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This is the Cross-company Parallel Half-Identical Region Engine (XPHIRE).

Please refer to the file 'INSTALL' for general installation instructions.

Please type `./xphire` for information on running the XPHIRE.

XPHIRE specific installation instructions
-----------------------------------------

If XPHIRE is to process CSV-files with certain DNA that are of no interest,
then XPHIRE can be configured to ignore such data (for a small performance
gain). For example any Y-DNA and MT-DNA of the human genome can be ignored with

  `./configure --enable-maxchr=23`

If only human AT-DNA is of interest, then any other DNA can be ignored with

  `./configure --enable-maxchr=22`

The default minimum length that a half-identical strand of DNA has to have in
order to be detected is 700 SNPs. This can be modified to for example 500 with

  `./configure --enable-minstrand=500`

For SSE 4.2 capable CPUs there is a severe performance penalty for setting
the minimum length to less than 31.

Parallelism can be disabled with

  `./configure --disable-openmp`

For additional XPHIRE-specific configure flags please run `./configure --help`

After having determined the relevant configure options the installation
can usually be done with the commands:

./configure my-configure-options-if-any
make
make install


XPHIRE portability
------------------

Although written for GCC and a CPU with SSE 4.2
XPHIRE is reasonably portable C99 and works with a variety of CPUs
(i386, x86_64, PPC, ARM), Operating Systems (Linux, Darwin, Solaris)
and free compilers (gcc, clang and Sun Studio):

List of successful build + testing (of version 0.9.2):
CPU           Kernel          Compiler           SSE4.2    OpenMP/Threads
i7-3770K      Linux 3.8.00    GCC 4.7.3          Yes       Yes/8

List of successful build + testing (of version 0.9.0):
CPU           Kernel          Compiler           SSE4.2    OpenMP/Threads
i386          Linux 2.6.24    GCC 4.2.4          no        Yes/1
Xeon E7540    Linux 2.6.18    GCC 4.8.1          Yes       Yes/48
i7-3770K      Linux 2.6.35    GCC 4.6.0          Yes       Yes/8
x86_64        Linux 2.6.35    Sun Studio 12.1    No        Yes/2
i5-2520M      Linux 3.2.0     clang 3.0          Yes       No
Athlon 64 X2  Linux 3.2.6     GCC 4.6.3          No        Yes/2
x86_64        Darwin 12.3.0   GCC 4.8.0          No        Yes/2
i386          Darwin 10.8.0   GCC 4.2.1          No        Yes/1
PowerPC       Darwin 9.8.0    GCC 4.0.1          No        No
i386          SunOS 5.10      GCC 3.4.3          No        No
ARMv7         Linux 2.6.28    GCC 4.2.1          No        Yes/1
Source: README, updated 2013-08-23