mirror of
https://gitlab.univ-nantes.fr/glicid-public/glicid-non-free.git
synced 2025-04-28 17:28:35 +02:00
507 lines
21 KiB
Scheme
507 lines
21 KiB
Scheme
(define-module (glicid-tainted packages chemistry)
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#:use-module (guix packages)
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#:use-module (guix download)
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#:use-module (guix gexp)
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#:use-module (guix utils)
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#:use-module (guix build-system cmake)
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#:use-module ((guix licenses) #:prefix license:)
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#:use-module (gnu packages)
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#:use-module (gnu packages algebra)
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#:use-module (gnu packages mpi)
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#:use-module (gnu packages maths)
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#:use-module (gnu packages perl)
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#:use-module (gnu packages xml)
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#:use-module (gnu packages chemistry)
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#:use-module (gnu packages documentation)
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#:use-module (gnu packages graphviz)
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#:use-module (gnu packages pkg-config)
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#:use-module (gnu packages python)
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#:use-module (gnu packages python-xyz)
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#:use-module (gnu packages sphinx)
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#:use-module (gnu packages check)
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#:use-module (gnu packages gcc)
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#:use-module (gnu packages ssh)
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#:use-module (guix-science-nonfree packages cuda)
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#:use-module (glicid packages mpi)
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#:use-module (nongnu packages nvidia)
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)
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(define-public gromacs+cuda
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(package
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(inherit gromacs)
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(name "gromacs+cuda")
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(arguments
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(list #:configure-flags
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#~(list "-DGMX_DEVELOPER_BUILD=on" ; Needed to run tests
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;; Unbundling
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"-DGMX_USE_LMFIT=EXTERNAL"
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"-DGMX_BUILD_OWN_FFTW=off"
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"-DGMX_EXTERNAL_BLAS=on"
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"-DGMX_EXTERNAL_LAPACK=on"
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"-DGMX_EXTERNAL_TNG=on"
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"-DGMX_EXTERNAL_ZLIB=on"
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; "-DGMX_HWLOC=ON"
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"-DGMX_GPU=CUDA"
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(string-append "-DCUDA_TOOLKIT_ROOT_DIR=" #$(this-package-input "cuda-toolkit"))
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"-DGMX_EXTERNAL_TINYXML2=on"
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(string-append "-DTinyXML2_DIR="
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#$(this-package-input "tinyxml2"))
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;; Workaround for cmake/FindSphinx.cmake version parsing that does
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;; not understand the guix-wrapped `sphinx-build --version' answer
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(string-append "-DSPHINX_EXECUTABLE_VERSION="
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#$(package-version python-sphinx)))
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#:phases
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#~(modify-phases %standard-phases
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(add-after 'unpack 'fixes
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(lambda* (#:key inputs #:allow-other-keys)
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;; Still bundled: part of gromacs, source behind registration
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;; but free software anyways
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;;(delete-file-recursively "src/external/vmd_molfile")
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;; Still bundled: threads-based OpenMPI-compatible fallback
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;; designed to be bundled like that
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;;(delete-file-recursively "src/external/thread_mpi")
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;; Unbundling
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(delete-file-recursively "src/external/lmfit")
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(delete-file-recursively "src/external/clFFT")
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(delete-file-recursively "src/external/fftpack")
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(delete-file-recursively "src/external/build-fftw")
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(delete-file-recursively "src/external/tng_io")
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(delete-file-recursively "src/external/tinyxml2")
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(delete-file-recursively "src/external/googletest")
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(copy-recursively #$(package-source googletest)
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"src/external/googletest")
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;; This test warns about the build host hardware, disable
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(substitute* "src/gromacs/hardware/tests/hardwaretopology.cpp"
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(("TEST\\(HardwareTopologyTest, HwlocExecute\\)")
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"void __guix_disabled()"))
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)))))
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(inputs
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(modify-inputs (package-inputs gromacs)
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(append cuda
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;hwloc
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))))
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)
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(define-public gromacs+cuda-v1
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(package
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(inherit gromacs)
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(name "gromacs+cuda-v1")
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(arguments
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(list #:configure-flags
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#~(list "-DGMX_DEVELOPER_BUILD=on" ; Needed to run tests
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;; Unbundling
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"-DGMX_USE_LMFIT=EXTERNAL"
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"-DGMX_BUILD_OWN_FFTW=off"
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"-DGMX_EXTERNAL_BLAS=on"
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"-DGMX_EXTERNAL_LAPACK=on"
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"-DGMX_EXTERNAL_TNG=on"
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"-DGMX_EXTERNAL_ZLIB=on"
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"-DGMX_HWLOC=ON"
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"-DGMX_GPU=CUDA"
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(string-append "-DCUDA_TOOLKIT_ROOT_DIR=" #$(this-package-input "cuda-toolkit"))
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"-DGMX_EXTERNAL_TINYXML2=on"
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(string-append "-DTinyXML2_DIR="
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#$(this-package-input "tinyxml2"))
