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phylo
fastcodeml
Commits
f08ea9c2
Commit
f08ea9c2
authored
Jun 21, 2016
by
oshahmir
Browse files
A BG/Q compatible version (can be cross-compiled with XL compiler)
parent
51c4dc5b
Changes
5
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Inline
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BayesTest.cpp
View file @
f08ea9c2
...
...
@@ -547,14 +547,14 @@ double MfgBayesTest::getGridParams(const std::vector<double> &aVars,
}
// Fill the matrices and compute their eigendecomposition.
//
#ifdef _MSC_VER
//
#pragma omp parallel sections default(none) shared( \
#ifdef _MSC_VER
#pragma omp parallel sections default(none) shared( \
omega_fg, omega_bg, kappa, q_fg, q_bg, omega_fg_is_one, omega_bg_is_one)
//
#else
//
#pragma omp parallel sections default(shared)
//
#endif
#else
#pragma omp parallel sections default(shared)
#endif
{
//
#pragma omp section
#pragma omp section
{
if
(
omega_fg_is_one
)
q_fg
.
fillMatrix
(
kappa
);
...
...
@@ -563,7 +563,7 @@ double MfgBayesTest::getGridParams(const std::vector<double> &aVars,
q_fg
.
eigenQREV
();
}
//
#pragma omp section
#pragma omp section
{
if
(
omega_bg_is_one
)
q_bg
.
fillMatrix
(
kappa
);
...
...
CMakeLists.txt
View file @
f08ea9c2
...
...
@@ -193,9 +193,4 @@ target_link_libraries(fast ${EXTRA_LIBS})
if
(
MPI_LIBRARY
)
target_link_libraries
(
fast
${
MPI_LIBRARY
}
)
endif
(
MPI_LIBRARY
)
add_subdirectory
(
bad_cases
)
\ No newline at end of file
endif
(
MPI_LIBRARY
)
\ No newline at end of file
Forest.cpp
View file @
f08ea9c2
...
...
@@ -906,16 +906,16 @@ void Forest::computeLikelihoods(const mfgProbabilityMatrixSet &aSet,
const
int
len
=
static_cast
<
int
>
(
ivs
->
size
());
const
unsigned
int
*
tmp_ivs
=
&
(
*
ivs
)[
0
];
//
#ifdef _MSC_VER
//
#pragma omp parallel for default(none) shared(aSet, len, tmp_ivs, tmp_roots, \
#ifdef _MSC_VER
#pragma omp parallel for default(none) shared(aSet, len, tmp_ivs, tmp_roots, \
likelihoods) schedule(static)
//
#else
//
#pragma omp parallel for default(shared)
//
#endif
#else
#pragma omp parallel for default(shared)
#endif
for
(
int
i
=
0
;
i
<
len
;
++
i
)
{
//
#ifndef _MSC_VER
//
#pragma omp task untied
//
#endif
#ifndef _MSC_VER
#pragma omp task untied
#endif
{
// Compute likelihood array at the root of one tree (the access order is
// the fastest)
...
...
MathSupport.h
View file @
f08ea9c2
...
...
@@ -44,8 +44,8 @@ inline void SetSeedCodeml(int seed, int PrintSeed) {
seed
=
1234567891
*
(
int
)
time
(
NULL
)
+
1
;
}
seed
=
abs
(
seed
);
//
seed = abs(seed);
if
(
seed
<
0
)
seed
=-
seed
;
// if(PrintSeed) {
// fseed = fopen("SeedUsed", "w");
// if(fseed == NULL) std::cout << "can't open file SeedUsed.";
...
...
@@ -73,7 +73,12 @@ inline double rndu2Codeml(void) {
// 32-bit integer assumed.
// From Ripley (1987) table 2.4 line 4.
w_rndu
=
abs
(
w_rndu
*
16807
)
%
2147483647
;
//w_rndu = abs(w_rndu * 16807) % 2147483647;
if
(
w_rndu
>=
0
)
w_rndu
=
(
w_rndu
*
16807
)
%
2147483647
;
else
w_rndu
=
((
-
w_rndu
)
*
16807
)
%
2147483647
;
if
(
w_rndu
==
0
)
w_rndu
=
13
;
return
w_rndu
/
2147483647
.
0
;
...
...
SETPATHS
View file @
f08ea9c2
...
...
@@ -13,10 +13,10 @@
# 2) BG /Q
export
BLAS_LIB_DIR
=
"/bgsys/local/lib64;/opt/ibmcmp/xlf/bg/14.1/lib64"
export
LAPACK_LIB_DIR
=
"/bgsys/local/lib64;/opt/ibmcmp/xlf/bg/14.1/lib64"
export
NLOPT_LIB_DIR
=
"/home/
kali/FastCodeML-1.2.0/FCM-10.06.2014/nlopt-release
/lib"
export
NLOPT_INCLUDE_DIR
=
"/home/
kali/FastCodeML-1.2.0/FCM-10.06.2014/nlopt-release
/include"
export
NLOPT_LIB_DIR
=
"/home/
shahmirz
/lib"
export
NLOPT_INCLUDE_DIR
=
"/home/
shahmirz
/include"
export
MATH_LIB_NAMES
=
"esslbg;lapack;m;xlf90_r;xl;xlfmath;esslbg;dl"
export
BOOST_ROOT
=
"/
home/kali/FastCodeML-1.2.0/FCM-10.06.2014/boost-release
"
export
BOOST_ROOT
=
"/
bgsys/local/boost/1_59_0
"
export
INCLUDE_DIR_MKL
=
"/bgsys/ibm_essl/prod/opt/ibmmath/essl/5.1/include"
export
CXX
=
"/bgsys/drivers/ppcfloor/comm/xl/bin/mpixlcxx"
export
CXXFLAGS
=
"-qstrict -qthreaded -qhalt=e -D_BGQ_COMPILER"
...
...
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