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authorV3n3RiX <venerix@redcorelinux.org>2020-08-25 10:45:55 +0100
committerV3n3RiX <venerix@redcorelinux.org>2020-08-25 10:45:55 +0100
commit3cf7c3ef441822c889356fd1812ebf2944a59851 (patch)
treec513fe68548b40365c1c2ebfe35c58ad431cdd77 /sci-chemistry/gromacs
parent05b8b0e0af1d72e51a3ee61522941bf7605cd01c (diff)
gentoo resync : 25.08.2020
Diffstat (limited to 'sci-chemistry/gromacs')
-rw-r--r--sci-chemistry/gromacs/Manifest17
-rw-r--r--sci-chemistry/gromacs/gromacs-2018.8.ebuild18
-rw-r--r--sci-chemistry/gromacs/gromacs-2019.5-r1.ebuild18
-rw-r--r--sci-chemistry/gromacs/gromacs-2019.6.ebuild18
-rw-r--r--sci-chemistry/gromacs/gromacs-2020.1-r1.ebuild24
-rw-r--r--sci-chemistry/gromacs/gromacs-2020.2.ebuild24
-rw-r--r--sci-chemistry/gromacs/gromacs-2020.3.ebuild341
-rw-r--r--sci-chemistry/gromacs/gromacs-2020.9999.ebuild24
-rw-r--r--sci-chemistry/gromacs/gromacs-9999.ebuild24
9 files changed, 426 insertions, 82 deletions
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest
index 54979d004776..015a4eab9de9 100644
--- a/sci-chemistry/gromacs/Manifest
+++ b/sci-chemistry/gromacs/Manifest
@@ -4,6 +4,7 @@ DIST gromacs-2019.5.tar.gz 33445791 BLAKE2B 1e2e2764b0c8774c878abf4f32c2fa7ddd9b
DIST gromacs-2019.6.tar.gz 33446147 BLAKE2B adc21fb6b841b06d499607f8c0166a673645ef5af0b40bd823d0fff5ea24397e6301c5e1e0070986ae1ce1deba8a42052b66da148b071c1e21f2fe3908fee275 SHA512 7c227a9539e5775d5d128ae9e872a24181d79cdcd2852b86453597987e8d7332ecec371da65d089f6e610c54aafbccc8824ce298743383dd6240719ebee692a8
DIST gromacs-2020.1.tar.gz 29153989 BLAKE2B b1c0313da945c57c74040c2bcd50495b238b0e131cc4ebecd74ae0d01465b47d732ea456a52a2f9d998cd37e2bfdb93d52bd15177328c4b7a14e6b1d8bc00117 SHA512 130394ec70e5d75ea451e9fa77c4ea2dd4adb0c51cc7663ac8579972bab7a0b75d9143d0eebb21802fc93305deca8831393a8cb3f51b6d01f9477f3dadece037
DIST gromacs-2020.2.tar.gz 29144614 BLAKE2B cd20b031dcec32d9a797d66f2679779077910c184702f12f12093d92e8417d42e07bfb17a8fe63e9d29a889d5f57461b5f86e11adfc26635f8d2b5a5df19473a SHA512 348c80fad93b34e6703906fec97c6c2294c0803c326d6145776b732e1c33cd58e0967ddb2ec4799e3583542c09e7a6a015e4d084d60cf97b81b3a92253cca76c
+DIST gromacs-2020.3.tar.gz 29143950 BLAKE2B ea88fcacc3958f1123c1fe4852f7160a04e4daff15dd2eb87c23197bff2e6379f396df0747b078dc86e7bb909ecbb4b6d98530a34234c989a636dbdb2327562d SHA512 8dbd13f8c6dd9ac337e0bea683aeff38010ee9b4ef438de230beb76e5a54884a5c1eda72f20294b7920758978e247900ac3db32b95c7452350fc1f5ef0a4bcc8
DIST manual-2018.8.pdf 10025023 BLAKE2B afb0a6e6a72d78df743fcb57e7c1716848589e571dd35167b957a9b407ca27978ccfb6cb9e0df9c9439b888f352501a00ba32281ed1e0b4193bd606f1d77152e SHA512 b1972f7ce965bfc9377542993c5943ea4868a8ed23a969d4203264746d6bea3a7a65c6379196ece37fd6d68ec7ec80f827bde87d1049284af7082759a124f1d5
DIST manual-2019.5.pdf 12702361 BLAKE2B cb80429a59019b190115bf2af689c0df23b0fec6e41a9ebc9eba20977d1b06eed79044c906c41228883767f673140e15d3a5ef947a0c1ec4fe84012089f4fa91 SHA512 baf27961b87e6120c49abc9dc58e25d12a15588b4ac787e1a086748d488692d4a1262229ac66e550d3cca3a6042545fb6ec472a2c98d6a8698b7a18b4397f605
DIST manual-2019.6.pdf 12702376 BLAKE2B c350127bc06a9eb3dee73da39037c84daeb89500e23cb131bd19a150bf60602d4dde7611e0c6f0f344af4093e96a899303dac71b4df56fd0c44c3a48a56606b7 SHA512 dfdff67c2c1c9ce1f1c236b7686c5331b0fe86951da6c98eddd6a3e748815e0be0a9653ae4318469fcdd913c4e7c355d64a997cc80b9d9fbe6282ef6d98e61eb
@@ -12,11 +13,13 @@ DIST regressiontests-2019.5.tar.gz 67643634 BLAKE2B c4d9535d9a8a650869d67544ad5f
DIST regressiontests-2019.6.tar.gz 67643195 BLAKE2B 1e054e24b187946f7ea28090d4f20cf8e1d79a26253f57ba07d130e0773d8541b8a1552a38023d31a68ce8bc62d8e0af1d98609234bb3e7d3e6d567307ebb386 SHA512 eacf1c55b982515a305c29459fe80a7cd558a8481e5689962aa956148af542568b1d1ce59c6784ecb0afd4768c2b664afa21e12af2d89ae2b06b1ba61ad72036
DIST regressiontests-2020.1.tar.gz 48541809 BLAKE2B 0fec2f0fb7fad0ad48bb790d7df6487e2c1931a0a2134795bf7da4a9087f0f2a3743288fc4ec057fa6b22412c2d8f312cfa3af38be8c5bea51d7a06afb5ac9f0 SHA512 664d29ce39629ed218de65179ce4a73e479d73d30bc96f5ae57624d7e4447298c6122dc09e7873b8cad458eaee0530866411fab20e009e46bf39b133e0de47e8
DIST regressiontests-2020.2.tar.gz 48539492 BLAKE2B 08222ec18e70f551194fc0a060facda394c0d9999e162dace06029aa5f36e7237aeb2468a80d1198257a45fb076f8f633a7279a85976484900bf4154176aa070 SHA512 3066d92a59dafade78807612681d82a7b8a0bd9b74fa7e8784063a908418c55b4427482dc7feb261ff6981fabb2d64a800d3e90ed647ab45e201f4847347bac7
-EBUILD gromacs-2018.8.ebuild 7012 BLAKE2B c54d0bce4d4ffca3365f6f574313ebdf9b0a7e71a8bd7e10c3ffe10f7bddce9854cc4707d1c9f0611e3a0d353fe4ec215d3ee385459748d5266d98f1b5e861a6 SHA512 1de3a0dbba1c03730f7709013515d2282951e0e87e962dce8c46f227bf0e9ddc2034b28ac797c3c2feb81a1c27f1fa10136ea60c861d266ca708e3aac687b8df
