Received: from localhost (localhost [127.0.0.1]) by mail.netbsd.org (Postfix) with ESMTP id AC3CA84D17 for ; Sat, 20 May 2023 14:42:13 +0000 (UTC) X-Virus-Scanned: amavisd-new at netbsd.org Received: from mail.netbsd.org ([127.0.0.1]) by localhost (mail.netbsd.org [127.0.0.1]) (amavisd-new, port 10025) with ESMTP id t1Ox28piAojf for ; Sat, 20 May 2023 14:42:12 +0000 (UTC) Received: from cvs.NetBSD.org (ivanova.NetBSD.org [IPv6:2001:470:a085:999:28c:faff:fe03:5984]) by mail.netbsd.org (Postfix) with ESMTP id 203C984D58 for ; Sat, 20 May 2023 14:42:12 +0000 (UTC) Received: by cvs.NetBSD.org (Postfix, from userid 500) id 13E30FA87; Sat, 20 May 2023 14:42:12 +0000 (UTC) Content-Transfer-Encoding: 7bit Content-Type: multipart/mixed; boundary="_----------=_168459373222760" MIME-Version: 1.0 Date: Sat, 20 May 2023 14:42:12 +0000 From: "Jason Bacon" Subject: CVS commit: pkgsrc/biology/canu To: pkgsrc-changes@NetBSD.org Approved: commit_and_comment Reply-To: bacon@netbsd.org X-Mailer: log_accum Message-Id: <20230520144212.13E30FA87@cvs.NetBSD.org> This is a multi-part message in MIME format. --_----------=_168459373222760 Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="US-ASCII" Module Name: pkgsrc Committed By: bacon Date: Sat May 20 14:42:11 UTC 2023 Modified Files: pkgsrc/biology/canu: Makefile PLIST distinfo pkgsrc/biology/canu/patches: patch-Makefile patch-pipelines_canu_Defaults.pm patch-pipelines_canu_Execution.pm patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp patch-utility_src_utility_files.H patch-utility_src_utility_logging.H patch-utility_src_utility_system.H patch-utility_src_utility_types.H Added Files: pkgsrc/biology/canu/files: cpuid_arm.c cpuid_ppc.c Log Message: biology/canu: Fix build on Darwin aarch64 Replace SIMDE with upstream source hacks from FreeBSD port Should also work on powerpc, but untested No changes to existing binaries To generate a diff of this commit: cvs rdiff -u -r1.20 -r1.21 pkgsrc/biology/canu/Makefile cvs rdiff -u -r1.3 -r1.4 pkgsrc/biology/canu/PLIST cvs rdiff -u -r1.6 -r1.7 pkgsrc/biology/canu/distinfo cvs rdiff -u -r0 -r1.1 pkgsrc/biology/canu/files/cpuid_arm.c \ pkgsrc/biology/canu/files/cpuid_ppc.c cvs rdiff -u -r1.3 -r1.4 pkgsrc/biology/canu/patches/patch-Makefile \ pkgsrc/biology/canu/patches/patch-pipelines_canu_Defaults.pm \ pkgsrc/biology/canu/patches/patch-pipelines_canu_Execution.pm cvs rdiff -u -r1.2 -r1.3 \ pkgsrc/biology/canu/patches/patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp \ pkgsrc/biology/canu/patches/patch-utility_src_utility_files.H \ pkgsrc/biology/canu/patches/patch-utility_src_utility_logging.H \ pkgsrc/biology/canu/patches/patch-utility_src_utility_system.H \ pkgsrc/biology/canu/patches/patch-utility_src_utility_types.H Please note that diffs are not public domain; they are subject to the copyright notices on the relevant files. --_----------=_168459373222760 Content-Disposition: inline Content-Length: 10371 Content-Transfer-Encoding: binary Content-Type: text/x-diff; charset=us-ascii Modified files: Index: pkgsrc/biology/canu/Makefile diff -u pkgsrc/biology/canu/Makefile:1.20 pkgsrc/biology/canu/Makefile:1.21 --- pkgsrc/biology/canu/Makefile:1.20 Sat May 20 11:27:27 2023 +++ pkgsrc/biology/canu/Makefile Sat May 20 14:42:11 2023 @@ -1,4 +1,4 @@ -# $NetBSD: