diff options
Diffstat (limited to 'sci-chemistry/gromacs')
-rw-r--r-- | sci-chemistry/gromacs/Manifest | 32 | ||||
-rw-r--r-- | sci-chemistry/gromacs/gromacs-2018.8-r1.ebuild | 12 | ||||
-rw-r--r-- | sci-chemistry/gromacs/gromacs-2019.6-r1.ebuild | 14 | ||||
-rw-r--r-- | sci-chemistry/gromacs/gromacs-2019.6-r2.ebuild | 14 | ||||
-rw-r--r-- | sci-chemistry/gromacs/gromacs-2020.4-r1.ebuild | 12 | ||||
-rw-r--r-- | sci-chemistry/gromacs/gromacs-2020.7.ebuild | 12 | ||||
-rw-r--r-- | sci-chemistry/gromacs/gromacs-2021.3-r1.ebuild | 12 | ||||
-rw-r--r-- | sci-chemistry/gromacs/gromacs-2021.5.ebuild | 12 | ||||
-rw-r--r-- | sci-chemistry/gromacs/gromacs-2021.6.ebuild | 14 | ||||
-rw-r--r-- | sci-chemistry/gromacs/gromacs-2021.9999.ebuild | 12 | ||||
-rw-r--r-- | sci-chemistry/gromacs/gromacs-2022.3.ebuild | 12 | ||||
-rw-r--r-- | sci-chemistry/gromacs/gromacs-2022.4.ebuild | 12 | ||||
-rw-r--r-- | sci-chemistry/gromacs/gromacs-2022.9999.ebuild | 34 | ||||
-rw-r--r-- | sci-chemistry/gromacs/gromacs-2023.9999.ebuild | 36 | ||||
-rw-r--r-- | sci-chemistry/gromacs/gromacs-2023_rc1.ebuild | 36 | ||||
-rw-r--r-- | sci-chemistry/gromacs/gromacs-9999.ebuild | 36 |
16 files changed, 158 insertions, 154 deletions
diff --git a/sci-chemistry/gromacs/Manifest b/sci-chemistry/gromacs/Manifest index 4bda80af8443..08e12d33c9f3 100644 --- a/sci-chemistry/gromacs/Manifest +++ b/sci-chemistry/gromacs/Manifest @@ -20,7 +20,7 @@ DIST manual-2021.5.pdf 12253641 BLAKE2B 8850715a2bb21345e1c9735aca1a5dd2ad916e5a DIST manual-2021.6.pdf 12256595 BLAKE2B 5d808e38571b38c1f6e0d115f6e604238206cc001f59d05ed855e80c324c0e6fd7767adb723b3d0edd1267ae5973a3b83b76bd04d2dc99769e6440600d8e2146 SHA512 64fe56422d7417f6f61b10346c99e24c3f423f0cedc3794e0809250282bc87ef692b47ae6c3f95ad7994aa3860ed82035cbacc76eb78a2f54a29052a05260af2 DIST manual-2022.3.pdf 13080874 BLAKE2B 3e70da8f70281c78084f5f9af86cdcda187c7b3085f08d95487992a65e31b7dae0b3e66d914dc0bccaf1bfe4c672d2018f38d0bde679759545aca55d1df1f554 SHA512 f634eac722d4a6f77820ef46024d9209de97fb6afb52333f200c2717049d8d09e31f0ef7bac8f154d79ae43fa31541ed6c3d839dd088433222ebdace298b5fae DIST manual-2022.4.pdf 13080976 BLAKE2B 45685fa1d727aa30425e946ac72e0bd723528032e3fb45525d3c025316ee2682ea3c9cc2fd75b5cd4e900adbc6e7f577e3368d9e0681294fd1515df3d2e5d840 SHA512 a7ac3a80a90f14b6917e15633d77230d24cdcf19ade38d14b35c6451074848a7754b33c612e2a26a657f2edd3d6710e5a8130cacb107d4085d1bd934267ad623 -DIST manual-2023_rc1.pdf 13506754 BLAKE2B 9487753e788fa5b2d01255717769e0b01cf7adcb4ae99a1f37f4ad0f8acccfbf4eff0a4c76add63bc82bffdf844cf8dd1d858d15a6bacd6635ec3a3474e10f6f SHA512 f26df914402793c656a798847524c0b9207a4163bb36d6cb90740a699418719f7b124343b4886e50d92023c14f8c1e61e950c12b8e1e4702007e34677cd17ef2 +DIST manual-2023-rc1.pdf 13506754 BLAKE2B 9487753e788fa5b2d01255717769e0b01cf7adcb4ae99a1f37f4ad0f8acccfbf4eff0a4c76add63bc82bffdf844cf8dd1d858d15a6bacd6635ec3a3474e10f6f SHA512 f26df914402793c656a798847524c0b9207a4163bb36d6cb90740a699418719f7b124343b4886e50d92023c14f8c1e61e950c12b8e1e4702007e34677cd17ef2 DIST regressiontests-2018.8.tar.gz 67855469 BLAKE2B 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8158822224006946b320786b17f607d4f561a0427a5f44dcfd69cba2feb5aee7d3e1b86a4ebd9f712ea8a475cd166d29e1e1441e2160a703662fa324b2f7db53 SHA512 22561e31e3abbbc834a0478e43fcc533d7a3d51352e46cf202adb0714953d257f8f8b75034289c8ba6755de7e29f3c0dbfbbb275cd4997d631b280045881d9ca +EBUILD gromacs-2022.4.ebuild 9590 BLAKE2B 8158822224006946b320786b17f607d4f561a0427a5f44dcfd69cba2feb5aee7d3e1b86a4ebd9f712ea8a475cd166d29e1e1441e2160a703662fa324b2f7db53 SHA512 22561e31e3abbbc834a0478e43fcc533d7a3d51352e46cf202adb0714953d257f8f8b75034289c8ba6755de7e29f3c0dbfbbb275cd4997d631b280045881d9ca +EBUILD gromacs-2022.9999.ebuild 9590 BLAKE2B 8158822224006946b320786b17f607d4f561a0427a5f44dcfd69cba2feb5aee7d3e1b86a4ebd9f712ea8a475cd166d29e1e1441e2160a703662fa324b2f7db53 SHA512 22561e31e3abbbc834a0478e43fcc533d7a3d51352e46cf202adb0714953d257f8f8b75034289c8ba6755de7e29f3c0dbfbbb275cd4997d631b280045881d9ca +EBUILD gromacs-2023.9999.ebuild 9534 BLAKE2B 1ebe091e96c5cf231de9edb6659089ee84f49f06d9c093a099cd1c30ce0e03b35db34477c7d8f27f4c68a598376cc6f8df834aee8c3c56ec191fb54d246d4545 