-EBUILD gromacs-2019.5-r1.ebuild 7334 BLAKE2B 1f53f81589e531a292a8bf191064b446ea7b021c73df2645e1f8a2d793d7b7020f6908c7b90066f3e328eb78ed42eed91fb40ec98a08254c7538b29c31f9bdf3 SHA512 f57ebd19ee8f5653b7ec80e6981fced22014b8dc7f54be0a438ffe5db0de94f8b1db13b8698cce616544d04b65672465402a4057ee47924478a4d5dd59901c0f
-EBUILD gromacs-2019.6.ebuild 7337 BLAKE2B c12b7eb0e5a53c8b215fc1862b229c75d723865340d0eabd5b660feb613a9dec1482632a975a3f3689c90ada28096a04b819ebd8616f1de35fb1224b92ef85ea SHA512 4bee46c3a389251149573e391214cf3a8a394cca0ccd1c29f5bf827106580007f7e6dbad319a39fe637db5d7a96f4c9883bb81f0975dc214f8af89f0f1d50930
-EBUILD gromacs-2020.1-r1.ebuild 9916 BLAKE2B 1bface90982f6c78c024e92d9741b97a4658f037e73b9126a9cca33ee0169baec055ecbe21d307e3b79488241cd98b2d0a3df644fb330ffdc2819d360ddc981c SHA512 a41b93992725a08eea05125c4685b0c726fa0f1e284879d5ae6c20327ff19d681c135f736829fd546d122dd50587f9fff387220dc685f5989ceca1b45b2c4eba
-EBUILD gromacs-2020.2.ebuild 9916 BLAKE2B 1bface90982f6c78c024e92d9741b97a4658f037e73b9126a9cca33ee0169baec055ecbe21d307e3b79488241cd98b2d0a3df644fb330ffdc2819d360ddc981c SHA512 a41b93992725a08eea05125c4685b0c726fa0f1e284879d5ae6c20327ff19d681c135f736829fd546d122dd50587f9fff387220dc685f5989ceca1b45b2c4eba
-EBUILD gromacs-2020.9999.ebuild 9831 BLAKE2B 0d20f9e04a318eb2313d1b84adb9a747f4b70cc57446031da410e05bc37d2e3b53489110b803b69bcb235ea87dd913e9a7de6531c2e32b6afb9505c44a4d2dbe SHA512 c2edca500cd77e9b88f6b83cb4b3f11819adf313e4b68250d8b446466187e963bdd925665ca3aa532ae2c88b611f15b860f722cdf17c2b145d7cd58a56cb2c17
-EBUILD gromacs-9999.ebuild 9827 BLAKE2B 20a6e2e5b0d70a1c0ada0cafcb12eb170b99ebb37778f467dda1800cabb05d6a34d0dfef9bfaa04b5e6f3b781ed2e5eb97a1f61044e54e526559a9f9093be648 SHA512 19c73f34eda0ed83e58b67c7feb87e6540fb441806c27ae3b6b7d0e59c33cd220d87873fa3b3b9b5c72e8f9f73b778d41d69f21a3fded51a030d1ac6854bc2a2
+DIST regressiontests-2020.3.tar.gz 48541439 BLAKE2B c8b3840b76b7974e5efd518d02da2be3c8e685a420462962cf4ffb7b234bd5ffec0fb83adc962e4ce4716098667e1431f7bc46911bf5400f369881c697c1d0cb SHA512 84848210b2c4c0387c3f347237d58a114bd28c2d248f359e40a4a5b3557fca7763c431d1e03f167dcf22296a48dd47413a644238d72edc1414e3f830dd732416
+EBUILD gromacs-2018.8.ebuild 6958 BLAKE2B 17452127d480265b57b435d84de5860729860e72a47f89ced75cfa18e9efc1b6dc478785545a86313e9fc6a93647d1ae9f4b78167654acc0a95288215df3d35a SHA512 a2c23b418af81162c22b06d4b5fe2114d09288f314dacb6ca7a5b0fecd50a3bf0069237ec036da8c420b133daaf1eef43d40d1b13c525df8f362f9a0a7b9ec51
+EBUILD gromacs-2019.5-r1.ebuild 7280 BLAKE2B 9d26c304b6e67d00a69d6919daf2bde5b542c9e1c5e1e2f44a2fb1350986a1175737bc9f7325c71cca8479a3e90fca63a0debb01eff5bb94113533a0be364839 SHA512 c991901aed3149fa7872f02647aaff424bd93508157c0f734cc0b14b9f81fe55ff996d8a5a7fb7ba1514cf737047cfbd389a54804d2b5659d728df6f004a847e
+EBUILD gromacs-2019.6.ebuild 7283 BLAKE2B 00055c4ba5cf660237d73232aa7a76857bc141eaa79fdbf81985d337c134123ad7fd92b69d017425ec3f11eb2f367a25e8c4168b948f1092b2a1e538cb991886 SHA512 c307ea57a5b7c468ddd454ee97743643363121757c50cda948398090fa9368dc7b52255e6c3a261565894edd77f91d62c221841c1aca3644691c7fb9a0a8d5ef
+EBUILD gromacs-2020.1-r1.ebuild 9844 BLAKE2B 9568558d0558311ed7a8b8d523ec287dea6682ff5eccb6b780e90739f876d262d20b9f938999bb3283a7c05677aa3a33e7c35071822be05fdd4cf4c74d9ec1d9 SHA512 86e3d58bedb8a87210a81bad1450c11dbfbc99623beac78a498c39dcef2628b2a9a6a7b85c036a79ead38e56ce40d3d15beba6072c4fa8cd62011181eacef97f
+EBUILD gromacs-2020.2.ebuild 9844 BLAKE2B 9568558d0558311ed7a8b8d523ec287dea6682ff5eccb6b780e90739f876d262d20b9f938999bb3283a7c05677aa3a33e7c35071822be05fdd4cf4c74d9ec1d9 SHA512 86e3d58bedb8a87210a81bad1450c11dbfbc99623beac78a498c39dcef2628b2a9a6a7b85c036a79ead38e56ce40d3d15beba6072c4fa8cd62011181eacef97f
+EBUILD gromacs-2020.3.ebuild 9844 BLAKE2B 9568558d0558311ed7a8b8d523ec287dea6682ff5eccb6b780e90739f876d262d20b9f938999bb3283a7c05677aa3a33e7c35071822be05fdd4cf4c74d9ec1d9 SHA512 86e3d58bedb8a87210a81bad1450c11dbfbc99623beac78a498c39dcef2628b2a9a6a7b85c036a79ead38e56ce40d3d15beba6072c4fa8cd62011181eacef97f
+EBUILD gromacs-2020.9999.ebuild 9759 BLAKE2B bf1d5b859c466f05b4909113c90faaed916512809ec9563c474461906d49261baeca9b8f7e5bdf85a3fffd32b1b84b4ec47d4523105bba3ed32ce73491d6e7d1 SHA512 cac942e6effce1c0c7ff99ac56c88d9422a89b1b275d3555c5a15a00640c253bd3a98301b9509daf14b3e4d3f1577a8fe6647aab10bf645645ccf35b57470208
+EBUILD gromacs-9999.ebuild 9755 BLAKE2B ee04718fea528c500f797f0ee1ebfb2307772ff5ab4cfc3293f3bf6f93a25ee6155c0b888a4d25371c6a9c4fb022d9e79da9a9df85d7fc82a97442755314ff28 SHA512 5338d8d45908e0b618c21908162e16fff4fba74d671a756229f1f05bce9fd578e923d6289609344cd4a28a78995e2609908de0598cc5d60d45a029ac97b7bba4