Makefile,v 1.20 2023/05/20 11:27:27 bacon Exp $ +# $NetBSD: Makefile,v 1.21 2023/05/20 14:42:11 bacon Exp $ DISTNAME= canu-2.2 CATEGORIES= biology java @@ -31,7 +31,7 @@ REPLACE_PERL+= fastq-utilities/*.pl REPLACE_PERL+= *.pl # May work on other 64-bit processors, but untested -ONLY_FOR_PLATFORM= *-*-x86_64 *-*-aarch64 +ONLY_FOR_PLATFORM= *-*-x86_64 *-*-aarch64 *-*-powerpc64 USE_LANGUAGES= c c++ USE_JAVA= run @@ -46,8 +46,15 @@ SITE_PERL_REL= lib/perl5/site_perl JAVAJARDIR= share/java/classes INSTALLATION_DIRS= bin lib/perl5 ${JAVAJARDIR} +.include "../../mk/bsd.prefs.mk" + post-extract: ${CHMOD} -R g-w ${WRKDIR} +.if ${MACHINE_ARCH} == "aarch64" + ${CP} ${FILESDIR}/cpuid_arm.c ${WRKSRC}/utility/src/parasail/cpuid.c +.elif ${MACHINE_ARCH} == "powerpc64" + ${CP} ${FILESDIR}/cpuid_ppc.c ${WRKSRC}/utility/src/parasail/cpuid.c +.endif # Upstream does not want to use lib/perl5/site_perl post-build: @@ -59,8 +66,6 @@ do-install: cd ${TMP_INST}/lib/perl5 && ${PAX} -wr * ${DESTDIR}${PREFIX}/lib/perl5 cd ${TMP_INST}/share && ${PAX} -wr * ${DESTDIR}${PREFIX}/share -.include "../../mk/bsd.prefs.mk" - # Xcode supports -Xpreprocessor -fopenmp, but does not supply OpenMP libs # parallel/openmp installs an entire llvm # Maybe a libomp package would suffice? @@ -69,6 +74,5 @@ do-install: .endif .include "../../devel/boost-libs/buildlink3.mk" -.include "../../devel/simde/buildlink3.mk" .include "../../lang/perl5/module.mk" .include "../../mk/bsd.pkg.mk" Index: pkgsrc/biology/canu/PLIST diff -u pkgsrc/biology/canu/PLIST:1.3 pkgsrc/biology/canu/PLIST:1.4 --- pkgsrc/biology/canu/PLIST:1.3 Sat May 20 11:27:27 2023 +++ pkgsrc/biology/canu/PLIST Sat May 20 14:42:11 2023 @@ -1,4 +1,4 @@ -@comment $NetBSD: PLIST,v 1.3 2023/05/20 11:27:27 bacon Exp $ +@comment $NetBSD: PLIST,v 1.4 2023/05/20 14:42:11 bacon Exp $ bin/alignGFA bin/bogart bin/canu Index: pkgsrc/biology/canu/distinfo diff -u pkgsrc/biology/canu/distinfo:1.6 pkgsrc/biology/canu/distinfo:1.7 --- pkgsrc/biology/canu/distinfo:1.6 Sat May 20 11:27:27 2023 +++ pkgsrc/biology/canu/distinfo Sat May 20 14:42:11 2023 @@ -1,4 +1,4 @@ -$NetBSD: distinfo,v 1.6 2023/05/20 11:27:27 bacon Exp $ +$NetBSD: distinfo,v 1.7 2023/05/20 14:42:11 bacon Exp $ BLAKE2s (canu-2.2.tar.xz) = 5b585a2e0a31c2181817798b5f267dd4cf43c3ffeba4b0a04ffc8021a4603aed SHA512 (canu-2.2.tar.xz) = af08874a319dd5fd6bbe666c8a5d0a43b7c0caaaca3a3cbf4d3fe022d6d6b8c14cd967c2e26f4fbf571129be240dcb65e92fe61fad1e51d554f15254d0b6ce8f @@ -7,8 +7,6 @@ SHA1 (patch-Makefile) = 54a3a216948fea81 SHA1 (patch-pipelines_canu_Defaults.pm) = 5ecea8ebac667499916b0243f34dc25838992444 SHA1 (patch-pipelines_canu_Execution.pm) = 75c019a93f5b6a4491191b4f32931ac0b8435421 SHA1 (patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp) = fd219645141ebe9d6f23153a2a2b0f56abc103af -SHA1 (patch-utility_src_parasail_internal__sse.h) = 3eca097b64273ada2df6f9be895823980ea79902 -SHA1 (patch-utility_src_utility_align-ssw.H) = 146e1959207dfe1deaae7f8f9809ed72be116841 SHA1 (patch-utility_src_utility_files.H) = bc28dfd6957a2e2928b5df6a0e1d08c8ba5b2c27 SHA1 (patch-utility_src_utility_logging.H) = 13e9ced966710cef4a2d38fd2b752f8a726ba07b SHA1 (patch-utility_src_utility_system.H) = e0bab7ed20431948845fac907584215c0b891406 Index: pkgsrc/biology/canu/patches/patch-Makefile diff -u pkgsrc/biology/canu/patches/patch-Makefile:1.3 