diff options
| -rw-r--r-- | gnu/local.mk | 1 | ||||
| -rw-r--r-- | gnu/packages/chemistry.scm | 90 | ||||
| -rw-r--r-- | gnu/packages/patches/gromacs-tinyxml2.patch | 67 |
3 files changed, 158 insertions, 0 deletions
diff --git a/gnu/local.mk b/gnu/local.mk index 3c9a10b6bc..827e186501 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -1006,6 +1006,7 @@ dist_patch_DATA = \ %D%/packages/patches/gpsbabel-qstring.patch \ %D%/packages/patches/grantlee-merge-theme-dirs.patch \ %D%/packages/patches/grep-timing-sensitive-test.patch \ + %D%/packages/patches/gromacs-tinyxml2.patch \ %D%/packages/patches/groovy-add-exceptionutilsgenerator.patch \ %D%/packages/patches/grub-efi-fat-serial-number.patch \ %D%/packages/patches/gsl-test-i686.patch \ diff --git a/gnu/packages/chemistry.scm b/gnu/packages/chemistry.scm index 5b21e3309c..0540dfceb6 100644 --- a/gnu/packages/chemistry.scm +++ b/gnu/packages/chemistry.scm @@ -30,15 +30,20 @@ #:use-module (gnu packages) #:use-module (gnu packages algebra) #:use-module (gnu packages boost) + #:use-module (gnu packages check) #:use-module (gnu packages compression) #:use-module (gnu packages documentation) #:use-module (gnu packages gl) + #:use-module (gnu packages graphviz) #:use-module (gnu packages gv) #:use-module (gnu packages maths) + #:use-module (gnu packages mpi) + #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages python) #:use-module (gnu packages python-xyz) #:use-module (gnu packages qt) + #:use-module (gnu packages sphinx) #:use-module (gnu packages xml) #:use-module (guix build-system cmake) #:use-module (guix build-system gnu) @@ -336,6 +341,91 @@ optionally velocities and the H-matrix. Coordinates and velocities are stored with user-specified precision.") (license license:bsd-3))) +(define-public gromacs + (package + (name "gromacs") + (version "2020.2") + (source (origin + (method url-fetch) + (uri (string-append "http://ftp.gromacs.org/pub/gromacs/gromacs-" + version ".tar.gz")) + (sha256 + (base32 + "1wyjgcdl30wy4hy6jvi9lkq53bqs9fgfq6fri52dhnb3c76y8rbl")) + ;; Our version of tinyxml2 is far newer than the bundled one and + ;; require fixing `testutils' code. See patch header for more info + (patches (search-patches "gromacs-tinyxml2.patch")))) + (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" + (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))) + #: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))))) + (native-inputs + `(("doxygen" ,doxygen) + ("googletest-source" ,(package-source googletest)) + ("graphviz" ,graphviz) + ("pkg-config" ,pkg-config) + ("python" ,python) + ("python-pygments" ,python-pygments) + ("python-sphinx" ,python-sphinx))) + (inputs + `(("fftwf" ,fftwf) + ("hwloc" ,hwloc-2 "lib") + ("lmfit" ,lmfit) + ("openblas" ,openblas) + ("perl" ,perl) + ("tinyxml2" ,tinyxml2) + ("tng" ,tng))) + (home-page "http://www.gromacs.org/") + (synopsis "Molecular dynamics software package") + (description "GROMACS is a versatile package to perform molecular dynamics, +i.e. simulate the Newtonian equations of motion for systems with hundreds to +millions of particles. It is primarily designed for biochemical molecules like +proteins, lipids and nucleic acids that have a lot of complicated bonded +interactions, but since GROMACS is extremely fast at calculating the nonbonded +interactions (that usually dominate simulations) many groups are also using it +for research on non-biological systems, e.g. polymers. GROMACS supports all the +usual algorithms you expect from a modern molecular dynamics implementation.") + (license license:lgpl2.1+))) + (define-public openbabel (package (name "openbabel") diff --git a/gnu/packages/patches/gromacs-tinyxml2.patch b/gnu/packages/patches/gromacs-tinyxml2.patch new file mode 100644 index 0000000000..cc7d7459a8 --- /dev/null +++ b/gnu/packages/patches/gromacs-tinyxml2.patch @@ -0,0 +1,67 @@ +Unbundling tinyxml2 from gromacs and using our own, which is newer, broke gromacs +build. + +This patch fixes three issues: + +- cmake now errors out if using multiple target_link_libraries with mixed styles + of signatures. + +- Error handling API changed, fix the testutils/refdata_xml.cpp code by using the + new API: document.ErrorStr() & tinyxml2::XML_SUCCESS. + +Those fixes will be submitted for inclusion to upstream, but may not be suitable +there as long as they still keep the old version bundled. + +First hunk has already been requested for merging. Third is in discussion. Second +will only be sent if third is OK'ed. + +diff -ruN gromacs-2020.2/src/testutils/CMakeLists.txt gromacs-2020.2-fixed/src/testutils/CMakeLists.txt +--- gromacs-2020.2/src/testutils/CMakeLists.txt 2020-04-30 18:33:44.000000000 +0200 ++++ gromacs-2020.2-fixed/src/testutils/CMakeLists.txt 2020-05-01 22:52:16.356000000 +0200 +@@ -73,7 +73,7 @@ + + if(HAVE_TINYXML2) + include_directories(SYSTEM ${TinyXML2_INCLUDE_DIR}) +- target_link_libraries(testutils ${TinyXML2_LIBRARIES}) ++ target_link_libraries(testutils PRIVATE ${TinyXML2_LIBRARIES}) + else() + include_directories(BEFORE SYSTEM "../external/tinyxml2") + endif() +diff -ruN gromacs-2020.2/src/testutils/refdata_xml.cpp gromacs-2020.2-fixed/src/testutils/refdata_xml.cpp +--- gromacs-2020.2/src/testutils/refdata_xml.cpp 2020-04-30 18:33:44.000000000 +0200 ++++ gromacs-2020.2-fixed/src/testutils/refdata_xml.cpp 2020-05-01 23:17:09.556000000 +0200 +@@ -206,21 +206,12 @@ + document.LoadFile(path.c_str()); + if (document.Error()) + { +- const char* errorStr1 = document.GetErrorStr1(); +- const char* errorStr2 = document.GetErrorStr2(); ++ const char* errorStr = document.ErrorStr(); + std::string errorString("Error was "); +- if (errorStr1) +- { +- errorString += errorStr1; +- } +- if (errorStr2) +- { +- errorString += errorStr2; +- } +- if (!errorStr1 && !errorStr2) +- { ++ if (errorStr) ++ errorString += errorStr; ++ else + errorString += "not specified."; +- } + GMX_THROW(TestException("Reference data not parsed successfully: " + path + "\n." + + errorString + "\n")); + } +@@ -371,7 +362,7 @@ + XMLElementPtr rootElement = createRootElement(&document); + createChildElements(rootElement, rootEntry); + +- if (document.SaveFile(path.c_str()) != tinyxml2::XML_NO_ERROR) ++ if (document.SaveFile(path.c_str()) != tinyxml2::XML_SUCCESS) + { + GMX_THROW(TestException("Reference data saving failed in " + path)); + } |