MISC metadata.xml 1192 BLAKE2B 560c1c792102747fc16c22d475114480b9897263405da05946721dae5b781c599a02e1401adfa4d929bfb41b4d52791376438aa37d33de18beabc9edbeb779fa SHA512 136c49bfaca76e714e811077c7f7d214a5984c7b6c891c79ad4a754c304752e17450c9aee100dafce04d7bf3893a53224ef9b54504a278654d59fae9acdd0f77
diff --git a/sci-chemistry/gromacs/gromacs-2018.8.ebuild b/sci-chemistry/gromacs/gromacs-2018.8.ebuild
index feaa75c10bff..f124a0eac166 100644
--- a/sci-chemistry/gromacs/gromacs-2018.8.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2018.8.ebuild
@@ -5,7 +5,7 @@ EAPI=7
CMAKE_MAKEFILE_GENERATOR="ninja"
-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils
+inherit bash-completion-r1 cmake cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils
SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${PV/_/-}.pdf )
@@ -68,7 +68,7 @@ src_prepare() {
xdg_environment_reset #591952
- cmake-utils_src_prepare
+ cmake_src_prepare
use cuda && cuda_src_prepare
@@ -158,7 +158,7 @@ src_configure() {
-DGMX_BINARY_SUFFIX="${suffix}"
-DGMX_LIBS_SUFFIX="${suffix}"
)
- BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
+ BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure
[[ ${CHOST} != *-darwin* ]] || \
sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
use mpi || continue
@@ -176,7 +176,7 @@ src_configure() {
-DGMX_BINARY_SUFFIX="_mpi${suffix}"
-DGMX_LIBS_SUFFIX="_mpi${suffix}"
)
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
+ BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake_src_configure
[[ ${CHOST} != *-darwin* ]] || \
sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die
done
@@ -186,31 +186,31 @@ src_compile() {
for x in ${GMX_DIRS}; do
einfo "Compiling for ${x} precision"
BUILD_DIR="${WORKDIR}/${P}_${x}"\
- cmake-utils_src_compile
+ cmake_src_compile
use mpi || continue
einfo "Compiling for ${x} precision with mpi"
BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
- cmake-utils_src_compile
+ cmake_src_compile
done
}
src_test() {
for x in ${GMX_DIRS}; do
BUILD_DIR="${WORKDIR}/${P}_${x}"\
- cmake-utils_src_make check
+ cmake_src_make check
done
}
src_install() {
for x in ${GMX_DIRS}; do
BUILD_DIR="${WORKDIR}/${P}_${x}" \
- cmake-utils_src_install
+ cmake_src_install
if use doc; then
newdoc "${DISTDIR}/manual-${PV/_/-}.pdf" "${PN}-manual-${PV}.pdf"
fi
use mpi || continue
BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
- cmake-utils_src_install
+ cmake_src_install
done
if use tng; then
diff --git a/sci-chemistry/gromacs/gromacs-2019.5-r1.ebuild b/sci-chemistry/gromacs/gromacs-2019.5-r1.ebuild
index d5258ab6f232..7ea93b91af9f 100644
--- a/sci-chemistry/gromacs/gromacs-2019.5-r1.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2019.5-r1.ebuild
@@ -5,7 +5,7 @@ EAPI=7
CMAKE_MAKEFILE_GENERATOR="ninja"
-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils
+inherit bash-completion-r1 cmake cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils
SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${PV/_/-}.pdf )
@@ -71,7 +71,7 @@ src_prepare() {
xdg_environment_reset #591952
- cmake-utils_src_prepare
+ cmake_src_prepare
use cuda && cuda_src_prepare
@@ -170,7 +170,7 @@ src_configure() {
-DGMX_BINARY_SUFFIX="${suffix}"
-DGMX_LIBS_SUFFIX="${suffix}"
)
- BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
+ BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure
[[ ${CHOST} != *-darwin* ]] || \
sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
use mpi || continue
@@ -189,7 +189,7 @@ src_configure() {
-DGMX_BINARY_SUFFIX="_mpi${suffix}"
-DGMX_LIBS_SUFFIX="_mpi${suffix}"
)
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
+ BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake_src_configure
[[ ${CHOST} != *-darwin* ]] || \
sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die
done
@@ -199,31 +199,31 @@ src_compile() {
for x in ${GMX_DIRS}; do
einfo "Compiling for ${x} precision"
BUILD_DIR="${WORKDIR}/${P}_${x}"\
- cmake-utils_src_compile
+ cmake_src_compile
use mpi || continue
einfo "Compiling for ${x} precision with mpi"
BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
- cmake-utils_src_compile
+ cmake_src_compile
done
}
src_test() {
for x in ${GMX_DIRS}; do
BUILD_DIR="${WORKDIR}/${P}_${x}"\
- cmake-utils_src_make check
+ cmake_src_make check
done
}
src_install() {
for x in ${GMX_DIRS}; do
BUILD_DIR="${WORKDIR}/${P}_${x}" \
- cmake-utils_src_install
+ cmake_src_install
if use doc; then
newdoc "${DISTDIR}/manual-${PV/_/-}.pdf" "${PN}-manual-${PV}.pdf"
fi
use mpi || continue
BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
- cmake-utils_src_install
