Replace posix_memalign with std::aligned_alloc (BlueBrain/CoreNeuron#859

)

* Replace posix_memalign with std::aligned_alloc

Unfortunately aligned_alloc does not allow aligning buffers that are not
a multiple of the alignment. To help with this, we allocate slightly
larger buffers (up to the next multiple of the alignment) where necessary.

CoreNEURON Repo SHA: BlueBrain/CoreNeuron@414479d

src/coreneuron/utils/memory.h

@@ -173,14 +173,15 @@ class MemoryManaged {
     // does nothing by default
 };
 
-#include <stdlib.h>
+#include <cstdlib>
 
 inline void alloc_memory(void*& pointer, size_t num_bytes, size_t alignment) {
-#if defined(MINGW)
-    nrn_assert((pointer = _aligned_malloc(num_bytes, alignment)) != nullptr);
-#else
-    nrn_assert(posix_memalign(&pointer, alignment, num_bytes) == 0);
-#endif
+    size_t fill = 0;
+    if (num_bytes % alignment != 0) {
+        size_t multiple = num_bytes / alignment;
+        fill = alignment * (multiple + 1) - num_bytes;
+    }
+    nrn_assert((pointer = std::aligned_alloc(alignment, num_bytes + fill)) != nullptr);
 }
 
 inline void calloc_memory(void*& pointer, size_t num_bytes, size_t alignment) {

src/coreneuron/utils/nrnoc_aux.cpp

@@ -101,14 +101,7 @@ void* erealloc(void* ptr, size_t size) {
 }
 
 void* nrn_cacheline_alloc(void** memptr, size_t size) {
-#if HAVE_MEMALIGN
-    if (posix_memalign(memptr, 64, size) != 0) {
-        fprintf(stderr, "posix_memalign not working\n");
-        assert(0);
-    }
-#else
-    *memptr = emalloc(size);
-#endif
+    alloc_memory(*memptr, size, 64);
     return *memptr;
 }