Fixing generation of documentation

.gitignore

+# Compiled source #
+###################
+*.com
+*.class
+*.dll
+*.exe
+*.o
+*.so
+
+# Packages #
+############
+# it's better to unpack these files and commit the raw source
+# git has its own built in compression methods
+*.7z
+*.dmg
+*.gz
+*.iso
+*.jar
+*.rar
+*.tar
+*.zip
+
+# Logs and databases #
+######################
+*.log
+*.sql
+*.sqlite
+
+# OS generated files #
+######################
+.DS_Store
+.DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+ehthumbs.db
+Thumbs.db
+
+###### Other
+
+*.vtk
+AUTHORS
+COPYING
+ChangeLog
+INSTALL
+NEWS
+README
+Makefile
+Makefile.in
+config.status
+configure
+numerics
+**/.deps
+**/src/config
+aclocal.m4
+**/autom4te.cache

src/MPI_wrapper/MPI_IsendW.hpp

@@ -16,7 +16,7 @@
 class MPI_IsendWB
 {
 public:
-	static inline void send(size_t proc , size_t tag ,void * buf, size_t sz, MPI_Request & req)
+	static inline void send(size_t proc , size_t tag ,const void * buf, size_t sz, MPI_Request & req)
 	{
 		MPI_Isend(buf, sz,MPI_BYTE, proc, tag , MPI_COMM_WORLD,&req);
 	}

src/VCluster_object_array.hpp

@@ -37,7 +37,7 @@ public:
 	 * \return the size of the array
 	 *
 	 */
-	size_t size()
+	size_t size() const
 	{
 		return objects.size();
 	}
@@ -172,6 +172,16 @@ public:
 		return objects[j];
 	}
 
+	/*! \brief Return the object j in the array
+	 *
+	 * \param j element j
+	 *
+	 */
+	const T & operator[](size_t j) const
+	{
+		return objects[j];
+	}
+
 	/*! \brief Resize the array
 	 *
 	 * \param size

src/VCluster_unit_test_util.hpp

@@ -43,7 +43,7 @@ void * msg_alloc(size_t msg_i ,size_t total_msg, size_t total_p, size_t i,size_t
 	if (global_v_cluster->getProcessingUnits() <= 8)
 	{if (totp_check) BOOST_REQUIRE_EQUAL(total_p,global_v_cluster->getProcessingUnits()-1);}
 	else
-	{if (totp_check) BOOST_REQUIRE_EQUAL(total_p,8);}
+	{if (totp_check) BOOST_REQUIRE_EQUAL(total_p,(size_t)8);}
 
 	BOOST_REQUIRE_EQUAL(msg_i, global_step);
 	v->get(i).resize(msg_i);
@@ -221,7 +221,7 @@ template<unsigned int ip> void test_no_send_some_peer()
 		}
 		else
 		{
-			BOOST_REQUIRE_EQUAL(0,recv_message.get(p_id).size());
+			BOOST_REQUIRE_EQUAL((size_t)0,recv_message.get(p_id).size());
 		}
 	}
 }
@@ -320,7 +320,7 @@ template<unsigned int ip> void test()
 				}
 				else
 				{
-					BOOST_REQUIRE_EQUAL(0,recv_message.get(p_id).size());
+					BOOST_REQUIRE_EQUAL((size_t)0,recv_message.get(p_id).size());
 				}
 			}
 		}
@@ -532,7 +532,7 @@ template<unsigned int ip> void test()
 				}
 				else
 				{
-					BOOST_REQUIRE_EQUAL(0,recv_message.get(p_id).size());
+					BOOST_REQUIRE_EQUAL((size_t)0,recv_message.get(p_id).size());
 				}
 			}
 		}
@@ -547,6 +547,8 @@ template<unsigned int ip> void test()
  */
 void test_send_recv_complex(const size_t n, Vcluster & vcl)
 {
+	//! [Send and receive vectors of complex]
+
 	// Point test typedef
 	typedef Point_test<float> p;
 
