From nobody Tue Dec 12 19:04:17 2023 X-Original-To: dev-commits-ports-all@mlmmj.nyi.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2610:1c1:1:606c::19:1]) by mlmmj.nyi.freebsd.org (Postfix) with ESMTP id 4SqShf12vDz54K1R; Tue, 12 Dec 2023 19:04:18 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from mxrelay.nyi.freebsd.org (mxrelay.nyi.freebsd.org [IPv6:2610:1c1:1:606c::19:3]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256 client-signature RSA-PSS (4096 bits) client-digest SHA256) (Client CN "mxrelay.nyi.freebsd.org", Issuer "R3" (verified OK)) by mx1.freebsd.org (Postfix) with ESMTPS id 4SqShf0bbYz3XVk; Tue, 12 Dec 2023 19:04:18 +0000 (UTC) (envelope-from git@FreeBSD.org) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1702407858; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=yBLI8YNbX+b3HkaoeZuc2TXmY5YfGKnVnRgFO+47orc=; b=FqCpOjby0o7Yz/IxLdl+P64r8yG/JPCE8AmYAUEwQ+wH74DAY7fLcD7L7pJmAtW8LjnKpJ ioCJAhYBxdr4DdooY1e+yw3dtai+dkfyh49gkmpUs8U8zRMKn8JNHzKDgOqfyRuiLExR+x W7WZYXISzYwF6CiVH6a26KIoQ1YX21V6CQFKEw7gtxAS7FDnn7hYr1AnWBwOcnvKKFrUU8 SZOaA4s8jPUJKb1CH2BmVp5pCJFVK9N5p5MvA1kvPCOXrjHRl54GzAasqsONnRGS6ierVT eLT73vs28BWBw8PR431AQJGMtV62E5NYFZvSvSGHzZ8+a+T0kHJMoBjivlDVXw== ARC-Seal: i=1; s=dkim; d=freebsd.org; t=1702407858; a=rsa-sha256; cv=none; b=oBPjSLEdXwQqgwggWM2juMLCurIxKVCvKcbXMGoN4lnza3sH4OCeEhcl5A4tAoBNK38+Hj KnkLdLDrx8RnCZWkkLW7LOjbuNzdot35R/v+n8C+hxftHNz3j1tBT1PGetdwOsKVBo4uEs Gmm84Hox+29mFdQm35F9cjNgjTDaMV4Jf9FFWRJd7nX30hgJDFBWk7qGIJqnKBx24w503i Ao+mkIdxoEbDNQ7vLZhCdolUPutYv1jbNzRn3EZQc9yDhCMnzYgwuszvbtZBCE/0XyFkDB DWX9nX+Vlcbe/p+NRbCcjeMOcppIXVszaWnrGVZIgBUGLYxRgfT+f9tvjtNeYQ== ARC-Authentication-Results: i=1; mx1.freebsd.org; none ARC-Message-Signature: i=1; a=rsa-sha256; c=relaxed/relaxed; d=freebsd.org; s=dkim; t=1702407858; h=from:from:reply-to:subject:subject:date:date:message-id:message-id: to:to:cc:mime-version:mime-version:content-type:content-type: content-transfer-encoding:content-transfer-encoding; bh=yBLI8YNbX+b3HkaoeZuc2TXmY5YfGKnVnRgFO+47orc=; b=VVbQslWtbdKBqCCh7mHTnWnbJ49RHSzJJT2iNifYsU0iq3teRQeDLJUjPzhWRCmGT4X3AT tPh/Nya2DumDj1st78G199n/LGFXCsjfxHZX2qL0KO2Y6QJuDbMZt/qFEDNRTBQEQAKkRG jyYRQa2UXxU3BIsqdX3psyIGkHbn/F1MoH6qxGlkU1ZahO2geDbXpxYjqRQ55d0utdWYeF 9M8+648RLYfR53oBDwGi+/PqhuKYZNqfPgtYTEFxBpPdYJcAFyNt+cmOdSPjfA4EoaoyDF nkmr5jyrcp4Xxuq/OyAFhFOK9v6zbf+ZtXrOPQAKQrHDQyo5sUPWWfKo1yzSbA== Received: from gitrepo.freebsd.org (gitrepo.freebsd.org [IPv6:2610:1c1:1:6068::e6a:5]) (using TLSv1.3 with cipher TLS_AES_256_GCM_SHA384 (256/256 bits) key-exchange X25519 server-signature RSA-PSS (4096 bits) server-digest SHA256) (Client did not present a certificate) by mxrelay.nyi.freebsd.org (Postfix) with ESMTPS id 4SqShd6p73zCNL; Tue, 12 Dec 2023 19:04:17 +0000 (UTC) (envelope-from git@FreeBSD.org) Received: from gitrepo.freebsd.org ([127.0.1.44]) by gitrepo.freebsd.org (8.17.1/8.17.1) with ESMTP id 3BCJ4HTW070090; Tue, 12 Dec 2023 19:04:17 GMT (envelope-from git@gitrepo.freebsd.org) Received: (from git@localhost) by gitrepo.freebsd.org (8.17.1/8.17.1/Submit) id 3BCJ4H8l070087; Tue, 12 Dec 2023 19:04:17 GMT (envelope-from git) Date: Tue, 12 Dec 2023 19:04:17 GMT Message-Id: <202312121904.3BCJ4H8l070087@gitrepo.freebsd.