llvm-clang needed for gromacs-2016-1

diff -uNr llvm-3.9.0.src.orig/cmake/config-ix.cmake llvm-3.9.0.src/cmake/config-ix.cmake
--- llvm-3.9.0.src.orig/cmake/config-ix.cmake	2015-09-21 08:59:14.000000000 -0400
+++ llvm-3.9.0.src/cmake/config-ix.cmake	2015-09-21 09:42:08.000000000 -0400
@@ -323,6 +323,12 @@
 set(LLVM_HOST_TRIPLE "${LLVM_INFERRED_HOST_TRIPLE}" CACHE STRING
     "Host on which LLVM binaries will run")
 
+if( APPLE )
+get_host_osx_version(LLVM_INFERRED_OSX_VERSION)
+set(LLVM_HOST_OSX_VERSION "${LLVM_INFERRED_OSX_VERSION}" CACHE STRING
+    "Host version of Mac OS X")
+endif( APPLE )
+
 # Determine the native architecture.
 string(TOLOWER "${LLVM_TARGET_ARCH}" LLVM_NATIVE_ARCH)
 if( LLVM_NATIVE_ARCH STREQUAL "host" )
diff -uNr llvm-3.9.0.src.orig/cmake/modules/GetHostTriple.cmake llvm-3.9.0.src/cmake/modules/GetHostTriple.cmake
--- llvm-3.9.0.src.orig/cmake/modules/GetHostTriple.cmake	2015-07-04 14:35:51.000000000 -0400
+++ llvm-3.9.0.src/cmake/modules/GetHostTriple.cmake	2015-09-21 09:42:08.000000000 -0400
@@ -28,3 +28,15 @@
   set( ${var} ${value} PARENT_SCOPE )
   message(STATUS "Target triple: ${value}")
 endfunction( get_host_triple var )
+
+# Mac OS X only: get the host version
+function( get_host_osx_version var )
+  if( APPLE )
+    execute_process(COMMAND sw_vers -productVersion COMMAND cut -d. -f1-2
+      RESULT_VARIABLE TT_RV
+      OUTPUT_VARIABLE value
+      OUTPUT_STRIP_TRAILING_WHITESPACE)
+    set( ${var} ${value} PARENT_SCOPE )
+    message(STATUS "Host OS X version: ${value}")
+  endif ( APPLE )
+endfunction( get_host_osx_version var )
diff -uNr llvm-3.9.0.src.orig/utils/lit/lit/TestRunner.py llvm-3.9.0.src/utils/lit/lit/TestRunner.py
--- llvm-3.9.0.src.orig/utils/lit/lit/TestRunner.py	2015-09-21 08:56:28.000000000 -0400
+++ llvm-3.9.0.src/utils/lit/lit/TestRunner.py	2015-09-21 09:42:08.000000000 -0400
@@ -484,11 +484,16 @@
                     return str(line_number - int(match.group(2)))
             ln = re.sub('%\(line *([\+-]) *(\d+)\)', replace_line_number, ln)
 
+            ln1 = ln.split(' ')[1];
             # Collapse lines with trailing '\\'.
             if script and script[-1][-1] == '\\':
                 script[-1] = script[-1][:-1] + ln
-            else:
+            # do not commit this patch
+            # exception: built-in shell commands and operators
+            elif ln[1] == '(' or ln[1] == '{' or ln[1] == '!' or ln[1] == '|' or ln1 == 'export' or ln1 == 'env' or ln1 == 'cd' or ln1 == 'pushd' or ln1 == 'set' or ln1 == 'test' or ln1 == 'umask' or ln1 == '%clang_profgen' or 'LLVM_PROFILE_FILE=' in ln1 or 'LLVM_PROFILE_VERBOSE_ERRORS=' in ln1:
                 script.append(ln)
+            else:
+                script.append('gtimeout 1m ' +ln)
         elif command_type == 'XFAIL':
             test.xfails.extend([s.strip() for s in ln.split(',')])
         elif command_type == 'REQUIRES':

