From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id B6C32138334 for ; Fri, 4 Oct 2019 21:46:08 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 0B11DE0845; Fri, 4 Oct 2019 21:46:08 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id D4AADE0845 for ; Fri, 4 Oct 2019 21:46:07 +0000 (UTC) Received: from oystercatcher.gentoo.org (unknown [IPv6:2a01:4f8:202:4333:225:90ff:fed9:fc84]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 78BD534B92D for ; Fri, 4 Oct 2019 21:46:06 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 8215C7E7 for ; Fri, 4 Oct 2019 21:46:04 +0000 (UTC) From: "Alexey Shvetsov" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Alexey Shvetsov" Message-ID: <1570225541.32a93a6cf9c5d508b67d7257c940234949e58eab.alexxy@gentoo> Subject: [gentoo-commits] repo/gentoo:master commit in: sci-chemistry/gromacs/ X-VCS-Repository: repo/gentoo X-VCS-Files: sci-chemistry/gromacs/Manifest sci-chemistry/gromacs/gromacs-2018.8.ebuild sci-chemistry/gromacs/gromacs-2018.9999.ebuild X-VCS-Directories: sci-chemistry/gromacs/ X-VCS-Committer: alexxy X-VCS-Committer-Name: Alexey Shvetsov X-VCS-Revision: 32a93a6cf9c5d508b67d7257c940234949e58eab X-VCS-Branch: master Date: Fri, 4 Oct 2019 21:46:04 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Auto-Response-Suppress: DR, RN, NRN, OOF, AutoReply X-Archives-Salt: f010529e-24d5-4d6a-a74d-288c342867f8 X-Archives-Hash: 5f977826370779bdc3d44d639267e8ac commit: 32a93a6cf9c5d508b67d7257c940234949e58eab Author: Alexey Shvetsov gentoo org> AuthorDate: Fri Oct 4 21:45:18 2019 +0000 Commit: Alexey Shvetsov gentoo org> CommitDate: Fri Oct 4 21:45:41 2019 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=32a93a6c sci-chemistry/gromacs: Version bump for 2018.x series Package-Manager: Portage-2.3.76, Repoman-2.3.17 Signed-off-by: Alexey Shvetsov gentoo.org> sci-chemistry/gromacs/Manifest | 2 ++ ...macs-2018.9999.ebuild => gromacs-2018.8.ebuild} | 37 ++++++++++++++++++---- sci-chemistry/gromacs/gromacs-2018.9999.ebuild | 37 ++++++++++++++++++---- 3 files changed, 62 insertions(+), 14 deletions(-) diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest index 43ad2677e51..a3e67a7d98a 100644 --- a/sci-chemistry/gromacs/Manifest +++ b/sci-chemistry/gromacs/Manifest @@ -1,8 +1,10 @@ DIST gromacs-2018.7.tar.gz 29912662 BLAKE2B 0714b28ec2443f3201275fc2fa6db1202a059161362134d4de03a900a3a67fe9d31ba8c058d5ee971198fecd69379fcd389f03d25c61f50b8460c43ba5c564d5 SHA512 fbc3b847b70b1396f412b8f4a1b977268651f8d53a222dcf6349fe563ff6319e096484209a24351e382bc9162a949b3900591f5b469c32dd9effeb894f03c172 +DIST gromacs-2018.8.tar.gz 29913703 BLAKE2B 8780032305928067fbfe1559efe9eedc4d47e27ab2f6ab54d6dba39edfcbeefbee4673d8910009048a850620b5a08ba8feb622db652c439cfa50a149ec5f0015 SHA512 6717895942f2ab7b54019511ed2aebadadde8e96d3c4b7414bb9168ffe418432d2dee330192e199f7b9d2f665c71f5d4f1ef0911aa7243d525a2ca182ef5b122 DIST gromacs-2019.2.tar.gz 33437869 BLAKE2B bebe4942688dace148856d4491b687b8e0fd2c86d7fbd9eecdb46824d316a0fc3854464ecafa79d8db92327ee8467be204b050c11f1e71132184efd812c3bf09 