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View Code? Open in Web Editor NEWRing network model test to demonstrate the use of CoreNEURON
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ringtest's Issues
NEURON: NetCon and NetCon source with no gid are not in the same thread
When I run this python ringtest.py -nt=2 on JURECA-DC login, I get this message:
$ python ringtest.py -nt=2
[10, 20] [1, 1]
nring=16
cell per ring=8
ncell_per_type=8
ntype=16
created coredat/
0.02s created rings
2224 non-zero area compartments
0s initialized
NEURON: NetCon and NetCon source with no gid are not in the same thread
near line 0
^
ParallelContext[1].nrnbbcore_write("coredat/")
Traceback (most recent call last):
File "ringtest.py", line 201, in <module>
pc.nrnbbcore_write(bbcorewrite_folder)
RuntimeError: hoc error
The code is basically at d3b40f9
Building a network of astrocytes via a gap junction
How do I re-use the gid in ParallelContext::source_var(), which in my understanding, does not allow it?
Cannot build coreneuron executable
after
cd $SOURCE_DIR/ringtest
mkdir -p coreneuron_x86 && cd coreneuron_x86
cmake $BASE_DIR/sources/CoreNeuron -DADDITIONAL_MECHPATH=$SOURCE_DIR/ringtest/mod
make -j
I cannot find coreneuron_core in ./coreneuron_x86/bin. There are only mod2c_core, nrnivmodl_core and a folder called x86_64. Below is the make -j output:
(test)tony@Aurora-R11:~/coreneuron_tutorial/sources/ringtest/coreneuron_x86$ make -j
make[1]: Entering directory '/home/tony/coreneuron_tutorial/sources/ringtest/coreneuron_x86'
make[2]: Entering directory '/home/tony/coreneuron_tutorial/sources/ringtest/coreneuron_x86'
make[2]: Entering directory '/home/tony/coreneuron_tutorial/sources/ringtest/coreneuron_x86'
make[2]: Entering directory '/home/tony/coreneuron_tutorial/sources/ringtest/coreneuron_x86'
[ 2%] [FLEX][lex] Building scanner with flex 2.6.4
[ 2%] [BISON][diffeq] Building parser with bison 3.7
Scanning dependencies of target kin_deriv_header
Scanning dependencies of target scopmath
[ 3%] [BISON][parse1] Building parser with bison 3.7
make[2]: Leaving directory '/home/tony/coreneuron_tutorial/sources/ringtest/coreneuron_x86'
make[2]: Entering directory '/home/tony/coreneuron_tutorial/sources/ringtest/coreneuron_x86'
diffeq.y: warning: 5 shift/reduce conflicts [-Wconflicts-sr]
diffeq.y: note: rerun with option '-Wcounterexamples' to generate conflict counterexamples
make[2]: Leaving directory '/home/tony/coreneuron_tutorial/sources/ringtest/coreneuron_x86'
make[2]: Entering directory '/home/tony/coreneuron_tutorial/sources/ringtest/coreneuron_x86'
[ 4%] Generating kinderiv.h by inspecting MOD files
[ 5%] Building CXX object coreneuron/CMakeFiles/scopmath.dir/sim/scopmath/abort.cpp.o
[ 6%] Building CXX object coreneuron/CMakeFiles/scopmath.dir/sim/scopmath/newton_thread.cpp.o
[ 7%] Building CXX object coreneuron/CMakeFiles/scopmath.dir/sim/scopmath/crout_thread.cpp.o
[ 8%] Building CXX object coreneuron/CMakeFiles/scopmath.dir/sim/scopmath/sparse_thread.cpp.o
[ 9%] Building CXX object coreneuron/CMakeFiles/scopmath.dir/sim/scopmath/ssimplic_thread.cpp.o
make[2]: Leaving directory '/home/tony/coreneuron_tutorial/sources/ringtest/coreneuron_x86'
[ 9%] Built target kin_deriv_header
make[2]: Entering directory '/home/tony/coreneuron_tutorial/sources/ringtest/coreneuron_x86'
Scanning dependencies of target coreneuron
make[2]: Leaving directory '/home/tony/coreneuron_tutorial/sources/ringtest/coreneuron_x86'
make[2]: Entering directory '/home/tony/coreneuron_tutorial/sources/ringtest/coreneuron_x86'
[ 10%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/io/mem_layout_util.cpp.o
[ 11%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/apps/corenrn_parameters.cpp.o
[ 13%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/gpu/nrn_acc_manager.cpp.o
[ 13%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/apps/main1.cpp.o
[ 14%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/io/core2nrn_data_return.cpp.o
[ 15%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/io/global_vars.cpp.o
[ 16%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/io/file_utils.cpp.o
[ 17%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/io/mk_mech.cpp.o
[ 18%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/io/nrn_checkpoint.cpp.o