SHA512 79f8655ddc978812628a3fbc7927928e1bf6b7baa91c47c0d8fce81966d894bd04a0b152bb19be20b25734986c4d8da37b6586b9e82f66c56275c52cef05265a +EBUILD gromacs-2023_rc1.ebuild 9534 BLAKE2B 1ebe091e96c5cf231de9edb6659089ee84f49f06d9c093a099cd1c30ce0e03b35db34477c7d8f27f4c68a598376cc6f8df834aee8c3c56ec191fb54d246d4545 SHA512 79f8655ddc978812628a3fbc7927928e1bf6b7baa91c47c0d8fce81966d894bd04a0b152bb19be20b25734986c4d8da37b6586b9e82f66c56275c52cef05265a +EBUILD gromacs-9999.ebuild 9534 BLAKE2B 1ebe091e96c5cf231de9edb6659089ee84f49f06d9c093a099cd1c30ce0e03b35db34477c7d8f27f4c68a598376cc6f8df834aee8c3c56ec191fb54d246d4545 SHA512 79f8655ddc978812628a3fbc7927928e1bf6b7baa91c47c0d8fce81966d894bd04a0b152bb19be20b25734986c4d8da37b6586b9e82f66c56275c52cef05265a MISC metadata.xml 1375 BLAKE2B 321b7db8536061655a6efaa40110f4858633921292eba465b85fe0cb50280842e511f2f11385fe5d62bbdfb40e9c0c76e8e986a1efce8eac25d52c438d7ed5f4 SHA512 cc61e0b477f6576079a0f7910475b9091c1c521fbb48efab365d355e3c0a80cd19e1ea9028cb269d37c2572546b1be66a210512e40ff0f2d6314d1b0138cdba6 diff --git a/sci-chemistry/gromacs/gromacs-2018.8-r1.ebuild b/sci-chemistry/gromacs/gromacs-2018.8-r1.ebuild index fb79ed729b5a..255810902b42 100644 --- a/sci-chemistry/gromacs/gromacs-2018.8-r1.ebuild +++ b/sci-chemistry/gromacs/gromacs-2018.8-r1.ebuild @@ -8,15 +8,15 @@ CMAKE_MAKEFILE_GENERATOR="ninja" inherit bash-completion-r1 cmake cuda readme.gentoo-r1 toolchain-funcs xdg-utils SRC_URI=" - http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz - doc? ( http://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf ) + https://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz + doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf ) test? ( https://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" KEYWORDS="amd64 arm x86 ~amd64-linux ~x86-linux ~x64-macos" ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" DESCRIPTION="The ultimate molecular dynamics simulation package" -HOMEPAGE="http://www.gromacs.org/" +HOMEPAGE="https://www.gromacs.org/" # see COPYING for details # https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING @@ -48,6 +48,7 @@ RDEPEND="${CDEPEND}" REQUIRED_USE=" || ( single-precision double-precision ) cuda? ( single-precision ) + opencl? ( single-precision ) cuda? ( !opencl ) mkl? ( !blas !fftw !lapack )" @@ -106,11 +107,6 @@ src_configure() { 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 diff --git a/sci-chemistry/gromacs/gromacs-2019.6-r1.ebuild b/sci-chemistry/gromacs/gromacs-2019.6-r1.ebuild index b04308aaa907..bf9f493d1163 100644 --- a/sci-chemistry/gromacs/gromacs-2019.6-r1.ebuild +++ b/sci-chemistry/gromacs/gromacs-2019.6-r1.ebuild @@ -8,15 +8,15 @@ CMAKE_MAKEFILE_GENERATOR="ninja" inherit bash-completion-r1 cmake cuda readme.gentoo-r1 toolchain-funcs xdg-utils SRC_URI=" - http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz - doc? ( http://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf ) - test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" + https://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz + doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf ) + test? ( https://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" KEYWORDS="amd64 arm x86 ~amd64-linux ~x86-linux ~x64-macos" 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/" +HOMEPAGE="https://www.gromacs.org/" # see COPYING for details # https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING @@ -50,6 +50,7 @@ RDEPEND="${CDEPEND}" REQUIRED_USE=" || ( single-precision double-precision ) cuda? ( single-precision ) + opencl? ( single-precision ) cuda? ( !opencl ) mkl? ( !blas !fftw !lapack ) ${PYTHON_REQUIRED_USE}" @@ -109,11 +110,6 @@ src_configure() { if use fftw; then fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) - elif use mkl && has_version "=sci-libs/mkl-10*"; then - fft_opts=( -DGMX_FFT_LIBRARY=mkl - -DMKL_INCLUDE_DIR="${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=$(get_libdir) fft_opts=( -DGMX_FFT_LIBRARY=mkl diff --git a/sci-chemistry/gromacs/gromacs-2019.6-r2.ebuild b/sci-chemistry/gromacs/gromacs-2019.6-r2.ebuild index 71a5399a8a70..ea9f998593a4 