Install directions

This section covers the basics of how to download and install TIMBIR.

Dependencies

  • MPI compiler (Intel or Open MPI)
  • OpenMP
  • make utility

Dependencies Install

  • Install MPI ( Here I use openMPI as a example):

    $ wget https://www.open-mpi.org/software/ompi/v1.10/downloads/openmpi-1.10.2.tar.gz
$ tar xvzf openmpi-1.10.2.tar.gz
$ cd <openmpi path>
$ ./configure --prefix=<your mpi install path>
$ make all install

  • Install HDF5 library. First go to https://www.hdfgroup.org/HDF5/release/obtainsrc.html#conf to find the appropriate hdf5 library for your platform (here we use hdf5-1.8.16.tar as example:

    $ tar xvf hdf5-1.8.16.tar
$ cd <hdf5 path>
$ ./configure --prefix=/clhome/KYUE/lib/hdf5 --enable-fortran --enable-cxx
$ make
$ make install

  • Set your library path with HDF5 library and MPI library (here we use bash as example):

    $ vi env.sh (create a bash script)
$ export HDF5_BASE=<hdf5 full path>
$ export MPI_BASE=<MPI full path>
$ export PATH = ${MPI_BASE}/bin:${HDF5_BASE}/bin:$PATH
$ export LD_LIBRARY_PATH= = ${MPI_BASE}/lib:${HDF5_BASE}/lib64:$PATH
$ source env.sh

Compiling TIMBIR

To compile the MBIR algorithm code:

$ git clone https://github.com/adityamnk/timbir.git timbir
$ cd timbir/src/MBIR_4D

This generates library files in timbir/src/lib. For more information, read the README in timbir/src/MBIR_4D.

Running the reconstruction algorithm

If the input data format is a standard binary, run the code in timbir/src/reconstruct/bin_data. For more information on data format and running the code, read the README in timbir/src/reconstruct/basic:

$ cd timbir/src/reconstruct/bin_data
$ make

This generates executables in the same folder.

If the input data is in HDF format used at APS, run the code in timbir/src/reconstruct/aps_data. For more information on data format and running the code, read the README in timbir/src/reconstruct/aps_data:

$ cd timbir/src/reconstruct/aps_data
$ make

This generates executables in the same folder.

If the input data is in standard HDF format, run the code in timbir/src/reconstruct/std_data. For more informantion on data format and running the code, read the README in timbir/src/reconstruct/std_data:

$ cd timbir/src/reconstruct/std_data
$ make #Generates executables in the same folder