Installing

Table of Contents

• Installation
  • Requirements
  • Initial (one-time) set-up
    • System File
• Compiling
  • make arguments
  • ALGLIB

A guide to installing and compiling FlowSieve.

Installation

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Requirements

• netcdf4 (tested on versions 4.7 and 4.8)
  • requires parallel installation
  • hdf5-mpi required
• mpi (openmpi or intel mpi, not mpich)
• compilers: either gcc or icpc (intel compiler)
  • For gcc, tested on gcc8 and gcc9. When tested, FlowSieve compiled without warnings or errors.
    • Note that FlowSieve currently **does not support for gcc10+**.
  • If Intel compilers are available, they are recommended, since the additional compiler optimizations provide a minor performance improvement.
  • Intended to be compiled with c++14 standard (this is specified in the compiler flags in the system.mk file)
• curl

The following, while not required to run FlowSieve itself, are required to run the tutorial. These requirements are outline in Tutorials/environment.yml to facility create an anaconda environment. Note that these exact package versions may not be required, but they are sufficient. That is, other package versions may work, but have not been tested.

• python=3.7
• numpy=1.17
• matplotlib=3.1
• netCDF4=1.4
• scipy=1.3
• pip

  ---

Initial (one-time) set-up

First, you will need to copy the FlowSieve source files onto your HPC system. The source files are available through git (https://github.com/husseinaluie/FlowSieve), allowing you to directly copy/fork the repository, or download a zipped version.

System File

Next, you will need to create a system.mk file in the main code directory that specifies the compilers and provides the compiler flags needed to link to the appropriate libraries.

Some system files are already provided in the Systems directory for a few computing environments, and may be a helpful reference. Where appropraite, they specify which modules are needed to compile and run the code (note: these modules need to be loaded both when you compile the code and also when you run the code).

If you create a system file for a computing environment that was not previously included, please consider submitting it to the repository so that others can benefit from it.

The Systems directory contains a few sample system files. To prepare a system file for your machine, there are a few steps.

1. Copy the most appropraite system file from Systems to system.mk into the main directory.
2. Compilers: Indicate your chosen compilers (CXX for C++ and MPICXX for C++ with mpi)
3. Links: these may need to change depending on your compiler (e.g. -fopenmp to -qopenmp for intel compilers)
4. EXTRA_OPT_FLAGS: this is for other optimizations that you may not want on by default. For example, -ip -ipo for intel compilers.
5. Depending on how your libraries are set up, you may need to add various library and include directories to LIB_DIRS and INC_DIRS

If you are unsure of how to make an appropriate system.mk file, please feel free to contact the FlowSieve developers for support.

Compiling

A makefile is included to simplify compiling. As a first test of your install, try make clean; make Case_Files/coarse_grain.x. If the executable compiles successfully, then a good next step is to check out the tutorials that are provided to familiarize yourself with the code usage.

make arguments

• make clean
  • This removes all object files (*.o) in the source tree
• make hardclean
  • In addition to the clean removals, also removes the executables, symbol table (dSYM)
• make Case_Files/<filename>.x
  • Makes the specified executable. Case_Files contains the main files that can be compiled into executables.
• make docs
  • Makes the doxygen-produced documentation. Note: doxygen and dot must be installed and on the path
• make cleandocs
  • Removes the previous documentation build

ALGLIB

Some of the executables (such as interpolator.x and helmholtz_projection.x) require the use of a third-party library, ALGLIB. To compile this library, simply call make ALGLIB (should only need to be done once, unless you call make hardclean, change system libraries, etc.).