@@ -568,6 +570,8 @@ void test_send_recv_complex(const size_t n, Vcluster & vcl)
 
 	vcl.execute();
 
+	//! [Send and receive vectors of complex]
+
 	// Check the received buffers (careful at negative modulo)
 	for (size_t i = 0 ; i < 8 ; i++)
 	{
@@ -609,7 +613,7 @@ template<typename T> void test_send_recv_primitives(size_t n, Vcluster & vcl)
 	openfpm::vector<T> v_send = allocate_openfpm_primitive<T>(n,vcl.getProcessUnitID());
 
 	{
-	//! [ Send and receive vectors data ]
+	//! [Sending and receiving primitives]
 
 	// Send to 8 processors
 	for (size_t i = 0 ; i < 8 ; i++)
@@ -627,6 +631,8 @@ template<typename T> void test_send_recv_primitives(size_t n, Vcluster & vcl)
 
 	vcl.execute();
 
+	//! [Sending and receiving primitives]
+
 	// Check the received buffers (careful at negative modulo)
 	for (size_t i = 0 ; i < 8 ; i++)
 	{
@@ -640,12 +646,10 @@ template<typename T> void test_send_recv_primitives(size_t n, Vcluster & vcl)
 		}
 	}
 
-	//! [ Send and receive vectors data ]
-
 	}
 
 	{
-	//! [ Send and receive plain buffer data ]
+	//! [Send and receive plain buffer data]
 
 	// Send to 8 processors
 	for (size_t i = 0 ; i < 8 ; i++)
@@ -663,6 +667,8 @@ template<typename T> void test_send_recv_primitives(size_t n, Vcluster & vcl)
 
 	vcl.execute();
 
+	//! [Send and receive plain buffer data]
+
 	// Check the received buffers (careful at negative modulo)
 	for (size_t i = 0 ; i < 8 ; i++)
 	{
@@ -676,7 +682,6 @@ template<typename T> void test_send_recv_primitives(size_t n, Vcluster & vcl)
 		}
 	}
 
-	//! [ Send and receive plain buffer data ]
 	}
 }
 
@@ -691,7 +696,7 @@ template<typename T>  void test_single_all_gather_primitives(Vcluster & vcl)
 	vcl.execute();
 
 	for (size_t i = 0 ; i < vcl.getProcessingUnits() ; i++)
-		BOOST_REQUIRE_EQUAL(i,clt.get(i));
+		BOOST_REQUIRE_EQUAL(i,(size_t)clt.get(i));
 
 	//! [allGather numbers]
 

src/VCluster_unit_tests.hpp

@@ -89,22 +89,22 @@ BOOST_AUTO_TEST_CASE( VCluster_use_reductions)
 	vcl.execute();
 
 	if ( vcl.getProcessingUnits() < 128 )
-	{BOOST_REQUIRE_EQUAL(c_max,vcl.getProcessingUnits()-1);}
+	{BOOST_REQUIRE_EQUAL(c_max,(char)vcl.getProcessingUnits()-1);}
 	if ( vcl.getProcessingUnits() < 256 )
-	{BOOST_REQUIRE_EQUAL(uc_max,vcl.getProcessingUnits()-1);}
+	{BOOST_REQUIRE_EQUAL(uc_max,(unsigned char)vcl.getProcessingUnits()-1);}
 	if ( vcl.getProcessingUnits() < 32768 )
-	{BOOST_REQUIRE_EQUAL(s_max,vcl.getProcessingUnits()-1);}
+	{BOOST_REQUIRE_EQUAL(s_max,(short int) vcl.getProcessingUnits()-1);}
 	if ( vcl.getProcessingUnits() < 65536 )
-	{BOOST_REQUIRE_EQUAL(us_max,vcl.getProcessingUnits()-1);}
+	{BOOST_REQUIRE_EQUAL(us_max,(unsigned short)vcl.getProcessingUnits()-1);}
 	if ( vcl.getProcessingUnits() < 2147483648 )
-	{BOOST_REQUIRE_EQUAL(i_max,vcl.getProcessingUnits()-1);}
+	{BOOST_REQUIRE_EQUAL(i_max,(int)vcl.getProcessingUnits()-1);}
 	if ( vcl.getProcessingUnits() < 4294967296 )
-	{BOOST_REQUIRE_EQUAL(ui_max,vcl.getProcessingUnits()-1);}
+	{BOOST_REQUIRE_EQUAL(ui_max,(unsigned int)vcl.getProcessingUnits()-1);}
 
