Merge branch 'develop'

.gitignore

@@ -4,9 +4,10 @@ build_*
 test
 doc/webdocs/site
 install*
-rapidjson
 *.swp
 regression*
 *.sh
 *DS_Store
 concurrentqueue
+perfstubs
+rapidjson

CMakeLists.txt

@@ -654,7 +654,7 @@ include(GitExternal)
 git_external(concurrentqueue
     https://github.com/cameron314/concurrentqueue.git
     master
-    VERBOSE)
+    VERBOSE NO_UPDATE)
 
 find_file(
     CONCURRENTQUEUE_HEADER
@@ -677,12 +677,12 @@ git_external(perfstubs
 
 find_file(
     PERFSTUBS_HEADER
-    NAMES perfstubs_api/Tool.h
+    NAMES perfstubs_api/tool.h
     PATHS ${PROJECT_SOURCE_DIR}/perfstubs)
 
 if(PERFSTUBS_HEADER)
     message(INFO " Found perfstubs at ${PROJECT_SOURCE_DIR}/perfstubs")
-    include_directories(${PROJECT_SOURCE_DIR})
+    include_directories(${PROJECT_SOURCE_DIR}/perfstubs)
 else()
     message(FATAL_ERROR " perfstubs not found. This should have been checked out automatically. "
             "Try manually check out https://github.com/khuck/perfstubs.git to ${PROJECT_SOURCE_DIR}")
@@ -817,7 +817,7 @@ CONFIGURE_FILE(${CMAKE_SOURCE_DIR}/pkgconfig/apex.pc.in
                ${CMAKE_BINARY_DIR}/pkgconfig/apex.pc @ONLY)
 INSTALL_FILES(/lib/pkgconfig FILES pkgconfig/apex.pc)
 
-if (APEX_USE_WEAK_SYMBOLS) 
+if (APEX_USE_WEAK_SYMBOLS)
     add_definitions(-DAPEX_USE_WEAK_SYMBOLS)
 else()
     find_library(DYNAMICLIB dl)

cmake/Modules/GitExternal.cmake

@@ -19,12 +19,12 @@
 #
 # [optional] Flags which control behaviour
 #  NO_UPDATE
-#    When set, GitExternal will not change a repo that has already been checked out. 
-#    The purpose of this is to allow one to set a default branch to be checked out, 
-#    but stop GitExternal from changing back to that branch if the user has checked 
+#    When set, GitExternal will not change a repo that has already been checked out.
+#    The purpose of this is to allow one to set a default branch to be checked out,
+#    but stop GitExternal from changing back to that branch if the user has checked
 #    out and is working on another.
-#  VERBOSE 
-#    When set, displays information about git commands that are executed  
+#  VERBOSE
+#    When set, displays information about git commands that are executed
 #
 
 find_package(Git)
@@ -101,15 +101,15 @@ function(GIT_EXTERNAL DIR REPO TAG)
       endif()
 
       # update tag
-#      GIT_EXTERNAL_MESSAGE("git rebase FETCH_HEAD")
-#      execute_process(COMMAND ${GIT_EXECUTABLE} rebase FETCH_HEAD
-#        RESULT_VARIABLE RESULT OUTPUT_VARIABLE OUTPUT ERROR_VARIABLE OUTPUT
-#        WORKING_DIRECTORY "${DIR}")
-#      if(RESULT)
-#        message(STATUS "git rebase failed, aborting ${DIR} merge")
-#        execute_process(COMMAND ${GIT_EXECUTABLE} rebase --abort
-#          WORKING_DIRECTORY "${DIR}")
-#      endif()
+      GIT_EXTERNAL_MESSAGE("git rebase FETCH_HEAD")
+      execute_process(COMMAND ${GIT_EXECUTABLE} rebase FETCH_HEAD
+        RESULT_VARIABLE RESULT OUTPUT_VARIABLE OUTPUT ERROR_VARIABLE OUTPUT
+        WORKING_DIRECTORY "${DIR}")
+      if(RESULT)
+        message(STATUS "git rebase failed, aborting ${DIR} merge")
+        execute_process(COMMAND ${GIT_EXECUTABLE} rebase --abort
+          WORKING_DIRECTORY "${DIR}")
+      endif()
 
