Let all DEBUG being compiled (#657)

Nicolas Cornu · pramodk · web-flow · commit 0efca7a3ab70 · 2021-10-31T08:37:53.000+01:00
* Fixes for running with all debugs enabled
 * Change #if DEBUG to #if CORENRN_DEBUG to compile the code
 * mk_cell_indices() should be used with only cell-permute one
 * fix bug in CHKPNTDEBUG where ntc.bcptype[i] was accessed by
   mechanism index rather than index for point process (vector
   is allocated only for number of point processes)
 * Do not add user visible option but use -DCORENRN_ENABLE_DEBUG_CODE=ON
   to enable all debugging code: -DCORENRN_DEBUG -DCHKPNTDEBUG -DCORENRN_DEBUG_QUEUE -DINTERLEAVE_DEBUG
 * Enable one Github CI configuration with all debugging code

Co-authored-by: Pramod Kumbhar &lt;pramod.s.kumbhar@gmail.com&gt;
diff --git a/.github/workflows/coreneuron-ci.yml b/.github/workflows/coreneuron-ci.yml
@@ -34,7 +34,7 @@ jobs:
         os: [ ubuntu-18.04, macOS-10.15 ]
         config:
           # Defaults: CORENRN_ENABLE_MPI=ON
-          - {cmake_option: "-DCORENRN_ENABLE_MPI=ON", documentation: ON}
+          - {cmake_option: "-DCORENRN_ENABLE_MPI=ON -DCORENRN_ENABLE_DEBUG_CODE=ON", documentation: ON}
           - {cmake_option: "-DCORENRN_ENABLE_MPI_DYNAMIC=ON"}
           - {cmake_option: "-DCORENRN_ENABLE_MPI_DYNAMIC=ON -DCORENRN_ENABLE_SHARED=OFF"}
           - {cmake_option: "-DCORENRN_ENABLE_MPI=OFF"}
diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
@@ -36,7 +36,7 @@ jobs:
         working-directory: ${{runner.workspace}}/CoreNeuron
         run:  |
           mkdir build && cd build
-          cmake .. -DCORENRN_ENABLE_MPI=ON -DCMAKE_C_FLAGS="-coverage -O0" -DCMAKE_CXX_FLAGS="-coverage -O0";
+          cmake .. -DCORENRN_ENABLE_MPI=ON -DCORENRN_ENABLE_DEBUG_CODE=ON -DCMAKE_C_FLAGS="-coverage -O0" -DCMAKE_CXX_FLAGS="-coverage -O0";
           make -j2
           (cd ..;  lcov --capture  --initial --directory . --no-external --output-file build/coverage-base.info)
           make test
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -395,6 +395,11 @@ if(CORENRN_ENABLE_LIKWID_PROFILING)
   add_definitions("-DLIKWID_PERFMON")
 endif()
 
+# enable debugging code with extra logs to stdout
+if(CORENRN_ENABLE_DEBUG_CODE)
+  add_definitions(-DCORENRN_DEBUG -DCHKPNTDEBUG -DCORENRN_DEBUG_QUEUE -DINTERLEAVE_DEBUG)
+endif()
+
 # =============================================================================
 # Common CXX flags : ignore unknown pragma warnings
 # =============================================================================
diff --git a/coreneuron/io/global_vars.cpp b/coreneuron/io/global_vars.cpp
@@ -161,7 +161,7 @@ void set_globals(const char* path, bool cli_global_seed, int cli_global_seed_val
         }
     }
 
-#if DEBUG
+#if CORENRN_DEBUG
     for (const auto& item: *n2v) {
         printf("%s %ld %p\n", item.first.c_str(), item.second.first, item.second.second);
     }
diff --git a/coreneuron/io/nrn2core_data_init.cpp b/coreneuron/io/nrn2core_data_init.cpp
@@ -170,7 +170,9 @@ static void nrn2core_tqueue() {
                     case 2: {  // NetCon
                         int ncindex = ncte->intdata[idat++];
                         NetCon* nc = nt.netcons + ncindex;
+#ifndef CORENRN_DEBUG_QUEUE
 #define CORENRN_DEBUG_QUEUE 0
+#endif
 #if CORENRN_DEBUG_QUEUE
                         printf("nrn2core_tqueue tid=%d i=%zd type=%d tdeliver=%g NetCon %d\n",
                                tid,
diff --git a/coreneuron/io/nrn_checkpoint.hpp b/coreneuron/io/nrn_checkpoint.hpp
@@ -76,7 +76,7 @@ extern int patstimtype;
 // nrn_setup.cpp and debugging only information which is retrievable from
 // NrnThread and Memb_list. Ideally, this should all go away
 
