glicid-non-free/glicid-tainted/packages/chemistry.scm

(define-module (glicid-tainted packages chemistry)
  #:use-module (guix packages)
  #:use-module (guix download)
#:use-module (guix gexp)
#:use-module (guix utils)
#:use-module (guix build-system cmake)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (gnu packages)
#:use-module (gnu packages algebra)
#:use-module (gnu packages mpi)
#:use-module (gnu packages maths)
#:use-module (gnu packages perl)
#:use-module (gnu packages xml)
#:use-module (gnu packages chemistry)
#:use-module (gnu packages documentation)
#:use-module (gnu packages graphviz)
#:use-module (gnu packages pkg-config)
#:use-module (gnu packages python)
#:use-module (gnu packages python-xyz)
#:use-module (gnu packages sphinx)
#:use-module (gnu packages check)
#:use-module (gnu packages gcc)
#:use-module (guix-science-nonfree packages cuda)
#:use-module (glicid packages mpi)

)

(define-public gromacs+cuda
  (package
    (inherit gromacs)
    (name "gromacs+cuda")
    (arguments
     (list #:configure-flags
           #~(list "-DGMX_DEVELOPER_BUILD=on"     ; Needed to run tests
                   ;; Unbundling
                   "-DGMX_USE_LMFIT=EXTERNAL"
                   "-DGMX_BUILD_OWN_FFTW=off"
                   "-DGMX_EXTERNAL_BLAS=on"
                   "-DGMX_EXTERNAL_LAPACK=on"
                   "-DGMX_EXTERNAL_TNG=on"
                   "-DGMX_EXTERNAL_ZLIB=on"
;                   "-DGMX_HWLOC=ON"
                   "-DGMX_GPU=CUDA"
                   (string-append "-DCUDA_TOOLKIT_ROOT_DIR=" #$(this-package-input "cuda-toolkit"))
                   "-DGMX_EXTERNAL_TINYXML2=on"
                   (string-append "-DTinyXML2_DIR="
                                  #$(this-package-input "tinyxml2"))
                   ;; Workaround for cmake/FindSphinx.cmake version parsing that does
                   ;; not understand the guix-wrapped `sphinx-build --version' answer
                   (string-append "-DSPHINX_EXECUTABLE_VERSION="
                                  #$(package-version python-sphinx)))
 #:phases
           #~(modify-phases %standard-phases
               (add-after 'unpack 'fixes
                 (lambda* (#:key inputs #:allow-other-keys)
                   ;; Still bundled: part of gromacs, source behind registration
                   ;; but free software anyways
                   ;;(delete-file-recursively "src/external/vmd_molfile")
                   ;; Still bundled: threads-based OpenMPI-compatible fallback
                   ;; designed to be bundled like that
                   ;;(delete-file-recursively "src/external/thread_mpi")
                   ;; Unbundling
                   (delete-file-recursively "src/external/lmfit")
                   (delete-file-recursively "src/external/clFFT")
                   (delete-file-recursively "src/external/fftpack")
                   (delete-file-recursively "src/external/build-fftw")
                   (delete-file-recursively "src/external/tng_io")
                   (delete-file-recursively "src/external/tinyxml2")
                   (delete-file-recursively "src/external/googletest")
                   (copy-recursively #$(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()"))

		   )))))

    (inputs
         (modify-inputs (package-inputs gromacs)
              (append cuda 
;hwloc
))))
)

(define-public gromacs+cuda-v2
  (package
    (inherit gromacs)
    (name "gromacs+cuda-v2")
    (arguments
     (list #:configure-flags
           #~(list "-DGMX_DEVELOPER_BUILD=on"     ; Needed to run tests
                   ;; Unbundling
                   "-DGMX_USE_LMFIT=EXTERNAL"
                   "-DGMX_BUILD_OWN_FFTW=off"
                   "-DGMX_EXTERNAL_BLAS=on"
                   "-DGMX_EXTERNAL_LAPACK=on"
                   "-DGMX_EXTERNAL_TNG=on"
                   "-DGMX_EXTERNAL_ZLIB=on"
                   "-DGMX_HWLOC=ON"
                   "-DGMX_GPU=CUDA"
                   (string-append "-DCUDA_TOOLKIT_ROOT_DIR=" #$(this-package-input "cuda-toolkit"))
                   "-DGMX_EXTERNAL_TINYXML2=on"
                   (string-append "-DTinyXML2_DIR="
                                  #$(this-package-input "tinyxml2"))
                   ;; Workaround for cmake/FindSphinx.cmake version parsing that does
                   ;; not understand the guix-wrapped `sphinx-build --version' answer
                   (string-append "-DSPHINX_EXECUTABLE_VERSION="
                                  #$(package-version python-sphinx)))
 #:phases
           #~(modify-phases %standard-phases
               (add-after 'unpack 'fixes
                 (lambda* (#:key inputs #:allow-other-keys)
                   ;; Still bundled: part of gromacs, source behind registration
                   ;; but free software anyways
                   ;;(delete-file-recursively "src/external/vmd_molfile")
                   ;; Still bundled: threads-based OpenMPI-compatible fallback
                   ;; designed to be bundled like that
                   ;;(delete-file-recursively "src/external/thread_mpi")
                   ;; Unbundling
                   (delete-file-recursively "src/external/lmfit")
                   (delete-file-recursively "src/external/clFFT")
                   (delete-file-recursively "src/external/fftpack")
                   (delete-file-recursively "src/external/build-fftw")
                   (delete-file-recursively "src/external/tng_io")
                   (delete-file-recursively "src/external/tinyxml2")
                   (delete-file-recursively "src/external/googletest")
                   (copy-recursively #$(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()"))




		   )))))

    (inputs
         (modify-inputs (package-inputs gromacs)
              (append cuda 
hwloc openmpi-glicid-waves
))))
)

gromacs+cuda-v2