Switch to C++11 threading API

This removes dependencies on the POSIX threads API and uses exclusively
the C++11 standard for multi-threading. This is not complete yet,
compilation flags still need to be worked out and tested for MacOSX and
Windows.

build

@@ -11,7 +11,7 @@ dependencies = False
 verbose = False
 targets = []
 
-global todo, headers, object_deps, file_flags, thread_cflags, thread_ldflags, lock, print_lock, stop
+global todo, headers, object_deps, file_flags, lock, print_lock, stop
 global include_paths
 todo, headers, object_deps, file_flags = {}, {}, {}, {}
 lock = threading.Lock()
@@ -287,7 +287,7 @@ class Entry:
     self.deps = list_cmd_deps(cc_file)
 
     skip = False
-    flags = copy.copy (gsl_ldflags+ thread_ldflags)
+    flags = copy.copy (gsl_ldflags)
     if 'Q' in file_flags[cc_file]: flags += qt_ldflags
 
     if not skip: 
@@ -315,7 +315,7 @@ class Entry:
     self.action = 'CC'
     cc_file = self.name[:-len(obj_suffix)] + cpp_suffix
     self.deps = set([ cc_file ])
-    flags = copy.copy (gsl_cflags + thread_cflags)
+    flags = copy.copy (gsl_cflags)
 
     if is_moc (cc_file):
       src_header = cc_file[:-len(moc_cpp_suffix)] + h_suffix

cmd/dwi2fod.cpp

@@ -1,9 +1,7 @@
 #include "command.h"
 #include "ptr.h"
 #include "progressbar.h"
-#include "thread/exec.h"
-#include "thread/queue.h"
-#include "image/loop.h"
+#include "image/threaded_loop.h"
 #include "image/buffer.h"
 #include "image/buffer_preload.h"
 #include "image/voxel.h"

cmd/dwi2response.cpp

@@ -39,7 +39,7 @@
 #include "math/SH.h"
 #include "math/vector.h"
 
-#include "thread/queue.h"
+#include "thread_queue.h"
 
 #include "dwi/directions/set.h"
 #include "dwi/gradient.h"

cmd/dwi2tensor.cpp

@@ -24,8 +24,7 @@
 
 #include "command.h"
 #include "progressbar.h"
-#include "thread/exec.h"
-#include "thread/queue.h"
+#include "image/threaded_loop.h"
 #include "image/voxel.h"
 #include "image/buffer.h"
 #include "image/buffer_preload.h"

cmd/fod2metric.cpp

@@ -37,7 +37,7 @@
 #include "math/SH.h"
 #include "math/vector.h"
 
-#include "thread/queue.h"
+#include "thread_queue.h"
 
 #include "dwi/fmls.h"
 #include "dwi/directions/set.h"

cmd/sh2peaks.cpp

@@ -22,8 +22,7 @@
 #include "command.h"
 #include "math/SH.h"
 #include "progressbar.h"
-#include "thread/exec.h"
-#include "thread/queue.h"
+#include "thread_queue.h"
 #include "image/loop.h"
 #include "image/buffer.h"
 #include "image/voxel.h"

cmd/tck2connectome.cpp

@@ -41,7 +41,7 @@
 #include "image/loop.h"
 #include "image/voxel.h"
 
-#include "thread/queue.h"
+#include "thread_queue.h"
 
 
 

cmd/tckedit.cpp

@@ -27,8 +27,7 @@
 #include "exception.h"
 #include "mrtrix.h"
 
-#include "thread/exec.h"
-#include "thread/queue.h"
+#include "thread_queue.h"
 
 #include "dwi/tractography/file.h"
 #include "dwi/tractography/properties.h"

cmd/tckmap.cpp

@@ -31,8 +31,7 @@
 #include "image/header.h"
 #include "image/voxel.h"
 #include "math/matrix.h"
-#include "thread/exec.h"
-#include "thread/queue.h"
+#include "thread_queue.h"
 
 #include "dwi/tractography/file.h"
 #include "dwi/tractography/properties.h"

cmd/tcknodeextract.cpp

@@ -44,7 +44,7 @@
 #include "image/transform.h"
 #include "image/voxel.h"
 
-#include "thread/queue.h"
+#include "thread_queue.h"
 
 
 

cmd/tcknormalise.cpp

@@ -27,7 +27,7 @@
 #include "get_set.h"
 #include "image/buffer_preload.h"
 #include "image/voxel.h"
-#include "thread/queue.h"
+#include "thread_queue.h"
 #include "dwi/tractography/file.h"
 #include "dwi/tractography/properties.h"
 

configure

@@ -105,10 +105,6 @@ LDFLAGS         Any additional flags to the linker.
 