-struct Memb_list_ckpnt {
+struct Memb_list_chkpnt {
     // debug only
     double* data_not_permuted;
     Datum* pdata_not_permuted;
diff --git a/coreneuron/io/nrn_setup.cpp b/coreneuron/io/nrn_setup.cpp
@@ -524,7 +524,10 @@ void nrn_setup(const char* filesdat,
         nrn_setup_cleanup();
 
 #if INTERLEAVE_DEBUG
-    mk_cell_indices();
+    // mk_cell_indices debug code is supposed to be used with cell-per-core permutations
+    if (corenrn_param.cell_interleave_permute == 1) {
+        mk_cell_indices();
+    }
 #endif
 
     /// Allocate memory for fast_imem calculation
@@ -614,7 +617,7 @@ void read_phasegap(NrnThread& nt, UserParams& userParams) {
         F.read_array<int>(si.tar_index.data(), ntar);
     }
 
-#if DEBUG
+#if CORENRN_DEBUG
     printf("%d read_phasegap tid=%d nsrc=%d ntar=%d\n", nrnmpi_myid, nt.id, nsrc, ntar);
     for (int i = 0; i < nsrc; ++i) {
         printf("src %z %d %d\n", size_t(si.src_sid[i]), si.src_type[i], si.src_index[i]);
diff --git a/coreneuron/io/phase2.cpp b/coreneuron/io/phase2.cpp
@@ -707,7 +707,7 @@ void Phase2::set_dependencies(const NrnThread& nt, const std::vector<Memb_func>&
     free(mech_deps);
 }
 
-void Phase2::handle_weights(NrnThread& nt, int n_netcon) {
+void Phase2::handle_weights(NrnThread& nt, int n_netcon, NrnThreadChkpnt& ntc) {
     nt.n_weight = weights.size();
     // weights in netcons order in groups defined by Point_process target type.
     nt.weights = (double*) ecalloc_align(nt.n_weight, sizeof(double));
@@ -731,21 +731,24 @@ void Phase2::handle_weights(NrnThread& nt, int n_netcon) {
 
 #if CHKPNTDEBUG
     ntc.delay = new double[n_netcon];
-    memcpy(ntc.delay, delay, n_netcon * sizeof(double));
+    memcpy(ntc.delay, delay.data(), n_netcon * sizeof(double));
 #endif
     for (int i = 0; i < n_netcon; ++i) {
         NetCon& nc = nt.netcons[i];
         nc.delay_ = delay[i];
     }
 }
 
-void Phase2::get_info_from_bbcore(NrnThread& nt, const std::vector<Memb_func>& memb_func) {
+void Phase2::get_info_from_bbcore(NrnThread& nt,
+                                  const std::vector<Memb_func>& memb_func,
+                                  NrnThreadChkpnt& ntc) {
     // BBCOREPOINTER information
 #if CHKPNTDEBUG
     ntc.nbcp = num_point_process;
-    ntc.bcpicnt = new int[num_point_process];
-    ntc.bcpdcnt = new int[num_point_process];
-    ntc.bcptype = new int[num_point_process];
+    ntc.bcpicnt = new int[n_mech];
+    ntc.bcpdcnt = new int[n_mech];
+    ntc.bcptype = new int[n_mech];
+    size_t point_proc_id = 0;
 #endif
     for (size_t i = 0; i < n_mech; ++i) {
         int type = mech_types[i];
@@ -754,9 +757,10 @@ void Phase2::get_info_from_bbcore(NrnThread& nt, const std::vector<Memb_func>& m
         }
         type = tmls[i].type;  // This is not an error, but it has to be fixed I think
 #if CHKPNTDEBUG
-        ntc.bcptype[i] = type;
-        ntc.bcpicnt[i] = icnt;
-        ntc.bcpdcnt[i] = dcnt;
+        ntc.bcptype[point_proc_id] = type;
+        ntc.bcpicnt[point_proc_id] = tmls[i].iArray.size();
+        ntc.bcpdcnt[point_proc_id] = tmls[i].dArray.size();
+        point_proc_id++;
 #endif
         int ik = 0;
         int dk = 0;
@@ -792,7 +796,7 @@ void Phase2::get_info_from_bbcore(NrnThread& nt, const std::vector<Memb_func>& m
     }
 }
 
