Merge pull request #261 from intel/develop

Develop bug fixes

docs/api/html/classyask_1_1yk__env-members.html

@@ -74,14 +74,15 @@
 <p>This is the complete list of members for <a class="el" href="classyask_1_1yk__env.html">yask::yk_env</a>, including all inherited members.</p>
 <table class="directory">
   <tr class="even"><td class="entry"><a class="el" href="classyask_1_1yk__env.html#ab14fa168dc78346ac61b54c9a509099b">disable_debug_output</a>()</td><td class="entry"><a class="el" href="classyask_1_1yk__env.html">yask::yk_env</a></td><td class="entry"><span class="mlabel">static</span></td></tr>
-  <tr><td class="entry"><a class="el" href="classyask_1_1yk__env.html#a69eac2bb8a841f6259697a7dcc8cf386">get_debug_output</a>()</td><td class="entry"><a class="el" href="classyask_1_1yk__env.html">yask::yk_env</a></td><td class="entry"><span class="mlabel">static</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classyask_1_1yk__env.html#add8b12cd6d10f964665a41acedbb9b14">get_num_ranks</a>() const =0</td><td class="entry"><a class="el" href="classyask_1_1yk__env.html">yask::yk_env</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
-  <tr><td class="entry"><a class="el" href="classyask_1_1yk__env.html#a93deb7b62612742f5a85fd8e319df38c">get_rank_index</a>() const =0</td><td class="entry"><a class="el" href="classyask_1_1yk__env.html">yask::yk_env</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classyask_1_1yk__env.html#a2384185b4d346418a62db1310a3dddca">global_barrier</a>() const =0</td><td class="entry"><a class="el" href="classyask_1_1yk__env.html">yask::yk_env</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
-  <tr><td class="entry"><a class="el" href="classyask_1_1yk__env.html#abe162669b192b8c650ee7dbfbd62bb7d">is_trace_enabled</a>()</td><td class="entry"><a class="el" href="classyask_1_1yk__env.html">yask::yk_env</a></td><td class="entry"><span class="mlabel">static</span></td></tr>
-  <tr class="even"><td class="entry"><a class="el" href="classyask_1_1yk__env.html#aa5cf0e8d885f4d9ebde6539d5246cda1">set_debug_output</a>(yask_output_ptr debug)</td><td class="entry"><a class="el" href="classyask_1_1yk__env.html">yask::yk_env</a></td><td class="entry"><span class="mlabel">static</span></td></tr>
-  <tr><td class="entry"><a class="el" href="classyask_1_1yk__env.html#ac6b39c25ae59e27dcdb405a9fe24e763">set_trace_enabled</a>(bool enable)</td><td class="entry"><a class="el" href="classyask_1_1yk__env.html">yask::yk_env</a></td><td class="entry"><span class="mlabel">static</span></td></tr>
-  <tr bgcolor="#f0f0f0" class="even"><td class="entry"><b>~yk_env</b>() (defined in <a class="el" href="classyask_1_1yk__env.html">yask::yk_env</a>)</td><td class="entry"><a class="el" href="classyask_1_1yk__env.html">yask::yk_env</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr>
+  <tr><td class="entry"><a class="el" href="classyask_1_1yk__env.html#ab2d17018fe9fadd9bfdc091d8bf32feb">finalize</a>()=0</td><td class="entry"><a class="el" href="classyask_1_1yk__env.html">yask::yk_env</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classyask_1_1yk__env.html#a69eac2bb8a841f6259697a7dcc8cf386">get_debug_output</a>()</td><td class="entry"><a class="el" href="classyask_1_1yk__env.html">yask::yk_env</a></td><td class="entry"><span class="mlabel">static</span></td></tr>
+  <tr><td class="entry"><a class="el" href="classyask_1_1yk__env.html#add8b12cd6d10f964665a41acedbb9b14">get_num_ranks</a>() const =0</td><td class="entry"><a class="el" href="classyask_1_1yk__env.html">yask::yk_env</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classyask_1_1yk__env.html#a93deb7b62612742f5a85fd8e319df38c">get_rank_index</a>() const =0</td><td class="entry"><a class="el" href="classyask_1_1yk__env.html">yask::yk_env</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+  <tr><td class="entry"><a class="el" href="classyask_1_1yk__env.html#a2384185b4d346418a62db1310a3dddca">global_barrier</a>() const =0</td><td class="entry"><a class="el" href="classyask_1_1yk__env.html">yask::yk_env</a></td><td class="entry"><span class="mlabel">pure virtual</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classyask_1_1yk__env.html#abe162669b192b8c650ee7dbfbd62bb7d">is_trace_enabled</a>()</td><td class="entry"><a class="el" href="classyask_1_1yk__env.html">yask::yk_env</a></td><td class="entry"><span class="mlabel">static</span></td></tr>
+  <tr><td class="entry"><a class="el" href="classyask_1_1yk__env.html#aa5cf0e8d885f4d9ebde6539d5246cda1">set_debug_output</a>(yask_output_ptr debug)</td><td class="entry"><a class="el" href="classyask_1_1yk__env.html">yask::yk_env</a></td><td class="entry"><span class="mlabel">static</span></td></tr>
+  <tr class="even"><td class="entry"><a class="el" href="classyask_1_1yk__env.html#ac6b39c25ae59e27dcdb405a9fe24e763">set_trace_enabled</a>(bool enable)</td><td class="entry"><a class="el" href="classyask_1_1yk__env.html">yask::yk_env</a></td><td class="entry"><span class="mlabel">static</span></td></tr>
+  <tr bgcolor="#f0f0f0"><td class="entry"><b>~yk_env</b>() (defined in <a class="el" href="classyask_1_1yk__env.html">yask::yk_env</a>)</td><td class="entry"><a class="el" href="classyask_1_1yk__env.html">yask::yk_env</a></td><td class="entry"><span class="mlabel">inline</span><span class="mlabel">virtual</span></td></tr>
 </table></div><!-- contents -->
 <!-- start footer part -->
 <hr class="footer"/><address class="footer"><small>