[ 21%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/io/output_spikes.cpp.o
[ 21%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/io/nrn_filehandler.cpp.o
[ 22%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/io/nrn_setup.cpp.o
[ 23%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/io/phase2.cpp.o
[ 24%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/io/phase1.cpp.o
[ 25%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/io/prcellstate.cpp.o
[ 26%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/io/reports/nrnreport.cpp.o
[ 28%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/io/reports/binary_report_handler.cpp.o
[ 28%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/io/reports/report_configuration_parser.cpp.o
[ 29%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/io/reports/report_event.cpp.o
[ 30%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/io/reports/report_handler.cpp.o
[ 31%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/io/reports/sonata_report_handler.cpp.o
[ 32%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/io/setup_fornetcon.cpp.o
[ 33%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/permute/balance.cpp.o
[ 34%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/mechanism/patternstim.cpp.o
[ 35%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/network/partrans_setup.cpp.o
[ 36%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/mpi/mpispike.cpp.o
[ 37%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/mechanism/eion.cpp.o
[ 42%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/network/netpar.cpp.o
[ 38%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/network/multisend.cpp.o
[ 40%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/mechanism/capac.cpp.o
[ 41%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/network/partrans.cpp.o
[ 43%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/network/cvodestb.cpp.o
[ 45%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/network/multisend_setup.cpp.o
[ 46%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/mechanism/register_mech.cpp.o
[ 46%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/network/tqueue.cpp.o
[ 47%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/network/netcvode.cpp.o
[ 48%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/mechanism/mech_mapping.cpp.o
[ 49%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/mpi/nrnmpi.cpp.o
[ 50%] Linking CXX static library ../lib/libscopmath.a
Scanning dependencies of target mod2c_core
make[2]: Leaving directory '/home/tony/coreneuron_tutorial/sources/ringtest/coreneuron_x86'
make[2]: Entering directory '/home/tony/coreneuron_tutorial/sources/ringtest/coreneuron_x86'
[ 51%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/permute/cellorder.cpp.o
make[2]: Leaving directory '/home/tony/coreneuron_tutorial/sources/ringtest/coreneuron_x86'
[ 52%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/permute/data_layout.cpp.o
[ 53%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/permute/cellorder1.cpp.o
[ 55%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/permute/cellorder2.cpp.o
[ 56%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/permute/node_permute.cpp.o
[ 57%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/sim/fadvance_core.cpp.o
[ 58%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/sim/fast_imem.cpp.o
[ 60%] Building C object external/mod2c/src/mod2c_core/CMakeFiles/mod2c_core.dir/io.c.o
[ 54%] Building C object external/mod2c/src/mod2c_core/CMakeFiles/mod2c_core.dir/consist.c.o
[ 60%] Built target scopmath
[ 61%] Building C object external/mod2c/src/mod2c_core/CMakeFiles/mod2c_core.dir/list.c.o
/home/tony/coreneuron_tutorial/sources/coreNeuron/coreneuron/io/reports/report_configuration_parser.cpp: In function ‘std::vector<coreneuron::ReportConfiguration> coreneuron::create_report_configurations(const char*, const char*, std::string&)’:
/home/tony/coreneuron_tutorial/sources/coreNeuron/coreneuron/io/reports/report_configuration_parser.cpp:104:48: warning: format ‘%d’ expects argument of type ‘int*’, but argument 9 has type ‘coreneuron::TargetType*’ [-Wformat=]
104 | sscanf(raw_line, "\n%s %s %s %s %s %s %d %lf %lf %lf %d %d %s\n", report.name,
