HemeXtract

HemeXtract was developed for a fork of HemeLB and is not compatible with this newer version. For the current version, use the CSV extraction method described below.

HemeLB stores output data in compressed .dat or .xtr files. To make this human-readable, use the hemeXtract tool provided in the download files.

Installation Steps

Applicable for Commit ece1265

git clone https://github.com/UCL-CCS/hemeXtract.git
sudo apt-get install libtirpc-dev
sudo apt-get install rpcbind

Then modify the Makefile: add -ltirpc at the end of each g++ execution line. The modified compile command should look like:

g++ -Wall -O3 hemeXtract.cc -o hemeXtract -ltirpc

Then run:

make

Usage

./hemeXtract -X output.xtr --output=readable_output.txt

Visualization

To visualize the converted files, use ParaView. It is recommended to install it from the official website.

For further information, refer to the HemeLB Simulation Tutorial Section 3.

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Extract Information (Newer Version)

First, activate the conda environment:

conda activate gmy-tool

Then run the extraction command:

hlb-dump-extracted-properties <path-to-xtr-file> > <output-path>.csv

Example:

hlb-dump-extracted-properties whole.xtr > whole.csv