-	BOOST_REQUIRE_EQUAL(li_max,vcl.getProcessingUnits()-1);
-	BOOST_REQUIRE_EQUAL(uli_max,vcl.getProcessingUnits()-1);
-	BOOST_REQUIRE_EQUAL(f_max,vcl.getProcessingUnits()-1);
-	BOOST_REQUIRE_EQUAL(d_max,vcl.getProcessingUnits()-1);
+	BOOST_REQUIRE_EQUAL(li_max,(long int)vcl.getProcessingUnits()-1);
+	BOOST_REQUIRE_EQUAL(uli_max,(unsigned long int)vcl.getProcessingUnits()-1);
+	BOOST_REQUIRE_EQUAL(f_max,(float)vcl.getProcessingUnits()-1);
+	BOOST_REQUIRE_EQUAL(d_max,(double)vcl.getProcessingUnits()-1);
 }
 
 #define N_V_ELEMENTS 16

src/unused/ComUnit.cpp

-#include "ComUnit.hpp"
-
-#define SERVICE_TAG	0xFFFFFFF
-
-/*! \brief Send some data globally to one processor when the other side
- *         do not know about the other side
- *
- * Send some data globally to one processor when the other side
- * do not know about the other side
- *
- * \Warning if you already call this function with p, will overwrite the request
- *
- * \param p is the processor number
- * \param buf is the buffer pointer
- * \param sz is the size of the communication
- *
- */
-
-bool SentToU(size_t p, void * buf,size_t sz)
-{
-	// before complete the communication we have to notify to the other
-	// processor that we have some data to send.
-
-	if (p >= comReq.size())
-	{
-		std::cerr << "Error: file: " << __FILE__ << " line: " << __LINE__ << " processor " << p << " does not exist";
-		return false;
-	}
-
-	return true;
-}
-
-/*! \brief Send some data locally (to its neighborhood) to one processor
- *
- * Send some data locally to one processor
- *
- */
-
-bool SendToNU(void * buf, size_t sz)
-{
-	return true;
-}
-
-/*! \brief Send some data globally to one processor when the other side
- *         know about the other side
- *
- * Send some data globally to one processor when the other side
- * know about the other side
- *
- * \Warning if you already call this function with p, will overwrite the request
- *
- * \param p is the processor number
- * \param buf is the buffer pointer
- * \param sz is the size of the communication
- *
- */
-
-bool SendTo(size_t p, void * buf, size_t sz)
-{
-	MPI_ISend(p,buf,sz);
-}
-
-/*! \brief Wait for all communication to complete
- *
- * Wait for all communication to complete
- *
- * \return true if no error occur
- *
- */
-
-bool wait()
-{
-	// Here we have to type of communication to handle
-
-	// Type 1 One side does not know that the other side want to communcate
-	// Type 2 The other side know that want to communicate
-
-	// The reqs structure handle the communication of type 2
-	// comReq and comSize store request of type 2
-
-	// For the type 1 we have to reduce scatter the comReq this
-	// for each processor K return the number of processors that need
-	// to communicate with K
-
-	MPI_ireduce_scatter();
-
-	// For the type 2 we already have recv coupled to send so just wait to complete
-
-	//! wait for all request to complete
-	MPI_Waitall(reqs.size(),&reqs[0],&status[0]);
-
-	//! For the number of incoming request queue an MPI_IRecv with MPI_ANY_SOURCE
-	//! It is going to receive the length of the message that each processor need
-	//! communicate
-
-	for (int i = 0 ; i < 5; i++)
-	{
-
-	}
-
-	//! For the number of outcomming request queue MPI_ISend sending the length of
-	//! the message the processor need to comunicate
-
-	for (int i = 0 ; i < 5; i++)
-	{
-
-	}
-
-	//! wait for all request to complete
-	MPI_Waitall(reqs.size(),&reqs[0],&status[0]);
-
-	//! finally send and receive the data
-
-	for (int i = 0 ; i < 5; i++)
-	{
-
-	}
-
-	for (int i = 0 ; i < 5; i++)
-	{
-
-	}
-
-	//! wait for all request to complete
-	MPI_Waitall(reqs.size(),&reqs[0],&status[0]);
-
-	return true;
-}

