MPI-Rockstar - Autotools Build Guide

If you prefer to use Makefile provided in scripts directory, please follow the instruction described in Get Started.

Requirements and Dependencies

Software	Notes
C/C++ compiler (GCC / Intel / Clang)	Must support OpenMP
MPI implementation (Open MPI / MPICH, etc., >= MPI-2.2)	`mpicc` / `mpicxx` wrappers must be available
autoconf >= 2.69	Used by `./bootstrap.sh`
automake	Used by `./bootstrap.sh`
libtool	Used by `./bootstrap.sh`
libtirpc + development headers	Required when `<rpc/xdr.h>` is absent (TIPSY I/O)
HDF5 library (optional, >= 1.8.0)	Required only when `--with-hdf5` is specified
pkg-config (optional)	Used for automatic HDF5 detection

File Layout

The following files are added or modified for the Autotools build:

mpi-rockstar/
├── bootstrap.sh        ← runs autoreconf -fi to generate the configure script
├── configure.ac        ← autoconf configuration file
├── Makefile.am         ← top-level Automake file (SUBDIRS = src)
└── src/
    ├── Makefile.am     ← build target definitions (faithfully reproduces src/Makefile)
    └── ...  (source files)

Build Instructions

Basic Build (out-of-tree build recommended)

# 1. Generate the configure script (only needed once, or after editing configure.ac)
./bootstrap.sh

# 2. Create and enter a build directory
mkdir build && cd build

# 3. Run configure, specifying MPI wrappers for CC and CXX
../configure CC=mpicc CXX=mpicxx

# 4. Compile
make -j$(nproc)

Note: Binaries are placed under build/src/.

Build with HDF5 Support

./bootstrap.sh
mkdir build && cd build

# Auto-detect HDF5 via pkg-config
../configure CC=mpicc CXX=mpicxx --with-hdf5

# Specify the HDF5 installation prefix manually
../configure CC=mpicc CXX=mpicxx --with-hdf5=/path/to/hdf5

make -j$(nproc)

When HDF5 is enabled, both mpi-rockstar and mpi-rockstar_hdf5 are built.

Adding optimization flags via `CFLAGS` / `CXXFLAGS` (set at `configure` time)

With Autotools, the standard way to add optimization flags is to pass them as environment variables when running configure. For example,

../configure CC=mpicc CXX=mpicxx CFLAGS="-O3" CXXFLAGS="-O3"

When HDF5 support is enabled, you can add optimization flags in the same way—just set CFLAGS and CXXFLAGS at configure time, and they will be applied to the HDF5-enabled build as well.
OpenMP flags are auto-detected by configure (via AC_OPENMP) and added to both compile and link steps, so you usually do not need to put OpenMP flags (e.g., -fopenmp) into CFLAGS/CXXFLAGS yourself.

configure Options

Run ../configure --help to list all available options.

New Compiling Options

These flags correspond to the “New Compiling Options” described in the upstream README.

configure flag	Preprocessor macro	Effect
`--enable-output-rvmax`	`-DOUTPUT_RVMAX`	Add $R_{\rm vmax}$ (radius of maximum circular velocity) to ASCII output
`--enable-output-nfw-chi2`	`-DOUTPUT_NFW_CHI2`	Output the χ² of the NFW density profile fit
`--enable-output-intermediate-axis`	`-DOUTPUT_INTERMEDIATE_AXIS`	Output the 6 components of the intermediate shape ellipsoid axis (within Rvir and R500c)
`--enable-output-inertia-tensor`	`-DOUTPUT_INERTIA_TENSOR`	Output the 12 components of the inertia tensor (within Rvir and R500c)

Note: --enable-output-intermediate-axis and --enable-output-inertia-tensor are mutually exclusive. Specifying both causes configure to abort with an error.

HDF5 Options

configure flag	Effect
(not specified)	HDF5 disabled (default)
`--with-hdf5`	Enable HDF5; locate it automatically via pkg-config
`--with-hdf5=/path/to/hdf5`	Enable HDF5 using the specified installation prefix
`--without-hdf5`	Explicitly disable HDF5

Enabling Multiple Options at Once

Multiple --enable-* / --with-* flags can be combined on a single configure command line, separated by spaces. For example,

# Enable OUTPUT_RVMAX, OUTPUT_NFW_CHI2, and the inertia tensor output together
../configure CC=mpicc CXX=mpicxx \
  --enable-output-rvmax \
  --enable-output-nfw-chi2 \
  --enable-output-inertia-tensor

# Add HDF5 support as well
../configure CC=mpicc CXX=mpicxx \
  --enable-output-rvmax \
  --enable-output-nfw-chi2 \
  --enable-output-inertia-tensor\
  --with-hdf5=/path/to/hdf5

After configure completes, a summary of enabled options is printed:

--- New Compiling Options ---
  OUTPUT_RVMAX             : yes
  OUTPUT_NFW_CHI2          : yes
  OUTPUT_INTERMEDIATE_AXIS : no
  OUTPUT_INERTIA_TENSOR    : yes
-----------------------------

make install

# Default installation prefix: /usr/local
make install

# To install to a custom prefix, pass --prefix to configure
../configure CC=mpicc CXX=mpicxx --prefix=/opt/mpi-rockstar
make -j$(nproc)
make install

Installed files:

File	Installed to
`mpi-rockstar`	`$(prefix)/bin/`
`mpi-rockstar_hdf5`	`$(prefix)/bin/` (only when HDF5 is enabled)
`find_parents`	`$(prefix)/bin/`

To uninstall, run make uninstall.

Generated Binaries and Libraries

For an out-of-tree build, all outputs are placed under build/src/.

File	When generated
`mpi-rockstar`	Always
`find_parents`	Always
`mpi-rockstar_hdf5`	Only when `--with-hdf5` is specified
`libmpi_rockstar.a`	Always (internal use)
`libmpi_rockstar_hdf5.a`	Only when `--with-hdf5` is specified (internal use)

Cleaning the Build

# Remove compiled object files only
make clean

# Remove all files generated by configure and make (restores the build directory to a clean state)
make distclean

# Also remove files generated by bootstrap.sh (configure script, Makefile.in, etc.)
make maintainer-clean
# or manually: rm -rf autom4te.cache configure Makefile.in

Troubleshooting

`u_int` undefined error (tirpc)

/usr/include/tirpc/rpc/xdr.h: error: unknown type name 'u_int'

configure.ac prefers the system <rpc/xdr.h> and adds -I/usr/include/tirpc only when that header is absent.
If the error persists, try prepending sys/types.h:

CPPFLAGS="-include sys/types.h" ../configure CC=mpicc CXX=mpicxx

OpenMP not found

OpenMP is required but the C compiler does not support it.

Verify that mpicc/mpicxx wraps an OpenMP-capable compiler (GCC, Intel, or Clang):

mpicc --version   # check whether it wraps GCC, Clang, or icc

HDF5 not found

HDF5 requested via --with-hdf5, but pkg-config could not find package 'hdf5'.

Possible fixes:

# Specify the installation prefix explicitly
../configure CC=mpicc CXX=mpicxx --with-hdf5=/path/to/hdf5

# Or install the HDF5 development package
sudo apt-get install libhdf5-dev    # Ubuntu/Debian
sudo dnf install hdf5-devel         # RHEL/Rocky Linux