Enzo v2.0 documentation

Obtaining and Building Enzo

Enzo Compilation Requirements

Enzo can be compiled on any POSIX-compatible operating system, such as Linux, BSD (including Mac OS X), and AIX. In addition to a C/C++ and Fortran-90 compiler, the following libraries are necessary:

  • HDF5, the hierarchical data format. Note that HDF5 also may require the szip and zlib libraries, which can be found at the HDF5 website. Note that compiling with HDF5 1.8 or greater requires that the compiler directive H5_USE_16_API be specified; typically this is done with -DH5_USE_16_API and it’s set in most of the provided makefiles.
  • MPI, for multi-processor parallel jobs. Note that Enzo will compile without MPI, but it’s fine to compile with MPI and only run oon a single processor.

Mercurial Check Out Instructions

Enzo is provided in both a stable and an unstable form. It is highly recommended that for any production run the stable version is used. Additionally, we encourage anyone who uses Enzo to sign up for the Enzo Users’ List. A source browser is also available.

Please visit the Google Code project website to access the Enzo source tree and read the latest source checkout instructions.

http://enzo.googlecode.com/

Before you try to build Enzo, you may wish to verify your system meets the compilation requirements?.

Updating a source tree with Mercurial is beyond the scope of this document; for more information, please peruse How To Develop Enzo and the Mercurial documentation. The `mercurial <http://mercurial.selenic.com/`_ commands of most use are pull, update and incoming.

Building Enzo

This is a quick, line by line example of checking out and building Enzo using current build system. A comprehensive list of the make system arguments can be found in The Enzo Makefile System.

This assumes that we’re working from a checkout from the Enzo project page, located at http://enzo.googlecode.com/ . Checkout instructions can be found there, and for more detailed information about the structure of the Enzo source control repository, see CheckOutInstructions.

Initializing the Build System

This just clears any existing configurations left over from a previous machine, and creates a couple of files for building.

~ $ cd enzo/
~/enzo $ ./configure

This should output a brief message saying that the build system has been initialized. To confirm that it ran, there should be a file called Make.config.machine in the src/enzo subdirectory.

Go to the Source Directory

The source code for the various Enzo components are laid out in the src/ directory.

~/enzo/src $ cd src/
~/enzo/src $ ls
Makefile      P-GroupFinder anyl          enzo          enzohop       inits
lcaperf       mpgrafic      ring
~/enzo/src $

Right now, we’re just building the main executable (the one that does the simulations), so we need the enzo/ directory.

~/enzo/src $ cd enzo/

Find the Right Machine File

We’ve chosen to go with configurations files based on specific machines. This means we can provide configurations files for most of the major NSF resources, and examples for many of the one-off (clusters, laptops, etc.).

These machine-specific configuration files are named Make.mach.machinename.

~/enzo/src/enzo $ ls Make.mach.*
Make.mach.darwin          Make.mach.nasa-discover   Make.mach.ncsa-cobalt
Make.mach.ornl-jaguar-pgi Make.mach.tacc-ranger     Make.mach.unknown
Make.mach.kolob           Make.mach.nasa-pleiades   Make.mach.nics-kraken
Make.mach.scinet          Make.mach.triton
Make.mach.linux-gnu       Make.mach.ncsa-abe        Make.mach.orange
Make.mach.sunnyvale       Make.mach.triton-intel
~/enzo/src/enzo $

In this example, we choose Make.mach.darwin, which is appropriate for Mac OS X machines.

Porting

If there’s no machine file for the machine you’re on, you will have to do a small amount of porting. However, we have attempted to provide a wide base of Makefiles, so you should be able to find one that is close, if not identical, to the machine you are attempting to run Enzo on. The basic steps are as follows:

  1. Find a Make.mach file from a similar platform.
  2. Copy it to Make.mach.site-machinename (site = sdsc or owner, machinename = hostname).
  3. Edit the machine-specific settings (compilers, libraries, etc.).
  4. Build and test.

If you expect that you will have multiple checkouts of the Enzo source code, you should feel free to create the directory $HOME/.enzo/ and place your custom makefiles there, and Enzo’s build system will use any machine name-matching Makefile in that directory to provide or override Make settings.