     endif()
   else()

etc/buildbot.sh

@@ -39,7 +39,7 @@ yes_otf=" -DUSE_OTF2=TRUE -DOTF2_ROOT=/usr/local/otf2/2.1"
 yes_ompt=" -DUSE_OMPT=TRUE -DOMPT_ROOT=/usr/local/ompt/5.0"
 #yes_mpi=" -DUSE_MPI=TRUE -DCMAKE_C_COMPILER=mpicc -DCMAKE_CXX_COMPILER=mpicxx"
 yes_mpi=" -DUSE_MPI=TRUE"
-yes_papi=" -DUSE_PAPI=TRUE -DPAPI_ROOT=/usr/local/papi/5.5.0"
+yes_papi=" -DUSE_PAPI=TRUE -DPAPI_ROOT=/usr"
 yes_tau=" -DUSE_TAU=TRUE -DTAU_ROOT=/usr/local/tau/git -DTAU_ARCH=x86_64 -DTAU_OPTIONS=-pthread"
 
 # set defaults

src/apex/apex.cpp

@@ -1818,16 +1818,16 @@ using namespace apex;
 
 extern "C" {
 
-    int apex_init(const char * thread_name, unsigned long int comm_rank,
-        unsigned long int comm_size) {
+    int apex_init(const char * thread_name, const uint64_t comm_rank,
+        const uint64_t comm_size) {
         return init(thread_name, comm_rank, comm_size);
     }
 
-    int apex_init_(unsigned long int comm_rank, unsigned long int comm_size) {
+    int apex_init_(const uint64_t comm_rank, const uint64_t comm_size) {
         return init("FORTRAN thread", comm_rank, comm_size);
     }
 
-    int apex_init__(unsigned long int comm_rank, unsigned long int comm_size) {
+    int apex_init__(const uint64_t comm_rank, const uint64_t comm_size) {
         return init("FORTRAN thread", comm_rank, comm_size);
     }
 

src/apex/apex.h

@@ -26,6 +26,7 @@
 #include "apex_types.h"
 #include "apex_export.h"
 #include "stdbool.h"
+#include "stdint.h"
 
 #ifdef __cplusplus
 extern "C" {
@@ -53,8 +54,8 @@ extern "C" {
  \return APEX_NOERROR on success, or APEX_ERROR on failure.
  \sa @ref apex_finalize
  */
-APEX_EXPORT int apex_init(const char * thread_name, const unsigned int
-    comm_rank, const unsigned int comm_size);
+APEX_EXPORT int apex_init(const char * thread_name, const uint64_t comm_rank,
+    const uint64_t comm_size);
 
 /**
  \brief Dump output from APEX.

src/apex/apex_types.h

@@ -183,6 +183,7 @@ typedef struct _profile
     double maximum;       /*!< Maximum value seen by the timer or counter */
     apex_profile_type type; /*!< Whether this is a timer or a counter */
     double papi_metrics[8];  /*!< Array of accumulated PAPI hardware metrics */
+    int times_reset;      /*!< How many times was this timer reset */
 } apex_profile;
 
 /** Rather than use void pointers everywhere, be explicit about

src/apex/perftool_implementation.cpp

@@ -4,7 +4,7 @@
 //  file LICENSE_1_0.txt or copy at http://www.boost.org/LICENSE_1_0.txt)
 //
 
-#include "perfstubs/perfstubs_api/Tool.h"
+#include "perfstubs_api/tool.h"
 #include <stdlib.h>
 #include "apex.h"
 #include "thread_instance.hpp"
@@ -15,54 +15,54 @@ std::mutex my_mutex;
 
 extern "C" {
     // library function declarations
-    void perftool_init(void) {
+    void ps_initialize(void) {
         apex_init("PerfStubs API", 0, 1);
     }
-    void perftool_register_thread(void) {
+    void ps_register_thread(void) {
         apex_register_thread("PerfStubs Thread");
     }
-    void perftool_exit(void) {
+    void ps_finalize(void) {
         apex_exit_thread();
     }
-    void perftool_dump(void) {
+    void ps_dump_data(void) {
         apex_dump(false);
     }
 