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org From: Thierry Thomas Subject: git: 22df0dbcfa87 - main - biology/gcta: chase the upgrade of OpenBLAS List-Id: Commit messages for all branches of the ports repository List-Archive: https://lists.freebsd.org/archives/dev-commits-ports-all List-Help: List-Post: List-Subscribe: List-Unsubscribe: Sender: owner-dev-commits-ports-all@freebsd.org X-BeenThere: dev-commits-ports-all@freebsd.org MIME-Version: 1.0 Content-Type: text/plain; charset=utf-8 Content-Transfer-Encoding: 8bit X-Git-Committer: thierry X-Git-Repository: ports X-Git-Refname: refs/heads/main X-Git-Reftype: branch X-Git-Commit: 22df0dbcfa877e85bf5c29d7ff6808f7116cafb7 Auto-Submitted: auto-generated The branch main has been updated by thierry: URL: https://cgit.FreeBSD.org/ports/commit/?id=22df0dbcfa877e85bf5c29d7ff6808f7116cafb7 commit 22df0dbcfa877e85bf5c29d7ff6808f7116cafb7 Author: Eijiro Shibusawa AuthorDate: 2023-12-12 18:53:43 +0000 Commit: Thierry Thomas CommitDate: 2023-12-12 19:03:50 +0000 biology/gcta: chase the upgrade of OpenBLAS GCTA should modify the LAPACK functios calls, this is a temporary fix. See . PR: 273219 Approved by: jwb@ --- biology/gcta/Makefile | 1 + biology/gcta/files/patch-include_Matrix.hpp | 24 ++++++++++++++++++++++++ biology/gcta/files/patch-include_cpu.h | 7 ++++--- biology/gcta/files/patch-main_mkl.cpp | 24 ++++++++++++++++++++++++ biology/gcta/files/patch-src_StatLib.cpp | 19 +++++++++++++++++++ 5 files changed, 72 insertions(+), 3 deletions(-) diff --git a/biology/gcta/Makefile b/biology/gcta/Makefile index c9aef3210017..a1721656f2ae 100644 --- a/biology/gcta/Makefile +++ b/biology/gcta/Makefile @@ -1,6 +1,7 @@ PORTNAME= gcta DISTVERSIONPREFIX= v DISTVERSION= 1.94.1 +PORTREVISION= 1 CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org diff --git a/biology/gcta/files/patch-include_Matrix.hpp b/biology/gcta/files/patch-include_Matrix.hpp new file mode 100644 index 000000000000..5039c75580bb --- /dev/null +++ b/biology/gcta/files/patch-include_Matrix.hpp @@ -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){ diff --git a/biology/gcta/files/patch-include_cpu.h b/biology/gcta/files/patch-include_cpu.h index 41c192d4c5f7..92a8e4dd1212 100644 --- a/biology/gcta/files/patch-include_cpu.h +++ b/biology/gcta/files/patch-include_cpu.h @@ -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 #endif diff --git a/biology/gcta/files/patch-main_mkl.cpp b/biology/gcta/files/patch-main_mkl.cpp new file mode 100644 index 000000000000..a74cbecfa6fd --- /dev/null +++ b/biology/gcta/files/patch-main_mkl.cpp @@ -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 ); diff --git a/biology/gcta/files/patch-src_StatLib.cpp b/biology/gcta/files/patch-src_StatLib.cpp new file mode 100644 index 000000000000..bde6badd351a --- /dev/null +++ b/biology/gcta/files/patch-src_StatLib.cpp @@ -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;