SHA512 da7ff24e8485774e22d1c2464fbe64675c3305ef0e21a3d17e363201031952e5d4a9b81f572d5284fb6f2596ed99daf62fe78d653387d9d714274f46bc750183 DIST gromacs-2019.3.tar.gz 33441419 BLAKE2B 79319dd23982c65c7c4d8e5f633cef0c7fd99a38a4e0cc9030a3ffb0fdfc07a4fbfbcfa942896f23a143b747e044fae645498a3e6992497d1f1a7d966f80b2b0 SHA512 de9f54d095b45ea7efd1043f83a40f6c778a6e3e2067a01f48d1ce843d68d226061933ca28a3edb635b795a8ddd5ef9deb8ed1114aa3235bc8039db8ff7d0218 DIST gromacs-2019.4.tar.gz 33444527 BLAKE2B 5a01ed0e38faade037de701b72e8d52fd5a947a23228f0b5170a170dc963b00068a6b6880dd9a3f6f2a73140a3787952741dcbcc862bc357a8be8bf5640faa16 SHA512 adc6dea187b7f3a3c13fcd39445ae45248d46d56b0102fda47b1850b83ff1fb77a3fec99d4a4124b01ed04646dab6ab67749eae1bec36d1ba6f2205855cd29f8 DIST regressiontests-2018.7.tar.gz 67856738 BLAKE2B 955ae8b5e74f90fec704cf41fbd00bd8c09d754f950551fe0adfcd407db6fdb4491a3815149ea37d36c747316c79d462e823b9f6b26f2376bf90d87aad95731b SHA512 c2ff390750bd99faebcd8d5dd8ad6dbf2b00113ed888bddddf985dbf95d7f347093adb67f3c396547b3e2990de330fddb7efe83ded91a72cf97c82a1dac7e826 +DIST regressiontests-2018.8.tar.gz 67855469 BLAKE2B 34c9b339f6229f483afbb5192ee6ba8b8f72d5c26907a853af9c53dfece0d88739e48f6b44b78d1c010f988f9385d077285300522164f533a5861e9dda879275 SHA512 3642389d27bd1942cd0f091c940ae97b197b94856a387fe581dc516b0d4169480f16551d4ba357f9282b3337d605c286d51dd38112ac87c826dda634904836bb DIST regressiontests-2019.2.tar.gz 67643003 BLAKE2B 4178de5d62f194a81f97e442c10f123dc59c5e63f2078f7f07135709f3f6e530e0d237bf40264b285c084519d5ace75dfcbcddc16dc740c4f17233dc33542e45 SHA512 c1f25bc770d3f0a873c887d5563c1cd88179e81211b70ce6f5015696e6fa0b6931a8da7a449f2b223f3105b9e2e7eca67248e96fbfc2a7fd5fb360ba616f22ff DIST regressiontests-2019.3.tar.gz 67640462 BLAKE2B ed6c176a144e0407be66585be5d6090c31c047498bc5f48f59685108de91f2f9ddb2d22b291a15e6ffa1db848aae19b94a79c8c3d34b1067680f759a179953dd SHA512 822e905fb488ce308eb9324d93f78106da5252c773c7941d49c6162e73bdff109aeca1f0d57216c6dd6536a4c41d80013fa1cee2f5206b0c4160a3e5b4a31315 DIST regressiontests-2019.4.tar.gz 67639728 BLAKE2B aba912863669a4a6a6a74e385f9b0974d0c0aa30d3aea7834d77c8bb3f4f59effcbe10a480e74e7aa31fe32d64ba6628d67703ca1894839ce7ddfc8da93902dc SHA512 45de03d368da4e6e5c647f3fea61d64defe6d1cbc1c4219eeac2db27559e3cea7f15f9acb3e56ab934b44ca3ae4ce199b4e4969f704776bb9f0b23f1a34ff56d diff --git a/sci-chemistry/gromacs/gromacs-2018.9999.ebuild b/sci-chemistry/gromacs/gromacs-2018.8.ebuild similarity index 86% copy from sci-chemistry/gromacs/gromacs-2018.9999.ebuild copy to sci-chemistry/gromacs/gromacs-2018.8.ebuild index 0f1504ebd16..4db9e9672b0 100644 --- a/sci-chemistry/gromacs/gromacs-2018.9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-2018.8.ebuild @@ -1,7 +1,7 @@ # Copyright 1999-2019 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 CMAKE_MAKEFILE_GENERATOR="ninja" @@ -47,7 +47,7 @@ CDEPEND=" mkl? ( sci-libs/mkl ) mpi? ( virtual/mpi ) " -DEPEND="${CDEPEND} +BDEPEND="${CDEPEND} virtual/pkgconfig doc? ( app-doc/doxygen @@ -113,6 +113,27 @@ src_prepare() { fi DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" + # try to create policy for imagemagik + mkdir -p ${HOME}/.config/ImageMagick + cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF + + + !ATTLIST policymap xmlns CDATA #FIXED ''> + + + ]> + + + + + + + + + EOF } src_configure() { @@ -196,11 +217,13 @@ src_configure() { mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_THREAD_MPI=OFF - -DGMX_MPI=ON ${cuda} + -DGMX_MPI=ON -DGMX_OPENMM=OFF -DGMX_BUILD_MDRUN_ONLY=ON -DBUILD_SHARED_LIBS=OFF -DGMX_BUILD_MANUAL=OFF + "${opencl[@]}" + "${cuda[@]}" -DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" ) @@ -251,14 +274,14 @@ src_install() { doins src/external/tng_io/include/tng/*h fi # drop unneeded stuff - rm "${ED}"usr/bin/GMXRC* || die - for x in "${ED}"usr/bin/gmx-completion-*.bash ; do + rm "${ED}"/usr/bin/GMXRC* || die + for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do local n=${x##*/gmx-completion-} n="${n%.bash}" - cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die + cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die newbashcomp "${T}"/"${n}" "${n}" done - rm "${ED}"usr/bin/gmx-completion*.bash || die + rm "${ED}"/usr/bin/gmx-completion*.bash || die readme.gentoo_create_doc } diff --git a/sci-chemistry/gromacs/gromacs-2018.9999.ebuild b/sci-chemistry/gromacs/gromacs-2018.9999.ebuild index 0f1504ebd16..4db9e9672b0 100644 --- a/sci-chemistry/gromacs/gromacs-2018.9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-2018.9999.ebuild @@ -1,7 +1,7 @@ # Copyright 1999-2019 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 CMAKE_MAKEFILE_GENERATOR="ninja" @@ -47,7 +47,7 @@ CDEPEND=" mkl? ( sci-libs/mkl ) mpi? ( virtual/mpi ) " -DEPEND="${CDEPEND} +BDEPEND="${CDEPEND} virtual/pkgconfig doc? ( app-doc/doxygen @@ -113,6 +113,27 @@ src_prepare() { fi DOC_CONTENTS="Gromacs can use sci-chemistry/vmd to read additional file formats" + # try to create policy for imagemagik + mkdir -p ${HOME}/.config/ImageMagick + cat >> ${HOME}/.config/ImageMagick/policy.xml <<- EOF + + + !ATTLIST policymap xmlns CDATA #FIXED ''> + + + ]> + + + + + + + + + EOF } src_configure() { @@ -196,11 +217,13 @@ src_configure() { mycmakeargs=( ${mycmakeargs_pre[@]} ${p} -DGMX_THREAD_MPI=OFF - -DGMX_MPI=ON ${cuda} + -DGMX_MPI=ON -DGMX_OPENMM=OFF -DGMX_BUILD_MDRUN_ONLY=ON -DBUILD_SHARED_LIBS=OFF -DGMX_BUILD_MANUAL=OFF + "${opencl[@]}" + "${cuda[@]}" -DGMX_BINARY_SUFFIX="_mpi${suffix}" -DGMX_LIBS_SUFFIX="_mpi${suffix}" ) @@ -251,14 +274,14 @@ src_install() { doins src/external/tng_io/include/tng/*h fi # drop unneeded stuff - rm "${ED}"usr/bin/GMXRC* || die - for x in "${ED}"usr/bin/gmx-completion-*.bash ; do + rm "${ED}"/usr/bin/GMXRC* || die + for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do local n=${x##*/gmx-completion-} n="${n%.bash}" - cat "${ED}"usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die + cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die newbashcomp "${T}"/"${n}" "${n}" done - rm "${ED}"usr/bin/gmx-completion*.bash || die + rm "${ED}"/usr/bin/gmx-completion*.bash || die readme.gentoo_create_doc }