Make sure you save your configuration file! If you’re on a big system (multiple Enzo users), please post your file to the Enzo mailing list, and it will be considered for inclusion with the base Enzo distribution.

HDF5 Versions

If your system uses a version of HDF5 greater than or equal to 1.8, you probably need to add a flag to your compile settings, unless your HDF5 library was compiled using –with-default-api-version=v16. The simplest thing to do is to find the line in your Make.mach file that sets up MACH_DEFINES, which may look like this

MACH_DEFINES   = -DLINUX # Defines for the architecture; e.g. -DSUN, -DLINUX, etc.

and change it to

MACH_DEFINES   = -DLINUX -DH5_USE_16_API # Defines for the architecture; e.g. -DSUN, -DLINUX, etc.

This will ensure that the HDF5 header files expose the correct API for Enzo.

Build the Makefile

Now that you have your configuration file, tell the build system to use it:

~/enzo/src/enzo $ make machine-darwin

 *** Execute 'gmake clean' before rebuilding executables ***

   MACHINE: Darwin (OSX Leopard)

~/enzo/src/enzo $

You may also to know the settings (precision, etc.) that’s being use. You can find this out using make show-config. For a detailed explanation of what these mean, see The Enzo Makefile System.

~/enzo/src/enzo $ make show-config

MACHINE: Darwin (OSX Leopard)
MACHINE-NAME: darwin

PARAMETER_MAX_SUBGRIDS:       100000
PARAMETER_MAX_BARYONS:        20
PARAMETER_MAX_TASKS_PER_NODE: 8
PARAMETER_MEMORY_POOL_SIZE:   100000

CONFIG_PRECISION:             64
CONFIG_PARTICLES:             64
CONFIG_INTEGERS:              64
CONFIG_PARTICLE_IDS:          64
CONFIG_INITS:                 64
CONFIG_IO:                    32
CONFIG_USE_MPI:               yes
CONFIG_OBJECT_MODE:           64
CONFIG_TASKMAP:               no
CONFIG_PACKED_AMR:            yes
CONFIG_PACKED_MEM:            no
CONFIG_LCAPERF:               no
CONFIG_PAPI:                  no
CONFIG_PYTHON:                no
CONFIG_ECUDA:                 no
CONFIG_OOC_BOUNDARY:          no
CONFIG_OPT:                   debug
CONFIG_TESTING:               no
CONFIG_TPVEL:                 no
CONFIG_PHOTON:                yes
CONFIG_HYPRE:                 no
CONFIG_EMISSIVITY:            no
CONFIG_USE_HDF4:              no
CONFIG_NEW_GRID_IO:           yes
CONFIG_BITWISE_IDENTICALITY:  yes
CONFIG_FAST_SIB:              yes
CONFIG_FLUX_FIX:              yes

~/enzo/src/enzo $

Build Enzo

The default build target is the main executable, Enzo.

~/enzo/src/enzo $ make
Updating DEPEND
pdating DEPEND
Compiling enzo.C
Compiling acml_st1.src
... (skipping) ...
Compiling Zeus_zTransport.C
Linking
Success!
~/enzo/src/enzo $

After compiling, you will have enzo.exe in the current directory.

Building other Tools

Building other tools is typically very straightforward; they rely on the same Makefiles, and so should require no porting or modifications to configuration.

Inits

~/enzo/src/ring $ cd ../inits/
~/enzo/src/inits $ make
Compiling enzo_module.src90
Updating DEPEND
Compiling acml_st1.src
...
Compiling XChunk_WriteIntField.C
Linking
Success!

This will produce inits.exe.

Ring

~/enzo/src/enzo $ cd ../ring/
~/enzo/src/ring $ make
Updating DEPEND
Compiling Ring_Decomp.C
Compiling Enzo_Dims_create.C
Compiling Mpich_V1_Dims_create.c
Linking
Success!

This will produce ring.exe.

YT

To install yt, you can use the installation script provided with the yt source distribution. See Installation or Using the Installation Script for more information.