-void Phase2::set_vec_play(NrnThread& nt) {
+void Phase2::set_vec_play(NrnThread& nt, NrnThreadChkpnt& ntc) {
     // VecPlayContinuous instances
     // No attempt at memory efficiency
     nt.n_vecplay = vec_play_continuous.size();
@@ -851,7 +855,7 @@ void Phase2::populate(NrnThread& nt, const UserParams& userParams) {
     auto& memb_func = corenrn.get_memb_funcs();
 #if CHKPNTDEBUG
     ntc.mlmap = new Memb_list_chkpnt*[memb_func.size()];
-    for (int i = 0; i < _memb_func.size(); ++i) {
+    for (int i = 0; i < memb_func.size(); ++i) {
         ntc.mlmap[i] = nullptr;
     }
 #endif
@@ -994,7 +998,7 @@ void Phase2::populate(NrnThread& nt, const UserParams& userParams) {
             mech_data_layout_transform<int>(ml->pdata, n, szdp, layout);
 
 #if CHKPNTDEBUG  // Not substantive. Only for debugging.
-            Memb_list_ckpnt* mlc = ntc.mlmap[type];
+            Memb_list_chkpnt* mlc = ntc.mlmap[type];
             mlc->pdata_not_permuted = (int*) coreneuron::ecalloc_align(n * szdp, sizeof(int));
             if (layout == Layout::AoS) {  // only copy
                 for (int i = 0; i < n; ++i) {
@@ -1064,7 +1068,7 @@ void Phase2::populate(NrnThread& nt, const UserParams& userParams) {
         permute_ptr(nt._v_parent_index, nt.end, p);
         node_permute(nt._v_parent_index, nt.end, p);
 
-#if DEBUG
+#if CORENRN_DEBUG
         for (int i = 0; i < nt.end; ++i) {
             printf("parent[%d] = %d\n", i, nt._v_parent_index[i]);
         }
@@ -1129,15 +1133,15 @@ void Phase2::populate(NrnThread& nt, const UserParams& userParams) {
     // nt.presyns order same as output_vindex order
 #if CHKPNTDEBUG
     ntc.output_vindex = new int[nt.n_presyn];
-    memcpy(ntc.output_vindex, output_vindex, nt.n_presyn * sizeof(int));
+    memcpy(ntc.output_vindex, output_vindex.data(), nt.n_presyn * sizeof(int));
 #endif
     if (nt._permute) {
         // only indices >= 0 (i.e. _actual_v indices) will be changed.
         node_permute(output_vindex.data(), nt.n_presyn, nt._permute);
     }
 #if CHKPNTDEBUG
     ntc.output_threshold = new double[nt.ncell];
-    memcpy(ntc.output_threshold, output_threshold, nt.ncell * sizeof(double));
+    memcpy(ntc.output_threshold, output_threshold.data(), nt.ncell * sizeof(double));
 #endif
     for (int i = 0; i < nt.n_presyn; ++i) {  // real cells
         PreSyn* ps = nt.presyns + i;
@@ -1182,8 +1186,8 @@ void Phase2::populate(NrnThread& nt, const UserParams& userParams) {
 #if CHKPNTDEBUG
     ntc.pnttype = new int[nnetcon];
     ntc.pntindex = new int[nnetcon];
-    memcpy(ntc.pnttype, pnttype, nnetcon * sizeof(int));
-    memcpy(ntc.pntindex, pntindex, nnetcon * sizeof(int));
+    memcpy(ntc.pnttype, pnttype.data(), nnetcon * sizeof(int));
+    memcpy(ntc.pntindex, pntindex.data(), nnetcon * sizeof(int));
 #endif
     for (int i = 0; i < nnetcon; ++i) {
         int type = pnttype[i];
@@ -1196,11 +1200,11 @@ void Phase2::populate(NrnThread& nt, const UserParams& userParams) {
         }
     }
 
-    handle_weights(nt, nnetcon);
+    handle_weights(nt, nnetcon, ntc);
 
-    get_info_from_bbcore(nt, memb_func);
+    get_info_from_bbcore(nt, memb_func, ntc);
 