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;; Workaround for cmake/FindSphinx.cmake version parsing that does
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;; not understand the guix-wrapped `sphinx-build --version' answer
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(string-append "-DSPHINX_EXECUTABLE_VERSION="
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#$(package-version python-sphinx)))
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#:phases
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#~(modify-phases %standard-phases
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(add-after 'unpack 'fixes
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(lambda* (#:key inputs #:allow-other-keys)
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;; Still bundled: part of gromacs, source behind registration
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;; but free software anyways
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;;(delete-file-recursively "src/external/vmd_molfile")
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;; Still bundled: threads-based OpenMPI-compatible fallback
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;; designed to be bundled like that
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;;(delete-file-recursively "src/external/thread_mpi")
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;; Unbundling
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(delete-file-recursively "src/external/lmfit")
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(delete-file-recursively "src/external/clFFT")
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(delete-file-recursively "src/external/fftpack")
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(delete-file-recursively "src/external/build-fftw")
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(delete-file-recursively "src/external/tng_io")
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(delete-file-recursively "src/external/tinyxml2")
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(delete-file-recursively "src/external/googletest")
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(copy-recursively #$(package-source googletest)
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"src/external/googletest")
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;; This test warns about the build host hardware, disable
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(substitute* "src/gromacs/hardware/tests/hardwaretopology.cpp"
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(("TEST\\(HardwareTopologyTest, HwlocExecute\\)")
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"void __guix_disabled()"))
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(substitute* "src/gromacs/hardware/tests/hardwaretopology.cpp"
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(("TEST\\(HardwareTopologyTest, NumaCacheSelfconsistency\\)")
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"void __guix_disabledv2()")) ;; really not sure it's the best way…
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)))))
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(inputs
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(modify-inputs (package-inputs gromacs)
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(append cuda
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hwloc ;; openmpi-glicid-waves openssh-sans-x ;; ssh is because openmpi use rsh and tests use it !
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))))
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)
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(define-public gromacs+cuda-v1-zen3
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(package
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(inherit gromacs)
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(name "gromacs+cuda-v1-zen3")
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(arguments
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(list #:configure-flags
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#~(list "-DGMX_DEVELOPER_BUILD=on" ; Needed to run tests
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;; Unbundling
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"-DGMX_USE_LMFIT=EXTERNAL"
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"-DGMX_BUILD_OWN_FFTW=off"
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"-DGMX_EXTERNAL_BLAS=on"
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"-DGMX_EXTERNAL_LAPACK=on"
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"-DGMX_EXTERNAL_TNG=on"
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"-DGMX_EXTERNAL_ZLIB=on"
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"-DGMX_HWLOC=ON"
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"-DGMX_GPU=CUDA"
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"-DGMX_SIMD=AVX2_256"
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(string-append "-DCUDA_TOOLKIT_ROOT_DIR=" #$(this-package-input "cuda-toolkit"))
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"-DGMX_EXTERNAL_TINYXML2=on"
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(string-append "-DTinyXML2_DIR="
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#$(this-package-input "tinyxml2"))
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;; Workaround for cmake/FindSphinx.cmake version parsing that does
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;; not understand the guix-wrapped `sphinx-build --version' answer
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(string-append "-DSPHINX_EXECUTABLE_VERSION="
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#$(package-version python-sphinx)))
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#:phases
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#~(modify-phases %standard-phases
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(add-after 'unpack 'fixes
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(lambda* (#:key inputs #:allow-other-keys)
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;; Still bundled: part of gromacs, source behind registration
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;; but free software anyways
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;;(delete-file-recursively "src/external/vmd_molfile")
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;; Still bundled: threads-based OpenMPI-compatible fallback
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;; designed to be bundled like that
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;;(delete-file-recursively "src/external/thread_mpi")
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;; Unbundling
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(delete-file-recursively "src/external/lmfit")
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(delete-file-recursively "src/external/clFFT")
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(delete-file-recursively "src/external/fftpack")
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(delete-file-recursively "src/external/build-fftw")
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(delete-file-recursively "src/external/tng_io")
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(delete-file-recursively "src/external/tinyxml2")
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(delete-file-recursively "src/external/googletest")
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(copy-recursively #$(package-source googletest)
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"src/external/googletest")
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;; This test warns about the build host hardware, disable
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(substitute* "src/gromacs/hardware/tests/hardwaretopology.cpp"
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(("TEST\\(HardwareTopologyTest, HwlocExecute\\)")
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"void __guix_disabled()"))
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(substitute* "src/gromacs/hardware/tests/hardwaretopology.cpp"
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(("TEST\\(HardwareTopologyTest, NumaCacheSelfconsistency\\)")
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"void __guix_disabledv2()")) ;; really not sure it's the best way…
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)))))
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(inputs
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(modify-inputs (package-inputs gromacs)
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(append cuda
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hwloc ;; openmpi-glicid-waves openssh-sans-x ;; ssh is because openmpi use rsh and tests use it !
