Gap junction fix (#213)

* Avoid running the read_phase<gap> if the _fat.dat file hasn't opened
* Check in phase gap if the <gid>_gap.dat exists and then try to
  open the .dat file
* Improve output and fix issue with closing file when it doesn't exist
* Class member initialisation to avoid garbage values resulting into undefined behaviour

Author: iomaganaris

coreneuron/nrniv/nrn_filehandler.cpp

@@ -36,6 +36,11 @@ FileHandler::FileHandler(const char* filename, bool reorder) {
     stored_chkpnt = 0;
 }
 
+bool FileHandler::file_exist(const char* filename) const {
+    struct stat buffer;
+    return (stat(filename, &buffer) == 0);
+}
+
 void FileHandler::open(const char* filename, bool reorder, std::ios::openmode mode) {
     nrn_assert((mode & (std::ios::in | std::ios::out)));
     reorder_bytes = reorder;

coreneuron/nrniv/nrn_filehandler.h

@@ -32,6 +32,7 @@ THE POSSIBILITY OF SUCH DAMAGE.
 #include <iostream>
 #include <fstream>
 #include <vector>
+#include <sys/stat.h>
 #include "coreneuron/utils/endianness.h"
 #include "coreneuron/utils/swap_endian.h"
 #include "coreneuron/nrniv/nrn_assert.h"
@@ -85,6 +86,8 @@ class FileHandler {
         return F.fail();
     }
 
+    bool file_exist(const char* filename) const;
+
     /** nothing more to read */
     bool eof();
 

coreneuron/nrniv/nrn_setup.h

@@ -131,8 +131,14 @@ inline void* phase_wrapper_w(NrnThread* nt) {
                                     std::string("%s/%d_" + getPhaseName<P>() + ".dat").c_str(),
                                     data_dir, gidgroups_w[i]);
 
-            // if no file failed to open or not opened at all
-            file_reader_w[i].open(fname, byte_swap_w);
+            // Avoid trying to open the gid_gap.dat file if it doesn't exist when there are no
+            // gap junctions in this gid
+            if (P == gap && !file_reader_w[i].file_exist(fname)) {
+                file_reader_w[i].close();
+            } else {
+                // if no file failed to open or not opened at all
+                file_reader_w[i].open(fname, byte_swap_w);
+            }
         }
         read_phase_aux<P>(file_reader_w[i], imult_w[i], *nt);
         if (!no_open) {

coreneuron/nrniv/partrans.h

@@ -16,10 +16,10 @@ typedef int sgid_t;
 #endif
 
 struct HalfGap_Info {
-    int layout;
-    int type;
-    int ix_vpre; /* AoS index for vpre from beginning of a HalfGap instance */
-    int sz;      /* size of a HalfGap instance */
+    int layout = 0;
+    int type = 0;
+    int ix_vpre = 0; /* AoS index for vpre from beginning of a HalfGap instance */
+    int sz = 0;      /* size of a HalfGap instance */
 };
 extern HalfGap_Info* halfgap_info;
 
@@ -38,13 +38,13 @@ class TransferThreadData {
 extern TransferThreadData* transfer_thread_data_; /* array for threads */
 
 struct SetupInfo {
-    int nsrc;  // number of sources in this thread
-    int ntar;  // equal to memb_list nodecount
-    int type;
-    int ix_vpre;
-    sgid_t* sid_src;
-    int* v_indices;      // increasing order
-    sgid_t* sid_target;  // aleady in memb_list order
+    int nsrc = 0;  // number of sources in this thread
+    int ntar = 0;  // equal to memb_list nodecount
+    int type = 0;
+    int ix_vpre = 0;
+    sgid_t* sid_src = nullptr;
+    int* v_indices = nullptr;      // increasing order
+    sgid_t* sid_target = nullptr;  // aleady in memb_list order
 };
 extern SetupInfo* setup_info_; /* array for threads exists only during setup*/
 

coreneuron/nrniv/partrans_setup.cpp

@@ -231,9 +231,11 @@ void nrn_partrans::gap_mpi_setup(int ngroup) {
     // cleanup
     for (int tid = 0; tid < ngroup; ++tid) {
         SetupInfo& si = setup_info_[tid];
-        delete[] si.sid_src;
-        delete[] si.v_indices;
-        delete[] si.sid_target;
+        if (si.ntar) {
+            delete[] si.sid_src;
+            delete[] si.v_indices;
+            delete[] si.sid_target;
+        }
     }
     delete[] send_to_want;
     delete[] recv_from_have;
@@ -244,7 +246,11 @@ void nrn_partrans::gap_thread_setup(NrnThread& nt) {
     // printf("%d gap_thread_setup tid=%d\n", nrnmpi_myid, nt.id);
     nrn_partrans::TransferThreadData& ttd = transfer_thread_data_[nt.id];
 
-    ttd.halfgap_ml = nt._ml_list[halfgap_info->type];
+    if (transfer_thread_data_[nt.id].ntar) {
+        ttd.halfgap_ml = nt._ml_list[halfgap_info->type];
+    } else {
+        ttd.halfgap_ml = nullptr;
+    }
 #if 0
   int ntar = ttd.halfgap_ml->nodecount;
   assert(ntar == ttd.ntar);