add zen3 variant

glicid-tainted/packages/chemistry.scm

@@ -139,6 +139,71 @@
 
 
 
+		   )))))
+
+    (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+cuda-v1-zen3
+  (package
+    (inherit gromacs)
+    (name "gromacs+cuda-v1")
+    (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"
+		   "-DGMX_SIMD=AVX2_256"
+                   (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()")) ;; really not sure it's the best way…
+
+
+
+
 		   )))))
 
     (inputs