your simulation files, as /path/to/mysolver N solver.inp to run on N processes
   • note that solver.inp must be in your console's current working directory, flowsolver does not accept a path for solver.inp.

# Running postsolver

• For Linux builds, you will first need to rename postsolver.exe to postsolver in the bin/ folder.
• To reduce the output timesteps into one file, and generate a pht file that can be visualized in paraview, use the multipostsolver script in the scripts/ directory.
• First, edit the line in the multipostsolver script that calls the postsolver binary, make the path to the binary match where the executable is on your machine, a full path should be used.
  • e.g., the loop that calls postsolver should look something like this: sh ... # reduce the restarts for each time step requested k=0 for ((i=$1 ;i<=$2; i+=$3)); do echo "Multipostsolver is reducing timestep: $i" let k++ /home/alex2/CRIMSONFlowsolver/bin/postsolver -sn $i -newsn $i -ph -td -bflux -wss $5 $6 $7 $8 $9 $10 $11 done ...
• Then run the multipostsolver script, with parameters in the form multipostsolver start_index end_index increment folder_name
• e.g., multipostsolver 0 95 5 outputfolder in your N-procs-case folder (where N is the number of processes you set for simulation)
• multipostsolver will store the results in a folder named restarts-outputfolder-0-95-5, in the parent folder of the one you ran it in.