pkgsrc/biology/canu/patches/patch-Makefile:1.4 --- pkgsrc/biology/canu/patches/patch-Makefile:1.3 Sat May 20 11:27:27 2023 +++ pkgsrc/biology/canu/patches/patch-Makefile Sat May 20 14:42:11 2023 @@ -1,4 +1,4 @@ -$NetBSD: patch-Makefile,v 1.3 2023/05/20 11:27:27 bacon Exp $ +$NetBSD: patch-Makefile,v 1.4 2023/05/20 14:42:11 bacon Exp $ # Portability Index: pkgsrc/biology/canu/patches/patch-pipelines_canu_Defaults.pm diff -u pkgsrc/biology/canu/patches/patch-pipelines_canu_Defaults.pm:1.3 pkgsrc/biology/canu/patches/patch-pipelines_canu_Defaults.pm:1.4 --- pkgsrc/biology/canu/patches/patch-pipelines_canu_Defaults.pm:1.3 Sat May 20 11:27:27 2023 +++ pkgsrc/biology/canu/patches/patch-pipelines_canu_Defaults.pm Sat May 20 14:42:11 2023 @@ -1,4 +1,4 @@ -$NetBSD: patch-pipelines_canu_Defaults.pm,v 1.3 2023/05/20 11:27:27 bacon Exp $ +$NetBSD: patch-pipelines_canu_Defaults.pm,v 1.4 2023/05/20 14:42:11 bacon Exp $ # Better task limit control under slurm Index: pkgsrc/biology/canu/patches/patch-pipelines_canu_Execution.pm diff -u pkgsrc/biology/canu/patches/patch-pipelines_canu_Execution.pm:1.3 pkgsrc/biology/canu/patches/patch-pipelines_canu_Execution.pm:1.4 --- pkgsrc/biology/canu/patches/patch-pipelines_canu_Execution.pm:1.3 Sat May 20 11:27:27 2023 +++ pkgsrc/biology/canu/patches/patch-pipelines_canu_Execution.pm Sat May 20 14:42:11 2023 @@ -1,4 +1,4 @@ -$NetBSD: patch-pipelines_canu_Execution.pm,v 1.3 2023/05/20 11:27:27 bacon Exp $ +$NetBSD: patch-pipelines_canu_Execution.pm,v 1.4 2023/05/20 14:42:11 bacon Exp $ # Better task limit control under slurm Index: pkgsrc/biology/canu/patches/patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp diff -u pkgsrc/biology/canu/patches/patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp:1.2 pkgsrc/biology/canu/patches/patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp:1.3 --- pkgsrc/biology/canu/patches/patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp:1.2 Sat May 20 11:27:27 2023 +++ pkgsrc/biology/canu/patches/patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp Sat May 20 14:42:11 2023 @@ -1,4 +1,4 @@ -$NetBSD: patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp,v 1.2 2023/05/20 11:27:27 bacon Exp $ +$NetBSD: patch-utgcns_libboost_boost_smart__ptr_detail_shared__count.hpp,v 1.3 2023/05/20 14:42:11 bacon Exp $ # Portability Index: pkgsrc/biology/canu/patches/patch-utility_src_utility_files.H diff -u pkgsrc/biology/canu/patches/patch-utility_src_utility_files.H:1.2 pkgsrc/biology/canu/patches/patch-utility_src_utility_files.H:1.3 --- pkgsrc/biology/canu/patches/patch-utility_src_utility_files.H:1.2 Sat May 20 11:27:27 2023 +++ pkgsrc/biology/canu/patches/patch-utility_src_utility_files.H Sat May 20 14:42:11 2023 @@ -1,4 +1,4 @@ -$NetBSD: patch-utility_src_utility_files.H,v 1.2 2023/05/20 11:27:27 bacon Exp $ +$NetBSD: patch-utility_src_utility_files.H,v 1.3 2023/05/20 14:42:11 bacon Exp $ # Portability Index: pkgsrc/biology/canu/patches/patch-utility_src_utility_logging.H diff -u pkgsrc/biology/canu/patches/patch-utility_src_utility_logging.H:1.2 pkgsrc/biology/canu/patches/patch-utility_src_utility_logging.H:1.3 --- pkgsrc/biology/canu/patches/patch-utility_src_utility_logging.H:1.2 Sat May 20 11:27:27 2023 +++ pkgsrc/biology/canu/patches/patch-utility_src_utility_logging.H