diff -uNr cfe-3.9.0.src.orig/lib/Driver/Tools.cpp cfe-3.9.0.src/lib/Driver/Tools.cpp
--- cfe-3.9.0.src.orig/lib/Driver/Tools.cpp	2016-08-13 16:43:56.000000000 -0400
+++ cfe-3.9.0.src/lib/Driver/Tools.cpp	2016-11-01 20:08:04.000000000 -0400
@@ -3061,12 +3061,18 @@
 
   switch (getOpenMPRuntime(TC, Args)) {
   case OMPRT_OMP:
+    // Help clang find libomp.dylib
+    CmdArgs.push_back("-L@FINK_PREFIX@/lib/libomp");
     CmdArgs.push_back("-lomp");
     break;
   case OMPRT_GOMP:
+    // Help clang find libgomp.dylib
+    CmdArgs.push_back("-L@FINK_PREFIX@/lib/libomp");
     CmdArgs.push_back("-lgomp");
     break;
   case OMPRT_IOMP5:
+    // Help clang find libiomp5.dylib
+    CmdArgs.push_back("-L@FINK_PREFIX@/lib/libomp");
     CmdArgs.push_back("-liomp5");
     break;
   case OMPRT_Unknown:
@@ -5031,6 +5037,8 @@
     case OMPRT_OMP:
     case OMPRT_IOMP5:
       // Clang can generate useful OpenMP code for these two runtime libraries.
+      // Automatically find omp.h from libomp-dev
+      CmdArgs.push_back("-I@FINK_PREFIX@/include/libomp");
       CmdArgs.push_back("-fopenmp");
 
       // If no option regarding the use of TLS in OpenMP codegeneration is
@@ -9524,9 +9532,13 @@
         // Also link the particular OpenMP runtimes.
         switch (getOpenMPRuntime(ToolChain, Args)) {
         case OMPRT_OMP:
+	  // Help clang find libomp.dylib
+	  CmdArgs.push_back("-L@FINK_PREFIX@/lib/libomp");
           CmdArgs.push_back("-lomp");
           break;
         case OMPRT_GOMP:
+	  // Help clang find libgomp.dylib
+	  CmdArgs.push_back("-L@FINK_PREFIX@/lib/libomp");
           CmdArgs.push_back("-lgomp");
 
           // FIXME: Exclude this for platforms with libgomp that don't require
@@ -9534,6 +9546,8 @@
           CmdArgs.push_back("-lrt");
           break;
         case OMPRT_IOMP5:
+	  // Help clang find libiomp5.dylib
+	  CmdArgs.push_back("-L@FINK_PREFIX@/lib/libomp");
           CmdArgs.push_back("-liomp5");
           break;
         case OMPRT_Unknown:

diff -uNr cfe-3.9.0.src.orig/lib/Driver/Tools.cpp cfe-3.9.0.src/lib/Driver/Tools.cpp
--- cfe-3.9.0.src.orig/lib/Driver/Tools.cpp	2016-08-13 16:43:56.000000000 -0400
+++ cfe-3.9.0.src/lib/Driver/Tools.cpp	2016-10-29 07:57:22.000000000 -0400
@@ -7637,22 +7637,22 @@
       CmdArgs.push_back("-object_path_lto");
       CmdArgs.push_back(TmpPath);
     }
+  }
 