+ cmake_src_install
done
if use tng; then
diff --git a/sci-chemistry/gromacs/gromacs-2019.6.ebuild b/sci-chemistry/gromacs/gromacs-2019.6.ebuild
index e8541e9964ed..85004d2644a2 100644
--- a/sci-chemistry/gromacs/gromacs-2019.6.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2019.6.ebuild
@@ -5,7 +5,7 @@ EAPI=7
CMAKE_MAKEFILE_GENERATOR="ninja"
-inherit bash-completion-r1 cmake-utils cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils
+inherit bash-completion-r1 cmake cuda eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils
SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
doc? ( ftp://ftp.gromacs.org/pub/manual/manual-${PV/_/-}.pdf )
@@ -71,7 +71,7 @@ src_prepare() {
xdg_environment_reset #591952
- cmake-utils_src_prepare
+ cmake_src_prepare
use cuda && cuda_src_prepare
@@ -170,7 +170,7 @@ src_configure() {
-DGMX_BINARY_SUFFIX="${suffix}"
-DGMX_LIBS_SUFFIX="${suffix}"
)
- BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
+ BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure
[[ ${CHOST} != *-darwin* ]] || \
sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
use mpi || continue
@@ -189,7 +189,7 @@ src_configure() {
-DGMX_BINARY_SUFFIX="_mpi${suffix}"
-DGMX_LIBS_SUFFIX="_mpi${suffix}"
)
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
+ BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake_src_configure
[[ ${CHOST} != *-darwin* ]] || \
sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die
done
@@ -199,31 +199,31 @@ src_compile() {
for x in ${GMX_DIRS}; do
einfo "Compiling for ${x} precision"
BUILD_DIR="${WORKDIR}/${P}_${x}"\
- cmake-utils_src_compile
+ cmake_src_compile
use mpi || continue
einfo "Compiling for ${x} precision with mpi"
BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
- cmake-utils_src_compile
+ cmake_src_compile
done
}
src_test() {
for x in ${GMX_DIRS}; do
BUILD_DIR="${WORKDIR}/${P}_${x}"\
- cmake-utils_src_make check
+ cmake_src_make check
done
}
src_install() {
for x in ${GMX_DIRS}; do
BUILD_DIR="${WORKDIR}/${P}_${x}" \
- cmake-utils_src_install
+ cmake_src_install
if use doc; then
newdoc "${DISTDIR}/manual-${PV/_/-}.pdf" "${PN}-manual-${PV}.pdf"
fi
use mpi || continue
BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
- cmake-utils_src_install
+ cmake_src_install
done
if use tng; then
diff --git a/sci-chemistry/gromacs/gromacs-2020.1-r1.ebuild b/sci-chemistry/gromacs/gromacs-2020.1-r1.ebuild
index 9d71d0f73354..ba456196edd8 100644
--- a/sci-chemistry/gromacs/gromacs-2020.1-r1.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2020.1-r1.ebuild
@@ -9,7 +9,7 @@ PYTHON_COMPAT=( python3_{6,7,8} )
DISTUTILS_SINGLE_IMPL=1
-inherit bash-completion-r1 cmake-utils cuda distutils-r1 eutils flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils
+inherit bash-completion-r1 cmake cuda distutils-r1 eutils flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils
if [[ $PV = *9999* ]]; then
EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
@@ -116,7 +116,7 @@ src_prepare() {
xdg_environment_reset #591952
- cmake-utils_src_prepare
+ cmake_src_prepare
use cuda && cuda_src_prepare
@@ -244,7 +244,7 @@ src_configure() {
-DGMX_LIBS_SUFFIX="${suffix}"
-DGMX_PYTHON_PACKAGE=$(usex python)
)
- BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
+ BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure
[[ ${CHOST} != *-darwin* ]] || \
sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
use mpi || continue
@@ -263,7 +263,7 @@ src_configure() {
-DGMX_BINARY_SUFFIX="_mpi${suffix}"
-DGMX_LIBS_SUFFIX="_mpi${suffix}"
)
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
+ BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake_src_configure
[[ ${CHOST} != *-darwin* ]] || \
sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die
done
@@ -273,46 +273,46 @@ src_compile() {
for x in ${GMX_DIRS}; do
einfo "Compiling for ${x} precision"
BUILD_DIR="${WORKDIR}/${P}_${x}"\
- cmake-utils_src_compile
+ cmake_src_compile
if use python; then
BUILD_DIR="${WORKDIR}/${P}_${x}"\
- cmake-utils_src_compile python_packaging/all
+ cmake_src_compile python_packaging/all
BUILD_DIR="${WORKDIR}/${P}" \
distutils-r1_src_compile
fi
# not 100% necessary for rel ebuilds as available from website
if use doc; then
BUILD_DIR="${WORKDIR}/${P}_${x}"\
- cmake-utils_src_compile manual
+ cmake_src_compile manual
fi
use mpi || continue
einfo "Compiling for ${x} precision with mpi"
BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
- cmake-utils_src_compile
+ cmake_src_compile
done
}
src_test() {
for x in ${GMX_DIRS}; do
BUILD_DIR="${WORKDIR}/${P}_${x}"\
- cmake-utils_src_make check
+ cmake_src_make check
done
}
src_install() {
for x in ${GMX_DIRS}; do