Sat May 20 14:42:11 2023 @@ -1,4 +1,4 @@ -$NetBSD: patch-utility_src_utility_logging.H,v 1.2 2023/05/20 11:27:27 bacon Exp $ +$NetBSD: patch-utility_src_utility_logging.H,v 1.3 2023/05/20 14:42:11 bacon Exp $ # Portability Index: pkgsrc/biology/canu/patches/patch-utility_src_utility_system.H diff -u pkgsrc/biology/canu/patches/patch-utility_src_utility_system.H:1.2 pkgsrc/biology/canu/patches/patch-utility_src_utility_system.H:1.3 --- pkgsrc/biology/canu/patches/patch-utility_src_utility_system.H:1.2 Sat May 20 11:27:27 2023 +++ pkgsrc/biology/canu/patches/patch-utility_src_utility_system.H Sat May 20 14:42:11 2023 @@ -1,4 +1,4 @@ -$NetBSD: patch-utility_src_utility_system.H,v 1.2 2023/05/20 11:27:27 bacon Exp $ +$NetBSD: patch-utility_src_utility_system.H,v 1.3 2023/05/20 14:42:11 bacon Exp $ # Portability Index: pkgsrc/biology/canu/patches/patch-utility_src_utility_types.H diff -u pkgsrc/biology/canu/patches/patch-utility_src_utility_types.H:1.2 pkgsrc/biology/canu/patches/patch-utility_src_utility_types.H:1.3 --- pkgsrc/biology/canu/patches/patch-utility_src_utility_types.H:1.2 Sat May 20 11:27:27 2023 +++ pkgsrc/biology/canu/patches/patch-utility_src_utility_types.H Sat May 20 14:42:11 2023 @@ -1,4 +1,4 @@ -$NetBSD: patch-utility_src_utility_types.H,v 1.2 2023/05/20 11:27:27 bacon Exp $ +$NetBSD: patch-utility_src_utility_types.H,v 1.3 2023/05/20 14:42:11 bacon Exp $ # Portability Added files: Index: pkgsrc/biology/canu/files/cpuid_arm.c diff -u /dev/null pkgsrc/biology/canu/files/cpuid_arm.c:1.1 --- /dev/null Sat May 20 14:42:12 2023 +++ pkgsrc/biology/canu/files/cpuid_arm.c Sat May 20 14:42:11 2023 @@ -0,0 +1,57 @@ +/** + * @file + * + * @author jeffrey.daily@gmail.com + * + * Copyright (c) 2015 Battelle Memorial Institute. + * + * For non-intel platforms, stub out the intel feature tests. + */ +#include "config.h" + +#include "parasail/cpuid.h" + +int parasail_can_use_avx512vbmi() +{ + return 0; +} + +int parasail_can_use_avx512bw() +{ + return 0; +} + +int parasail_can_use_avx512f() +{ + return 0; +} + +int parasail_can_use_avx2() +{ + return 0; +} + +int parasail_can_use_sse41() +{ + return 0; +} + +int parasail_can_use_sse2() +{ + return 0; +} + +int parasail_can_use_altivec() +{ + return 0; +} + +int parasail_can_use_neon() +{ +#if HAVE_NEON + return 1; +#else + return 0; +#endif +} + Index: pkgsrc/biology/canu/files/cpuid_ppc.c diff -u /dev/null pkgsrc/biology/canu/files/cpuid_ppc.c:1.1 --- /dev/null Sat May 20 14:42:12 2023 +++ pkgsrc/biology/canu/files/cpuid_ppc.c Sat May 20 14:42:11 2023 @@ -0,0 +1,57 @@ +/** + * @file + * + * @author jeffrey.daily@gmail.com + * + * Copyright (c) 2015 Battelle Memorial Institute. + * + * For non-intel platforms, stub out the intel feature tests. + */ +#include "config.h" + +#include "parasail/cpuid.h" + +int parasail_can_use_avx512vbmi() +{ + return 0; +} + +int parasail_can_use_avx512bw() +{ + return 0; +} + +int parasail_can_use_avx512f() +{ + return 0; +} + +int parasail_can_use_avx2() +{ + return 0; +} + +int parasail_can_use_sse41() +{ + return 0; +} + +int parasail_can_use_sse2() +{ + return 0; +} + +int parasail_can_use_altivec() +{ +#if HAVE_ALTIVEC + return 1; +#else + return 0; +#endif +} + +int parasail_can_use_neon() +{ + return 0; +} + --_----------=_168459373222760--