Merge "fix a segfault in sse_mask_init" into release-4-6

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 16830abb7b19655bb5f76ae800fb3590c8737e0c..0eef9de6fd7d448813dcd4914845bd5b2562ec1b 100644 (file)
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -55,7 +55,6 @@ set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Gromacs - a toolkit for high-performance
 if (NOT GMX_USE_RELATIVE_INSTALL_PATH)
     set(CPACK_SET_DESTDIR "ON")
 endif()
-set(CPACK_INCLUDE_TOPLEVEL_DIRECTORY 0)
 set(CPACK_RESOURCE_FILE_WELCOME "${CMAKE_SOURCE_DIR}/admin/InstallWelcome.txt")
 # Its GPL/LGPL, so they do not have to agree to a license for mere usage, but some installers require this...
 set(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/admin/InstallLicense.txt")
@@ -1020,7 +1019,6 @@ endif()
 
 add_subdirectory(share)
 add_subdirectory(include)
-add_subdirectory(man)
 add_subdirectory(src)
 add_subdirectory(scripts)
 

diff --git a/CPackInit.cmake b/CPackInit.cmake
index d0f255a8bd6f879fc307b8b1f3f3a384cad78359..20d2c2369510a415d03d9a2bf2327d70c5fcc946 100644 (file)
--- a/CPackInit.cmake
+++ b/CPackInit.cmake
@@ -4,5 +4,5 @@ if(CPACK_SOURCE_PACKAGE_FILE_NAME AND NOT EXISTS "${CMAKE_BINARY_DIR}/man/man1/n
     message(FATAL_ERROR 
         "To generate correct source package all man pages need to be generated. "
         "The man pages are automatically build together with the binaries. "
-        "Make sure to build all binaries (e.g. GMX_X11=on). ${CMAKE_SOURCE_DIR}/man/man1/ngmx.1")
+        "Make sure to build all binaries (e.g. GMX_X11=on).")
 endif()

diff --git a/cmake/BuildManPages.cmake b/cmake/BuildManPages.cmake
index bd3f5937b46e92ee5e057f01bd5602e7604ed72f..65ac6540755dd81a702b9e3130f8ea3696dfa5af 100644 (file)
--- a/cmake/BuildManPages.cmake
+++ b/cmake/BuildManPages.cmake
@@ -35,6 +35,10 @@ if(GMX_BUILD_MANPAGES)
     configure_file(${CMAKE_SOURCE_DIR}/man/man7/gromacs.7.cmakein ${CMAKE_BINARY_DIR}/man/man7/gromacs.7)
     install(FILES ${CMAKE_BINARY_DIR}/man/man7/gromacs.7 DESTINATION
         ${MAN_INSTALL_DIR}/man7)
+#man-pages are only avalaible if they are either build or this is a source archive
+elseif(NOT EXISTS "${CMAKE_SOURCE_DIR}/admin/.isreposource")
+    install(FILES ${CMAKE_SOURCE_DIR}/man/man7/gromacs.7 DESTINATION
+        ${MAN_INSTALL_DIR}/man7)
 endif()
 
 function (gmx_add_man_page EXENAME)
@@ -56,5 +60,8 @@ function (gmx_add_man_page EXENAME)
                 -P ${CMAKE_SOURCE_DIR}/cmake/Filter.cmake)
         install(FILES ${MAN1_PATH}/${EXENAME}.1 DESTINATION 
             ${MAN_INSTALL_DIR}/man1)
+    elseif(NOT EXISTS "${CMAKE_SOURCE_DIR}/admin/.isreposource")
+        install(FILES ${CMAKE_SOURCE_DIR}/man/man1/${EXENAME}.1 DESTINATION 
+            ${MAN_INSTALL_DIR}/man1)
     endif()
 endfunction ()

diff --git a/man/CMakeLists.txt b/man/CMakeLists.txt
deleted file mode 100644 (file)
index 82953fe..0000000
--- a/man/CMakeLists.txt
+++ /dev/null
@@ -1,8 +0,0 @@
-# Man pages: Nothing to build, just installation
-install(DIRECTORY . DESTINATION ${MAN_INSTALL_DIR}
-  COMPONENT data
-  PATTERN "Makefile*" EXCLUDE
-  PATTERN "CMake*" EXCLUDE
-  PATTERN "cmake*" EXCLUDE
-  PATTERN "*~" EXCLUDE
-)

