Merge "Fixes linkage with FFTW + MKL for BLAS/LAPACK" into release-4-6

diff --git a/src/gmxlib/CMakeLists.txt b/src/gmxlib/CMakeLists.txt
index f7a174b84f9582d27dbb60ea942b59721b21e69a..735ce020ff8ab53a14174af570898f65abfd64d9 100644 (file)
--- a/src/gmxlib/CMakeLists.txt
+++ b/src/gmxlib/CMakeLists.txt
@@ -113,7 +113,7 @@ endif()
 
 # NONBONDED_SOURCES is imported from the nonbonded subdirectory.
 add_library(gmx ${GMXLIB_SOURCES} ${BLAS_SOURCES} ${LAPACK_SOURCES} ${THREAD_MPI_SRC} ${NONBONDED_SOURCES})
-target_link_libraries(gmx ${GMX_GPU_LIBRARIES} ${GMX_EXTRA_LIBRARIES} ${FFT_LIBRARIES} ${THREAD_LIB} ${OpenMP_SHARED_LINKER_FLAGS})
+target_link_libraries(gmx ${FFT_LIBRARIES} ${GMX_GPU_LIBRARIES} ${GMX_EXTRA_LIBRARIES} ${THREAD_LIB} ${OpenMP_SHARED_LINKER_FLAGS})
 if(USE_VERSION_H)
        add_dependencies(gmx gmx_version) 
 endif()

diff --git a/src/kernel/CMakeLists.txt b/src/kernel/CMakeLists.txt
index 01e290c9c534a1e0bbe78d3e19a357dee3ac8800..50624792f1189c574ad7d61ea40092ead9851b41 100644 (file)
--- a/src/kernel/CMakeLists.txt
+++ b/src/kernel/CMakeLists.txt
@@ -102,8 +102,6 @@ if(GMX_FAHCORE)
   add_library(fahcore ${MDRUN_SOURCES})
 else(GMX_FAHCORE)
 
-list(APPEND GMX_EXTRA_LIBRARIES gmxpreprocess md ${OpenMP_LINKER_FLAGS})
-
 set(GMX_KERNEL_PROGRAMS
     grompp tpbconv pdb2gmx g_protonate gmxdump g_x2top gmxcheck)
 if (NOT GMX_NO_QUOTES)
@@ -116,13 +114,13 @@ foreach(PROGRAM ${GMX_KERNEL_PROGRAMS})
     if (NOT ${PROGRAM} STREQUAL "g_luck")
         gmx_add_man_page(${PROGRAM})
     endif()
-    target_link_libraries(${PROGRAM} ${GMX_EXTRA_LIBRARIES})
+    target_link_libraries(${PROGRAM} gmxpreprocess md gmx ${OpenMP_LINKER_FLAGS})
     set_target_properties(${PROGRAM} PROPERTIES OUTPUT_NAME "${PROGRAM}${GMX_BINARY_SUFFIX}")
 endforeach()
 
 add_executable(mdrun ${MDRUN_SOURCES} main.c)
 gmx_add_man_page(mdrun)
-target_link_libraries(mdrun ${GMX_EXTRA_LIBRARIES})
+target_link_libraries(mdrun gmxpreprocess md gmx ${OpenMP_LINKER_FLAGS})
 set_target_properties(mdrun PROPERTIES OUTPUT_NAME "mdrun${GMX_BINARY_SUFFIX}" COMPILE_FLAGS "${OpenMP_C_FLAGS}")
 
 # Construct component groups for installation; note that a component may

diff --git a/src/mdlib/CMakeLists.txt b/src/mdlib/CMakeLists.txt
index 732624a99147b908ae4ddca1041baa350d27aaa7..617a0c7796bee3f247248d111cc983dfd8f17080 100644 (file)
--- a/src/mdlib/CMakeLists.txt
+++ b/src/mdlib/CMakeLists.txt
@@ -57,7 +57,7 @@ endif()
 
 add_library(md ${MDLIB_SOURCES})
 