| ~^
| |
| int*
105 | report.target_name, report.type_str, report_on, report.unit, report.format, &target_type,
| ~~~~~~~~~~~~
| |
| coreneuron::TargetType*
[ 62%] Building C object external/mod2c/src/mod2c_core/CMakeFiles/mod2c_core.dir/nocpout.c.o
[ 63%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/sim/finitialize.cpp.o
[ 64%] Building C object external/mod2c/src/mod2c_core/CMakeFiles/mod2c_core.dir/partial.c.o
[ 66%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/sim/multicore.cpp.o
[ 65%] Building C object external/mod2c/src/mod2c_core/CMakeFiles/mod2c_core.dir/solve.c.o
[ 70%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/utils/ivocvect.cpp.o
[ 69%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/utils/ispc/globals.cpp.o
[ 71%] Building C object external/mod2c/src/mod2c_core/CMakeFiles/mod2c_core.dir/discrete.c.o
[ 67%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/sim/solve_core.cpp.o
[ 68%] Building C object external/mod2c/src/mod2c_core/CMakeFiles/mod2c_core.dir/version.c.o
[ 72%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/sim/treeset_core.cpp.o
[ 73%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/utils/lpt.cpp.o
[ 74%] Building C object external/mod2c/src/mod2c_core/CMakeFiles/mod2c_core.dir/kinetic.c.o
[ 75%] Building C object external/mod2c/src/mod2c_core/CMakeFiles/mod2c_core.dir/modl.c.o
/home/tony/coreneuron_tutorial/sources/coreNeuron/coreneuron/io/reports/report_configuration_parser.cpp:95:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
95 | fgets(raw_line, REPORT_MAX_FILEPATH_LEN, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/tony/coreneuron_tutorial/sources/coreNeuron/coreneuron/io/reports/report_configuration_parser.cpp:103:14: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
103 | fgets(raw_line, REPORT_MAX_FILEPATH_LEN, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/tony/coreneuron_tutorial/sources/coreNeuron/coreneuron/io/reports/report_configuration_parser.cpp:171:18: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
171 | fread(gids, sizeof(int), report.num_gids, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/tony/coreneuron_tutorial/sources/coreNeuron/coreneuron/io/reports/report_configuration_parser.cpp:173:18: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
173 | fgets(raw_line, REPORT_MAX_FILEPATH_LEN, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/tony/coreneuron_tutorial/sources/coreNeuron/coreneuron/io/reports/report_configuration_parser.cpp:180:10: warning: ignoring return value of ‘char* fgets(char*, int, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
180 | fgets(raw_line, REPORT_MAX_NAME_LEN, fp);
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 76%] Building C object external/mod2c/src/mod2c_core/CMakeFiles/mod2c_core.dir/parsact.c.o
[ 77%] Building C object external/mod2c/src/mod2c_core/CMakeFiles/mod2c_core.dir/sens.c.o
[ 78%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/utils/memory_utils.cpp.o
[ 80%] Building C object external/mod2c/src/mod2c_core/CMakeFiles/mod2c_core.dir/symbol.c.o
[ 81%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/utils/nrn_stats.cpp.o
[ 82%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/utils/nrnoc_aux.cpp.o
[ 83%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/utils/nrntimeout.cpp.o
/home/tony/coreneuron_tutorial/sources/coreNeuron/external/mod2c/src/mod2c_core/sens.c: In function ‘sensmassage’:
/home/tony/coreneuron_tutorial/sources/coreNeuron/external/mod2c/src/mod2c_core/sens.c:150:6: warning: type of ‘fn’ defaults to ‘int’ [-Wimplicit-int]
150 | void sensmassage(type, qfun, fn)
| ^~~~~~~~~~~
[ 84%] Building C object external/mod2c/src/mod2c_core/CMakeFiles/mod2c_core.dir/deriv.c.o
[ 85%] Building C object external/mod2c/src/mod2c_core/CMakeFiles/mod2c_core.dir/simultan.c.o
[ 88%] Building C object external/mod2c/src/mod2c_core/CMakeFiles/mod2c_core.dir/units.c.o
[ 86%] Building C object coreneuron/CMakeFiles/coreneuron.dir/utils/progressbar/progressbar.c.o
[ 87%] Building C object external/mod2c/src/mod2c_core/CMakeFiles/mod2c_core.dir/noccout.c.o
[ 89%] Building C object external/mod2c/src/mod2c_core/CMakeFiles/mod2c_core.dir/init.c.o
[ 90%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/utils/randoms/nrnran123.cpp.o
