Merge pull request #287 from intel/develop

Develop

Author: chuckyount

README.md

@@ -68,6 +68,8 @@ and Intel(R) graphics processors.
 
 ## Backward-compatibility notices
 ### Version 4
+* Version 4.05.00 removes the "out-of-band" genetic-algorithm tuning script
+    due to lack of resources for maintenance and testing.
 * Version 4.04.00 deprecates the existing `void* {set,get}_elements_in_slice()`
     APIs and provides safer `float*` and `double*` versions.
 * Version 4.03.00 is a significant release with the following notices:

docs/YASK-tutorial.pdf

@@ -47,7 +47,7 @@ namespace yask {
     // https://semver.org/.
 
     // Format: "major.minor.patch[-alpha|-beta]".
-    const string version = "4.04.09";
+    const string version = "4.05.00";
 
     string yask_get_version_string() {
         return version;

src/common/common_utils.cpp

@@ -58,7 +58,7 @@ namespace yask {
         int m_idx = (order+1)*num_points;
         int n_idx = num_points;
         int dsz = m_idx * n_idx;
-        double d[dsz];
+        vector<double> d(dsz);
 
         for (int i = 1; i < dsz; i++)
             d[i] = 0.0;

src/contrib/coefficients/fd_coeff.cpp

@@ -516,13 +516,12 @@ namespace yask {
             auto* var_send_reqs = var_mpi_data.send_reqs.data();
             auto* var_recv_stats = var_mpi_data.recv_stats.data();
             auto* var_send_stats = var_mpi_data.send_stats.data();
+            auto* stats = var_mpi_data.stats.data();
+            auto* indices = var_mpi_data.indices.data();
 
             #ifndef USE_INDIV_MPI_TESTS
 
             // Bulk testing.
-            auto asize = max(var_mpi_data.recv_reqs.size(), var_mpi_data.send_reqs.size());
-            int indices[asize];
-            MPI_Status stats[asize];
             int n = 0;
             MPI_Testsome(int(var_mpi_data.recv_reqs.size()), var_recv_reqs, &n, indices, stats);
             num_tests++;

src/kernel/lib/halo.cpp

@@ -570,6 +570,8 @@ namespace yask {
         std::vector<MPI_Request> send_reqs;
         std::vector<MPI_Status> recv_stats;
         std::vector<MPI_Status> send_stats;
+        std::vector<MPI_Status> stats;
+        std::vector<int> indices;
 
         MPIData(MPIInfoPtr mpi_info) :
             _mpi_info(mpi_info) {
@@ -586,6 +588,8 @@ namespace yask {
             memset(&nullst, 0, sizeof(nullst));
             recv_stats.resize(n, nullst);
             send_stats.resize(n, nullst);
+            stats.resize(n, nullst);
+            indices.resize(n, 0);
         }
 
         void reset_locks() {

src/kernel/lib/settings.hpp

@@ -254,8 +254,12 @@ namespace yask {
         rank_domain_offsets.set_vals_same(0);
 
         // Tables to share data across ranks.
-        idx_t coords[nr][nddims]; // rank indices.
-        idx_t rsizes[nr][nddims]; // rank sizes.
+        vector<vector<idx_t>> coords(nr); // rank indices.
+        vector<vector<idx_t>> rsizes(nr); // rank sizes.
+        for (int rn = 0; rn < nr; rn++) {
+            coords[rn].resize(nddims);
+            rsizes[rn].resize(nddims);
+        }
 
         // Two passes over ranks:
         // 0: sum all specified local sizes.
@@ -274,9 +278,9 @@ namespace yask {
 
             // Exchange coord and size info between all ranks.
             for (int rn = 0; rn < nr; rn++) {
-                MPI_Bcast(&coords[rn][0], nddims, MPI_INTEGER8,
+                MPI_Bcast(coords[rn].data(), nddims, MPI_INTEGER8,
                           rn, env->comm);
-                MPI_Bcast(&rsizes[rn][0], nddims, MPI_INTEGER8,
+                MPI_Bcast(rsizes[rn].data(), nddims, MPI_INTEGER8,
                           rn, env->comm);
             }
             // Now, the tables are filled in for all ranks.