BUILD_DIR="${WORKDIR}/${P}_${x}" \
- cmake-utils_src_install
+ cmake_src_install
if use python; then
BUILD_DIR="${WORKDIR}/${P}_${x}" \
- cmake-utils_src_install python_packaging/install
+ cmake_src_install python_packaging/install
fi
if use doc; then
newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
fi
use mpi || continue
BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
- cmake-utils_src_install
+ cmake_src_install
done
if use tng; then
diff --git a/sci-chemistry/gromacs/gromacs-2020.2.ebuild b/sci-chemistry/gromacs/gromacs-2020.2.ebuild
index 9d71d0f73354..ba456196edd8 100644
--- a/sci-chemistry/gromacs/gromacs-2020.2.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2020.2.ebuild
@@ -9,7 +9,7 @@ PYTHON_COMPAT=( python3_{6,7,8} )
DISTUTILS_SINGLE_IMPL=1
-inherit bash-completion-r1 cmake-utils cuda distutils-r1 eutils flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils
+inherit bash-completion-r1 cmake cuda distutils-r1 eutils flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils
if [[ $PV = *9999* ]]; then
EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
@@ -116,7 +116,7 @@ src_prepare() {
xdg_environment_reset #591952
- cmake-utils_src_prepare
+ cmake_src_prepare
use cuda && cuda_src_prepare
@@ -244,7 +244,7 @@ src_configure() {
-DGMX_LIBS_SUFFIX="${suffix}"
-DGMX_PYTHON_PACKAGE=$(usex python)
)
- BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
+ BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure
[[ ${CHOST} != *-darwin* ]] || \
sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
use mpi || continue
@@ -263,7 +263,7 @@ src_configure() {
-DGMX_BINARY_SUFFIX="_mpi${suffix}"
-DGMX_LIBS_SUFFIX="_mpi${suffix}"
)
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
+ BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake_src_configure
[[ ${CHOST} != *-darwin* ]] || \
sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die
done
@@ -273,46 +273,46 @@ src_compile() {
for x in ${GMX_DIRS}; do
einfo "Compiling for ${x} precision"
BUILD_DIR="${WORKDIR}/${P}_${x}"\
- cmake-utils_src_compile
+ cmake_src_compile
if use python; then
BUILD_DIR="${WORKDIR}/${P}_${x}"\
- cmake-utils_src_compile python_packaging/all
+ cmake_src_compile python_packaging/all
BUILD_DIR="${WORKDIR}/${P}" \
distutils-r1_src_compile
fi
# not 100% necessary for rel ebuilds as available from website
if use doc; then
BUILD_DIR="${WORKDIR}/${P}_${x}"\
- cmake-utils_src_compile manual
+ cmake_src_compile manual
fi
use mpi || continue
einfo "Compiling for ${x} precision with mpi"
BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
- cmake-utils_src_compile
+ cmake_src_compile
done
}
src_test() {
for x in ${GMX_DIRS}; do
BUILD_DIR="${WORKDIR}/${P}_${x}"\
- cmake-utils_src_make check
+ cmake_src_make check
done
}
src_install() {
for x in ${GMX_DIRS}; do
BUILD_DIR="${WORKDIR}/${P}_${x}" \
- cmake-utils_src_install
+ cmake_src_install
if use python; then
BUILD_DIR="${WORKDIR}/${P}_${x}" \
- cmake-utils_src_install python_packaging/install
+ cmake_src_install python_packaging/install
fi
if use doc; then
newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
fi
use mpi || continue
BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
- cmake-utils_src_install
+ cmake_src_install
done
if use tng; then
diff --git a/sci-chemistry/gromacs/gromacs-2020.3.ebuild b/sci-chemistry/gromacs/gromacs-2020.3.ebuild
new file mode 100644
index 000000000000..ba456196edd8
--- /dev/null
+++ b/sci-chemistry/gromacs/gromacs-2020.3.ebuild
@@ -0,0 +1,341 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+CMAKE_MAKEFILE_GENERATOR="ninja"
+
+PYTHON_COMPAT=( python3_{6,7,8} )
+
+DISTUTILS_SINGLE_IMPL=1
+
+inherit bash-completion-r1 cmake cuda distutils-r1 eutils flag-o-matic multilib readme.gentoo-r1 toolchain-funcs xdg-utils
+
+if [[ $PV = *9999* ]]; then
+ EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
+ https://gerrit.gromacs.org/gromacs.git
+ https://github.com/gromacs/gromacs.git
+ https://repo.or.cz/r/gromacs.git"
+ [[ $PV = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="release-${PV:0:4}"
+ inherit git-r3
+else
+ SRC_URI="ftp://ftp.gromacs.org/pub/${PN}/${PN}-${PV/_/-}.tar.gz
+ test? ( http://gerrit.gromacs.org/download/regressiontests-${PV/_/-}.tar.gz )"
+ KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+fi
+
+ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2"
+
+DESCRIPTION="The ultimate molecular dynamics simulation package"
+HOMEPAGE="http://www.gromacs.org/"
+
+# see COPYING for details
+# https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING
+# base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib
+LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )"