docs/api/html/classyask_1_1yk__env.html

@@ -91,6 +91,9 @@
 <tr class="memitem:a2384185b4d346418a62db1310a3dddca"><td class="memItemLeft" align="right" valign="top">virtual void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classyask_1_1yk__env.html#a2384185b4d346418a62db1310a3dddca">global_barrier</a> () const =0</td></tr>
 <tr class="memdesc:a2384185b4d346418a62db1310a3dddca"><td class="mdescLeft">&#160;</td><td class="mdescRight">Wait until all ranks have reached this element.  <a href="#a2384185b4d346418a62db1310a3dddca">More...</a><br /></td></tr>
 <tr class="separator:a2384185b4d346418a62db1310a3dddca"><td class="memSeparator" colspan="2">&#160;</td></tr>
+<tr class="memitem:ab2d17018fe9fadd9bfdc091d8bf32feb"><td class="memItemLeft" align="right" valign="top">virtual void&#160;</td><td class="memItemRight" valign="bottom"><a class="el" href="classyask_1_1yk__env.html#ab2d17018fe9fadd9bfdc091d8bf32feb">finalize</a> ()=0</td></tr>
+<tr class="memdesc:ab2d17018fe9fadd9bfdc091d8bf32feb"><td class="mdescLeft">&#160;</td><td class="mdescRight">Finalize the environment.  <a href="#ab2d17018fe9fadd9bfdc091d8bf32feb">More...</a><br /></td></tr>
+<tr class="separator:ab2d17018fe9fadd9bfdc091d8bf32feb"><td class="memSeparator" colspan="2">&#160;</td></tr>
 </table><table class="memberdecls">
 <tr class="heading"><td colspan="2"><h2 class="groupheader"><a name="pub-static-methods"></a>
 Static Public Member Functions</h2></td></tr>
@@ -357,6 +360,34 @@ <h2 class="memtitle"><span class="permalink"><a href="#a2384185b4d346418a62db131
 <p>Wait until all ranks have reached this element. </p>
 <p>If MPI is enabled, calls <code>MPI_Barrier()</code>. Otherwise, has no effect. </p>
 
