doc/doxygen: improve doc

doc/doxygen/chapters/advanced_examples.doxy

@@ -973,7 +973,8 @@ renderbuffer objects into CUDA.  CUDA however imposes some technical
 constraints: peer memcpy has to be disabled, and the thread that runs OpenGL has
 to be the one that runs CUDA computations for that GPU.
 
-To achieve this with StarPU, pass the option \ref disable-cuda-memcpy-peer
+To achieve this with StarPU, pass the option
+\ref disable-cuda-memcpy-peer "--disable-cuda-memcpy-peer"
 to <c>./configure</c> (TODO: make it dynamic), OpenGL/GLUT has to be initialized
 first, and the interoperability mode has to
 be enabled by using the field
@@ -1126,7 +1127,7 @@ directory <c>examples/interface/</c>.
 
 The number of data a task can manage is fixed by the environment variable
 \ref STARPU_NMAXBUFS which has a default value which can be changed
-through the configure option \ref enable-maxbuffers.
+through the configure option \ref enable-maxbuffers "--enable-maxbuffers".
 
 However, it is possible to define tasks managing more data by using
 the field starpu_task::dyn_handles when defining a task and the field

doc/doxygen/chapters/api/codelet_and_tasks.doxy

@@ -214,7 +214,8 @@ Is an array of ::starpu_data_access_mode. It describes the required
 access modes to the data neeeded by the codelet (e.g. ::STARPU_RW). The
 number of entries in this array must be specified in the field
 starpu_codelet::nbuffers, and should not exceed \ref STARPU_NMAXBUFS. If
-unsufficient, this value can be set with the configure option \ref enable-maxbuffers.
+unsufficient, this value can be set with the configure option
+\ref enable-maxbuffers "--enable-maxbuffers".
 
 \var starpu_codelet::dyn_modes
 Is an array of ::starpu_data_access_mode. It describes the required
@@ -288,7 +289,7 @@ Is an array of ::starpu_data_handle_t. It specifies the handles to the
 different pieces of data accessed by the task. The number of entries
 in this array must be specified in the field starpu_codelet::nbuffers,
 and should not exceed \ref STARPU_NMAXBUFS. If unsufficient, this value can
-be set with the configure option \ref enable-maxbuffers.
+be set with the configure option \ref enable-maxbuffers "--enable-maxbuffers".
 \var starpu_task::dyn_handles
 Is an array of ::starpu_data_handle_t. It specifies the handles to the
 different pieces of data accessed by the task. The number of entries

doc/doxygen/chapters/api/initialization.doxy

@@ -140,14 +140,16 @@ AMD implementation of OpenCL is known to fail when copying
 data asynchronously. When using this implementation, it is
 therefore necessary to disable asynchronous data transfers.
 This can also be specified at compilation time by giving to
-the configure script the option \ref disable-asynchronous-copy. (default = 0)
+the configure script the option
+\ref disable-asynchronous-copy "--disable-asynchronous-copy". (default = 0)
 \var starpu_conf::disable_asynchronous_cuda_copy
 This flag should be set to 1 to disable
 asynchronous copies between CPUs and CUDA accelerators.
 This can also be specified with the environment variable
 \ref STARPU_DISABLE_ASYNCHRONOUS_CUDA_COPY.
 This can also be specified at compilation time by giving to
-the configure script the option \ref disable-asynchronous-cuda-copy. (default = 0)
+the configure script the option
+\ref disable-asynchronous-cuda-copy "--disable-asynchronous-cuda-copy". (default = 0)
 \var starpu_conf::disable_asynchronous_opencl_copy
 This flag should be set to 1 to disable
 asynchronous copies between CPUs and OpenCL accelerators.
@@ -158,8 +160,8 @@ when copying data asynchronously. When using this
 implementation, it is therefore necessary to disable
 asynchronous data transfers. This can also be specified at
 compilation time by giving to the configure script the
-option \ref disable-asynchronous-opencl-copy. (default
-= 0)
+option \ref disable-asynchronous-opencl-copy "--disable-asynchronous-opencl-copy".
+(default = 0)
 
 \var starpu_conf::disable_asynchronous_mic_copy
 indicate if asynchronous copies to MIC devices should be disabled

doc/doxygen/chapters/api/profiling.doxy

@@ -171,6 +171,6 @@ called automatically by starpu_shutdown().
 \ingroup API_Profiling
 Display statistics about the current data handles registered
 within StarPU. StarPU must have been configured with the configure
-option \ref enable-memory-stats (see \ref MemoryFeedback).
+option \ref enable-memory-stats "--enable-memory-stats" (see \ref MemoryFeedback).
 
 */

doc/doxygen/chapters/building.doxy

@@ -39,10 +39,10 @@ performance.  <c>hwloc</c> is available in major free operating system
 distributions, and for most operating systems.
 
 If <c>hwloc</c> is not available on your system, the option
-\ref without-hwloc should be explicitely given when calling the
+\ref without-hwloc "--without-hwloc" should be explicitely given when calling the
 <c>configure</c> script. If <c>hwloc</c> is installed with a <c>pkg-config</c> file,
 no option is required, it will be detected automatically, otherwise
-\ref with-hwloc should be used to specify the location of
+\ref with-hwloc "--with-hwloc" should be used to specify the location of
 <c>hwloc</c>.
 