+SLOT="0/${PV}"
+IUSE="X blas cuda +custom-cflags +doc -double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack +lmfit mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}"
+
+CDEPEND="
+ X? (
+ x11-libs/libX11
+ x11-libs/libSM
+ x11-libs/libICE
+ )
+ blas? ( virtual/blas )
+ cuda? ( >=dev-util/nvidia-cuda-toolkit-6.5.14 )
+ opencl? ( virtual/opencl )
+ fftw? ( sci-libs/fftw:3.0 )
+ hwloc? ( sys-apps/hwloc )
+ lapack? ( virtual/lapack )
+ lmfit? ( sci-libs/lmfit )
+ mkl? ( sci-libs/mkl )
+ mpi? ( virtual/mpi )
+ ${PYTHON_DEPS}
+ !sci-chemistry/gmxapi
+ "
+BDEPEND="${CDEPEND}
+ virtual/pkgconfig
+ doc? (
+ app-doc/doxygen
+ $(python_gen_cond_dep '
+ dev-python/sphinx[${PYTHON_MULTI_USEDEP}]
+ ')
+ media-gfx/mscgen
+ media-gfx/graphviz
+ dev-texlive/texlive-latex
+ dev-texlive/texlive-latexextra
+ media-gfx/imagemagick
+ )"
+RDEPEND="${CDEPEND}"
+
+REQUIRED_USE="
+ || ( single-precision double-precision )
+ cuda? ( single-precision )
+ cuda? ( !opencl )
+ mkl? ( !blas !fftw !lapack )
+ ${PYTHON_REQUIRED_USE}"
+
+DOCS=( AUTHORS README )
+
+RESTRICT="!test? ( test )"
+
+if [[ ${PV} != *9999 ]]; then
+ S="${WORKDIR}/${PN}-${PV/_/-}"
+fi
+
+PATCHES=( "${FILESDIR}/${PN}-2020_beta1-pytest.patch" )
+
+pkg_pretend() {
+ [[ $(gcc-version) == "4.1" ]] && die "gcc 4.1 is not supported by gromacs"
+ use openmp && ! tc-has-openmp && \
+ die "Please switch to an openmp compatible compiler"
+}
+
+pkg_setup() {
+ python-single-r1_pkg_setup
+}
+
+src_unpack() {
+ if [[ ${PV} != *9999 ]]; then
+ default
+ else
+ git-r3_src_unpack
+ if use test; then
+ EGIT_REPO_URI="git://git.gromacs.org/regressiontests.git" \
+ EGIT_BRANCH="${EGIT_BRANCH}" \
+ EGIT_CHECKOUT_DIR="${WORKDIR}/regressiontests"\
+ git-r3_src_unpack
+ fi
+ fi
+}
+
+src_prepare() {
+ #notes/todos
+ # -on apple: there is framework support
+
+ xdg_environment_reset #591952
+
+ cmake_src_prepare
+
+ use cuda && cuda_src_prepare
+
+ GMX_DIRS=""
+ use single-precision && GMX_DIRS+=" float"
+ use double-precision && GMX_DIRS+=" double"
+
+ if use test; then
+ for x in ${GMX_DIRS}; do
+ mkdir -p "${WORKDIR}/${P}_${x}" || die
+ cp -al "${WORKDIR}/regressiontests"* "${WORKDIR}/${P}_${x}/tests" || die
+ done
+ 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
+ <?xml version="1.0" encoding="UTF-8"?>
+ <!DOCTYPE policymap [
+ <!ELEMENT policymap (policy)+>
+ !ATTLIST policymap xmlns CDATA #FIXED ''>
+ <!ELEMENT policy EMPTY>
+ <!ATTLIST policy xmlns CDATA #FIXED '' domain NMTOKEN #REQUIRED
+ name NMTOKEN #IMPLIED pattern CDATA #IMPLIED rights NMTOKEN #IMPLIED
+ stealth NMTOKEN #IMPLIED value CDATA #IMPLIED>
+ ]>
+ <policymap>
+ <policy domain="coder" rights="read | write" pattern="PS" />
+ <policy domain="coder" rights="read | write" pattern="PS2" />
+ <policy domain="coder" rights="read | write" pattern="PS3" />
+ <policy domain="coder" rights="read | write" pattern="EPS" />
+ <policy domain="coder" rights="read | write" pattern="PDF" />
+ <policy domain="coder" rights="read | write" pattern="XPS" />
+ </policymap>
+ EOF
+}
+
+src_configure() {
+ local mycmakeargs_pre=( ) extra fft_opts=( )
+
+ if use custom-cflags; then
+ #go from slowest to fastest acceleration
+ local acce="None"
+ use cpu_flags_x86_sse2 && acce="SSE2"
+ use cpu_flags_x86_sse4_1 && acce="SSE4.1"
+ use cpu_flags_x86_fma4 && acce="AVX_128_FMA"
+ use cpu_flags_x86_avx && acce="AVX_256"
+ use cpu_flags_x86_avx2 && acce="AVX2_256"
+ else
+ strip-flags
+ fi
+
+ #to create man pages, build tree binaries are executed (bug #398437)
+ [[ ${CHOST} = *-darwin* ]] && \
+ extra+=" -DCMAKE_BUILD_WITH_INSTALL_RPATH=OFF"
+
+ if use fftw; then
+ fft_opts=( -DGMX_FFT_LIBRARY=fftw3 )
+ elif use mkl && has_version "=sci-libs/mkl-10*"; then
+ fft_opts=( -DGMX_FFT_LIBRARY=mkl
+ -DMKL_INCLUDE_DIR="${MKLROOT}/include"
+ -DMKL_LIBRARIES="$(echo /opt/intel/mkl/10.0.5.025/lib/*/libmkl.so);$(echo /opt/intel/mkl/10.0.5.025/lib/*/libiomp*.so)"
+ )
+ elif use mkl; then
+ local bits=$(get_libdir)
+ fft_opts=( -DGMX_FFT_LIBRARY=mkl
+ -DMKL_INCLUDE_DIR="$(echo /opt/intel/*/mkl/include)"
+ -DMKL_LIBRARIES="$(echo /opt/intel/*/mkl/lib/*${bits/lib}/libmkl_rt.so)"
+ )
+ else
+ fft_opts=( -DGMX_FFT_LIBRARY=fftpack )
+ fi
+
+ if use lmfit; then
+ local lmfit_opts=( -DGMX_USE_LMFIT=EXTERNAL )
+ else
+ local lmfit_opts=( -DGMX_USE_LMFIT=INTERNAL )
+ fi
+
+ mycmakeargs_pre+=(
+ "${fft_opts[@]}"
+ "${lmfit_opts[@]}"
+ -DGMX_X11=$(usex X)
+ -DGMX_EXTERNAL_BLAS=$(usex blas)
+ -DGMX_EXTERNAL_LAPACK=$(usex lapack)
+ -DGMX_OPENMP=$(usex openmp)
+ -DGMX_COOL_QUOTES=$(usex offensive)
+ -DGMX_USE_TNG=$(usex tng)
+ -DGMX_BUILD_MANUAL=$(usex doc)
+ -DGMX_HWLOC=$(usex hwloc)
+ -DGMX_DEFAULT_SUFFIX=off
