autoibamr

The autoibamr.sh shell script downloads, configures, builds, and installs ibamr with common dependencies on Linux and macOS computers.

By default, autoibamr compiles everything with standard optimization flags (-O2 for C++ and Fortran). To use hardware-dependent optimization flags or disable optimizations for debugging use --enable-native-optimizations or --enable-debugging, respectively. These flags (and more) are documented under 'Advanced Configuration' below.

The default installation location is ~/autoibamr/. If you enable debugging then the default installation location is ~/autoibamr-debug/.

autoibamr is based on candi: https://github.com/dealii/candi

Dependencies

autoibamr requires that your present machine already have a working copy of MPI and the standard MPI compiler wrappers installed. If you want to use custom MPI compiler wrappers then you should set CC, CXX, and FC to full paths to the C, C++, and Fortran compilers, respectively.

Several IBAMR dependencies require using MPI compiler wrappers, so providing MPI_ROOT and using a separate compiler toolchain is presently not supported.

In addition to MPI, we require that the following build-time dependencies are available:

• python, e.g., python3-distutils on Ubuntu. Any system copy of Python should work.
• The standard Unix build tools: i.e., awk, sed, grep, make, and m4. These packages are typically installed automatically.
• If you want to use libMesh, an optional IBAMR dependency, then you need to have a system copy of XDR available. This library is typically installed by the command line tools SDK for macOS or by a package named something like libtirpc (Arch Linux), libtirpc-dev (Debian and Ubuntu), or libtirpc-devel (Read Hat).

If you are running on a mac then you may need to install Xcode's command-line tools. If you have not done this before then run

xcode-select --install

in the terminal. If you have already installed the command-line tools then we recommend ensuring the latest version is installed by checking with

softwareupdate --list

and installing any listed Xcode updates.

Quickstart

The following commands download the current stable version of the installer and then install the latest IBAMR release and common dependencies:

  git clone https://github.com/ibamr/autoibamr.git
  cd autoibamr
  ./autoibamr.sh

Follow the instructions on the screen (you can abort the process by pressing < CTRL > + C)

Most of IBAMR's dependencies are hosted on GitHub. If you have trouble accessing GitHub then you may need to install a workaround. Some users have reported that GitHub520 can help - see issue #73 for more information if this applies to you.

Installation

If you are on a cluster you will typically want to run module load mpi to set up the correct MPI environment. After that you can run

  ./autoibamr.sh

Fixing Common Problems with macOS

The most common sources of problem with macOS are:

1. Anaconda installs a conflicting and sometimes broken set of command-line tools
2. The operating system was updated but Xcode was not.

We highly recommend uninstalling anaconda (and related packages, like miniconda) since anaconda tries to replace the system-level development tools with its own. You may need to modify .bashrc to ensure no lingering references to conda remain after uninstalling it.

If you encounter problems such as

ld: library not found for -ld_classic

or things appear to stop working while compiling PETSc, then we recommend making sure that Xcode is up-to-date by running

xcode-select --install
softwareupdate --install xcode

or, alternatively, install and then update the full Xcode system from the App store.

Using the installed copy of IBAMR

This can be done in two ways:

1. source the enable.sh script installed in autoibamr/configuration:

   source ~/autoibamr/configuration/enable.sh

or, with a debug build:

   source ~/autoibamr-debug/configuration/enable.sh

This sets up the environment variables for each package. For example, this will set IBAMR_ROOT to the full path to the IBAMR installation. You can then configure your IBAMR application by running

   cmake -DIBAMR_ROOT="${IBAMR_ROOT}" .

in the normal way. Running enable.sh also sets up your PATH variable to include the copy of CMake provided by autoibamr.

2. Use the IBAMR installation directory directly: By default, IBAMR is installed in $HOME/autoibamr/packages/IBAMR-0.15.0/. You can configure your own IBAMR application by running

   $HOME/autoibamr/packages/cmake-3.20.5/bin/cmake -DIBAMR_ROOT="$HOME/autoibamr/packages/IBAMR-0.15.0/" .

or, with a debug build

   $HOME/autoibamr-debug/packages/cmake-3.20.5/bin/cmake -DIBAMR_ROOT="$HOME/autoibamr/packages/IBAMR-0.15.0/" .

in the normal way. That command uses the version of CMake installed by autoibamr - you can use another installed version if you wish (that is at least version 3.15).

Working with IBAMR examples

autoibamr sets up IBAMR and its dependencies for use in external projects. It can be used to develop IBAMR itself in two different ways:

1. The IBAMR source directory, is, by default, autoibamr/tmp/unpack/IBAMR-0.15.0/ and the build directory is autoibamr/tmp/build/v0.15.0/. As usual, the by default the prefix is autoibamr-debug when compiled in debug mode. While this is not the intended way to use autoibamr, you can compile and run examples from the build directory after installation.
2. You can install your own development copy of IBAMR that uses the dependencies installed by autoibamr. To do this you should provide the --dependencies-only flag when running the script (./autoibamr.sh --dependencies-only) and then download and compile IBAMR yourself after autoibamr finishes.
3. Finally, you could set up the IBAMR examples as external projects configured with CMake in the normal way by copying and pasting them.

Advanced Configuration

Command line options

Help: [-h], [--help]

You can get a list of all command line options by running

  ./autoibamr.sh -h
  ./autoibamr.sh --help

You can combine the command line options given below.

Prefix path: [-p <path>], [-p=<path>], [--prefix=<path>]

  ./autoibamr.sh -p "/path/to/install/dir"
  ./autoibamr.sh -p="/path/to/install/dir"
  ./autoibamr.sh --prefix="/path/to/install/dir"

Multiple build processes: [-j<N>], [-j <N>], [--jobs=<N>]

  ./autoibamr.sh -j<N>
  ./autoibamr.sh -j <N>
  ./autoibamr.sh --jobs=<N>

• Example: to use 2 build processes type ./autoibamr.sh -j 2.

Debug mode: --enable-debugging

  ./autoibamr.sh --enable-debugging

Sets up a debug build, where dependencies are compiled with assertion checking, debug symbols, and optimizations and IBAMR is compiled with assertions, no optimizations, and debug symbols. In this case autoibamr is installed into ~/autoibamr-debug by default (though this may be overridden with --prefix).

Platform-specific optimizations: --enable-native-optimizations

  ./autoibamr.sh --enable-native-optimizations

Turns on processor-specific optimizations. Incompatible with debug mode.

User interaction: [-y], [--yes], [--assume-yes]

  ./autoibamr.sh -y
  ./autoibamr.sh --yes
  ./autoibamr.sh --assume-yes

With this option you skip the user interaction. This might be useful if you submit the installation to the queueing system of a cluster.

By default both libMesh and SILO will be set up and used as dependencies. They can be disabled with --disable-libmesh and --disable-silo respectively.