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Commit 30712dda authored by Johanna Fink's avatar Johanna Fink
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Update README.md

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......@@ -10,37 +10,42 @@ some of the SHEMAT-Suite input arrays into hdf5-files.
## HDF5 Input ##
The option to use HDF5 input instead of serial ASCII input is now
available in branch `master` and Branches `mpi-sm-hdf5`. The
Python-script `convert_to_hdf5.py` converts parts of the standard
ASCII input file into and hdf5-file called `<input>_conv.h5`. Parts
which are not converted to hdf5-arrays are stored in a new ASCII-file
called `<input>_conv`. Due to changes in the SHEMAT-Suite reading
routines, most of the input data is then read from the HDF5-file which
is considerably faster than reading from the ASCII-file and has
advantages of parallel I/O.
# Input File Conversion to HDF5-format
How to use it:
The user input for SHEMAT-Suite is provided in an ASCII-file. For reducing the
reading time of larger input files, SHEMAT-Suite provides the option to read
HDF5 input instead. Theresore, we provide a Python-script for converting the
ASCII input file, which is created by the user, into an HDF5 input file.
1.) Copy the python code `convert_to_hdf5.py` from the code directory
to your model directory.
The script `convert_to_hdf5.py` converts parts of the standard ASCII input file
into and HDF5-file called `<input>_conv.h5`. Those parts which are not converted
to hdf5-arrays are stored in a new ASCII-file called `<input>_conv`.
Most of the input data, especially large arrays, is then read from the
HDF5-file, which is considerably faster than reading from the ASCII-file.
2.) For using the converter, the Python module has to be loaded.
**How to use it:**
3.) Conversion of standard SHEMAT-Suite input file:
0.) Prerequisite: Python
1.) Download the python scipt `convert_to_hdf5.py`
from https://git.rwth-aachen.de/SHEMAT-Suite/shemat-suite_scripts-open
2.) Conversion of standard SHEMAT-Suite input file:
`./convert_to_hdf5.py <inputfile>`
4.) The file shemade.job has to contain the name of the newly
generated ASCII-file `<inputfile>_conv`
3.) Write the name of the newly generated ASCII-file `<inputfile>_conv`
into the file `shemade.job `.
4.) Execute SHEMAT-Suite.
5.) Execute SHEMAT-Suite.
**Important note:**
Important note: The input of multiple values for e.g. boundary
conditions either has to be written in one line or the number of
entries has to be defined by using the keyword records. Otherwise the
converter will give an error!
The input of multiple values for e.g. boundary
conditions either has to be written in one line or the number of entries
has to be defined by using the keyword records. Otherwise the converter
will give an error!
Please test the HDF5 input option with your models and report any
difficulties like the one noted above, so that they can be adapted in
the future.
Please test the HDF5 input option with your models and report any
difficulties like the one noted above (e.g. as an issue),
so that they can be adapted in the future.
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