AGILE (gpu image reconstruction library)

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Attention: Research Computing Documentation has Moved
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Please use the new documentation url https://docs.rc.uab.edu/ for all Research Computing documentation needs.


As a result of this move, we have deprecated use of this wiki for documentation. We are providing read-only access to the content to facilitate migration of bookmarks and to serve as an historical record. All content updates should be made at the new documentation site. The original wiki will not receive further updates.

Thank you,

The Research Computing Team

AGILE (Environment for Linear and non-linear Image reconstruction using GPU Acceleration) is an open source library for GPU accelerated reconstruction problems in medical imaging. AGILE is developed at the Institute of Medical Engineering, Gratz University of Technology. It includes reconstruction code for Magnetic Resonance Imaging and Fluorescence Tomography, and was developed and tested on Linux systems.

Using AGILE

AGILE is available as a source code bundle and requires a GPU to execute.

AGILE on Cheaha

At this time, AGILE can only be run on Cheaha by building from source and running directly on the demonstration GPU node.

Preliminary Requirements

Before getting started, please review the Software Build Considerations to help create a sane, reproducible software product.

Using or building software for the GPU on Cheaha requires that you directly log into the GPU compute node. Start an SSH session with cheaha.uabgrid.uab.edu and after you log in execute a second SSH to the GPU compute node. 

ssh cheaha-compute-1-9

Set up Build Environment

The build instructions below will assume all commands are executed from a directory dedicated to the AGILE build, after you are logged into the GPU compute node, set up your build environment. In addition to your base build environment you will need the CUDA compiler utilities. 

mkdir agile-build
cd agile-build
bash
PATH=/bin:/usr/bin; unset LD_LIBRARY_PATH
module load cuda/cuda4.0

Install Dependencies for AGILE Build

CMake

CMake is a build management tool that provides utilities to support cross platform code. The CMake project provides a 32-bit binary for Linux that you can use. The utilities only control the build process, therefore the 32-bit code CMake code should not affect the 64-bit AGILE binaries produced below. 

wget http://www.cmake.org/files/v2.8/cmake-2.8.6-Linux-i386.tar.gz
tar xvfz cmake-2.8.6-Linux-i386.tar.gz
PATH=$PATH:$PWD/cmake-2.8.6-Linux-i386/bin
Boost

Boost is a collection of peer-reviewed portable C++ libraries that are targeted for standardization. Install boost with: 

wget http://downloads.sourceforge.net/project/boost/boost/1.48.0/boost_1_48_0.tar.gz?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fboost%2Ffiles%2Fboost%2F1.48.0%2F&ts=1322092023&use_mirror=cdnetworks-us-2
tar xvfz boost_1_48_0.tar.gz 
cd boost_1_48_0
./bootstrap.sh --prefix=$PWD/../boost
./b2 install
cd ..
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$PWD/boost/lib
Doxygen

Doxygen is a documentation system that supports many languages and builds documentation from source code and comments embedded in the source code, helping ensure accurate API documentation. 

wget http://ftp.stack.nl/pub/users/dimitri/doxygen-1.7.5.1.src.tar.gz
tar xvfz doxygen-1.7.5.1.src.tar.gz 
cd doxygen-1.7.5.1
./configure --prefix $PWD/../doxygen
make 
make install
cd ..
export PATH=$PATH:$PWD/doxygen/bin

Command to Build

The following build instructions were provided by Dr. Puri Bangalore 

ls
more INSTALL 
cd
wget http://downloads.sourceforge.net/project/flex/flex/flex-2.5.35/flex-2.5.35.tar.gz?r=http%3A%2F%2Fflex.sourceforge.net%2F&ts=1322094898&use_mirror=voxel
tar xvfz flex-2.5.35.tar.gz 
cd flex-2.5.35
./configure --prefix=/home/puri/flex
make install
cd
cd flex
ls
ls bin/
export PATH=$PATH:/home/puri/flex/bin
cd
cd doxygen-1.7.5.1
cd
cd agile
mkdir build
cd build
more ../readme.txt 
cmake -DBOOST_ROOT=/home/puri/boost -DCMAKE_INSTALL_PREFIX=/home/puri/apps/ ..
ccmake .
make
make tut01
make tut01-run
cd tutorial/tut01/tut01 
cd tutorial/tut01/
ls
./tut01 
cd ../tut02
ls
./tut02 
./tut02 
cd ../tut03
./tut03 
cd ../tut04
./tut04
cd ../tut05
./tut05
mpirun -np 2 ./tut05
mpirun -np 4 ./tut05
cd ../tut06
./tut06
mpirun -np 4 ./tut06
mpirun -np 2 ./tut06
mpirun -np 1 ./tut06
mpirun -np 2 compute-0-4 compute-0-7 ./tut06
mpirun -np 2 -host compute-0-4 compute-0-7 ./tut06
mpirun -help
mpirun -host compute-0-4 compute-0-7 -np 2 ./tut06
mpirun --host compute-0-4 compute-0-7 -np 2 ./tut06
mpirun -np 2 --host compute-0-4 compute-0-7 ./tut06
mpirun -help
cat > ~/hostfile
mpirun -np 2 -hostfile ~/hostfile ./tut06
cd ../tut07
ls
cd ../tut08
ls
./tut08 
cd
cd agile/apps/tgv_radial_image_recon/
/home/puri/agile/build/apps/tgv_radial_image_recon/nfft2d_tgv_recon_nogfx -param=recon_32_param.txt

AGILE Support

AGILE is not supported on Cheaha beyond the above build instructions provided for AGILE.

AGILE Tutorials

Please visit the AGILE web site for information on use.

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