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))))
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)
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(define-public gromacs+cuda-v2
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(package
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(inherit gromacs)
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(name "gromacs+cuda-v2")
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(arguments
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(list #:configure-flags
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#~(list "-DGMX_DEVELOPER_BUILD=on" ; Needed to run tests
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;; Unbundling
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"-DGMX_USE_LMFIT=EXTERNAL"
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"-DGMX_BUILD_OWN_FFTW=off"
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"-DGMX_EXTERNAL_BLAS=on"
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"-DGMX_EXTERNAL_LAPACK=on"
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"-DGMX_EXTERNAL_TNG=on"
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"-DGMX_EXTERNAL_ZLIB=on"
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"-DGMX_HWLOC=ON"
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"-DGMX_MPI=ON"
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"-DGMX_GPU=CUDA"
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(string-append "-DCUDA_TOOLKIT_ROOT_DIR=" #$(this-package-input "cuda-toolkit"))
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"-DGMX_EXTERNAL_TINYXML2=on"
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(string-append "-DTinyXML2_DIR="
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#$(this-package-input "tinyxml2"))
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;; Workaround for cmake/FindSphinx.cmake version parsing that does
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;; not understand the guix-wrapped `sphinx-build --version' answer
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(string-append "-DSPHINX_EXECUTABLE_VERSION="
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#$(package-version python-sphinx)))
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#:phases
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#~(modify-phases %standard-phases
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(add-after 'unpack 'fixes
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(lambda* (#:key inputs #:allow-other-keys)
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;; Still bundled: part of gromacs, source behind registration
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;; but free software anyways
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;;(delete-file-recursively "src/external/vmd_molfile")
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;; Still bundled: threads-based OpenMPI-compatible fallback
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;; designed to be bundled like that
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;;(delete-file-recursively "src/external/thread_mpi")
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;; Unbundling
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(delete-file-recursively "src/external/lmfit")
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(delete-file-recursively "src/external/clFFT")
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(delete-file-recursively "src/external/fftpack")
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(delete-file-recursively "src/external/build-fftw")
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(delete-file-recursively "src/external/tng_io")
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(delete-file-recursively "src/external/tinyxml2")
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(delete-file-recursively "src/external/googletest")
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(copy-recursively #$(package-source googletest)
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"src/external/googletest")
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;; This test warns about the build host hardware, disable
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(substitute* "src/gromacs/hardware/tests/hardwaretopology.cpp"
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(("TEST\\(HardwareTopologyTest, HwlocExecute\\)")
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"void __guix_disabled()"))
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(substitute* "src/gromacs/hardware/tests/hardwaretopology.cpp"
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(("TEST\\(HardwareTopologyTest, NumaCacheSelfconsistency\\)")
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"void __guix_disabledv2()")) ;; really not sure it's the best way…
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)))))
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(inputs
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(modify-inputs (package-inputs gromacs)
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(append cuda nvidia-driver hwloc openmpi openssh-sans-x ;; ssh is because openmpi use rsh and tests use it !