+</div>
+</div>
+<a id="ab2d17018fe9fadd9bfdc091d8bf32feb"></a>
+<h2 class="memtitle"><span class="permalink"><a href="#ab2d17018fe9fadd9bfdc091d8bf32feb">&#9670;&nbsp;</a></span>finalize()</h2>
+
+<div class="memitem">
+<div class="memproto">
+<table class="mlabels">
+  <tr>
+  <td class="mlabels-left">
+      <table class="memname">
+        <tr>
+          <td class="memname">virtual void yask::yk_env::finalize </td>
+          <td>(</td>
+          <td class="paramname"></td><td>)</td>
+          <td></td>
+        </tr>
+      </table>
+  </td>
+  <td class="mlabels-right">
+<span class="mlabels"><span class="mlabel">pure virtual</span></span>  </td>
+  </tr>
+</table>
+</div><div class="memdoc">
+
+<p>Finalize the environment. </p>
+<p>If MPI is enabled and YASK initialized the MPI communicator, calls <code>MPI_Finalize()</code>. This function is automatically called when a <a class="el" href="classyask_1_1yk__env.html" title="Kernel environment.">yk_env</a> object is destroyed. Cannot call <a class="el" href="classyask_1_1yk__env.html#a2384185b4d346418a62db1310a3dddca" title="Wait until all ranks have reached this element.">global_barrier()</a> or any MPI-dependent API after calling this. </p>
+
 </div>
 </div>
 <hr/>The documentation for this class was generated from the following file:<ul>

docs/api/html/functions_f.html

@@ -65,14 +65,17 @@
 <div class="textblock">Here is a list of all documented class members with links to the class documentation for each member:</div>
 
 <h3><a id="index_f"></a>- f -</h3><ul>
+<li>finalize()
+: <a class="el" href="classyask_1_1yk__env.html#ab2d17018fe9fadd9bfdc091d8bf32feb">yask::yk_env</a>
+</li>
 <li>first_domain_index()
 : <a class="el" href="classyask_1_1yc__solution__base.html#a56f644e7e6b4e96619245f217b3763b5">yask::yc_solution_base</a>
 </li>
 <li>format()
 : <a class="el" href="classyask_1_1yc__solution.html#a5f3624ded964c465724fd0221d5a2aaa">yask::yc_solution</a>
 </li>
 <li>format_indices()
-: <a class="el" href="classyask_1_1yk__var.html#ae929dea5359d07e7541abab78ca7b139">yask::yk_var</a>
+: <a class="el" href="classyask_1_1yk__var.html#a55d6c585b8384881065c01bb067c96dd">yask::yk_var</a>
 </li>
 <li>format_simple()
 : <a class="el" href="classyask_1_1yc__expr__node.html#a1af7948d0c2a977ed20c0b2d1d561052">yask::yc_expr_node</a>

docs/api/html/functions_func_f.html

@@ -65,14 +65,17 @@
  
 
 <h3><a id="index_f"></a>- f -</h3><ul>
+<li>finalize()
+: <a class="el" href="classyask_1_1yk__env.html#ab2d17018fe9fadd9bfdc091d8bf32feb">yask::yk_env</a>
+</li>
 <li>first_domain_index()
 : <a class="el" href="classyask_1_1yc__solution__base.html#a56f644e7e6b4e96619245f217b3763b5">yask::yc_solution_base</a>
 </li>
 <li>format()
 : <a class="el" href="classyask_1_1yc__solution.html#a5f3624ded964c465724fd0221d5a2aaa">yask::yc_solution</a>
 </li>
 <li>format_indices()
-: <a class="el" href="classyask_1_1yk__var.html#ae929dea5359d07e7541abab78ca7b139">yask::yk_var</a>
+: <a class="el" href="classyask_1_1yk__var.html#a55d6c585b8384881065c01bb067c96dd">yask::yk_var</a>
 </li>
 <li>format_simple()
 : <a class="el" href="classyask_1_1yc__expr__node.html#a1af7948d0c2a977ed20c0b2d1d561052">yask::yc_expr_node</a>