-target_link_libraries(md ${GMX_GPU_LIBRARIES} gmx ${GMX_EXTRA_LIBRARIES} ${FFT_LIBRARIES} ${OpenMP_SHARED_LINKER_FLAGS})
+target_link_libraries(md ${GMX_GPU_LIBRARIES} gmx)
 if(GMX_BUILD_OWN_FFTW)
     # This dependency has to be made here rather than the CMakeLists.txt that
     # does the FFTW build, because of the order in which

diff --git a/src/mdlib/nbnxn_cuda/CMakeLists.txt b/src/mdlib/nbnxn_cuda/CMakeLists.txt
index 27df5c76e837a88312cf620c7800f3b012219f25..bbabac0188b9ed9c790bc6bcafc9d40e50ac1b22 100644 (file)
--- a/src/mdlib/nbnxn_cuda/CMakeLists.txt
+++ b/src/mdlib/nbnxn_cuda/CMakeLists.txt
@@ -41,5 +41,6 @@ if(GMX_GPU)
             DEBUG -g -D_DEBUG_=1)
     #Because this is a static library linked into the (potential) shared library
     #it should have the export of the shared library.
+    target_link_libraries(nbnxn_cuda cuda_tools)
     SET_TARGET_PROPERTIES(nbnxn_cuda PROPERTIES DEFINE_SYMBOL "md_EXPORTS" )
 endif()

diff --git a/src/ngmx/CMakeLists.txt b/src/ngmx/CMakeLists.txt
index ed28c41a9663de1e64d317324a4868f06ffaca0b..cfb344f9b6e628be2579c2f490591893ddddfd55 100644 (file)
--- a/src/ngmx/CMakeLists.txt
+++ b/src/ngmx/CMakeLists.txt
@@ -54,7 +54,7 @@ set(NGMX_PROGRAMS
 foreach(PROG ${NGMX_PROGRAMS})
         add_executable(${PROG} ${PROG}.c ${NGMX_COMMON_SOURCE})
         gmx_add_man_page(${PROG})
-        target_link_libraries(${PROG} gmx ${GMX_EXTRA_LIBRARIES} ${X11_LIBRARIES})        
+        target_link_libraries(${PROG} gmx ${X11_LIBRARIES})
         set_target_properties(${PROG} PROPERTIES OUTPUT_NAME "${PROG}${GMX_BINARY_SUFFIX}")
 endforeach(PROG) 
 

diff --git a/src/tools/CMakeLists.txt b/src/tools/CMakeLists.txt
index 2faf622f44ea2426644c3237ab7813dd6eefe4ad..b323ef79de8149d02f29bde01583f713e5e88049 100644 (file)
--- a/src/tools/CMakeLists.txt
+++ b/src/tools/CMakeLists.txt
@@ -70,7 +70,7 @@ add_library(gmxana
             )
 
 
-target_link_libraries(gmxana md gmx ${GSL_LIBRARIES})
+target_link_libraries(gmxana md ${GSL_LIBRARIES})
 set_target_properties(gmxana PROPERTIES OUTPUT_NAME "gmxana${GMX_LIBS_SUFFIX}" SOVERSION ${SOVERSION} INSTALL_NAME_DIR "${LIB_INSTALL_DIR}"
     COMPILE_FLAGS "${OpenMP_C_FLAGS}")
 
@@ -107,7 +107,7 @@ foreach(TOOL ${GMX_TOOLS_PROGRAMS} ${GMX_TOOLS_PROGRAMS_NOT_FOR_INSTALLATION})
         endif()
     endif()
     add_executable(${TOOL} ${TOOL}.c)
-    target_link_libraries(${TOOL} gmxana ${OpenMP_LINKER_FLAGS})
+    target_link_libraries(${TOOL} gmxana md gmx ${OpenMP_LINKER_FLAGS})
     set_target_properties(${TOOL} PROPERTIES OUTPUT_NAME "${TOOL}${GMX_BINARY_SUFFIX}")
 endforeach()