From da13ce644ac19dd30ef4dd3357a1d72f650a827b Mon Sep 17 00:00:00 2001
From: Yann Dupont <yann@objoo.org>
Date: Mon, 25 May 2020 16:48:22 +0200
Subject: [PATCH] gromacs openmpi

---
 gnu/packages/glicid.scm | 65 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 65 insertions(+)

diff --git a/gnu/packages/glicid.scm b/gnu/packages/glicid.scm
index 0320ef0..411d5fd 100644
--- a/gnu/packages/glicid.scm
+++ b/gnu/packages/glicid.scm
@@ -206,6 +206,71 @@
 ;)
 
 
+(define-public glicid-gromacs-openmpi
+ (package
+  (inherit gromacs)
+  (name "glicid-gromacs-openmpi")
+  (inputs `(("openmpi", openmpi)
+            ("openssh", openssh)
+                    ,@(package-inputs gromacs)))
+  (build-system cmake-build-system)
+
+   (arguments
+       `(#: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_EXTERNAL_TINYXML2=on"
+               ;; special glicid
+               "-DGMX_MPI=on"
+               "-DCMAKE_C_COMPILER=mpicc"
+               "-DCMAKE_CXX_COMPILER=mpicxx"
+               (string-append "-DTinyXML2_DIR="
+                              (assoc-ref %build-inputs "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)))
+         #:tests? #f
+         #: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 (assoc-ref inputs "googletest-source")
+                                 "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()"))
+               #t)))))
+
+
+
+  )
+
+)
+
+
+
 ;; pour futures customisations.
 
 (define-public glicid-openmpi-gcc-8