     // measurement function declarations
-    void* perftool_timer_create(const char *timer_name) {
+    void* ps_timer_create(const char *timer_name) {
         return strdup(timer_name);
     }
-    void perftool_timer_start(const void *timer) {
+    void ps_timer_start(const void *timer) {
         apex_start(APEX_NAME_STRING, const_cast<void*>(timer));
     }
-    void perftool_timer_stop(const void *timer) {
+    void ps_timer_stop(const void *timer) {
         apex_stop(apex::thread_instance::instance().get_current_profiler());
     }
-    void perftool_dynamic_phase_start(const char *iteration_prefix,
+    void ps_dynamic_phase_start(const char *iteration_prefix,
                                       int iteration_number) {
         std::stringstream ss;
         ss << iteration_prefix << " " << iteration_number;
         apex_start(APEX_NAME_STRING, (void*)const_cast<char*>(ss.str().c_str()));
     }
-    void perftool_dynamic_phase_stop(const char *iteration_prefix,
+    void ps_dynamic_phase_stop(const char *iteration_prefix,
                                      int iteration_number) {
         apex_stop(apex::thread_instance::instance().get_current_profiler());
     }
-    void* perftool_create_counter(const char *counter_name) {
+    void* ps_create_counter(const char *counter_name) {
         return (void*)(strdup(counter_name));
     }
-    void perftool_sample_counter(const void *counter, double value) {
+    void ps_sample_counter(const void *counter, double value) {
         apex_sample_value((const char *)(counter), value);
     }
-    void perftool_metadata(const char *name, const char *value) {
+    void ps_set_metadata(const char *name, const char *value) {
         // do nothing
     }
 
     // data query function declarations
-    void perftool_get_timer_data(perftool_timer_data_t *timer_data) {
-        memset(timer_data, 0, sizeof(perftool_timer_data_t));
+    void ps_get_timer_data(ps_tool_timer_data_t *timer_data) {
+        memset(timer_data, 0, sizeof(ps_tool_timer_data_t));
     }
-    void perftool_free_timer_data(perftool_timer_data_t *timer_data) {
+    void ps_free_timer_data(ps_tool_timer_data_t *timer_data) {
         if (timer_data == nullptr)
         {
             return;
@@ -83,12 +83,12 @@ extern "C" {
             timer_data->values = nullptr;
         }
     }
-    void perftool_get_counter_data(perftool_counter_data_t *counter_data) {
-        memset(counter_data, 0, sizeof(perftool_counter_data_t));
+    void ps_get_counter_data(ps_tool_counter_data_t *counter_data) {
+        memset(counter_data, 0, sizeof(ps_tool_counter_data_t));
     }
-    void perftool_free_counter_data(perftool_counter_data_t *counter_data) {
+    void ps_free_counter_data(ps_tool_counter_data_t *counter_data) {
         if (counter_data == nullptr)
-        {   
+        {
             return;
         }
         if (counter_data->counter_names != nullptr)
@@ -122,10 +122,10 @@ extern "C" {
             counter_data->value_sumsqr = nullptr;
         }
     }
-    void perftool_get_metadata(perftool_metadata_t *metadata) {
-        memset(metadata, 0, sizeof(perftool_metadata_t));
+    void ps_get_metadata(ps_tool_metadata_t *metadata) {
+        memset(metadata, 0, sizeof(ps_tool_metadata_t));
     }
-    void perftool_free_metadata(perftool_metadata_t *metadata) {
+    void ps_free_metadata(ps_tool_metadata_t *metadata) {
         if (metadata == nullptr)
         {
             return;

src/apex/profile.hpp

@@ -61,13 +61,15 @@ class profile {
         _profile.sum_squares = 0.0;
         _profile.minimum = 0.0;
         _profile.maximum = 0.0;
+        _profile.times_reset++;
     };
     double get_calls() { return _profile.calls; }
     double get_mean() { return (_profile.accumulated / _profile.calls); }
     double get_accumulated() { return (_profile.accumulated); }
     double * get_papi_metrics() { return (_profile.papi_metrics); }
     double get_minimum() { return (_profile.minimum); }
     double get_maximum() { return (_profile.maximum); }
+    int get_times_reset() { return (_profile.times_reset); }
     double get_variance() {
         double mean = get_mean();
         double variance = ((_profile.sum_squares / _profile.calls) - (mean * mean));