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))))
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)
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(define-public gromacs-upstream-2205
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(package
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(inherit gromacs)
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(name "gromacs-upstream")
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(version "2022.5")
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(source (origin
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(method url-fetch)
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(uri (string-append "http://ftp.gromacs.org/pub/gromacs/gromacs-"
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version ".tar.gz"))
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(sha256
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(base32
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"08y233h7ajzjc63k7r8dabvckrmlwpim5y8jdklgz4xv4k2c6g08"))
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;; Our version of tinyxml2 is far newer than the bundled one and
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;; require fixing `testutils' code. See patch header for more info
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(patches (search-patches "gromacs-tinyxml2.patch"))))
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)
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)
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(define-public gromacs-upstream+cuda-2205
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(package
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(inherit gromacs+cuda)
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(version "2022.5")
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(name "gromacs-upstream+cuda")
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(source (origin
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(method url-fetch)
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(uri (string-append "http://ftp.gromacs.org/pub/gromacs/gromacs-"
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version ".tar.gz"))
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(sha256
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(base32
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"08y233h7ajzjc63k7r8dabvckrmlwpim5y8jdklgz4xv4k2c6g08"))
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;; Our version of tinyxml2 is far newer than the bundled one and
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;; require fixing `testutils' code. See patch header for more info
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(patches (search-patches "gromacs-tinyxml2.patch"))))
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)
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)
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(define-public gromacs-upstream+cuda-v2-2205
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(package
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(inherit gromacs+cuda-v2)
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(version "2022.5")
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(name "gromacs-upstream+cuda-v2")
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(source (origin
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(method url-fetch)
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(uri (string-append "http://ftp.gromacs.org/pub/gromacs/gromacs-"
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version ".tar.gz"))
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(sha256
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(base32
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"08y233h7ajzjc63k7r8dabvckrmlwpim5y8jdklgz4xv4k2c6g08"))
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;; Our version of tinyxml2 is far newer than the bundled one and
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;; require fixing `testutils' code. See patch header for more info
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(patches (search-patches "gromacs-tinyxml2.patch"))))
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)
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)
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(define-public gromacs-upstream+cuda-v1-2205
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(package
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(inherit gromacs+cuda-v1)
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(version "2022.5")
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(name "gromacs-upstream+cuda-v1")
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(source (origin
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(method url-fetch)
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(uri (string-append "http://ftp.gromacs.org/pub/gromacs/gromacs-"
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version ".tar.gz"))
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(sha256
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(base32
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"08y233h7ajzjc63k7r8dabvckrmlwpim5y8jdklgz4xv4k2c6g08"))
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;; Our version of tinyxml2 is far newer than the bundled one and
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;; require fixing `testutils' code. See patch header for more info
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(patches (search-patches "gromacs-tinyxml2.patch"))))
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)
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)
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(define-public gromacs-upstream-2300
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(package
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(inherit gromacs-upstream-2205)
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(version "2023")
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(source (origin
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(method url-fetch)
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(uri (string-append "http://ftp.gromacs.org/pub/gromacs/gromacs-"
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version ".tar.gz"))
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(sha256
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|
(base32
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|
"1a3vgckygd6gllnyvaydq721gkvfwmwxka6q9x0wmg7vfbdcd4mc"))
|
|
;; Our version of tinyxml2 is far newer than the bundled one and
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;; require fixing `testutils' code. See patch header for more info
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(patches (search-patches "gromacs-tinyxml2.patch"))))
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)
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)
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(define-public gromacs-upstream+cuda-2300
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(package
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(inherit gromacs-upstream+cuda-2205)
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(version "2023")
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|
(source (origin
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|
(method url-fetch)
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|