-    // Use -lto_library option to specify the libLTO.dylib path. Try to find
-    // it in clang installed libraries. If not found, the option is not used
-    // and 'ld' will use its default mechanism to search for libLTO.dylib.
-    if (Version[0] >= 133) {
-      // Search for libLTO in <InstalledDir>/../lib/libLTO.dylib
-      StringRef P = llvm::sys::path::parent_path(D.getInstalledDir());
-      SmallString<128> LibLTOPath(P);
-      llvm::sys::path::append(LibLTOPath, "lib");
-      llvm::sys::path::append(LibLTOPath, "libLTO.dylib");
-      if (llvm::sys::fs::exists(LibLTOPath)) {
-        CmdArgs.push_back("-lto_library");
-        CmdArgs.push_back(C.getArgs().MakeArgString(LibLTOPath));
-      } else {
-        D.Diag(diag::warn_drv_lto_libpath);
-      }
+  // Use -lto_library option to specify the libLTO.dylib path. Try to find
+  // it in clang installed libraries. If not found, the option is not used
+  // and 'ld' will use its default mechanism to search for libLTO.dylib.
+  if (Version[0] >= 133) {
+    // Search for libLTO in <InstalledDir>/../lib/libLTO.dylib
+    StringRef P = llvm::sys::path::parent_path(D.Dir);
+    SmallString<128> LibLTOPath(P);
+    llvm::sys::path::append(LibLTOPath, "lib");
+    llvm::sys::path::append(LibLTOPath, "libLTO.dylib");
+    if (llvm::sys::fs::exists(LibLTOPath)) {
+      CmdArgs.push_back("-lto_library");
+      CmdArgs.push_back(C.getArgs().MakeArgString(LibLTOPath));
+    } else {
+      D.Diag(diag::warn_drv_lto_libpath);
     }
   }
 
diff -uNr cfe-3.9.0.src.orig/test/Driver/darwin-ld-lto.c cfe-3.9.0.src/test/Driver/darwin-ld-lto.c
--- cfe-3.9.0.src.orig/test/Driver/darwin-ld-lto.c	2015-10-02 11:10:33.000000000 -0400
+++ cfe-3.9.0.src/test/Driver/darwin-ld-lto.c	2016-10-29 07:58:30.000000000 -0400
@@ -3,7 +3,7 @@
 // Check that ld gets "-lto_library" and warnings about libLTO.dylib path.
 
 // RUN: %clang -target x86_64-apple-darwin10 -### %s \
-// RUN:   -mlinker-version=133 -flto 2> %t.log
+// RUN:   -mlinker-version=133 2> %t.log
 // RUN: cat %t.log
 // RUN: FileCheck -check-prefix=LINK_LTOLIB_PATH %s < %t.log
 //
@@ -11,14 +11,14 @@
 // LINK_LTOLIB_PATH: "-lto_library"
 
 // RUN: %clang -target x86_64-apple-darwin10 -### %s \
-// RUN:   -ccc-install-dir %S/dummytestdir -mlinker-version=133 -flto 2> %t.log
+// RUN:   -ccc-install-dir %S/dummytestdir -mlinker-version=133 2> %t.log
 // RUN: cat %t.log
 // RUN: FileCheck -check-prefix=LINK_LTOLIB_PATH_WRN %s < %t.log
 //
 // LINK_LTOLIB_PATH_WRN: warning: libLTO.dylib relative to clang installed dir not found; using 'ld' default search path instead
 
 // RUN: %clang -target x86_64-apple-darwin10 -### %s \
-// RUN:   -ccc-install-dir %S/dummytestdir -mlinker-version=133 -Wno-liblto -flto 2> %t.log
+// RUN:   -ccc-install-dir %S/dummytestdir -mlinker-version=133 -Wno-liblto 2> %t.log
 // RUN: cat %t.log
 // RUN: FileCheck -check-prefix=LINK_LTOLIB_PATH_NOWRN %s < %t.log
 //

--- gromacs-2016/CMakeLists.txt.orig	2016-10-30 10:02:20.000000000 -0400
+++ gromacs-2016/CMakeLists.txt	2016-10-30 10:02:42.000000000 -0400
@@ -475,6 +475,7 @@
 # tests. This exports LIBXML2_FOUND, which we should not use because
 # it does not tell us that linking will succeed. Instead, we test that
 # next.
+set(LIBXML2_LIBRARIES @FINKPREFIX@/lib/libxml2.dylib)
 #if(DEFINED LIBXML2_LIBRARIES)
 #  set(LibXml2_FIND_QUIETLY TRUE)
 #endif()