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 on a single processor.
  • hg, a free, distributed source control management tool.
  • yt, the yt visualization and analysis suite. While it is not required to run enzo, yt enables the easiest analysis of its outputs, as well as the ability to run the enzo testing tools.

Downloading Enzo

We encourage anyone who uses Enzo to sign up for the Enzo Users’ List, where one can ask questions to the community of enzo users and developers.

Please visit the Enzo Project home page to learn more about the code and different installation methods. To directly access the source code, you can visit the Enzo Bitbucket page.

If you already have Fortran, C, C++ compilers, Mercurial, MPI, and HDF5 installed, then installation of Enzo should be straightforward. Simply run the following at the command line to get the latest stable version of the Enzo source using Mercurial. This command makes a copy of the existing enzo source code repository on your local computer in the current directory:

~ $ hg clone https://bitbucket.org/enzo/enzo-dev ./enzo

Later on, if you want to update your code and get any additional modifications which may have occurred since you originally cloned the source repository, you will have to pull them from the server and then update your local copy (in this example, no new changes have occurred):

By default, after you clone enzo you will be on the stable branch. If you wish to use the latest development version, you must update to the week-of-code branch:

~/ $ cd enzo
~/enzo $ hg update week-of-code

Enzo development continues regularly, and if you wish to use the latest changes, you can update the code as follows:

~/enzo $ hg pull
pulling from https://bitbucket.org/enzo/enzo-dev
searching for changes
no changes found

~/enzo $ hg update
0 files updated, 0 files merged, 0 files removed, 0 files unresolved

This covers the basics, but for more information about interacting with the mercurial version control system please peruse the Developer’s Guide, the Mercurial Documentation, and/or this entertaining tutorial on Mercurial.

Building Enzo

This is a quick, line by line example for building Enzo using the 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 (or download) of the source after following instructions on the Enzo Project home page, or the instructions in the last section. For more detailed information about the structure of the Enzo source control repository, see Introduction to Enzo Modification.

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
Configure complete.

This message just confirms that the build system has been initialized. To further 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 $ cd src
~/enzo/src $ ls
Makefile      P-GroupFinder      TREECOOL      anyl      enzo      enzohop
inits         lcaperf            mpgrafic      performance_tools   ring

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.arizona               Make.mach.darwin
Make.mach.hotfoot-condor        Make.mach.kolob
Make.mach.linux-gnu             Make.mach.nasa-discover
Make.mach.nasa-pleiades         Make.mach.ncsa-bluedrop
Make.mach.ncsa-bluewaters-gnu   Make.mach.ncsa-cobalt
Make.mach.nics-kraken           Make.mach.nics-kraken-gnu
Make.mach.nics-kraken-gnu-yt    Make.mach.nics-nautilus
Make.mach.orange                Make.mach.ornl-jaguar-pgi
Make.mach.scinet                Make.mach.sunnyvale
Make.mach.tacc-ranger           Make.mach.trestles
Make.mach.triton                Make.mach.triton-gnu
Make.mach.triton-intel          Make.mach.unknown

~/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 (remember to make clean if you change any previous settings):

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

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

   MACHINE: Darwin (OSX Leopard)

You may also want to know the settings (precision, etc.) that are 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  [max-subgrids-###]                : 100000
PARAMETER_MAX_BARYONS  [max-baryons-###]                  : 30
PARAMETER_MAX_TASKS_PER_NODE  [max-tasks-per-node-###]    : 8
PARAMETER_MEMORY_POOL_SIZE  [memory-pool-###]             : 100000

CONFIG_PRECISION  [precision-{32,64}]                     : 64
CONFIG_PARTICLES  [particles-{32,64,128}]                 : 64
CONFIG_INTEGERS  [integers-{32,64}]                       : 64
CONFIG_PARTICLE_IDS  [particle-id-{32,64}]                : 64
CONFIG_INITS  [inits-{32,64}]                             : 64
CONFIG_IO  [io-{32,64}]                                   : 32
CONFIG_USE_MPI  [use-mpi-{yes,no}]                        : yes
CONFIG_OBJECT_MODE  [object-mode-{32,64}]                 : 64
CONFIG_TASKMAP  [taskmap-{yes,no}]                        : no
CONFIG_PACKED_AMR  [packed-amr-{yes,no}]                  : yes
CONFIG_PACKED_MEM  [packed-mem-{yes,no}]                  : no
CONFIG_LCAPERF  [lcaperf-{yes,no}]                        : no
CONFIG_PAPI  [papi-{yes,no}]                              : no
CONFIG_PYTHON  [python-{yes,no}]                          : no
CONFIG_NEW_PROBLEM_TYPES  [new-problem-types-{yes,no}]    : no
CONFIG_ECUDA  [cuda-{yes,no}]                             : no
CONFIG_OOC_BOUNDARY  [ooc-boundary-{yes,no}]              : no
CONFIG_ACCELERATION_BOUNDARY  [acceleration-boundary-{yes,no}]    : yes
CONFIG_OPT  [opt-{warn,debug,cudadebug,high,aggressive}]  : debug
CONFIG_TESTING  [testing-{yes,no}]                        : no
CONFIG_TPVEL  [tpvel-{yes,no}]]                           : no
CONFIG_PHOTON  [photon-{yes,no}]                          : yes
CONFIG_HYPRE  [hypre-{yes,no}]                            : no
CONFIG_EMISSIVITY  [emissivity-{yes,no}]                  : no
CONFIG_USE_HDF4  [use-hdf4-{yes,no}]                      : no
CONFIG_NEW_GRID_IO  [newgridio-{yes,no}]                  : yes
CONFIG_BITWISE_IDENTICALITY  [bitwise-{yes,no}]           : no
CONFIG_FAST_SIB  [fastsib-{yes,no}]                       : yes
CONFIG_FLUX_FIX  [fluxfix-{yes,no}]                       : yes
CONFIG_GRAVITY_4S  [gravity-4s-{yes,no}]                  : no
CONFIG_ENZO_PERFORMANCE  [enzo-performance-{yes,no}]      : yes
CONFIG_LOG2ALLOC  [log2alloc-{yes,no}]                    : 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!

After compiling, you will have enzo.exe in the current directory. If you have a failure during the compiler process, you may get enough of an error message to track down what was responsible. If there is a failure during linking, examine the compile.out file to learn more about what caused the problem. A common problem is that you forgot to include the current location of the HDF5 libraries in your machine-specific makefile.

Congratulations! You now have a working executable and continue on the next step of running a test calculation.