100644 --- a/sci-chemistry/gromacs/gromacs-2019.6-r2.ebuild +++ b/sci-chemistry/gromacs/gromacs-2019.6-r2.ebuild @@ -8,15 +8,15 @@ CMAKE_MAKEFILE_GENERATOR="ninja" inherit bash-completion-r1 cmake cuda readme.gentoo-r1 toolchain-funcs xdg-utils SRC_URI=" - http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz - doc? ( http://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf ) - test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" + https://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz + doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf ) + test? ( https://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos" ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2" DESCRIPTION="The ultimate molecular dynamics simulation package" -HOMEPAGE="http://www.gromacs.org/" +HOMEPAGE="https://www.gromacs.org/" # see COPYING for details # https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING @@ -50,6 +50,7 @@ RDEPEND="${CDEPEND}" REQUIRED_USE=" || ( single-precision double-precision ) cuda? ( single-precision ) + opencl? ( single-precision ) cuda? ( !opencl ) mkl? ( !blas !fftw !lapack ) ${PYTHON_REQUIRED_USE}" @@ -111,11 +112,6 @@ src_configure() { if use fftw; then fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) - elif use mkl && has_version "=sci-libs/mkl-10*"; then - fft_opts=( -DGMX_FFT_LIBRARY=mkl - -DMKL_INCLUDE_DIR="${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 diff --git a/sci-chemistry/gromacs/gromacs-2020.4-r1.ebuild b/sci-chemistry/gromacs/gromacs-2020.4-r1.ebuild index 90ca3b46ae0a..a1a975ee8107 100644 --- a/sci-chemistry/gromacs/gromacs-2020.4-r1.ebuild +++ b/sci-chemistry/gromacs/gromacs-2020.4-r1.ebuild @@ -22,16 +22,16 @@ if [[ ${PV} = *9999* ]]; then inherit git-r3 else SRC_URI=" - http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz + https://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf ) - test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" + test? ( https://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" KEYWORDS="amd64 arm x86 ~amd64-linux ~x86-linux ~x64-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/" +HOMEPAGE="https://www.gromacs.org/" # see COPYING for details # https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING @@ -76,6 +76,7 @@ REQUIRED_USE=" || ( single-precision double-precision ) doc? ( !build-manual ) cuda? ( single-precision ) + opencl? ( single-precision ) cuda? ( !opencl ) mkl? ( !blas !fftw !lapack ) ${PYTHON_REQUIRED_USE}" @@ -181,11 +182,6 @@ src_configure() { if use fftw; then fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) - elif use mkl && has_version "=sci-libs/mkl-10*"; then - fft_opts=( -DGMX_FFT_LIBRARY=mkl - -DMKL_INCLUDE_DIR="${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 diff --git a/sci-chemistry/gromacs/gromacs-2020.7.ebuild b/sci-chemistry/gromacs/gromacs-2020.7.ebuild index ef73982121ff..afbf991e279f 100644 --- a/sci-chemistry/gromacs/gromacs-2020.7.ebuild +++ b/sci-chemistry/gromacs/gromacs-2020.7.ebuild @@ -22,16 +22,16 @@ if [[ ${PV} = *9999* ]]; then inherit git-r3 else SRC_URI=" - http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz + https://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf ) - test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" + test? ( https://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-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/" +HOMEPAGE="https://www.gromacs.org/" # see COPYING for details # https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING @@ -76,6 +76,7 @@ REQUIRED_USE=" || ( single-precision double-precision ) doc? ( !build-manual ) cuda? ( single-precision ) + opencl? ( single-precision ) cuda? ( !opencl ) mkl? ( !blas !fftw !lapack ) ${PYTHON_REQUIRED_USE}" @@ -181,11 +182,6 @@ src_configure() { if use fftw; then fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) - elif use mkl && has_version "=sci-libs/mkl-10*"; then - fft_opts=( -DGMX_FFT_LIBRARY=mkl - -DMKL_INCLUDE_DIR="${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 diff --git a/sci-chemistry/gromacs/gromacs-2021.3-r1.ebuild b/sci-chemistry/gromacs/gromacs-2021.3-r1.ebuild