README

Protinfo-cluster can be compiled with the following flags 

*simd flags -default is that scalar only options are enabled *
SSE2=1            enables SSE2 support for older CPUs (Pentium IV, AMD K8)
SSE3=1            enables SSE3 (and SSE2) support for most x86 CPUS (Pentium IV Prescott, AMD Opterons)
AVX=1             enables AVX (and SSE3/SSE2) support for recent CPUS (SandyBridge/IvyBridge, Bulldozer/Piledriver)

*compatibility flags - default is 64 bit with multithreaded options enabled using OpenMP* 
32BIT=1           compiles 32 bit binary - default is 64 bit 
SINGLE_THREADED=1 this flag is needed when OpenMP libraries are not installed or older gcc  (before gcc 4.2)

*GPU flags*
GPU=1 AMD=1       flags to compile GPU code - optimizations and library locations for AMD cards
GPU=1 NVIDIA=1    flags	to compile GPU code - optimizations and	library	locations for NVIDIA cards

*misc*
FAST_DIVISION=1   use the rcp function for SSE/AVX implementation of TMScore - slightly faster with small loss of accuracy in rare cases 
DEBUG=1           Debug mode

To compile;

make clean
make <options> (eg. make SSE3=1 FAST_DIVISION=1 GPU=1 AMD=1) 

For list of option flags

Protinfo_cluster --help

These are also listed in OPTIONS.txt 


For GPUs OpenCL must be installed and the path of the OpenCL library pointed to in the Makefile
AMD GPUs require installation of Catalyst drivers
NVIDIA requires installation of CUDA 4 and NVIDIA drivers
See separate README files for GPU

A set of test scripts have been included in the test directory which includes a set of candidate
structures from the Zhang test set and TMScores and RMSDs of those structures compared to the
experimental structure.

Output files:

History file for hierarchical clustering is a paired list of the clusters joined
History file for pruning is a list of the structures eliminated and the round.
Cluster file lists the structure name, cluster number that it is a member of the average distance to the members of each cluster

Hong Hung 8-18