docs/api/html/yk__var__api_8hpp_source.html

@@ -132,7 +132,7 @@
 <div class="ttc" id="ayask__kernel__api_8hpp_html"><div class="ttname"><a href="yask__kernel__api_8hpp.html">yask_kernel_api.hpp</a></div></div>
 <div class="ttc" id="aclassyask_1_1yk__var_html_a420e0dde2114ba663069b16d579072eb"><div class="ttname"><a href="classyask_1_1yk__var.html#a420e0dde2114ba663069b16d579072eb">yask::yk_var::is_fixed_size</a></div><div class="ttdeci">virtual bool is_fixed_size() const =0</div><div class="ttdoc">Determine whether this var is not automatically resized based on the solution.</div></div>
 <div class="ttc" id="aclassyask_1_1yk__var_html_a4a4e42c4cfc5b3b6a5d998611d0d8602"><div class="ttname"><a href="classyask_1_1yk__var.html#a4a4e42c4cfc5b3b6a5d998611d0d8602">yask::yk_var::get_raw_storage_buffer</a></div><div class="ttdeci">virtual void * get_raw_storage_buffer()=0</div><div class="ttdoc">[Advanced] Get pointer to raw data storage buffer.</div></div>
-<div class="ttc" id="agroup__yk_html_gab1c5abbc86c9fdde32def4217482cc63"><div class="ttname"><a href="group__yk.html#gab1c5abbc86c9fdde32def4217482cc63">yask::yk_grid</a></div><div class="ttdeci">YASK_DEPRECATED typedef yk_var yk_grid</div><div class="ttdoc">[Deprecated] Use yk_var.</div><div class="ttdef"><b>Definition:</b> yask_kernel_api.hpp:245</div></div>
+<div class="ttc" id="agroup__yk_html_gab1c5abbc86c9fdde32def4217482cc63"><div class="ttname"><a href="group__yk.html#gab1c5abbc86c9fdde32def4217482cc63">yask::yk_grid</a></div><div class="ttdeci">YASK_DEPRECATED typedef yk_var yk_grid</div><div class="ttdoc">[Deprecated] Use yk_var.</div><div class="ttdef"><b>Definition:</b> yask_kernel_api.hpp:257</div></div>
 <div class="ttc" id="aclassyask_1_1yk__var_html_ae62308be69ca643714879b0a1362de0e"><div class="ttname"><a href="classyask_1_1yk__var.html#ae62308be69ca643714879b0a1362de0e">yask::yk_var::get_left_extra_pad_size</a></div><div class="ttdeci">virtual idx_t get_left_extra_pad_size(const std::string &amp;dim) const =0</div><div class="ttdoc">Get the actual extra left padding in the specified dimension.</div></div>
 <div class="ttc" id="aclassyask_1_1yk__var_html_a3611ad6d130cb5ee7e030e6ad0c24f5b"><div class="ttname"><a href="classyask_1_1yk__var.html#a3611ad6d130cb5ee7e030e6ad0c24f5b">yask::yk_var::is_storage_layout_identical</a></div><div class="ttdeci">virtual bool is_storage_layout_identical(const yk_var_ptr other) const =0</div><div class="ttdoc">[Advanced] Determines whether storage layout is the same as another var.</div></div>
 <div class="ttc" id="aclassyask_1_1yk__var_html_aaf5b3f06b832bbf77b8f722fda8a2998"><div class="ttname"><a href="classyask_1_1yk__var.html#aaf5b3f06b832bbf77b8f722fda8a2998">yask::yk_var::get_first_local_index</a></div><div class="ttdeci">virtual idx_t get_first_local_index(const std::string &amp;dim) const =0</div><div class="ttdoc">Get the first valid index in this rank in the specified dimension.</div></div>

include/yask_kernel_api.hpp

@@ -238,6 +238,18 @@ namespace yask {
         virtual void
         global_barrier() const =0;
 
+        /// Finalize the environment.
+        /**
+           If MPI is enabled and YASK initialized the MPI communicator,
+           calls `MPI_Finalize()`.
+           This function is automatically called when a yk_env object
+           is destroyed.
+           Cannot call global_barrier() or any MPI-dependent API after
+           calling this.
+        */
+        virtual void
+        finalize() =0;
+
     }; // yk_env.
 
     /// **[Deprecated]** Use yk_var.

src/common/common_utils.cpp

@@ -43,7 +43,7 @@ namespace yask {
     // for numbers above 9 (at least up to 99).
 