 \subsection GettingSources Getting Sources

doc/doxygen/chapters/c_extensions.doxy

@@ -17,7 +17,7 @@ may need to install a specific <c>-dev</c> package of your distro, such
 as <c>gcc-4.6-plugin-dev</c> on Debian and derivatives.  In addition,
 the plug-in's test suite is only run when <a href="http://www.gnu.org/software/guile/">GNU Guile</a> is found at
 <c>configure</c>-time.  Building the GCC plug-in
-can be disabled by configuring with \ref disable-gcc-extensions.
+can be disabled by configuring with \ref disable-gcc-extensions "--disable-gcc-extensions".
 
 Those extensions include syntactic sugar for defining
 tasks and their implementations, invoking a task, and manipulating data

doc/doxygen/chapters/configure_options.doxy

@@ -157,7 +157,8 @@ Search for CUDA under <c>prefix</c>, which should notably contain the file
 \addindex __configure__--with-cuda-include-dir
 Search for CUDA headers under <c>dir</c>, which should
 notably contain the file <c>cuda.h</c>. This defaults to
-<c>/include</c> appended to the value given to \ref with-cuda-dir.
+<c>/include</c> appended to the value given to
+\ref with-cuda-dir "--with-cuda-dir".
 </dd>
 
 <dt>--with-cuda-lib-dir=<c>dir</c></dt>
@@ -166,7 +167,8 @@ notably contain the file <c>cuda.h</c>. This defaults to
 \addindex __configure__--with-cuda-lib-dir
 Search for CUDA libraries under <c>dir</c>, which should notably contain
 the CUDA shared libraries---e.g., <c>libcuda.so</c>.  This defaults to
-<c>/lib</c> appended to the value given to \ref with-cuda-dir.
+<c>/lib</c> appended to the value given to
+\ref with-cuda-dir "--with-cuda-dir".
 </dd>
 
 <dt>--disable-cuda-memcpy-peer</dt>
@@ -206,7 +208,8 @@ on Mac OS).
 \addindex __configure__--with-opencl-include-dir
 Search for OpenCL headers under <c>dir</c>, which should notably contain
 <c>CL/cl.h</c> (or <c>OpenCL/cl.h</c> on Mac OS).  This defaults to
-<c>/include</c> appended to the value given to \ref with-opencl-dir.
+<c>/include</c> appended to the value given to
+\ref with-opencl-dir "--with-opencl-dir".
 </dd>
 
 <dt>--with-opencl-lib-dir=<c>dir</c></dt>
@@ -215,7 +218,8 @@ Search for OpenCL headers under <c>dir</c>, which should notably contain
 \addindex __configure__--with-opencl-lib-dir
 Search for an OpenCL library under <c>dir</c>, which should notably
 contain the OpenCL shared libraries---e.g. <c>libOpenCL.so</c>. This defaults to
-<c>/lib</c> appended to the value given to \ref with-opencl-dir.
+<c>/lib</c> appended to the value given to
+\ref with-opencl-dir "--with-opencl-dir".
 </dd>
 
 <dt>--enable-opencl-simulator</dt>

doc/doxygen/chapters/environment_variables.doxy

@@ -387,7 +387,7 @@ StarPU, and finally in the source directory of StarPU.
 \anchor STARPU_SILENT
 \addindex __env__STARPU_SILENT
 This variable allows to disable verbose mode at runtime when StarPU
-has been configured with the option \ref enable-verbose. It also
+has been configured with the option \ref enable-verbose "--enable-verbose". It also
 disables the display of StarPU information and warning messages.
 </dd>
 

doc/doxygen/chapters/optimize_performance.doxy

@@ -452,8 +452,8 @@ times before the model is calibrated.
 
 \subsection Simulation Simulation
 
-Then, recompile StarPU, passing \ref enable-simgrid to <c>./configure</c>, and re-run the
-application:
+Then, recompile StarPU, passing \ref enable-simgrid "--enable-simgrid"
+to <c>./configure</c>, and re-run the application:
 
 \verbatim
 $ ./configure --enable-simgrid && make

doc/doxygen/chapters/performance_feedback.doxy

@@ -236,15 +236,15 @@ $ make install
 \endverbatim
 
 In order to have StarPU to generate traces, StarPU should be configured with
-the option \ref with-fxt :
+the option \ref with-fxt "--with-fxt" :
 
 \verbatim
 $ ./configure --with-fxt=$FXTDIR
 \endverbatim
 
 Or you can simply point the <c>PKG_CONFIG_PATH</c> to
-<c>$FXTDIR/lib/pkgconfig</c> and pass \ref with-fxt to
-<c>./configure</c>
+<c>$FXTDIR/lib/pkgconfig</c> and pass
+\ref with-fxt "--with-fxt" to <c>./configure</c>
 
 When FxT is enabled, a trace is generated when StarPU is terminated by calling
 starpu_shutdown()). The trace is a binary file whose name has the form
@@ -475,7 +475,7 @@ use this.
 \section MemoryFeedback Memory Feedback
 
 It is possible to enable memory statistics. To do so, you need to pass
-the option \ref enable-memory-stats when running configure. It is then
+the option \ref enable-memory-stats "--enable-memory-stats" when running configure. It is then
 possible to call the function starpu_display_memory_stats() to
 display statistics about the current data handles registered within StarPU.
 
@@ -547,8 +547,8 @@ Node #3
 \section DataStatistics Data Statistics
 
 Different data statistics can be displayed at the end of the execution
-of the application. To enable them, you need to pass the option \ref
-enable-stats when calling <c>configure</c>. When calling
+of the application. To enable them, you need to pass the option
+\ref enable-stats "--enable-stats" when calling <c>configure</c>. When calling
 starpu_shutdown() various statistics will be displayed,
 execution, MSI cache statistics, allocation cache statistics, and data
 transfer statistics. The display can be disabled by setting the