 LDLIB_FLAGS     Any additional flags to the linker to generate a shared library.
 
-PTHREAD_CFLAGS  Any flags required to compile with POSIX threads.
-
-PTHREAD_LDFLAGS Any flags required to link with POSIX threads.
-
 GSL_CFLAGS      Any flags required to compile with the GSL.
                 This may include in particular the path to the
                 include files, if not in a standard location
@@ -189,20 +185,17 @@ global cpp, cpp_cmd, ld, ld_args, ld_cmd
 
 cxx = [ 'g++' ]
 cxx_args = '-c CFLAGS SRC -o OBJECT'.split()
-cpp_flags = [ '-std=c++11' ]
+cpp_flags = [ '-std=c++11', '-pthread' ]
 
 ld = [ 'g++' ]
 ld_args = 'OBJECTS LDFLAGS -o EXECUTABLE'.split()
-ld_flags = []
+ld_flags = [ '-pthread' ]
 
 if static:
   ld_flags += [ '-static' ] 
 
 ld_lib_args = 'OBJECTS LDLIB_FLAGS -o LIB'.split()
-ld_lib_flags = [ ]
-
-thread_cflags = []
-thread_ldflags = [ '-lpthread' ]
+ld_lib_flags = [ '-pthread' ]
 
 zlib_cflags = []
 zlib_ldflags = [ '-lz' ]
@@ -477,52 +470,6 @@ else:
 
 
 
-report ('Checking for unordered_map: ')
-try:
-  compile ('''
-#include <unordered_map>
-
-int main() { 
-  std::unordered_map<int,int> map; 
-  return (map.size());
-}
-''', cpp_flags, ld_flags)
-  report ('present\n')
-except:
-  report ('no\n')
-  report ('Checking for TR1 unordered_map: ')
-  try:
-    compile ('''
-#include <tr1/unordered_map>
-
-int main() { 
-  std::tr1::unordered_map<int,int> map; 
-  return (map.size());
-}
-''', cpp_flags, ld_flags)
-    report ('present\n')
-    cpp_flags += [ '-DMRTRIX_USE_TR1' ]
-  except:
-    report ('no - will use SGI std::hash_map instead\n')
-    cpp_flags += [ '-DMRTRIX_USE_HASH_MAP' ]
-
-
-
-
-report ('Checking for 64-bit integer type: ')
-try:
-  compile ('''
-#include <stdint.h>
-
-int main() { 
-  int64_t t = 0; 
-  return (t); 
-}
-''', cpp_flags, ld_flags)
-  report ('yes\n')
-except:
-  report ('no\n')
-  error ('<stdint.h> is not C99 compliant - it does not define a int64_t type.')
 
 
 
@@ -614,49 +561,6 @@ ld_lib_flags += zlib_ldflags
 
 
 
-# POSIX threads:
-
-report ('Checking for POSIX threads: ')
-
-if 'PTHREAD_CFLAGS' in os.environ.keys(): thread_cflags = shlex.split (os.environ['PTHREAD_CFLAGS'])
-if 'PTHREAD_LDFLAGS' in os.environ.keys(): thread_ldflags = shlex.split (os.environ['PTHREAD_LDFLAGS'])
-
-try:
-  compile ('''
-#include <pthread.h>
-
-void* func (void*) { return (NULL); } 
-
-int main() { 
-  pthread_t t; 
-  if (pthread_create(&t, NULL, func, NULL)) return (1);
-  pthread_exit (NULL); 
-  return (0); 
-}
-''', cpp_flags + thread_cflags, ld_flags + thread_ldflags)
-  report ('yes\n')
-except CompileError:
-  error ('''compiler error!
-
-Use the PTHREAD_CFLAGS environment variable to set the path to
-the pthread include files and to set any required flags
-For example:
-     PTHREAD_CFLAGS="-I/usr/local/include" ./configure''')
-except LinkError:
-  error ('''linker error!
-
-Use the PTHREAD_LDFLAGS environment variable to set the path to
-the pthread libraries and to set the library to use
-For example:
-     PTHREAD_LDFLAGS="-L/usr/local/lib -lpthread" ./configure''')
-except RuntimeError:
-  error ('''runtime error!
-
-There is something wrong with your POSIX threads implementation!''')
-except:
-  error (' POSIX threads implementation not found!')
-
-
 