     // Format: "major.minor.patch[-alpha|-beta]".
-    const string version = "4.00.02";
+    const string version = "4.00.03";
 
     string yask_get_version_string() {
         return version;

src/kernel/Makefile

@@ -965,15 +965,19 @@ $(YK_API_TEST_EXEC): $(YK_TEST_SRC_DIR)/yask_kernel_api_test.cpp $(YK_LIB)
 	@ls -l $@
 
 # Build and run C++ tests.
+# First run on 1 rank, then multiple ranks if ranks>1.
 cxx-yk-api-test:
 	$(TEST_MAKE) $(YK_API_TEST_EXEC) allow_new_var_types=1
 	@echo '*** Running the C++ YASK kernel API test...'
 	$(RUN_PREFIX) $(YK_API_TEST_EXEC)
+	if (( $(ranks) > 1 )); then $(RUN_PREFIX) mpirun -np $(ranks) $(YK_API_TEST_EXEC); fi
 
 # Run Python kernel API test.
+# First run on 1 rank, then multiple ranks if ranks>1.
 py-yk-api-test: $(YK_TEST_SRC_DIR)/yask_kernel_api_test.py $(YK_PY_LIB)
 	@echo '*** Running the Python YASK kernel API test...'
 	$(RUN_PYTHON) $<
+	if (( $(ranks) > 1 )); then mpirun -np $(ranks) $(RUN_PYTHON) $<; fi
 
 # Build C++ kernel tests with exceptions.
 $(YK_API_TEST_EXEC_WITH_EXCEPTION): $(YK_TEST_SRC_DIR)/yask_kernel_api_exception_test.cpp $(YK_LIB)
@@ -1063,10 +1067,10 @@ yk-test-no-yc: kernel-no-yc $(YK_SCRIPT)
 
 # Run the kernel API tests for C++ and Python with and w/o expected exceptions.
 api-tests:
-	$(MAKE) clean; $(MAKE) cxx-yk-api-test real_bytes=8 stencil=iso3dfd
-	$(MAKE) clean; $(MAKE) py-yk-api-test stencil=iso3dfd
-	$(MAKE) clean; $(MAKE) cxx-yk-api-test-with-exception real_bytes=8 stencil=iso3dfd
-	$(MAKE) clean; $(MAKE) py-yk-api-test-with-exception stencil=iso3dfd
+	$(MAKE) clean; $(MAKE) cxx-yk-api-test real_bytes=8
+	$(MAKE) clean; $(MAKE) py-yk-api-test
+	$(MAKE) clean; $(MAKE) cxx-yk-api-test-with-exception real_bytes=8
+	$(MAKE) clean; $(MAKE) py-yk-api-test-with-exception
 
 # Run several stencils using built-in validation.
 # NB: set arch var as applicable.

src/kernel/lib/settings.hpp

@@ -70,6 +70,7 @@ namespace yask {
         MPI_Group group = MPI_GROUP_NULL;
         int num_ranks = 1;        // total number of ranks.
         int my_rank = 0;          // MPI-assigned index.
+        bool finalize_needed = false;
 
         // Vars for shared-mem ranks.
         MPI_Comm shm_comm = MPI_COMM_NULL; // shm communicator.
@@ -81,12 +82,24 @@ namespace yask {
         int max_threads=0;      // initial value from OMP.
 
         KernelEnv() { }
-        virtual ~KernelEnv() { }
+        virtual ~KernelEnv() {
+            finalize();
+        }
 
         // Init MPI, OMP, etc.
         // This is normally called very early in the program.
         virtual void init_env(int* argc, char*** argv, MPI_Comm comm);
 
+        virtual void finalize() {
+            TRACE_MSG("finalize_needed = " << finalize_needed);
+            if (comm != MPI_COMM_NULL && finalize_needed) {
+                MPI_Finalize();
+                comm = MPI_COMM_NULL;
+                shm_comm = MPI_COMM_NULL;
+            }
+            finalize_needed = false;
+        }
+
         // Lock.
         static void set_debug_lock() {
             if (!_debug_lock_init_done) {

src/kernel/lib/setup.cpp

@@ -61,6 +61,7 @@ namespace yask {
                     THROW_YASK_EXCEPTION("error: MPI_THREAD_SERIALIZED or MPI_THREAD_MULTIPLE not provided");
                 }
                 is_init = true;
+                finalize_needed = true;
             }
             comm = MPI_COMM_WORLD;
         }