mirror/freebsd-ports
1
0
Fork 0
mirror of https://git.FreeBSD.org/ports.git synced 2024-12-29 05:38:00 +00:00
Code Issues Releases Activity

biology/gcta: chase the upgrade of OpenBLAS

Browse Source 
GCTA should modify the LAPACK functios calls, this is a temporary fix.

See <https://github.com/jianyangqt/gcta/issues/59>.

PR:		273219
Approved by:	jwb@
This commit is contained in:
Eijiro Shibusawa 2023-12-12 19:53:43 +01:00 committed by Thierry Thomas
parent 84ca7effd3
commit 22df0dbcfa
5 changed files with 72 additions and 3 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

1
biology/gcta/Makefile
View File

@ -1,6 +1,7 @@
PORTNAME= gcta
DISTVERSIONPREFIX= v
DISTVERSION= 1.94.1
PORTREVISION= 1
CATEGORIES= biology
MAINTAINER= jwb@FreeBSD.org

24
biology/gcta/files/patch-include_Matrix.hpp Normal file
View File

@ -0,0 +1,24 @@
--- include/Matrix.hpp.orig 2022-08-03 06:01:52 UTC
+++ include/Matrix.hpp
@@ -32,7 +32,9 @@ bool _LLT(MatrixType &A, double &logdet){
#if GCTA_CPU_x86
dpotrf(&uplo, &cols, vi, &cols, &info);
#else
- dpotrf_(&uplo, &cols, vi, &cols, &info);
+ // OpenBLAS 0.3.25 requires a length argument. Is 1 the right value?
+ // Should all dgeqrf_() calls be patched?
+ dpotrf_(&uplo, &cols, vi, &cols, &info, 1);
#endif
//LOGGER << " LLT time: " << LOGGER.tp("LLT") << std::endl;
if(info == 0){
@@ -41,7 +43,9 @@ bool _LLT(MatrixType &A, double &logdet){
#if GCTA_CPU_x86
dpotri(&uplo, &cols, vi, &cols, &info);
#else
- dpotri_(&uplo, &cols, vi, &cols, &info);
+ // OpenBLAS 0.3.25 requires a length argument. Is 1 the right value?
+ // Should all doptri_() calls be patched?
+ dpotri_(&uplo, &cols, vi, &cols, &info, 1);
#endif
//LOGGER << " LLT inverse time: " << LOGGER.tp("LLT_INV") << std::endl;
if(info == 0){

7
biology/gcta/files/patch-include_cpu.h
View File

@ -1,15 +1,16 @@
--- include/cpu.h.orig 2023-10-13 13:09:13 UTC
--- include/cpu.h.orig 2022-08-03 06:01:52 UTC
+++ include/cpu.h
@@ -13,7 +13,7 @@
@@ -13,7 +13,8 @@
#define GCTA_ARCH_i386 0
#endif
-#if GCTA_ARCH_x86_64 || GCTA_ARCH_i386
+// GCTA_ARCH_x86 is used (mostly) to enable Intel's MKL library
+#if !defined(__FreeBSD__) && (GCTA_ARCH_x86_64 || GCTA_ARCH_i386)
#define GCTA_CPU_x86 1
#else
#define GCTA_CPU_x86 0
@@ -50,4 +50,4 @@
@@ -50,4 +51,4 @@
#include <lapack.h>
#endif

24
biology/gcta/files/patch-main_mkl.cpp Normal file
View File

@ -0,0 +1,24 @@
--- main/mkl.cpp.orig 2023-11-20 14:09:49 UTC
+++ main/mkl.cpp
@@ -365,7 +365,9 @@ bool gcta::comput_inverse_logdet_LDLT_mkl(eigenMatrix
#if GCTA_CPU_x86
dpotrf(&uplo, &int_n, Vi_mkl, &int_n, &info);
#else
- dpotrf_(&uplo, &int_n, Vi_mkl, &int_n, &info);
+ // OpenBLAS 0.3.25 requires a length argument. Is 1 the right value?
+ // Should all dpotrf_() calls be patched?
+ dpotrf_(&uplo, &int_n, Vi_mkl, &int_n, &info, 1);
#endif
//LOGGER << "Finished decompose" << endl;
//spotrf( &uplo, &n, Vi_mkl, &n, &info );
@@ -386,7 +388,9 @@ bool gcta::comput_inverse_logdet_LDLT_mkl(eigenMatrix
#if GCTA_CPU_x86
dpotri(&uplo, &int_n, Vi_mkl, &int_n, &info);
#else
- dpotri_(&uplo, &int_n, Vi_mkl, &int_n, &info);
+ // OpenBLAS 0.3.25 requires a length argument. Is 1 the right value?
+ // Should all dpotri_() calls be patched?
+ dpotri_(&uplo, &int_n, Vi_mkl, &int_n, &info, 1);
#endif
//LOGGER << "Inverse finished" << endl;
//spotri( &uplo, &n, Vi_mkl, &n, &info );

19
biology/gcta/files/patch-src_StatLib.cpp Normal file
View File

@ -0,0 +1,19 @@
--- src/StatLib.cpp.orig 2022-08-03 06:01:52 UTC
+++ src/StatLib.cpp
@@ -1,3 +1,4 @@
+
/*
GCTA: a tool for Genome-wide Complex Trait Analysis
@@ -117,8 +118,10 @@ namespace StatLib{
dormqr(&side, &t, &n, &n, &n, X, &lda, tau, c,
&lda, work, &lwork, &info);
#else
+ // OpenBLAS 0.3.25 requires a length argument. Is 1 the right value?
+ // Should all dormqr_() calls be patched?
dormqr_(&side, &t, &n, &n, &n, X, &lda, tau, c,
- &lda, work, &lwork, &info);
+ &lda, work, &lwork, &info, 1, 1);
#endif
if(info != 0){
return false;