src/unused/ComUnit.hpp

-#ifndef COM_UNIT_HPP
-#define COM_UNIT_HPP
-
-#include <mpi.h>
-#include <vector>
-
-/*! \brief This is the abstraction of the communication
- *          unit for the virtual cluster
- *
- * This with the abstraction of the communication
- *          unit of the virtual cluster
- *
- * When this unit is returned back, you must ensure that no other thread
- * is using MPI call
- *
- */
-
-class ComUnit
-{
-	// if this processor need to communicate with the processor K
-	// it put 1 at the position K
-	std::vector<unsigned int> comReq;
-
-	// if this processor need to communicate with the processor K
-	// a message to length m put m at position K
-	std::vector<size_t> sizeReq;
-
-	// List of all status request
-    std::vector<MPI_Request> reqs;
-
-    // List of the status of all the request
-    std::vector<MPI_Status> stat;
-
-	//! Send data
-	bool SentTo();
-
-	//! Send data to the neighborhood
-	bool SendToN();
-
-	//! wait for communication to complete
-	bool wait();
-};
-
-#endif

src/unused/TThread.cpp

-//
-//  Project   : ThreadPool
-//  File      : TThread.cc
-//  Author    : Ronald Kriemann
-//  Purpose   : baseclass for a thread-able class
-//
-// arch-tag: aec71576-f8d5-4573-ad31-f3dbddc59934
-//
-
-#include <unistd.h>
-#include <signal.h>
-#include <time.h>
-#include <sched.h>
-#include <string.h>
-
-#include <iostream>
-#include <cmath>
-
-#include "TThread.h"
-
-//
-// routine to call TThread::run() method
-//
-extern "C"
-void *
-_run_thread ( void *arg )
-{
-    if (arg != NULL)
-    {
-        ((TThread*) arg)->run();
-        ((TThread*) arg)->reset_running();
-    }// if
-
-    return NULL;
-}
-
-////////////////////////////////////////////
-//
-// constructor and destructor
-//
-    
-TThread::TThread ( const int thread_no )
-        : _running( false ), _thread_no(thread_no)
-{
-}
-
-TThread::~TThread ()
-{
-    // request cancellation of the thread if running
-    if ( _running )
-        cancel();
-}
-
-////////////////////////////////////////////
-//
-// access local data
-//
-
-void
-TThread::set_thread_no ( const int n )
-{
-    _thread_no = n;
-}
-    
-////////////////////////////////////////////
-//
-// thread management
-//
-
-//
-// create thread (actually start it)
-//
-void 
-TThread::create ( const bool detached, const bool sscope )
-{
-    if ( ! _running )
-    {
-        int status;
-        
-        if ((status = pthread_attr_init( & _thread_attr )) != 0)
-        {
-            std::cerr << "(TThread) create : pthread_attr_init ("
-                      << strerror( status ) << ")" << std::endl;
-            return;
-        }// if
-
-        if ( detached )
-        {
-            // detache created thread from calling thread
-            if ((status = pthread_attr_setdetachstate( & _thread_attr,
-                                                       PTHREAD_CREATE_DETACHED )) != 0)
-            {
-                std::cerr << "(TThread) create : pthread_attr_setdetachstate ("
-                          << strerror( status ) << ")" << std::endl;
-                return;
-            }// if
-        }// if
-
-        if ( sscope )
-        {
-            // use system-wide scheduling for thread
-            if ((status = pthread_attr_setscope( & _thread_attr, PTHREAD_SCOPE_SYSTEM )) != 0 )