[ 91%] Building C object external/mod2c/src/mod2c_core/CMakeFiles/mod2c_core.dir/diffeq.c.o
/home/tony/coreneuron_tutorial/sources/coreNeuron/external/mod2c/src/mod2c_core/sens.c:257:19: warning: ‘__builtin___sprintf_chk’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
257 | Sprintf(dname, "D%s", sname);
| ^~~~~
In file included from /usr/include/stdio.h:866,
from /home/tony/coreneuron_tutorial/sources/coreNeuron/external/mod2c/src/mod2c_core/modl.h:2,
from /home/tony/coreneuron_tutorial/sources/coreNeuron/external/mod2c/src/mod2c_core/sens.c:118:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output between 2 and 101 bytes into a destination of size 100
38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
39 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 93%] Building C object external/mod2c/src/mod2c_core/CMakeFiles/mod2c_core.dir/parse1.c.o
[ 92%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/utils/string_utils.cpp.o
[ 96%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/config/config.cpp.o
[ 94%] Building CXX object coreneuron/CMakeFiles/coreneuron.dir/utils/vrecord.cpp.o
[ 95%] Building C object external/mod2c/src/mod2c_core/CMakeFiles/mod2c_core.dir/lex.c.o
/home/tony/coreneuron_tutorial/sources/coreNeuron/external/mod2c/src/mod2c_core/units.c: In function ‘pu’:
/home/tony/coreneuron_tutorial/sources/coreNeuron/external/mod2c/src/mod2c_core/units.c:615:12: warning: type of ‘u’ defaults to ‘int’ [-Wimplicit-int]
615 | static int pu(u, i, f)
| ^~
/home/tony/coreneuron_tutorial/sources/coreNeuron/external/mod2c/src/mod2c_core/units.c:615:12: warning: type of ‘i’ defaults to ‘int’ [-Wimplicit-int]
/home/tony/coreneuron_tutorial/sources/coreNeuron/external/mod2c/src/mod2c_core/units.c:615:12: warning: type of ‘f’ defaults to ‘int’ [-Wimplicit-int]
/home/tony/coreneuron_tutorial/sources/coreNeuron/external/mod2c/src/mod2c_core/units.c: In function ‘lookup’:
/home/tony/coreneuron_tutorial/sources/coreNeuron/external/mod2c/src/mod2c_core/units.c:689:12: warning: type of ‘den’ defaults to ‘int’ [-Wimplicit-int]
689 | static int lookup(name, up, den, c)
| ^~~~~~
/home/tony/coreneuron_tutorial/sources/coreNeuron/external/mod2c/src/mod2c_core/units.c:689:12: warning: type of ‘c’ defaults to ‘int’ [-Wimplicit-int]
/home/tony/coreneuron_tutorial/sources/ringtest/coreneuron_x86/external/mod2c/src/mod2c_core/lex.c: In function ‘yy_init_buffer’:
/home/tony/coreneuron_tutorial/sources/ringtest/coreneuron_x86/external/mod2c/src/mod2c_core/lex.c:1612:40: warning: implicit declaration of function ‘isatty’ [-Wimplicit-function-declaration]
1612 | b->yy_is_interactive = file ? (isatty( fileno(file) ) > 0) : 0;
| ^~~~~~
/home/tony/coreneuron_tutorial/sources/coreNeuron/external/mod2c/src/mod2c_core/deriv.c: In function ‘next_forderiv’:
/home/tony/coreneuron_tutorial/sources/coreNeuron/external/mod2c/src/mod2c_core/deriv.c:392:16: warning: ‘^’ directive writing 1 byte into a region of size between 0 and 49 [-Wformat-overflow=]
392 | Sprintf(units, "%s/%s^%d", base_units, STR(indeplist->prev), indx);
| ^~~~~~~~~~
In file included from /usr/include/stdio.h:866,
from /home/tony/coreneuron_tutorial/sources/coreNeuron/external/mod2c/src/mod2c_core/modl.h:2,
from /home/tony/coreneuron_tutorial/sources/coreNeuron/external/mod2c/src/mod2c_core/deriv.c:30:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output 4 or more bytes (assuming 53) into a destination of size 50
38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
39 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/tony/coreneuron_tutorial/sources/coreNeuron/external/mod2c/src/mod2c_core/deriv.c:400:16: warning: ‘^’ directive writing 1 byte into a region of size between 0 and 49 [-Wformat-overflow=]
400 | Sprintf(units, "%s/%s^%d", base_units, STR(indeplist->prev), indx);
| ^~~~~~~~~~
In file included from /usr/include/stdio.h:866,
from /home/tony/coreneuron_tutorial/sources/coreNeuron/external/mod2c/src/mod2c_core/modl.h:2,
from /home/tony/coreneuron_tutorial/sources/coreNeuron/external/mod2c/src/mod2c_core/deriv.c:30:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output 4 or more bytes (assuming 53) into a destination of size 50
38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