index c8f88acab2c3..f55212f3bdc7 100644 --- a/sci-chemistry/gromacs/gromacs-2021.3-r1.ebuild +++ b/sci-chemistry/gromacs/gromacs-2021.3-r1.ebuild @@ -22,16 +22,16 @@ if [[ ${PV} = *9999* ]]; then inherit git-r3 else SRC_URI=" - http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz + https://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf ) - test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" + test? ( https://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" KEYWORDS="amd64 arm x86 ~amd64-linux ~x86-linux ~x64-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 cpu_flags_x86_avx512f cpu_flags_arm_neon" DESCRIPTION="The ultimate molecular dynamics simulation package" -HOMEPAGE="http://www.gromacs.org/" +HOMEPAGE="https://www.gromacs.org/" # see COPYING for details # https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING @@ -76,6 +76,7 @@ REQUIRED_USE=" || ( single-precision double-precision ) doc? ( !build-manual ) cuda? ( single-precision ) + opencl? ( single-precision ) cuda? ( !opencl ) mkl? ( !blas !fftw !lapack ) ${PYTHON_REQUIRED_USE}" @@ -189,11 +190,6 @@ src_configure() { if use fftw; then fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) - elif use mkl && has_version "=sci-libs/mkl-10*"; then - fft_opts=( -DGMX_FFT_LIBRARY=mkl - -DMKL_INCLUDE_DIR="${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 diff --git a/sci-chemistry/gromacs/gromacs-2021.5.ebuild b/sci-chemistry/gromacs/gromacs-2021.5.ebuild index c3df9c15d1d4..0a8e8fdc1642 100644 --- a/sci-chemistry/gromacs/gromacs-2021.5.ebuild +++ b/sci-chemistry/gromacs/gromacs-2021.5.ebuild @@ -22,16 +22,16 @@ if [[ ${PV} = *9999* ]]; then inherit git-r3 else SRC_URI=" - http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz + https://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf ) - test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" + test? ( https://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-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 cpu_flags_x86_avx512f cpu_flags_arm_neon" DESCRIPTION="The ultimate molecular dynamics simulation package" -HOMEPAGE="http://www.gromacs.org/" +HOMEPAGE="https://www.gromacs.org/" # see COPYING for details # https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING @@ -76,6 +76,7 @@ REQUIRED_USE=" || ( single-precision double-precision ) doc? ( !build-manual ) cuda? ( single-precision ) + opencl? ( single-precision ) cuda? ( !opencl ) mkl? ( !blas !fftw !lapack ) ${PYTHON_REQUIRED_USE}" @@ -189,11 +190,6 @@ src_configure() { if use fftw; then fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) - elif use mkl && has_version "=sci-libs/mkl-10*"; then - fft_opts=( -DGMX_FFT_LIBRARY=mkl - -DMKL_INCLUDE_DIR="${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 diff --git a/sci-chemistry/gromacs/gromacs-2021.6.ebuild b/sci-chemistry/gromacs/gromacs-2021.6.ebuild index c3df9c15d1d4..0614696b9b09 100644 --- a/sci-chemistry/gromacs/gromacs-2021.6.ebuild +++ b/sci-chemistry/gromacs/gromacs-2021.6.ebuild @@ -22,16 +22,16 @@ if [[ ${PV} = *9999* ]]; then inherit git-r3 else SRC_URI=" - http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz + https://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf ) - test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" - KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-macos" + test? ( https://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" + KEYWORDS="amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-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 cpu_flags_x86_avx512f cpu_flags_arm_neon" DESCRIPTION="The ultimate molecular dynamics simulation package" -HOMEPAGE="http://www.gromacs.org/" +HOMEPAGE="https://www.gromacs.org/" # see COPYING for details # https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING @@ -76,6 +76,7 @@ REQUIRED_USE=" || ( single-precision double-precision ) doc? ( !build-manual ) cuda? ( single-precision ) + opencl? ( single-precision ) cuda? ( !opencl ) mkl? ( !blas !fftw !lapack ) ${PYTHON_REQUIRED_USE}" @@ -189,11 +190,6 @@ src_configure() { if use fftw; then fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) - elif