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gnu: Add gromacs.

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* 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 2020-05-04 00:39:36 +02:00 • committed by Ludovic Courtès
parent feba2c9751
commit 06ed1dba35
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67
gnu/packages/patches/gromacs-tinyxml2.patch Normal file
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@ -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));
}