-    set_vec_play(nt);
+    set_vec_play(nt, ntc);
 
     if (!events.empty()) {
         userParams.checkPoints.restore_tqueue(nt, *this);
diff --git a/coreneuron/io/phase2.hpp b/coreneuron/io/phase2.hpp
@@ -19,6 +19,7 @@ struct NrnThread;
 struct NrnThreadMembList;
 struct Memb_func;
 struct Memb_list;
+class NrnThreadChkpnt;
 
 class Phase2 {
   public:
@@ -82,9 +83,11 @@ class Phase2 {
     void fill_before_after_lists(NrnThread& nt, const std::vector<Memb_func>& memb_func);
     void pdata_relocation(const NrnThread& nt, const std::vector<Memb_func>& memb_func);
     void set_dependencies(const NrnThread& nt, const std::vector<Memb_func>& memb_func);
-    void handle_weights(NrnThread& nt, int n_netcon);
-    void get_info_from_bbcore(NrnThread& nt, const std::vector<Memb_func>& memb_func);
-    void set_vec_play(NrnThread& nt);
+    void handle_weights(NrnThread& nt, int n_netcon, NrnThreadChkpnt& ntc);
+    void get_info_from_bbcore(NrnThread& nt,
+                              const std::vector<Memb_func>& memb_func,
+                              NrnThreadChkpnt& ntc);
+    void set_vec_play(NrnThread& nt, NrnThreadChkpnt& ntc);
 
     int n_output;
     int n_real_output;
diff --git a/coreneuron/mechanism/register_mech.cpp b/coreneuron/mechanism/register_mech.cpp
@@ -165,7 +165,7 @@ void nrn_writes_conc(int type, int /* unused */) {
     if (type == -1)
         return;
 
-#if DEBUG
+#if CORENRN_DEBUG
     printf("%s reordered from %d to %d\n", corenrn.get_memb_func(type).sym, type, lastion);
 #endif
     if (nrn_is_ion(type)) {
@@ -243,7 +243,7 @@ void hoc_register_dparam_semantics(int type, int ix, const char* name) {
             ion_write_depend(type, etype);
         }
     }
-#if DEBUG
+#if CORENRN_DEBUG
     printf("dparam semantics %s ix=%d %s %d\n",
            memb_func[type].sym,
            ix,
diff --git a/coreneuron/network/multisend_setup.cpp b/coreneuron/network/multisend_setup.cpp
@@ -10,8 +10,9 @@
 #include <cmath>
 #include <numeric>
 
-#if DEBUG
+#if CORENRN_DEBUG
 #include <fstream>
+#include <iomanip>
 #endif
 
 #include "coreneuron/utils/randoms/nrnran123.h"
@@ -36,7 +37,7 @@ namespace coreneuron {
 using Gid2IPS = std::map<int, InputPreSyn*>;
 using Gid2PS = std::map<int, PreSyn*>;
 
-#if DEBUG
+#if CORENRN_DEBUG
 template <typename T>
 static void celldebug(const char* p, T& map) {
     std::string fname = std::string("debug.") + std::to_string(nrnmpi_myid);
@@ -90,7 +91,7 @@ static void alltoalldebug(const char*,
                           const std::vector<int>&) {}
 #endif
 
-#if DEBUG
+#if CORENRN_DEBUG
 void phase1debug(int* targets_phase1) {
     std::string fname = std::string("debug.") + std::to_string(nrnmpi_myid);
     std::ofstream f(fname, std::ios::app);
diff --git a/coreneuron/network/partrans_setup.cpp b/coreneuron/network/partrans_setup.cpp
@@ -124,7 +124,7 @@ void nrn_partrans::gap_mpi_setup(int ngroup) {
         assert(tar2info.find(sgid) != tar2info.end());
     }
 
-#if DEBUG
+#if CORENRN_DEBUG
     printf("%d mpi outsrccnt_, outsrcdspl_, insrccnt, insrcdspl_\n", nrnmpi_myid);
     for (int i = 0; i < nrnmpi_numprocs; ++i) {
         printf("%d : %d %d %d %d\n",
@@ -203,10 +203,10 @@ void nrn_partrans::gap_mpi_setup(int ngroup) {
         }
     }
 
-#if DEBUG
+#if CORENRN_DEBUG
     // things look ok so far?
     for (int tid = 0; tid < ngroup; ++tid) {
-        nrn_partrans::SetupTransferInfo& si = setup_info_[tid];
+        SetupTransferInfo& si = setup_info_[tid];
         nrn_partrans::TransferThreadData& ttd = transfer_thread_data_[tid];
         for (size_t i = 0; i < si.src_sid.size(); ++i) {
             printf("%d %d src sid=%d v_index=%d %g\n",
@@ -217,7 +217,7 @@ void nrn_partrans::gap_mpi_setup(int ngroup) {
                    nrn_threads[tid]._data[ttd.src_indices[i]]);
         }
         for (size_t i = 0; i < ttd.tar_indices.size(); ++i) {
-            printf("%d %d src sid=i%z tar_index=%d %g\n",
+            printf("%d %d src sid=i%zd tar_index=%d %g\n",
                    nrnmpi_myid,
                    tid,
                    i,
diff --git a/coreneuron/permute/cellorder.hpp b/coreneuron/permute/cellorder.hpp
@@ -121,7 +121,9 @@ void copy_align_array(T*& dest, T* src, size_t n) {
     std::copy(src, src + n, dest);
 }
 
