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gnu: gromacs: Update to 2025.3.
Also unbundle libtirpc and muparser. The unbundling is now done in a snippet instead of a build phase. * gnu/packages/chemistry.scm (gromacs): Update to 2025.3. [source]: Switch to git-fetch. Add modules and snippet fields. [arguments]<#:configure-flags>: Add -DGMX_USE_MUPARSER=EXTERNAL and -DCMAKE_CXX_FLAGS. [phases]: Adjust 'fixes phase. Use the package source of googletest-1.13. [inputs]: Add libtirpc and muparser. * gnu/packages/patches/gromacs-tinyxml2.patch: Delete file. * gnu/local.mk (dist_patch_DATA): Deregister patch. Fixes: guix/guix#3584 Signed-off-by: Andreas Enge <andreas@enge.fr>
This commit is contained in:
David Elsing
Andreas Enge
parent
ad0c381841
commit
ad9d43baa0
3 changed files with 54 additions and 97 deletions
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@ -1519,7 +1519,6 @@ dist_patch_DATA = \
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%D%/packages/patches/grantlee-register-metaenumvariable.patch \
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%D%/packages/patches/grep-timing-sensitive-test.patch \
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%D%/packages/patches/grfcodec-gcc-compat.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/grub-hurd64.patch \
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@ -60,6 +60,7 @@
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#:use-module (gnu packages lisp)
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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 onc-rpc)
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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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@ -493,23 +494,47 @@ stored with user-specified precision.")
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(define-public gromacs
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(package
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(name "gromacs")
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(version "2022.4")
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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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"15vjwasxjq0h18dmzacjkdim51zrvr0ni42hbc30557j5xhbw4f5"))
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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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(version "2025.3")
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(source
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(origin
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(method git-fetch)
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(uri (git-reference
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(url "https://gitlab.com/gromacs/gromacs")
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(commit (string-append "v" version))))
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(file-name (git-file-name name version))
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(sha256
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(base32
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"1p9vvlbrysh8lwnbgy845pgx664k6mkw8p66f8bx468f7z2rp900"))
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(modules '((guix build utils)))
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(snippet
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'(begin
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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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;; Still bundled: Colvars is intended to be built as part of a
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;; molecular simulation program.
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;;(delete-file-recursively "src/external/colvars")
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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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(delete-file-recursively "src/external/muparser")
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(delete-file-recursively "src/external/rpc_xdr")
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(delete-file-recursively "src/external/vkfft")))))
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(build-system cmake-build-system)
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(arguments
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(list #: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_USE_MUPARSER=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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@ -521,31 +546,29 @@ stored with user-specified precision.")
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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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#$(package-version python-sphinx)))
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#$(package-version python-sphinx))
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(string-append
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"-DCMAKE_CXX_FLAGS=-I"
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(search-input-directory %build-inputs "/include/tirpc")))
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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 #$(package-source googletest)
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(lambda _
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(copy-recursively #$(package-source googletest-1.13)
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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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"void __guix_disabled()"))
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(substitute* "cmake/gmxTestXDR.cmake"
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(("TestXDR\\.cpp\"" orig)
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(string-append orig " LINK_LIBRARIES -ltirpc")))
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(substitute* "CMakeLists.txt"
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(("set\\(GMX_EXTRA_LIBRARIES.*" orig)
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(string-append
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orig "\nlist(APPEND GMX_EXTRA_LIBRARIES \"-ltirpc\")\n")))
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(substitute* "src/external/CMakeLists.txt"
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(("add_subdirectory\\(rpc_xdr\\)") "")))))))
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(native-inputs
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(list doxygen
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graphviz
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@ -556,7 +579,9 @@ stored with user-specified precision.")
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(inputs
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(list fftwf
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`(,hwloc-2 "lib")
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libtirpc
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lmfit
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muparser
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openblas
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perl
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tinyxml2
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@ -1,67 +0,0 @@
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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 this issue:
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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 --git a/CMakeLists.txt b/CMakeLists.txt
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index cd748c9..1e90c95 100644
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--- a/CMakeLists.txt
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+++ b/CMakeLists.txt
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@@ -539,9 +539,6 @@ if(GMX_EXTERNAL_TINYXML2)
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if(NOT HAVE_TINYXML2)
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message(FATAL_ERROR "External TinyXML-2 could not be found, please adjust your search paths")
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endif()
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- if (TinyXML2_FOUND AND TinyXML2_VERSION VERSION_GREATER "6")
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- message(FATAL_ERROR "External TinyXML-2 is later than the highest supported version 6. Please adjust your search paths to include a supported version")
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- endif()
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endif()
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option(GMX_EXTRAE "Add support for tracing using EXTRAE" OFF)
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diff --git a/src/testutils/refdata_xml.cpp b/src/testutils/refdata_xml.cpp
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index 0eb2209..57cebff 100644
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--- a/src/testutils/refdata_xml.cpp
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+++ b/src/testutils/refdata_xml.cpp
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@@ -206,21 +206,12 @@ ReferenceDataEntry::EntryPointer readReferenceDataFile(const std::string& path)
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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 @@ void writeReferenceDataFile(const std::string& path, const ReferenceDataEntry& r
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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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