 
 # GSL flags:
@@ -1208,8 +1112,6 @@ else:
   cache.write ('True\n')
   commit ('ld_lib', ld_lib);
   commit ('ld_lib_flags', ld_lib_flags);
-commit ('thread_cflags', thread_cflags)
-commit ('thread_ldflags', thread_ldflags)
 commit ('gsl_cflags', gsl_cflags)
 commit ('gsl_ldflags', gsl_ldflags)
 

lib/image/threaded_loop.h

@@ -27,8 +27,7 @@
 #include "image/loop.h"
 #include "image/utils.h"
 #include "image/iterator.h"
-#include "thread/mutex.h"
-#include "thread/exec.h"
+#include "thread.h"
 
 namespace MR
 {
@@ -361,7 +360,7 @@ namespace MR
 
         //! get next position in the outer loop
         bool next (Iterator& pos) {
-          Thread::Mutex::Lock lock (mutex);
+          std::lock_guard<std::mutex> lock (mutex);
           if (loop.ok()) {
             loop.set_position (dummy, pos);
             loop.next (dummy);
@@ -372,17 +371,16 @@ namespace MR
 
         //! invoke \a functor (const Iterator& pos) per voxel <em> in the outer axes only</em>
         template <class Functor> 
-          void run_outer (Functor&& functor, const std::string& thread_label = "unknown") 
+          void run_outer (Functor&& functor)
           {
             if (Thread::number_of_threads() == 0) {
               for (auto i = loop (dummy); i; ++i)
                 functor (dummy);
               return;
             }
 
-            __Outer<Functor> loop_thread (*this, functor);
-            Thread::Array<__Outer<Functor> > thread_list (loop_thread);
-            Thread::Exec threads (thread_list, thread_label);
+            __Outer<typename std::remove_reference<Functor>::type> loop_thread (*this, functor);
+            Thread::run (Thread::multi (loop_thread), "loop threads");
           }
 
 
@@ -391,43 +389,25 @@ namespace MR
         template <class Functor, class... VoxelType, typename std::enable_if<sizeof...(VoxelType) == 0, int>::type = 0> 
           void run (Functor&& functor, VoxelType&&... vox)
           {
-            if (Thread::number_of_threads() == 0) {
-              LoopInOrder inner_loop (axes);
-              for (auto i = loop (dummy); i; ++i) {
-                for (auto j = inner_loop (dummy); j; ++j)
-                  functor (dummy);
-              }
-              return;
-            }
-
-            __RunFunctorIter<Functor> loop_thread (*this, functor);
-            run_outer (loop_thread, "run thread");
+            __RunFunctorIter<typename std::remove_reference<Functor>::type> loop_thread (*this, functor);
+            run_outer (loop_thread);
           }
 
 
         template <class Functor, class... VoxelType, typename std::enable_if<sizeof...(VoxelType) != 0, int>::type = 0> 
           void run (Functor&& functor, VoxelType&&... vox)
           {
-            if (Thread::number_of_threads() == 0) {
-              LoopInOrder inner_loop (axes);
-              for (auto i = loop (vox...); i; ++i) {
-                for (auto j = inner_loop (vox...); j; ++j)
-                  functor (vox...);
-              }
-              return;
-            }
-
-            __RunFunctor<Functor, VoxelType...> 
+            __RunFunctor<typename std::remove_reference<Functor>::type, typename std::remove_reference<VoxelType>::type...> 
               loop_thread (*this, functor, vox...);
-            run_outer (loop_thread, "run thread");
+            run_outer (loop_thread);
           }
 
 
       protected:
         LoopInOrder loop;
         Iterator dummy;
         const std::vector<size_t> axes;
-        Thread::Mutex mutex;
+        std::mutex mutex;
 
         static std::vector<size_t> __get_axes_in_thread (
             const std::vector<size_t>& axes_in_loop,
@@ -471,7 +451,7 @@ namespace MR
        template <class Functor>
          class __Outer {
            public:
-             __Outer (ThreadedLoop& shared_info, const Functor& functor) :
+             __Outer (ThreadedLoop& shared_info, Functor& functor) :
                shared (shared_info),
                func (functor) { }
 
@@ -484,7 +464,7 @@ namespace MR
 
            protected:
              ThreadedLoop& shared;
-             Functor func;
+             typename std::remove_reference<Functor>::type func;
          };
 
 
@@ -505,7 +485,7 @@ namespace MR
              }
 
            protected:
-             Functor func;
+             typename std::remove_reference<Functor>::type func;
              LoopInOrder loop;
          };
 
@@ -528,7 +508,7 @@ namespace MR
              }
 
            protected:
-             Functor func;
+             typename std::remove_reference<Functor>::type func;
              LoopInOrder loop;
              const std::vector<size_t>& outer_axes;
              std::tuple<VoxelType...> vox;