+#ifndef INTERLEAVE_DEBUG
 #define INTERLEAVE_DEBUG 0
+#endif
 
 #if INTERLEAVE_DEBUG
 void mk_cell_indices();
diff --git a/coreneuron/permute/cellorder1.cpp b/coreneuron/permute/cellorder1.cpp
@@ -92,7 +92,7 @@ static void admin2(int ncell,
                    int*& nodebegin,
                    int*& ncycles);
 static void check(VecTNode&);
-#if DEBUG
+#if CORENRN_DEBUG
 static void prtree(VecTNode&);
 #endif
 
@@ -168,13 +168,13 @@ static void quality(VecTNode& nodevec, size_t max = 32) {
 
     // print result
     qcnt = 0;
-#if DEBUG
+#if CORENRN_DEBUG
     for (const auto& q: qual) {
         qcnt += q.second;
         printf("%6ld %6ld\n", q.first, q.second);
     }
 #endif
-#if DEBUG
+#if CORENRN_DEBUG
     printf("qual.size=%ld  qual total nodes=%ld  nodevec.size=%ld\n",
            qual.size(),
            qcnt,
@@ -209,7 +209,7 @@ static void quality(VecTNode& nodevec, size_t max = 32) {
             }
         }
     }
-#if DEBUG
+#if CORENRN_DEBUG
     printf("nrace = %ld (parent in same group of %ld nodes)\n", nrace1, max);
     printf("nrace = %ld (parent used more than once by same group of %ld nodes)\n", nrace2, max);
 #endif
@@ -342,7 +342,7 @@ int* node_order(int ncell,
     }
     check(nodevec);
 
-#if DEBUG
+#if CORENRN_DEBUG
     for (int i = 0; i < ncell; ++i) {
         TNode& nd = *nodevec[i];
         printf("%d size=%ld hash=%ld ix=%d\n", i, nd.treesize, nd.hash, nd.nodeindex);
@@ -411,7 +411,7 @@ void check(VecTNode& nodevec) {
     }
 }
 
-#if DEBUG
+#if CORENRN_DEBUG
 void prtree(VecTNode& nodevec) {
     size_t nnode = nodevec.size();
     for (size_t i = 0; i < nnode; ++i) {
@@ -501,7 +501,7 @@ void node_interleave_order(int ncell, VecTNode& nodevec) {
     // Traversal of nodevec: From root to leaves (this is why we compute the tree node order)
     std::sort(nodevec.begin() + ncell, nodevec.end(), interleave_comp);
 
-#if DEBUG
+#if CORENRN_DEBUG
     for (size_t i = 0; i < nodevec.size(); ++i) {
         TNode& nd = *nodevec[i];
         printf("%ld cell=%ld ix=%d\n", i, nd.cellindex, nd.nodeindex);
@@ -651,7 +651,7 @@ static void admin2(int ncell,
         }
     }
 
-#if DEBUG
+#if CORENRN_DEBUG
     printf("warp rootbegin nodebegin stridedispl\n");
     for (int i = 0; i <= nwarp; ++i) {
         printf("%4d %4d %4d %4d\n", i, rootbegin[i], nodebegin[i], stridedispl[i]);
diff --git a/coreneuron/permute/cellorder2.cpp b/coreneuron/permute/cellorder2.cpp
diff --git a/coreneuron/permute/node_permute.cpp b/coreneuron/permute/node_permute.cpp
diff --git a/coreneuron/sim/scopmath/sparse_thread.cpp b/coreneuron/sim/scopmath/sparse_thread.cpp
diff --git a/coreneuron/utils/nrntimeout.cpp b/coreneuron/utils/nrntimeout.cpp

Original file line number	Diff line number	Diff line change
`@@ -161,7 +161,7 @@ void set_globals(const char* path, bool cli_global_seed, int cli_global_seed_val`
`161`	`161`	`}`
`162`	`162`	`}`
`163`	`163`
`164`		`-#if DEBUG`
	`164`	`+#if CORENRN_DEBUG`
`165`	`165`	`for (const auto& item: *n2v) {`
`166`	`166`	`printf("%s %ld %p\n", item.first.c_str(), item.second.first, item.second.second);`
`167`	`167`	`}`