39 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/tony/coreneuron_tutorial/sources/coreNeuron/external/mod2c/src/mod2c_core/deriv.c: In function ‘massagederiv’:
/home/tony/coreneuron_tutorial/sources/coreNeuron/external/mod2c/src/mod2c_core/deriv.c:580:16: warning: ‘^’ directive writing 1 byte into a region of size between 0 and 49 [-Wformat-overflow=]
580 | Sprintf(units, "%s/%s^%d", base_units, STR(indeplist->prev), maxindx);
| ^~~~~~~~~~
In file included from /usr/include/stdio.h:866,
from /home/tony/coreneuron_tutorial/sources/coreNeuron/external/mod2c/src/mod2c_core/modl.h:2,
from /home/tony/coreneuron_tutorial/sources/coreNeuron/external/mod2c/src/mod2c_core/deriv.c:30:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:38:10: note: ‘__builtin___sprintf_chk’ output 4 or more bytes (assuming 53) into a destination of size 50
38 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
39 | __bos (__s), __fmt, __va_arg_pack ());
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
[ 97%] Linking C executable ../../../../bin/mod2c_core
make[2]: Leaving directory '/home/tony/coreneuron_tutorial/sources/ringtest/coreneuron_x86'
[ 97%] Built target mod2c_core
[ 98%] Linking CXX shared library ../lib/libcoreneuron.so
make[2]: Leaving directory '/home/tony/coreneuron_tutorial/sources/ringtest/coreneuron_x86'
[ 98%] Built target coreneuron
make[2]: Entering directory '/home/tony/coreneuron_tutorial/sources/ringtest/coreneuron_x86'
Scanning dependencies of target nrniv-core
make[2]: Leaving directory '/home/tony/coreneuron_tutorial/sources/ringtest/coreneuron_x86'
make[2]: Entering directory '/home/tony/coreneuron_tutorial/sources/ringtest/coreneuron_x86'
[100%] Running nrnivmodl-core with halfgap.mod
[INFO] Running: make -j4 -f /home/tony/coreneuron_tutorial/sources/ringtest/coreneuron_x86/share/coreneuron/nrnivmodl_core_makefile ROOT=/home/tony/coreneuron_tutorial/sources/ringtest/coreneuron_x86 MOD2CPP_BINARY=/home/tony/coreneuron_tutorial/sources/ringtest/coreneuron_x86/bin/mod2c_core MODS_PATH=x86_64/core/mods BUILD_TYPE=STATIC
make[3]: Entering directory '/home/tony/coreneuron_tutorial/sources/ringtest/coreneuron_x86/bin'
Default nmodl flags:
Translating x86_64/core/mods/exp2syn.mod into x86_64/corenrn/mod2c//exp2syn.cpp
Translating x86_64/core/mods/expsyn.mod into x86_64/corenrn/mod2c//expsyn.cpp
cvode_emit=0 cvode_not_allowed=0
cvode_emit=0 cvode_not_allowed=0
Thread Safe
Thread Safe
Translating x86_64/core/mods/halfgap.mod into x86_64/corenrn/mod2c//halfgap.cpp
Translating x86_64/core/mods/hh.mod into x86_64/corenrn/mod2c//hh.cpp
cvode_emit=0 cvode_not_allowed=0
Thread Safe
diff: x86_64/corenrn/mod2c/_mod_func.cpp: No such file or directory
cvode_emit=0 cvode_not_allowed=0
Thread Safe
Translating x86_64/core/mods/netstim.mod into x86_64/corenrn/mod2c//netstim.cpp
cvode_emit=0 cvode_not_allowed=0
Notice: ARTIFICIAL_CELL is a synonym for POINT_PROCESS which hints that it
only affects and is affected by discrete events. As such it is not
located in a section and is not associated with an integrator
Translating x86_64/core/mods/passive.mod into x86_64/corenrn/mod2c//passive.cpp
Thread Safe
cvode_emit=0 cvode_not_allowed=0
Translating x86_64/core/mods/pattern.mod into x86_64/corenrn/mod2c//pattern.cpp
Thread Safe
cvode_emit=0 cvode_not_allowed=0
Notice: ARTIFICIAL_CELL is a synonym for POINT_PROCESS which hints that it
only affects and is affected by discrete events. As such it is not
located in a section and is not associated with an integrator
Thread Safe
Translating x86_64/core/mods/stim.mod into x86_64/corenrn/mod2c//stim.cpp
cvode_emit=0 cvode_not_allowed=0
Translating x86_64/core/mods/svclmp.mod into x86_64/corenrn/mod2c//svclmp.cpp
Thread Safe
cvode_emit=0 cvode_not_allowed=0
Thread Safe
/home/tony/coreneuron_tutorial/sources/ringtest/coreneuron_x86/bin
=> Binary creating x86_64/special-core
make[3]: Leaving directory '/home/tony/coreneuron_tutorial/sources/ringtest/coreneuron_x86/bin'
[INFO] MOD files built successfully for CoreNEURON
make[2]: Leaving directory '/home/tony/coreneuron_tutorial/sources/ringtest/coreneuron_x86'
[100%] Built target nrniv-core
make[1]: Leaving directory '/home/tony/coreneuron_tutorial/sources/ringtest/coreneuron_x86'
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