-            {
-                std::cerr << "(TThread) create : pthread_attr_setscope ("
-                          << strerror( status ) << ")" << std::endl;
-                return;
-            }// if
-        }// if
-            
-#if defined(_POSIX_THREAD_PRIORITY_SCHEDULING) && defined(SUNOS)
-        //
-        // adjust thread-scheduling for Solaris
-        //
-        
-        struct sched_param  t_param;
-        
-        t_param.sched_priority = sched_get_priority_min( SCHED_RR );
-        
-        if ((status = pthread_attr_setschedpolicy(  & _thread_attr, SCHED_RR )) != 0)
-            std::cerr << "(TThread) create : pthread_attr_setschedpolicy ("
-                      << strerror( status ) << ")" << std::endl;
-        
-        if ((status = pthread_attr_setschedparam(   & _thread_attr, & t_param )) != 0)
-            std::cerr << "(TThread) create : pthread_attr_setschedparam ("
-                      << strerror( status ) << ")" << std::endl;
-
-        if ((status = pthread_attr_setinheritsched( & _thread_attr, PTHREAD_EXPLICIT_SCHED )) != 0)
-            std::cerr << "(TThread) create : pthread_attr_setinheritsched ("
-                      << strerror( status ) << ")" << std::endl;
-#endif
-
-#ifdef HPUX
-        // on HP-UX we increase the stack-size for a stable behaviour
-        // (need much memory for this !!!)
-        pthread_attr_setstacksize( & _thread_attr, 32 * 1024 * 1024 );
-#endif
-        
-        if ((status = pthread_create( & _thread_id, & _thread_attr, _run_thread, this ) != 0))
-            std::cerr << "(TThread) create : pthread_create ("
-                      << strerror( status ) << ")" << std::endl;
-        else
-            _running = true;
-    }// if
-    else
-        std::cout << "(TThread) create : thread is already running" << std::endl;
-}
-
-//
-// detach thread
-//
-void 
-TThread::detach ()
-{
-    if ( _running )
-    {
-        int status;
-        
-        // detach thread
-        if ((status = pthread_detach( _thread_id )) != 0)
-            std::cerr << "(TThread) detach : pthread_detach ("
-                      << strerror( status ) << ")" << std::endl;
-    }// if
-}
-
-//
-// synchronise with thread (wait until finished)
-//
-void 
-TThread::join ()
-{
-    if ( _running )
-    {
-        int status;
-    
-        // wait for thread to finish
-        if ((status = pthread_join( _thread_id, NULL )) != 0)
-            std::cerr << "(TThread) join : pthread_join ("
-                      << strerror( status ) << ")" << std::endl;
-
-        _running = false;
-    }// if
-}
-
-//
-// request cancellation of thread
-//
-void 
-TThread::cancel ()
-{
-    if ( _running )
-    {
-        int status;
-        
-        if ((status = pthread_cancel( _thread_id )) != 0)
-            std::cerr << "(TThread) cancel : pthread_cancel ("
-                      << strerror( status ) << ")" << std::endl;
-    }// if
-}
-
-////////////////////////////////////////////
-//
-// functions to be called by a thread itself
-//
-
-//
-// terminate thread
-//
-void 
-TThread::exit ()
-{
-    if ( _running && (pthread_self() == _thread_id))
-    {
-        void  * ret_val = NULL;
-
-        pthread_exit( ret_val );
-        
-        _running = false;
-    }// if
-}<