Enzo v2.0 documentation

Controlling Enzo data output

How and when Enzo outputs data is described below. There are five ways to control when data is output, two output formats, and two pitfalls when determining how to output data from your Enzo simulation.

Data Formats and Files

There are two output formats for Enzo data. In both cases, each data dump gets its own directory.

Each data dump writes several key files. NNNN denotes the dump number (i.e. 0001) and basename is something like RedshiftOutput or data or DD}.

All output files are also restart files. It’s not necessarily wise to write in 32 bit format if you’re computing in 64, though, as you’ll lose all the extra precision when you restart. (These are makefile flags.)

basenameNNNN:

The parameter file. This contains general simulation parameters,
dump time, cycle, and all the parameters defined here. It's worth
your time to be familiar with what's in this file.

basenameNNNN:

The hierarchy file. Contains a description of the hierarchy. One
entry for each grid, including information like the Grid Size, the
position in the volume, it's position in the hierarchy.

basenameNNNN.boundary:

A description of the boundary (plain text.) Basically a meta
description and filename for the next file

basenameNNNN.boundary.hdf5:

Actually contains the boundary information.

Other versions may output other files. It would be nice to have a description of them.

Packed AMR

This is the default output format. Each processor outputs all the grids it owns. In addition to the parameter, hierarchy, and boundary files which may or may not be described elsewhere, data is output in one basenameNNNN.taskmapCCCC} file for each processor, which contains a map between grid number and HDF5 file, and one basenameNNNN.cpuCCCC for each processor NNNN and CCCC are the dump number and cpu number, respectively.

basenameNNNN.cpuCCCC is an HDF5 file which contains an HDF5 group for each grid. Each grid in turn contains a dataset for each of the fields in the simulation.

~/DD0100>h5ls data0100.cpu0003
Grid00000002             Group
Grid00000026             Group
~/DD0100>h5ls data0100.cpu0003/Grid00000002
Density                  Dataset {16, 16, 32}
z-velocity               Dataset {16, 16, 32}

Pathnames

In previous versions of Enzo, the fully-qualified path to each file was output in the .hierarchy file, which requires modifying the .hierarchy file every time the data was moved. This has changed to be only the relative path to each data file, which largely eliminates the problem. To restore the old behavior, examine the parameters GlobalDir and LocalDir.

Timing Methods

There are 6 ways to trigger output from Enzo.

Cycle Based Output

CycleSkipDataDump = N
CycleLastDataDump = W
DataDumpName = data

One can trigger output every N cycles starting with cycle W using CycleSkipDataDump and CycleLastDataDump. Outputs are put in the directory DD0000 (or DD0001, etc.) and the basename is determined by DataDumpName.

CycleSkipDataDump <= 0 means cycle based output is skipped. The default is 0.

Pitfall 2: CycleLastDataDump defaults to zero and is incremented by CycleSkipDataDump every time output is done. If you change the value of CycleSkipDataDump and neglect to change CycleLastDataDump, Enzo will dump as long as CycleNumber >= CycleSkipDataDump + CycleLastDataDump. (So if you change CycleSkipDataDump from 0 to 10 from a Redshift dump at n=70, you’ll get an output every timestep for 7 timesteps.)

Time Based Output

TimeLastDataDump = V
dtDataDump = W

Exactly like Cycle based output, but triggered whenever time >= TimeLastDataDump + dtDataDump. The same pitfall applies.

Redshift Based Output

CosmologyOutputRedshift[ 0 ] = 12
CosmologyOutputRedshiftName[ 0 ] = Redshift12
RedshiftDumpName             = RedshiftOutput

Outputs at the specified redshift. Any number of these can be specified.

CosmologyOutputRedshift[ i ] is the only necessary parameter, and is the ith redshift to output.

Any outputs with CosmologyOutputRedshiftName[ i ] specified has that name used for the output, and no number is appended. (so if CosmologyOutputRedshiftName[ 6 ] = BaconHat, the outputs will be BaconHat, BaconHat.hierarchy, etc.)

If CosmologyOutputRedshiftName[ i ] is omitted, RedshiftDumpName is used for the basename, and the output number is taken from the array index. (So CosmologyOutputRedshift[19] = 2.34 and RedshiftDumpName = MonkeyOnFire, at dump will be made at z=2.34 with files called MonkeyOnFire0019.hierarchy, etc.)

Force Output Now

The following two options are run time driven. These are especially useful for very deep simulations that spend the majority of their time on lower levels. Note that unless you have the parameter FileDirectedOutput turned on, these will not be available.

To force an output as soon as the simulation finished the next step on the finest resolution, make a file called outputNow:

touch outputNow

This will remove the file as soon as the output has finished.

Sub Cycle Based Output

To get the simulation to output every 10 subsycles (again at the finest level of resolution) put the number of subcycles to skip in a file called subcycleCount:

echo 10 > subcycleCount

Time Based Interpolated Output

Even when you are running simulations with a long dtDataDump, sometimes you may want to see or analyze the interim datadumps. Using dtInterpolatedDataDump, you can control Enzo to check if it should start outputting interpolated data based on the time passed (dtInterpolatedDataDump < dtDataDump).

dtDataDump = 1e-4
dtInterpolatedDataDump = 1e-5

This is mostly for making movies or looking at the interim data where the TopGrid dt is too long, and in principle, this output shouldn’t be used for restart.

Friendly Note on Data Output

Enzo is content to output enough data to fill up a hard drive – for instance, your home directory. This should be noted before output parameters are set, particularly the Sub Cycle outputs, as Enzo has no prohibition against causing problems with quotas and file system size.