use mkl && has_version "=sci-libs/mkl-10*"; then - fft_opts=( -DGMX_FFT_LIBRARY=mkl - -DMKL_INCLUDE_DIR="${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 diff --git a/sci-chemistry/gromacs/gromacs-2021.9999.ebuild b/sci-chemistry/gromacs/gromacs-2021.9999.ebuild index 44a39087816b..31f880174588 100644 --- a/sci-chemistry/gromacs/gromacs-2021.9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-2021.9999.ebuild @@ -22,16 +22,16 @@ if [[ ${PV} = *9999* ]]; then inherit git-r3 else SRC_URI=" - http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz + https://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf ) - test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" + test? ( https://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" KEYWORDS="~amd64 ~arm ~x86 ~amd64-linux ~x86-linux ~x64-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 cpu_flags_x86_avx512f cpu_flags_arm_neon" DESCRIPTION="The ultimate molecular dynamics simulation package" -HOMEPAGE="http://www.gromacs.org/" +HOMEPAGE="https://www.gromacs.org/" # see COPYING for details # https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING @@ -76,6 +76,7 @@ REQUIRED_USE=" || ( single-precision double-precision ) doc? ( !build-manual ) cuda? ( single-precision ) + opencl? ( single-precision ) cuda? ( !opencl ) mkl? ( !blas !fftw !lapack ) ${PYTHON_REQUIRED_USE}" @@ -187,11 +188,6 @@ src_configure() { if use fftw; then fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) - elif use mkl && has_version "=sci-libs/mkl-10*"; then - fft_opts=( -DGMX_FFT_LIBRARY=mkl - -DMKL_INCLUDE_DIR="${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 diff --git a/sci-chemistry/gromacs/gromacs-2022.3.ebuild b/sci-chemistry/gromacs/gromacs-2022.3.ebuild index 8719a5c86554..d0f55aca4bc1 100644 --- a/sci-chemistry/gromacs/gromacs-2022.3.ebuild +++ b/sci-chemistry/gromacs/gromacs-2022.3.ebuild @@ -22,9 +22,9 @@ if [[ ${PV} = *9999* ]]; then inherit git-r3 else SRC_URI=" - http://ftp.gromacs.org/gromacs/${P}.tar.gz + https://ftp.gromacs.org/gromacs/${P}.tar.gz doc? ( https://ftp.gromacs.org/manual/manual-${PV}.pdf ) - test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV}.tar.gz )" + test? ( https://ftp.gromacs.org/regressiontests/regressiontests-${PV}.tar.gz )" # since 2022 arm support was dropped (but not arm64) KEYWORDS="~amd64 -arm ~arm64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" fi @@ -32,7 +32,7 @@ fi ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_avx512f cpu_flags_arm_neon" DESCRIPTION="The ultimate molecular dynamics simulation package" -HOMEPAGE="http://www.gromacs.org/" +HOMEPAGE="https://www.gromacs.org/" # see COPYING for details # https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING @@ -75,6 +75,7 @@ REQUIRED_USE=" || ( single-precision double-precision ) doc? ( !build-manual ) cuda? ( single-precision ) + opencl? ( single-precision ) cuda? ( !opencl ) clang-cuda? ( clang cuda ) mkl? ( !blas !fftw !lapack ) @@ -200,11 +201,6 @@ src_configure() { 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 diff --git a/sci-chemistry/gromacs/gromacs-2022.4.ebuild b/sci-chemistry/gromacs/gromacs-2022.4.ebuild index 8719a5c86554..d0f55aca4bc1 100644 --- a/sci-chemistry/gromacs/gromacs-2022.4.ebuild +++ b/sci-chemistry/gromacs/gromacs-2022.4.ebuild @@ -22,9 +22,9 @@ if [[ ${PV} = *9999* ]]; then inherit git-r3 else SRC_URI=" - http://ftp.gromacs.org/gromacs/${P}.tar.gz + https://ftp.gromacs.org/gromacs/${P}.tar.gz doc? ( https://ftp.gromacs.org/manual/manual-${PV}.pdf ) - test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV}.tar.gz )" + test? ( https://ftp.gromacs.org/regressiontests/regressiontests-${PV}.tar.gz )" # since 2022 arm support was dropped (but not arm64) KEYWORDS="~amd64 -arm ~arm64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" fi @@ -32,7 +32,7 @@ fi ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_avx512f cpu_flags_arm_neon" DESCRIPTION="The ultimate molecular dynamics simulation package" -HOMEPAGE="http://www.gromacs.org/" +HOMEPAGE="https://www.gromacs.org/" # see COPYING for details # https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING @@ -75,6 +75,7 @@ REQUIRED_USE=" || ( single-precision double-precision ) doc? ( !build-manual ) cuda? ( single-precision ) + opencl? ( single-precision ) cuda? ( !opencl ) clang-cuda? ( clang cuda ) mkl? ( !blas !fftw !lapack ) @@ -200,11 +201,6 @@ src_configure() { 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 diff --git a/sci-chemistry/gromacs/gromacs-2022.9999.ebuild b/sci-chemistry/gromacs/gromacs-2022.9999.ebuild index f8165b39b590..d0f55aca4bc1 100644 --- a/sci-chemistry/gromacs/gromacs-2022.9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-2022.9999.ebuild @@ -22,24 +22,24 @@ if [[ ${PV} = *9999* ]]; then inherit git-r3 else SRC_URI=" - http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz - doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf -> manual-${PV}.pdf ) - test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" + https://ftp.gromacs.org/gromacs/${P}.tar.gz + doc? ( https://ftp.gromacs.org/manual/manual-${PV}.pdf ) + test? ( https://ftp.gromacs.org/regressiontests/regressiontests-${PV}.tar.gz )" # since 2022 arm support was dropped (but not arm64) - KEYWORDS="~amd64 -arm ~x86 ~amd64-linux ~x86-linux ~x64-macos" + KEYWORDS="~amd64 -arm ~arm64 ~x86 ~amd64-linux ~x86-linux ~x64-macos" fi ACCE_IUSE="cpu_flags_x86_sse2 cpu_flags_x86_sse4_1 cpu_flags_x86_fma4 cpu_flags_x86_avx cpu_flags_x86_avx2 cpu_flags_x86_avx512f cpu_flags_arm_neon" DESCRIPTION="The ultimate molecular dynamics simulation package" -HOMEPAGE="http://www.gromacs.org/" +HOMEPAGE="https://www.gromacs.org/" # see COPYING for details # https://repo.or.cz/w/gromacs.git/blob/HEAD:/COPYING # base, vmd plugins, fftpack from numpy, blas/lapck from netlib, memtestG80 library, mpi_thread lib LICENSE="LGPL-2.1 UoI-NCSA !mkl? ( !fftw? ( BSD ) !blas? ( BSD ) !lapack? ( BSD ) ) cuda? ( LGPL-3 ) threads? ( BSD )" SLOT="0/${PV}" -IUSE="blas cuda +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" +IUSE="blas clang clang-cuda cuda +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" CDEPEND=" blas? ( virtual/blas ) @@ -56,6 +56,7 @@ CDEPEND=" " BDEPEND="${CDEPEND} virtual/pkgconfig + clang? ( >=sys-devel/clang-6:* ) build-manual? ( app-doc/doxygen $(python_gen_cond_dep ' @@ -74,7 +75,9 @@ REQUIRED_USE=" || ( single-precision double-precision ) doc? ( !build-manual ) cuda? ( single-precision ) + opencl? ( single-precision ) cuda? ( !opencl ) + clang-cuda? ( clang cuda ) mkl? ( !blas !fftw !lapack ) ${PYTHON_REQUIRED_USE}" @@ -115,6 +118,19 @@ src_prepare() { xdg_environment_reset #591952 + # we can use clang as default + if use clang && ! tc-is-clang ; then + export CC=${CHOST}-clang + export CXX=${CHOST}-clang++ + else + tc-export CXX CC + fi + # clang-cuda need to filter mfpmath + if use clang-cuda ; then + filter-mfpmath sse + filter-mfpmath i386 + fi + cmake_src_prepare use cuda && cuda_src_prepare @@ -185,11 +201,6 @@ src_configure() { if use fftw; then fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) - elif use mkl && has_version "=sci-libs/mkl-10*"; then - fft_opts=( -DGMX_FFT_LIBRARY=mkl - -DMKL_INCLUDE_DIR="${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 @@ -232,6 +243,7 @@ src_configure() { [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" local gpu=( "-DGMX_GPU=OFF" ) [[ ${x} = "float" ]] && use cuda && gpu=( "-DGMX_GPU=CUDA" ) + [[ ${x} = "float" ]] && use clang-cuda && gpu=( "-DGMX_GPU=CUDA" "-DGMX_CLANG_CUDA=ON" ) use opencl && gpu=( "-DGMX_GPU=OPENCL" ) mycmakeargs=( ${mycmakeargs_pre[@]} ${p} diff --git a/sci-chemistry/gromacs/gromacs-2023.9999.ebuild b/sci-chemistry/gromacs/gromacs-2023.9999.ebuild index 55fe829229e7..c69ff70b99d3 100644 --- a/sci-chemistry/gromacs/gromacs-2023.9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-2023.9999.ebuild @@ -22,24 +22,24 @@ if [[ ${PV} = *9999* ]]; then inherit git-r3 else SRC_URI=" - http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz - doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf -> manual-${PV}.pdf ) - test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" + https://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz + doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf ) + test? ( https://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" # since 2022 arm support was dropped (but not arm64) - KEYWORDS="~amd64 -arm ~x86 ~amd64-linux ~x86-linux ~x64-macos" + KEYWORDS="~amd64 -arm ~arm64 ~x86 ~amd64-linux ~x86-linux ~x64-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 cpu_flags_x86_avx512f cpu_flags_arm_neon" DESCRIPTION="The ultimate molecular dynamics simulation package" -HOMEPAGE="http://www.gromacs.org/" +HOMEPAGE="https://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="blas cuda +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" +IUSE="blas clang clang-cuda cuda +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" CDEPEND=" blas? ( virtual/blas ) @@ -51,11 +51,12 @@ CDEPEND=" mkl? ( sci-libs/mkl ) mpi? ( virtual/mpi[cxx] ) sci-libs/lmfit:= - >=dev-cpp/muParser-2.3.4:= + >=dev-cpp/muParser-2.3:= ${PYTHON_DEPS} " BDEPEND="${CDEPEND} virtual/pkgconfig + clang? ( >=sys-devel/clang-6:* ) build-manual? ( app-doc/doxygen $(python_gen_cond_dep ' @@ -73,7 +74,9 @@ REQUIRED_USE=" || ( single-precision double-precision ) doc? ( !build-manual ) cuda? ( single-precision ) + opencl? ( single-precision ) cuda? ( !opencl ) + clang-cuda? ( clang cuda ) mkl? ( !blas !fftw !lapack ) ${PYTHON_REQUIRED_USE}" @@ -114,6 +117,19 @@ src_prepare() { xdg_environment_reset #591952 + # we can use clang as default + if use clang && ! tc-is-clang ; then + export CC=${CHOST}-clang + export CXX=${CHOST}-clang++ + else + tc-export CXX CC + fi + # clang-cuda need to filter mfpmath + if use clang-cuda ; then + filter-mfpmath sse + filter-mfpmath i386 + fi + cmake_src_prepare use cuda && cuda_src_prepare @@ -184,11 +200,6 @@ src_configure() { if use fftw; then fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) - elif use mkl && has_version "=sci-libs/mkl-10*"; then - fft_opts=( -DGMX_FFT_LIBRARY=mkl - -DMKL_INCLUDE_DIR="${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 @@ -230,6 +241,7 @@ src_configure() { [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" local gpu=( "-DGMX_GPU=OFF" ) [[ ${x} = "float" ]] && use cuda && gpu=( "-DGMX_GPU=CUDA" ) + [[ ${x} = "float" ]] && use clang-cuda && gpu=( "-DGMX_GPU=CUDA" "-DGMX_CLANG_CUDA=ON" ) use opencl && gpu=( "-DGMX_GPU=OPENCL" ) mycmakeargs=( ${mycmakeargs_pre[@]} ${p} diff --git a/sci-chemistry/gromacs/gromacs-2023_rc1.ebuild b/sci-chemistry/gromacs/gromacs-2023_rc1.ebuild index 55fe829229e7..c69ff70b99d3 100644 --- a/sci-chemistry/gromacs/gromacs-2023_rc1.ebuild +++ b/sci-chemistry/gromacs/gromacs-2023_rc1.ebuild @@ -22,24 +22,24 @@ if [[ ${PV} = *9999* ]]; then inherit git-r3 else SRC_URI=" - http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz - doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf -> manual-${PV}.pdf ) - test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" + https://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz + doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf ) + test? ( https://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" # since 2022 arm support was dropped (but not arm64) - KEYWORDS="~amd64 -arm ~x86 ~amd64-linux ~x86-linux ~x64-macos" + KEYWORDS="~amd64 -arm ~arm64 ~x86 ~amd64-linux ~x86-linux ~x64-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 cpu_flags_x86_avx512f cpu_flags_arm_neon" DESCRIPTION="The ultimate molecular dynamics simulation package" -HOMEPAGE="http://www.gromacs.org/" +HOMEPAGE="https://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="blas cuda +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" +IUSE="blas clang clang-cuda cuda +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" CDEPEND=" blas? ( virtual/blas ) @@ -51,11 +51,12 @@ CDEPEND=" mkl? ( sci-libs/mkl ) mpi? ( virtual/mpi[cxx] ) sci-libs/lmfit:= - >=dev-cpp/muParser-2.3.4:= + >=dev-cpp/muParser-2.3:= ${PYTHON_DEPS} " BDEPEND="${CDEPEND} virtual/pkgconfig + clang? ( >=sys-devel/clang-6:* ) build-manual? ( app-doc/doxygen $(python_gen_cond_dep ' @@ -73,7 +74,9 @@ REQUIRED_USE=" || ( single-precision double-precision ) doc? ( !build-manual ) cuda? ( single-precision ) + opencl? ( single-precision ) cuda? ( !opencl ) + clang-cuda? ( clang cuda ) mkl? ( !blas !fftw !lapack ) ${PYTHON_REQUIRED_USE}" @@ -114,6 +117,19 @@ src_prepare() { xdg_environment_reset #591952 + # we can use clang as default + if use clang && ! tc-is-clang ; then + export CC=${CHOST}-clang + export CXX=${CHOST}-clang++ + else + tc-export CXX CC + fi + # clang-cuda need to filter mfpmath + if use clang-cuda ; then + filter-mfpmath sse + filter-mfpmath i386 + fi + cmake_src_prepare use cuda && cuda_src_prepare @@ -184,11 +200,6 @@ src_configure() { if use fftw; then fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) - elif use mkl && has_version "=sci-libs/mkl-10*"; then - fft_opts=( -DGMX_FFT_LIBRARY=mkl - -DMKL_INCLUDE_DIR="${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 @@ -230,6 +241,7 @@ src_configure() { [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" local gpu=( "-DGMX_GPU=OFF" ) [[ ${x} = "float" ]] && use cuda && gpu=( "-DGMX_GPU=CUDA" ) + [[ ${x} = "float" ]] && use clang-cuda && gpu=( "-DGMX_GPU=CUDA" "-DGMX_CLANG_CUDA=ON" ) use opencl && gpu=( "-DGMX_GPU=OPENCL" ) mycmakeargs=( ${mycmakeargs_pre[@]} ${p} diff --git a/sci-chemistry/gromacs/gromacs-9999.ebuild b/sci-chemistry/gromacs/gromacs-9999.ebuild index 55fe829229e7..c69ff70b99d3 100644 --- a/sci-chemistry/gromacs/gromacs-9999.ebuild +++ b/sci-chemistry/gromacs/gromacs-9999.ebuild @@ -22,24 +22,24 @@ if [[ ${PV} = *9999* ]]; then inherit git-r3 else SRC_URI=" - http://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz - doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf -> manual-${PV}.pdf ) - test? ( http://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" + https://ftp.gromacs.org/gromacs/${PN}-${PV/_/-}.tar.gz + doc? ( https://ftp.gromacs.org/manual/manual-${PV/_/-}.pdf ) + test? ( https://ftp.gromacs.org/regressiontests/regressiontests-${PV/_/-}.tar.gz )" # since 2022 arm support was dropped (but not arm64) - KEYWORDS="~amd64 -arm ~x86 ~amd64-linux ~x86-linux ~x64-macos" + KEYWORDS="~amd64 -arm ~arm64 ~x86 ~amd64-linux ~x86-linux ~x64-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 cpu_flags_x86_avx512f cpu_flags_arm_neon" DESCRIPTION="The ultimate molecular dynamics simulation package" -HOMEPAGE="http://www.gromacs.org/" +HOMEPAGE="https://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="blas cuda +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" +IUSE="blas clang clang-cuda cuda +custom-cflags +doc build-manual double-precision +fftw +gmxapi +gmxapi-legacy +hwloc lapack mkl mpi +offensive opencl openmp +python +single-precision test +threads +tng ${ACCE_IUSE}" CDEPEND=" blas? ( virtual/blas ) @@ -51,11 +51,12 @@ CDEPEND=" mkl? ( sci-libs/mkl ) mpi? ( virtual/mpi[cxx] ) sci-libs/lmfit:= - >=dev-cpp/muParser-2.3.4:= + >=dev-cpp/muParser-2.3:= ${PYTHON_DEPS} " BDEPEND="${CDEPEND} virtual/pkgconfig + clang? ( >=sys-devel/clang-6:* ) build-manual? ( app-doc/doxygen $(python_gen_cond_dep ' @@ -73,7 +74,9 @@ REQUIRED_USE=" || ( single-precision double-precision ) doc? ( !build-manual ) cuda? ( single-precision ) + opencl? ( single-precision ) cuda? ( !opencl ) + clang-cuda? ( clang cuda ) mkl? ( !blas !fftw !lapack ) ${PYTHON_REQUIRED_USE}" @@ -114,6 +117,19 @@ src_prepare() { xdg_environment_reset #591952 + # we can use clang as default + if use clang && ! tc-is-clang ; then + export CC=${CHOST}-clang + export CXX=${CHOST}-clang++ + else + tc-export CXX CC + fi + # clang-cuda need to filter mfpmath + if use clang-cuda ; then + filter-mfpmath sse + filter-mfpmath i386 + fi + cmake_src_prepare use cuda && cuda_src_prepare @@ -184,11 +200,6 @@ src_configure() { if use fftw; then fft_opts=( -DGMX_FFT_LIBRARY=fftw3 ) - elif use mkl && has_version "=sci-libs/mkl-10*"; then - fft_opts=( -DGMX_FFT_LIBRARY=mkl - -DMKL_INCLUDE_DIR="${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 @@ -230,6 +241,7 @@ src_configure() { [[ ${x} = "double" ]] && p="-DGMX_DOUBLE=ON" || p="-DGMX_DOUBLE=OFF" local gpu=( "-DGMX_GPU=OFF" ) [[ ${x} = "float" ]] && use cuda && gpu=( "-DGMX_GPU=CUDA" ) + [[ ${x} = "float" ]] && use clang-cuda && gpu=( "-DGMX_GPU=CUDA" "-DGMX_CLANG_CUDA=ON" ) use opencl && gpu=( "-DGMX_GPU=OPENCL" ) mycmakeargs=( ${mycmakeargs_pre[@]} ${p} |