gnu: Add gromacs.
* gnu/packages/chemistry.scm (gromacs): New variable. * gnu/packages/patches/gromacs-tinyxml2.patch: New file... * gnu/local.mk (dist_patch_DATA): ...add it here. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
This commit is contained in:
Vincent Legoll
Ludovic Courtès
parent
feba2c9751
commit
06ed1dba35
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@ -1006,6 +1006,7 @@ dist_patch_DATA = \
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%D%/packages/patches/gpsbabel-qstring.patch \
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%D%/packages/patches/grantlee-merge-theme-dirs.patch \
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%D%/packages/patches/grep-timing-sensitive-test.patch \
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%D%/packages/patches/gromacs-tinyxml2.patch \
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%D%/packages/patches/groovy-add-exceptionutilsgenerator.patch \
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%D%/packages/patches/grub-efi-fat-serial-number.patch \
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%D%/packages/patches/gsl-test-i686.patch \
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@ -30,15 +30,20 @@
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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 boost)
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#:use-module (gnu packages check)
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#:use-module (gnu packages compression)
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#:use-module (gnu packages documentation)
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#:use-module (gnu packages gl)
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#:use-module (gnu packages graphviz)
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#:use-module (gnu packages gv)
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#:use-module (gnu packages maths)
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#:use-module (gnu packages mpi)
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#:use-module (gnu packages perl)
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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 qt)
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#:use-module (gnu packages sphinx)
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#:use-module (gnu packages xml)
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#:use-module (guix build-system cmake)
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#:use-module (guix build-system gnu)
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@ -336,6 +341,91 @@ optionally velocities and the H-matrix. Coordinates and velocities are
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stored with user-specified precision.")
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(license license:bsd-3)))
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(define-public gromacs
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(package
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(name "gromacs")
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(version "2020.2")
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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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"1wyjgcdl30wy4hy6jvi9lkq53bqs9fgfq6fri52dhnb3c76y8rbl"))
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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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(build-system cmake-build-system)
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(arguments
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`(#: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_EXTERNAL_TINYXML2=on"
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(string-append "-DTinyXML2_DIR="
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(assoc-ref %build-inputs "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 (assoc-ref inputs "googletest-source")
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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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#t)))))
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(native-inputs
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`(("doxygen" ,doxygen)
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("googletest-source" ,(package-source googletest))
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("graphviz" ,graphviz)
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("pkg-config" ,pkg-config)
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("python" ,python)
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("python-pygments" ,python-pygments)
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("python-sphinx" ,python-sphinx)))
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(inputs
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`(("fftwf" ,fftwf)
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("hwloc" ,hwloc-2 "lib")
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("lmfit" ,lmfit)
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("openblas" ,openblas)
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("perl" ,perl)
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("tinyxml2" ,tinyxml2)
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("tng" ,tng)))
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(home-page "http://www.gromacs.org/")
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(synopsis "Molecular dynamics software package")
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(description "GROMACS is a versatile package to perform molecular dynamics,
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i.e. simulate the Newtonian equations of motion for systems with hundreds to
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millions of particles. It is primarily designed for biochemical molecules like
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proteins, lipids and nucleic acids that have a lot of complicated bonded
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interactions, but since GROMACS is extremely fast at calculating the nonbonded
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interactions (that usually dominate simulations) many groups are also using it
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for research on non-biological systems, e.g. polymers. GROMACS supports all the
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usual algorithms you expect from a modern molecular dynamics implementation.")
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(license license:lgpl2.1+)))
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(define-public openbabel
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(package
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(name "openbabel")
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@ -0,0 +1,67 @@
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Unbundling tinyxml2 from gromacs and using our own, which is newer, broke gromacs
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build.
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This patch fixes three issues:
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- cmake now errors out if using multiple target_link_libraries with mixed styles
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of signatures.
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- Error handling API changed, fix the testutils/refdata_xml.cpp code by using the
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new API: document.ErrorStr() & tinyxml2::XML_SUCCESS.
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Those fixes will be submitted for inclusion to upstream, but may not be suitable
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there as long as they still keep the old version bundled.
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First hunk has already been requested for merging. Third is in discussion. Second
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will only be sent if third is OK'ed.
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diff -ruN gromacs-2020.2/src/testutils/CMakeLists.txt gromacs-2020.2-fixed/src/testutils/CMakeLists.txt
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--- gromacs-2020.2/src/testutils/CMakeLists.txt 2020-04-30 18:33:44.000000000 +0200
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+++ gromacs-2020.2-fixed/src/testutils/CMakeLists.txt 2020-05-01 22:52:16.356000000 +0200
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@@ -73,7 +73,7 @@
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if(HAVE_TINYXML2)
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include_directories(SYSTEM ${TinyXML2_INCLUDE_DIR})
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- target_link_libraries(testutils ${TinyXML2_LIBRARIES})
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+ target_link_libraries(testutils PRIVATE ${TinyXML2_LIBRARIES})
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else()
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include_directories(BEFORE SYSTEM "../external/tinyxml2")
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endif()
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diff -ruN gromacs-2020.2/src/testutils/refdata_xml.cpp gromacs-2020.2-fixed/src/testutils/refdata_xml.cpp
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--- gromacs-2020.2/src/testutils/refdata_xml.cpp 2020-04-30 18:33:44.000000000 +0200
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+++ gromacs-2020.2-fixed/src/testutils/refdata_xml.cpp 2020-05-01 23:17:09.556000000 +0200
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@@ -206,21 +206,12 @@
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document.LoadFile(path.c_str());
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if (document.Error())
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{
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- const char* errorStr1 = document.GetErrorStr1();
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- const char* errorStr2 = document.GetErrorStr2();
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+ const char* errorStr = document.ErrorStr();
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std::string errorString("Error was ");
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- if (errorStr1)
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- {
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- errorString += errorStr1;
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- }
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- if (errorStr2)
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- {
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- errorString += errorStr2;
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- }
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- if (!errorStr1 && !errorStr2)
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- {
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+ if (errorStr)
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+ errorString += errorStr;
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+ else
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errorString += "not specified.";
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- }
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GMX_THROW(TestException("Reference data not parsed successfully: " + path + "\n."
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+ errorString + "\n"));
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}
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@@ -371,7 +362,7 @@
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XMLElementPtr rootElement = createRootElement(&document);
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createChildElements(rootElement, rootEntry);
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- if (document.SaveFile(path.c_str()) != tinyxml2::XML_NO_ERROR)
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+ if (document.SaveFile(path.c_str()) != tinyxml2::XML_SUCCESS)
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{
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GMX_THROW(TestException("Reference data saving failed in " + path));
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}
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