Discard spikes from forwardskip and improve for spike sorting (#195)

- Clear spike vectors after forwardskip to avoid spikes generated with negative timestamp
- Changed strcat to memcpy based to improve with millions of spikes
Co-Authored-By: Pramod Kumbhar <[email protected]>

Author: iomaganaris

coreneuron/nrniv/main1.cpp

@@ -355,6 +355,9 @@ void handle_forward_skip(double forwardskip, int prcellgid) {
     dt = savedt;
     t = savet;
     dt2thread(-1.);
+
+    // clear spikes generated during forward skip (with negative time) 
+    clear_spike_vectors();
 }
 
 const char* nrn_version(int) {

coreneuron/nrniv/output_spikes.cpp

@@ -40,6 +40,7 @@ THE POSSIBILITY OF SUCH DAMAGE.
 #include "coreneuron/nrniv/nrnmutdec.h"
 #include "coreneuron/nrnmpi/nrnmpi_impl.h"
 #include "coreneuron/nrnmpi/nrnmpidec.h"
+#include "coreneuron/utils/string_utils.h"
 
 namespace coreneuron {
 std::vector<double> spikevec_time;
@@ -176,9 +177,10 @@ void output_spikes_parallel(const char* outpath) {
 
     // populate buffer with all spike entries
     char spike_entry[SPIKE_RECORD_LEN];
+    unsigned spike_data_offset = 0;
     for (unsigned i = 0; i < num_spikes; i++) {
-        snprintf(spike_entry, 64, "%.8g\t%d\n", spikevec_time[i], spikevec_gid[i]);
-        strcat(spike_data, spike_entry);
+        int spike_entry_chars = snprintf(spike_entry, 64, "%.8g\t%d\n", spikevec_time[i], spikevec_gid[i]);
+        spike_data_offset = strcat_at_pos(spike_data, spike_data_offset, spike_entry, spike_entry_chars);
     }
 
     // calculate offset into global file. note that we don't write
@@ -250,6 +252,15 @@ void output_spikes(const char* outpath) {
 #endif
 }
 
+void clear_spike_vectors() {
+    auto spikevec_time_capacity = spikevec_time.capacity();
+    auto spikevec_gid_capacity = spikevec_gid.capacity();
+    spikevec_time.clear();
+    spikevec_gid.clear();
+    spikevec_time.reserve(spikevec_time_capacity);
+    spikevec_gid.reserve(spikevec_gid_capacity);
+}
+
 void validation(std::vector<std::pair<double, int> >& res) {
     for (unsigned i = 0; i < spikevec_gid.size(); ++i)
         if (spikevec_gid[i] > -1)

coreneuron/nrniv/output_spikes.h

@@ -38,6 +38,7 @@ void mk_spikevec_buffer(int);
 extern std::vector<double> spikevec_time;
 extern std::vector<int> spikevec_gid;
 
+void clear_spike_vectors();
 void validation(std::vector<std::pair<double, int> >& res);
 
 void spikevec_lock();

coreneuron/utils/string_utils.cpp

@@ -0,0 +1,35 @@
+/*
+Copyright (c) 2019, Blue Brain Project
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification,
+are permitted provided that the following conditions are met:
+1. Redistributions of source code must retain the above copyright notice,
+   this list of conditions and the following disclaimer.
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+3. Neither the name of the copyright holder nor the names of its contributors
+   may be used to endorse or promote products derived from this software
+   without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF
+THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
+#include <cstring>
+
+unsigned strcat_at_pos(char* dest, unsigned start_position, char* src, unsigned src_length) {
+    memcpy(dest + start_position, src, src_length);
+    dest[start_position + src_length] = '\0';
+    return start_position + src_length;
+}

coreneuron/utils/string_utils.h

@@ -0,0 +1,52 @@
+/*
+Copyright (c) 2019, Blue Brain Project
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification,
+are permitted provided that the following conditions are met:
+1. Redistributions of source code must retain the above copyright notice,
+   this list of conditions and the following disclaimer.
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+3. Neither the name of the copyright holder nor the names of its contributors
+   may be used to endorse or promote products derived from this software
+   without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
+LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF
+THE POSSIBILITY OF SUCH DAMAGE.
+*/
+
+/**
+ * @file string_utils.h
+ * @brief Utility functions for strings
+ *
+ */
+
+#ifndef CORENEURON_STRING_UTILS_HPP
+#define CORENEURON_STRING_UTILS_HPP
+
+/** @brief Appends a copy of the source string to the destination string.
+ *
+ *  A null-character is included at the end of the new string formed by the concatenation of both in destination.
+ *  It has similar behavior to strcat but better performance in case that it is needed to append a char array to
+ *  another very large char array.
+ *
+ *  @param dest Destination string
+ *  @param start_position Position of dest to start writing src
+ *  @param src Source string
+ *  @param src_length Length of src to append to dest
+ *  @return Position of the final character of dest after appending src (including the null terminating character)
+ */
+unsigned strcat_at_pos(char* dest, unsigned start_position, char* src, unsigned src_length);
+
+#endif /* ifndef CORENEURON_STRING_UTILS_HPP */