AGILE (gpu image reconstruction library)
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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
Command to Build
The following build instructions were provided by Dr. Puri Bangalore
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 cd cmake-2.8.6-Linux-i386 export PATH=$PATH:/home/puri/cmake-2.8.6-Linux-i386/bin echo $PATH cd wget http://downloads.sourceforge.net/project/boost/boost/1.48.0/boost_1_48_0.tar.gz?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fboost%2Ffiles%2Fboost%2F1.48.0%2F&ts=1322092023&use_mirror=cdnetworks-us-2 tar xvfz boost_1_48_0.tar.gz export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/puri/boost_1_48_0/libs cd cd boost_1_48_0 ./bootstrap.sh --prefix=/home/puri/boost ./b2 install export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/puri/boost/lib cd wget http://ftp.stack.nl/pub/users/dimitri/doxygen-1.7.5.1.src.tar.gz tar xvfz doxygen-1.7.5.1.src.tar.gz cd doxygen-1.7.5.1 ls more INSTALL cd wget http://downloads.sourceforge.net/project/flex/flex/flex-2.5.35/flex-2.5.35.tar.gz?r=http%3A%2F%2Fflex.sourceforge.net%2F&ts=1322094898&use_mirror=voxel tar xvfz flex-2.5.35.tar.gz cd flex-2.5.35 ./configure --prefix=/home/puri/flex make install cd cd flex ls ls bin/ export PATH=$PATH:/home/puri/flex/bin cd cd doxygen-1.7.5.1 ./configure --prefix /home/puri/doxygen make install make make install cd export PATH=$PATH:/home/puri/doxygen/bin 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.