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Short user manual

Welcome to use NBODY6++GPU, which is a MPI parallel version of NBODY6GPU developed by Sverre Aarseth and Keigo Nitadori, see www.sverre.com. The description of the code can be seen in Wang et al. (2015), MNRAS, 450, 4070: https://ui.adsabs.harvard.edu/abs/2015MNRAS.450.4070W/abstract.

Currently, this version of NBODY6++GPU has no further big update, because the main developer (Long Wang) now focuses on the development of the new N-body code PeTar (see https://github.com/lwang-astro/PeTar for detail). For users who are interested for using NBODY6++GPU, there is another active version maintained by team of Rainer Spurzem ([email protected] [email protected]). Please contact him and visit https://github.com/nbody6ppgpu/Nbody6PPGPU-beijing/blob/stable/README.md for detail.

Here is an example of current differences between the code version (May 2023), more changes and differences may occur in the future, if in doubt, ask the authors.

  • LW: implementation of Milky Way potential following the MWPotential2014 in Galpy (Bovy 2015).
  • RS: implementation of spin and mass dependent recoil kicks after GW merger (Arca Sedda et al. 2023 subm. MNRAS)
  • LW: implementation of python data reading interface for PeTar analysis tool.
  • RS: use of HDF5 output files with python data reading interfaces
  • RS: Namelist based input format, allowing also to read all stellar evolution and binary / collision parameters.
  • LW and RS: Some bug fixes related to Roche and GR radiation, in both versions slightly different ways.
  • LW and RS: implementation of BSE from Banerjee et al. 2019

If you find issues during using the code but not fully answered in the follow tips and manuals in doc/Nbody6++_manual.pdf, please use the GitHub issue to ask questions.

Install

Use the GNU configure tool to install:

./configure [options]
make
make install

The options for configure can be found by using

./configure --help

The options include the maximum size of data array, the switchers for using parallelization methods and HDF5 support.

some basic options

  • Install path:

    The default install path is /usr/local, if you want to change to another path, please use:

      ./configure --prefix=[YOURPATH]

    Replace [YOURPATH] to the full path that you want to install the code. There will be bin, doc, include and lib created in your install path.

  • GPU:

    The GPU support is enabled in the default case, if you want to disable the GPU acceleration, please use:

      ./configure --disable-gpu

  • MPI:

    The MPI is enabled in the default case, if you want to disable the MPI parallelization, please use:

      ./configure --disable-mpi

    Notice if no Fortran MPI compiler (mpif77) exist, the configure cannot pass, the --disable-mpi should be added manually

  • AVX/SSE:

    The AVX is enable in default case, you can choose no AVX/SSE, SSE and AVX, the option is:

      ./configure --enable-simd=[arg]

    Replace [arg] by no, sse, avx.

    Notice when the CPU don't support AVX/SSE, the code can still be compiled if the compiler support them. In such case a warning will appear during the configuration. Please be careful for this warning. It indicates that the code cannot be used in the current machine. In the case for running code on a computer cluster with a job manage system, the code may be compiled in the login node without AVX/SSE support but can be used on the working nodes that support AVX/SSE. Thus the configure does not switch off AVX/SSE even the CPU on the compiling node doesn't supports them.

  • HDF5 output format:

    The HDF5 is disabled in default case, if you want to enable it, please use:

      ./configure --enable-hdf5

    Notice when MPI is used, HDF5 compiler should be parallel version with Fortran enabled. If you want to use non-parallel version of HDF5 compiler with no MPI, please add --disable-mpi during the configuration.

  • Extra tools:

    There are some extra tools and libraries for reading conf.3 and do some basic analysis. It is disabled in the default case. If you want to switch on, please use:

      ./configure --enable-tools

Notice all configure options should be used together. For example:

./configure --prefix=/opt/nbody6++ --enable-tools --enable-hdf5

Important notice:

  • When large NMAX is used, sometimes the segmentation fault happens soon after the simulation starts. This is due to the stack memory overflow. In such case, you should always run

      ulimit -s unlimited

    before start the simulation in the same shell. Be careful that ulimit only affects the current shell you enter this commander, thus it's need to be used every time when a new shell is opened. You can add this line in the shell initialization file, e.g., in bash, usually it is .bashrc or .bash_profile in your home directory. After that, this commander is automatically loaded once a new shell is open.

  • In some Linux systems (e.g. Ubuntu), when the large NMAX is used, the compiling crash with the error:

      R_X86_64_PC32 against symbol

    This error is related to the memory model of the Linux system. The detail of memory model is shown in https://software.intel.com/en-us/node/579558 The solution is to add the configure option --enable-mcmodel=large

  • The stellar evolution package (SSE/BSE) in the current version is based on the new update of Banerjee et al. (2019) (http://arxiv.org/abs/1902.07718)