+ -DGMX_SIMD="$acce"
+ -DGMX_VMD_PLUGIN_PATH="${EPREFIX}/usr/$(get_libdir)/vmd/plugins/*/molfile/"
+ -DBUILD_TESTING=$(usex test)
+ -DGMX_BUILD_UNITTESTS=$(usex test)
+ -DPYTHON_EXECUTABLE="${EPREFIX}/usr/bin/${EPYTHON}"
+ ${extra}
+ )
+
+ for x in ${GMX_DIRS}; do
+ einfo "Configuring for ${x} precision"
+ local suffix=""
+ #if we build single and double - double is suffixed
+ use double-precision && use single-precision && \
+ [[ ${x} = "double" ]] && suffix="_d"
+ local p
+ [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF"
+ local cuda=( "-DGMX_GPU=OFF" )
+ [[ ${x} = "float" ]] && use cuda && \
+ cuda=( "-DGMX_GPU=ON" )
+ local opencl=( "-DGMX_USE_OPENCL=OFF" )
+ use opencl && opencl=( "-DGMX_USE_OPENCL=ON" ) cuda=( "-DGMX_GPU=ON" )
+ mycmakeargs=(
+ ${mycmakeargs_pre[@]} ${p}
+ -DGMX_MPI=OFF
+ -DGMX_THREAD_MPI=$(usex threads)
+ -DGMXAPI=$(usex gmxapi)
+ -DGMX_INSTALL_LEGACY_API=$(usex gmxapi-legacy)
+ "${opencl[@]}"
+ "${cuda[@]}"
+ "$(use test && echo -DREGRESSIONTEST_PATH="${WORKDIR}/${P}_${x}/tests")"
+ -DGMX_BINARY_SUFFIX="${suffix}"
+ -DGMX_LIBS_SUFFIX="${suffix}"
+ -DGMX_PYTHON_PACKAGE=$(usex python)
+ )
+ BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure
+ [[ ${CHOST} != *-darwin* ]] || \
+ sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
+ use mpi || continue
+ einfo "Configuring for ${x} precision with mpi"
+ mycmakeargs=(
+ ${mycmakeargs_pre[@]} ${p}
+ -DGMX_THREAD_MPI=OFF
+ -DGMX_MPI=ON
+ -DGMX_OPENMM=OFF
+ -DGMXAPI=OFF
+ "${opencl[@]}"
+ "${cuda[@]}"
+ -DGMX_BUILD_MDRUN_ONLY=ON
+ -DBUILD_SHARED_LIBS=OFF
+ -DGMX_BUILD_MANUAL=OFF
+ -DGMX_BINARY_SUFFIX="_mpi${suffix}"
+ -DGMX_LIBS_SUFFIX="_mpi${suffix}"
+ )
+ BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake_src_configure
+ [[ ${CHOST} != *-darwin* ]] || \
+ sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die
+ done
+}
+
+src_compile() {
+ for x in ${GMX_DIRS}; do
+ einfo "Compiling for ${x} precision"
+ BUILD_DIR="${WORKDIR}/${P}_${x}"\
+ cmake_src_compile
+ if use python; then
+ BUILD_DIR="${WORKDIR}/${P}_${x}"\
+ cmake_src_compile python_packaging/all
+ BUILD_DIR="${WORKDIR}/${P}" \
+ distutils-r1_src_compile
+ fi
+ # not 100% necessary for rel ebuilds as available from website
+ if use doc; then
+ BUILD_DIR="${WORKDIR}/${P}_${x}"\
+ cmake_src_compile manual
+ fi
+ use mpi || continue
+ einfo "Compiling for ${x} precision with mpi"
+ BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
+ cmake_src_compile
+ done
+}
+
+src_test() {
+ for x in ${GMX_DIRS}; do
+ BUILD_DIR="${WORKDIR}/${P}_${x}"\
+ cmake_src_make check
+ done
+}
+
+src_install() {
+ for x in ${GMX_DIRS}; do
+ BUILD_DIR="${WORKDIR}/${P}_${x}" \
+ cmake_src_install
+ if use python; then
+ BUILD_DIR="${WORKDIR}/${P}_${x}" \
+ cmake_src_install python_packaging/install
+ fi
+ if use doc; then
+ newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
+ fi
+ use mpi || continue
+ BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
+ cmake_src_install
+ done
+
+ if use tng; then
+ insinto /usr/include/tng
+ doins src/external/tng_io/include/tng/*h
+ fi
+ # drop unneeded stuff
+ rm "${ED}"/usr/bin/GMXRC* || die
+ for x in "${ED}"/usr/bin/gmx-completion-*.bash ; do
+ local n=${x##*/gmx-completion-}
+ n="${n%.bash}"
+ cat "${ED}"/usr/bin/gmx-completion.bash "$x" > "${T}/${n}" || die
+ newbashcomp "${T}"/"${n}" "${n}"
+ done
+ rm "${ED}"/usr/bin/gmx-completion*.bash || die
+ readme.gentoo_create_doc
+}
+
+pkg_postinst() {
+ einfo
+ einfo "Please read and cite:"
+ einfo "Gromacs 4, J. Chem. Theory Comput. 4, 435 (2008). "
+ einfo "https://dx.doi.org/10.1021/ct700301q"
+ einfo
+ readme.gentoo_print_elog
+}
diff --git a/sci-chemistry/gromacs/gromacs-2020.9999.ebuild b/sci-chemistry/gromacs/gromacs-2020.9999.ebuild
index a2dcda755c8b..92600477ee91 100644
--- a/sci-chemistry/gromacs/gromacs-2020.9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-2020.9999.ebuild
@@ -9,7 +9,7 @@ PYTHON_COMPAT=( python3_{6,7} )
DISTUTILS_SINGLE_IMPL=1
-inherit bash-completion-r1 cmake-utils cuda distutils-r1 eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils
+inherit bash-completion-r1 cmake cuda distutils-r1 eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils
if [[ $PV = *9999* ]]; then
EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
@@ -116,7 +116,7 @@ src_prepare() {
xdg_environment_reset #591952
- cmake-utils_src_prepare
+ cmake_src_prepare
use cuda && cuda_src_prepare
@@ -240,7 +240,7 @@ src_configure() {
-DGMX_LIBS_SUFFIX="${suffix}"
-DGMX_PYTHON_PACKAGE=$(usex python)
)
- BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
+ BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure
[[ ${CHOST} != *-darwin* ]] || \
sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
use mpi || continue
@@ -259,7 +259,7 @@ src_configure() {
-DGMX_BINARY_SUFFIX="_mpi${suffix}"
-DGMX_LIBS_SUFFIX="_mpi${suffix}"
)
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
+ BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake_src_configure
[[ ${CHOST} != *-darwin* ]] || \
sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die
done
@@ -269,46 +269,46 @@ src_compile() {
for x in ${GMX_DIRS}; do
einfo "Compiling for ${x} precision"
BUILD_DIR="${WORKDIR}/${P}_${x}"\
- cmake-utils_src_compile
+ cmake_src_compile
if use python; then
BUILD_DIR="${WORKDIR}/${P}_${x}"\
- cmake-utils_src_compile python_packaging/all
+ cmake_src_compile python_packaging/all
BUILD_DIR="${WORKDIR}/${P}" \
distutils-r1_src_compile
fi
# not 100% necessary for rel ebuilds as available from website
if use doc; then
BUILD_DIR="${WORKDIR}/${P}_${x}"\
- cmake-utils_src_compile manual
+ cmake_src_compile manual
fi
use mpi || continue
einfo "Compiling for ${x} precision with mpi"
BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
- cmake-utils_src_compile
+ cmake_src_compile
done
}
src_test() {
for x in ${GMX_DIRS}; do
BUILD_DIR="${WORKDIR}/${P}_${x}"\
- cmake-utils_src_make check
+ cmake_src_make check
done
}
src_install() {
for x in ${GMX_DIRS}; do
BUILD_DIR="${WORKDIR}/${P}_${x}" \
- cmake-utils_src_install
+ cmake_src_install
if use python; then
BUILD_DIR="${WORKDIR}/${P}_${x}" \
- cmake-utils_src_install python_packaging/install
+ cmake_src_install python_packaging/install
fi
if use doc; then
newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
fi
use mpi || continue
BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
- cmake-utils_src_install
+ cmake_src_install
done
if use tng; then
diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild
index 11c545362c66..203a0f716f57 100644
--- a/sci-chemistry/gromacs/gromacs-9999.ebuild
+++ b/sci-chemistry/gromacs/gromacs-9999.ebuild
@@ -9,7 +9,7 @@ PYTHON_COMPAT=( python3_{6,7} )
DISTUTILS_SINGLE_IMPL=1
-inherit bash-completion-r1 cmake-utils cuda distutils-r1 eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils
+inherit bash-completion-r1 cmake cuda distutils-r1 eutils multilib readme.gentoo-r1 toolchain-funcs xdg-utils
if [[ $PV = *9999* ]]; then
EGIT_REPO_URI="git://git.gromacs.org/gromacs.git
@@ -116,7 +116,7 @@ src_prepare() {
xdg_environment_reset #591952
- cmake-utils_src_prepare
+ cmake_src_prepare
use cuda && cuda_src_prepare
@@ -240,7 +240,7 @@ src_configure() {
-DGMX_LIBS_SUFFIX="${suffix}"
-DGMX_PYTHON_PACKAGE=$(usex python)
)
- BUILD_DIR="${WORKDIR}/${P}_${x}" cmake-utils_src_configure
+ BUILD_DIR="${WORKDIR}/${P}_${x}" cmake_src_configure
[[ ${CHOST} != *-darwin* ]] || \
sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}/gentoo_rules.cmake" || die
use mpi || continue
@@ -259,7 +259,7 @@ src_configure() {
-DGMX_BINARY_SUFFIX="_mpi${suffix}"
-DGMX_LIBS_SUFFIX="_mpi${suffix}"
)
- BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake-utils_src_configure
+ BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" CC="mpicc" cmake_src_configure
[[ ${CHOST} != *-darwin* ]] || \
sed -i '/SET(CMAKE_INSTALL_NAME_DIR/s/^/#/' "${WORKDIR}/${P}_${x}_mpi/gentoo_rules.cmake" || die
done
@@ -269,46 +269,46 @@ src_compile() {
for x in ${GMX_DIRS}; do
einfo "Compiling for ${x} precision"
BUILD_DIR="${WORKDIR}/${P}_${x}"\
- cmake-utils_src_compile
+ cmake_src_compile
if use python; then
BUILD_DIR="${WORKDIR}/${P}_${x}"\
- cmake-utils_src_compile python_packaging/all
+ cmake_src_compile python_packaging/all
BUILD_DIR="${WORKDIR}/${P}" \
distutils-r1_src_compile
fi
# not 100% necessary for rel ebuilds as available from website
if use doc; then
BUILD_DIR="${WORKDIR}/${P}_${x}"\
- cmake-utils_src_compile manual
+ cmake_src_compile manual
fi
use mpi || continue
einfo "Compiling for ${x} precision with mpi"
BUILD_DIR="${WORKDIR}/${P}_${x}_mpi"\
- cmake-utils_src_compile
+ cmake_src_compile
done
}
src_test() {
for x in ${GMX_DIRS}; do
BUILD_DIR="${WORKDIR}/${P}_${x}"\
- cmake-utils_src_make check
+ cmake_src_make check
done
}
src_install() {
for x in ${GMX_DIRS}; do
BUILD_DIR="${WORKDIR}/${P}_${x}" \
- cmake-utils_src_install
+ cmake_src_install
if use python; then
BUILD_DIR="${WORKDIR}/${P}_${x}" \
- cmake-utils_src_install python_packaging/install
+ cmake_src_install python_packaging/install
fi
if use doc; then
newdoc "${WORKDIR}/${P}_${x}"/docs/manual/gromacs.pdf "${PN}-manual-${PV}.pdf"
fi
use mpi || continue
BUILD_DIR="${WORKDIR}/${P}_${x}_mpi" \
- cmake-utils_src_install
+ cmake_src_install
done
if use tng; then
generated by cgit v1.2.3 (git 2.25.1) at 2024-06-13 11:50:03 +0000