diff --git a/src/mdlib/forcerec.c b/src/mdlib/forcerec.c
index d58d6edfff71d69cbfcbdf1fcab0adc2ba119ac9..ee164d229c5b56099845d5e858611e7b1663dfd4 100644 (file)
--- a/src/mdlib/forcerec.c
+++ b/src/mdlib/forcerec.c
@@ -1385,7 +1385,7 @@ void init_forcerec(FILE *fp,
         bNoSolvOpt         = TRUE;
     }
     
-    if( (getenv("GMX_DISABLE_ACCELERATION") != NULL) || (getenv("GMX_NOOPTIMIZEDKERNELS") != NULL) )
+    if (getenv("GMX_DISABLE_ACCELERATION") != NULL)
     {
         fr->use_acceleration = FALSE;
         if (fp != NULL)
@@ -1424,7 +1424,7 @@ void init_forcerec(FILE *fp,
     fr->bcoultab   = (!(fr->eeltype == eelCUT || EEL_RF(fr->eeltype)) ||
                       fr->eeltype == eelRF_ZERO);
     
-    if (getenv("GMX_FORCE_TABLES"))
+    if (getenv("GMX_REQUIRE_TABLES"))
     {
         fr->bvdwtab  = TRUE;
         fr->bcoultab = TRUE;

diff --git a/src/mdlib/shellfc.c b/src/mdlib/shellfc.c
index e3dc3fd7c9850616ce80f13f932049a6209cb0ba..5d9e7febe06264253742ee3c5860ee23d5a18dc0 100644 (file)
--- a/src/mdlib/shellfc.c
+++ b/src/mdlib/shellfc.c
@@ -77,8 +77,8 @@ typedef struct gmx_shellfc {
   int     nshell;          /* The number of local shells               */
   t_shell *shell;          /* The local shells                         */
   int     shell_nalloc;    /* The allocation size of shell             */
-  gmx_bool    bPredict;        /* Predict shell positions                  */
-  gmx_bool    bForceInit;      /* Force initialization of shell positions  */
+  gmx_bool bPredict;       /* Predict shell positions                  */
+  gmx_bool bRequireInit;   /* Require initialization of shell positions  */
   int     nflexcon;        /* The number of flexible constraints       */
   rvec    *x[2];           /* Array for iterative minimization         */
   rvec    *f[2];           /* Array for iterative minimization         */
@@ -407,13 +407,13 @@ gmx_shellfc_t init_shell_flexcon(FILE *fplog,
   shfc->shell_index_gl = shell_index;
 
   shfc->bPredict   = (getenv("GMX_NOPREDICT") == NULL);
-  shfc->bForceInit = FALSE;
+  shfc->bRequireInit = FALSE;
   if (!shfc->bPredict) {
     if (fplog)
       fprintf(fplog,"\nWill never predict shell positions\n");
   } else {
-    shfc->bForceInit = (getenv("GMX_FORCEINIT") != NULL);
-    if (shfc->bForceInit && fplog)
+    shfc->bRequireInit = (getenv("GMX_REQUIRE_SHELL_INIT") != NULL);
+    if (shfc->bRequireInit && fplog)
       fprintf(fplog,"\nWill always initiate shell positions\n");
   }
 
@@ -799,7 +799,7 @@ int relax_shell_flexcon(FILE *fplog,t_commrec *cr,gmx_bool bVerbose,
 #define  Try (1-Min)             /* At start Try = 1 */
 
   bCont        = (mdstep == inputrec->init_step) && inputrec->bContinuation;
-  bInit        = (mdstep == inputrec->init_step) || shfc->bForceInit;
+  bInit        = (mdstep == inputrec->init_step) || shfc->bRequireInit;
   ftol         = inputrec->em_tol;
   number_steps = inputrec->niter;
   nshell       = shfc->nshell;