(uri (string-append "http://ftp.gromacs.org/pub/gromacs/gromacs-"
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|
version ".tar.gz"))
|
|
(sha256
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|
(base32
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|
"1a3vgckygd6gllnyvaydq721gkvfwmwxka6q9x0wmg7vfbdcd4mc"))
|
|
;; Our version of tinyxml2 is far newer than the bundled one and
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|
;; require fixing `testutils' code. See patch header for more info
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(patches (search-patches "gromacs-tinyxml2.patch"))))
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)
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)
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(define-public gromacs-upstream+cuda-v1-2300
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(package
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(inherit gromacs-upstream+cuda-v1-2205)
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(version "2023")
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|
(source (origin
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|
(method url-fetch)
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|
(uri (string-append "http://ftp.gromacs.org/pub/gromacs/gromacs-"
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|
version ".tar.gz"))
|
|
(sha256
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|
(base32
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|
"1a3vgckygd6gllnyvaydq721gkvfwmwxka6q9x0wmg7vfbdcd4mc"))
|
|
;; Our version of tinyxml2 is far newer than the bundled one and
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;; require fixing `testutils' code. See patch header for more info
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(patches (search-patches "gromacs-tinyxml2.patch"))))
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)
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)
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(define-public gromacs-upstream+cuda-v2-2300
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(package
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(inherit gromacs-upstream+cuda-v2-2205)
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(version "2023")
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|
(source (origin
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(method url-fetch)
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(uri (string-append "http://ftp.gromacs.org/pub/gromacs/gromacs-"
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version ".tar.gz"))
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(sha256
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|
(base32
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|
"1a3vgckygd6gllnyvaydq721gkvfwmwxka6q9x0wmg7vfbdcd4mc"))
|
|
;; Our version of tinyxml2 is far newer than the bundled one and
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;; require fixing `testutils' code. See patch header for more info
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(patches (search-patches "gromacs-tinyxml2.patch"))))
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)
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)
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(define-public gromacs-upstream+cuda-v3-2300
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(package
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(inherit gromacs-upstream+cuda-v2-2300)
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(name "gromacs-upstream+cuda-v3")
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(arguments
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(list #:configure-flags
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#~(list "-DGMX_DEVELOPER_BUILD=on" ; Needed to run tests
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;; Unbundling
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"-DGMX_USE_LMFIT=EXTERNAL"
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"-DGMX_BUILD_OWN_FFTW=off"
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"-DGMX_EXTERNAL_BLAS=on"
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"-DGMX_EXTERNAL_LAPACK=on"
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"-DGMX_EXTERNAL_TNG=on"
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"-DGMX_EXTERNAL_ZLIB=on"
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"-DGMX_HWLOC=ON"
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"-DGMX_MPI=ON"
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"-DGMX_GPU=CUDA"
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|
(string-append "-DCUDA_TOOLKIT_ROOT_DIR=" #$(this-package-input "cuda-toolkit"))
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|
"-DGMX_EXTERNAL_TINYXML2=on"
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|
(string-append "-DTinyXML2_DIR="
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|
#$(this-package-input "tinyxml2"))
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|
"-DGMX_USE_CUFFTMP=on"
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|
(string-append "-DcuFFTMp_ROOT=" #$(this-package-input "cuda-toolkit"))
|
|
;; Workaround for cmake/FindSphinx.cmake version parsing that does
|
|
;; not understand the guix-wrapped `sphinx-build --version' answer
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|
(string-append "-DSPHINX_EXECUTABLE_VERSION="
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|
#$(package-version python-sphinx)))
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|
#:phases
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|
#~(modify-phases %standard-phases
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|
(add-after 'unpack 'fixes
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|
(lambda* (#:key inputs #:allow-other-keys)
|
|
;; Still bundled: part of gromacs, source behind registration
|
|
;; but free software anyways
|
|
;;(delete-file-recursively "src/external/vmd_molfile")
|
|
;; Still bundled: threads-based OpenMPI-compatible fallback
|
|
;; designed to be bundled like that
|
|
;;(delete-file-recursively "src/external/thread_mpi")
|
|
;; Unbundling
|
|
(delete-file-recursively "src/external/lmfit")
|
|
(delete-file-recursively "src/external/clFFT")
|
|
(delete-file-recursively "src/external/fftpack")
|
|
(delete-file-recursively "src/external/build-fftw")
|
|
(delete-file-recursively "src/external/tng_io")
|
|
(delete-file-recursively "src/external/tinyxml2")
|
|
(delete-file-recursively "src/external/googletest")
|
|
(copy-recursively #$(package-source googletest)
|
|
"src/external/googletest")
|
|
;; This test warns about the build host hardware, disable
|
|
(substitute* "src/gromacs/hardware/tests/hardwaretopology.cpp"
|
|
(("TEST\\(HardwareTopologyTest, HwlocExecute\\)")
|
|
"void __guix_disabled()"))
|
|
(substitute* "src/gromacs/hardware/tests/hardwaretopology.cpp"
|
|
(("TEST\\(HardwareTopologyTest, NumaCacheSelfconsistency\\)")
|
|
"void __guix_disabledv2()")) ;; really not sure it's the best way…
|
|
|
|
|
|
|
|
|
|
)))))
|
|
|
|
(inputs
|
|
(modify-inputs (package-inputs gromacs)
|
|
(append cuda
|
|
hwloc ;; openmpi-glicid-waves openssh-sans-x ;; ssh is because openmpi use rsh and tests use it !
|
|
)))))
|
|
|
|
(define-public gromacs-upstream gromacs-upstream-2300)
|
|
(define-public gromacs-upstream+cuda gromacs-upstream+cuda-2300)
|
|
(define-public gromacs-upstream+cuda-v2 gromacs-upstream+cuda-v2-2300)
|
|
|
|
|
|
|
|
gromacs-upstream+cuda-v3-2300
|