Minor fixes

coreneuron/io/nrn_setup.cpp

@@ -834,6 +834,8 @@ void nrn_cleanup() {
     if (!corenrn.get_pnttype2presyn().empty()) {
         corenrn.get_pnttype2presyn().clear();
     }
+
+    destroy_interleave_info();
 }
 
 void delete_trajectory_requests(NrnThread& nt) {

coreneuron/io/phase2.cpp

@@ -277,7 +277,10 @@ void Phase2::read_direct(int thread_id, const NrnThread& nt) {
         offset = nrn_soa_byte_align(offset);
 
         tml.type = type;
-        tml.nodeindices.resize(nodecounts[i]);
+        // artificial cell don't use nodeindices
+        if (!corenrn.get_is_artificial()[type]) {
+            tml.nodeindices.resize(nodecounts[i]);
+        }
         tml.pdata.resize(nodecounts[i] * dparam_sizes[type]);
 
         int* nodeindices_ = nullptr;

coreneuron/permute/cellorder.cpp

@@ -40,11 +40,11 @@ InterleaveInfo::InterleaveInfo(const InterleaveInfo& info) {
     nwarp = info.nwarp;
     nstride = info.nstride;
 
-    copy_array(stridedispl, info.stridedispl, nwarp + 1);
-    copy_array(stride, info.stride, nstride);
-    copy_array(firstnode, info.firstnode, nwarp + 1);
-    copy_array(lastnode, info.lastnode, nwarp + 1);
-    copy_array(cellsize, info.cellsize, nwarp);
+    copy_align_array(stridedispl, info.stridedispl, nwarp + 1);
+    copy_align_array(stride, info.stride, nstride);
+    copy_align_array(firstnode, info.firstnode, nwarp + 1);
+    copy_align_array(lastnode, info.lastnode, nwarp + 1);
+    copy_align_array(cellsize, info.cellsize, nwarp);
 
     copy_array(nnode, info.nnode, nwarp);
     copy_array(ncycle, info.ncycle, nwarp);

coreneuron/permute/cellorder.hpp

@@ -1,6 +1,7 @@
 #ifndef cellorder_h
 #define cellorder_h
 
+#include "coreneuron/utils/memory.h"
 #include <algorithm>
 namespace coreneuron {
 int* interleave_order(int ith, int ncell, int nnode, int* parent);
@@ -14,7 +15,7 @@ class InterleaveInfo {
     InterleaveInfo() = default;
     InterleaveInfo(const InterleaveInfo&);
     InterleaveInfo& operator=(const InterleaveInfo&);
-    virtual ~InterleaveInfo();
+    ~InterleaveInfo();
     int nwarp = 0;  // used only by interleave2
     int nstride = 0;
     int* stridedispl = nullptr;  // interleave2: nwarp+1
@@ -53,6 +54,13 @@ void copy_array(T*& dest, T* src, size_t n) {
     std::copy(src, src + n, dest);
 }
 
+// copy src array to dest with NRN_SOA_BYTE_ALIGN ecalloc_align allocation
+template <typename T>
+void copy_align_array(T*& dest, T* src, size_t n) {
+    dest = (T*)ecalloc_align(n, sizeof(T));
+    std::copy(src, src + n, dest);
+}
+
 #define INTERLEAVE_DEBUG 0
 
 #if INTERLEAVE_DEBUG