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20 hours ago •
nest
nest
Failing assertion upon `import nest`
The following issue was reported on the mailing list:
python: /home/neurobit/src/nest-simulator/nestkernel/model_manager.h:321: size_t nest::ModelManager::get_num_connection_models() const: Assertion `connection_models_[ 0 ].size() <= invalid_synindex' failed.
[dcccluster:979935] *** Process received signal ***
[dcccluster:979935] Signal: Aborted (6)
[dcccluster:979935] Signal code: (-6)
[dcccluster:979935] [ 0] /usr/lib64/libpthread.so.0(+0x12c20)[0x7f8c3a3cdc20]
[dcccluster:979935] [ 1] /usr/lib64/libc.so.6(gsignal+0x10f)[0x7f8c398a337f]
[dcccluster:979935] [ 2] /usr/lib64/libc.so.6(abort+0x127)[0x7f8c3988ddb5]
[dcccluster:979935] [ 3] /usr/lib64/libc.so.6(+0x21c89)[0x7f8c3988dc89]
[dcccluster:979935] [ 4] /usr/lib64/libc.so.6(+0x2fa76)[0x7f8c3989ba76]
[dcccluster:979935] [ 5] /home/neurobit/local/nest_3.3/lib64/python3.8/site-packages/nest/../../../nest/libnestkernel.so.3(+0x1aad22)[0x7f8c2a878d22]
[dcccluster:979935] [ 6] /home/neurobit/local/nest_3.3/lib64/python3.8/site-packages/nest/../../../nest/libnestkernel.so.3(_ZN4nest12ModelManager26register_connection_model_EPNS_14ConnectorModelE+0x32d)[0x7f8c2a80f07d]
[dcccluster:979935] [ 7] /home/neurobit/local/nest_3.3/lib64/python3.8/site-packages/nest/../../../nest/libmodels.so.3(_ZN4nest12ModelManager25register_connection_modelINS_24vogels_sprekeler_synapseEEEvRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEENS_28RegisterConnectionModelFlagsE+0x171)[0x7f8c2b04d071]
[dcccluster:979935] [ 8] /home/neurobit/local/nest_3.3/lib64/python3.8/site-packages/nest/../../../nest/libmodels.so.3(_ZN4nest12ModelsModule4initEP14SLIInterpreter+0x2c14)[0x7f8c2afa0404]
[dcccluster:979935] [ 9] /home/neurobit/local/nest_3.3/lib64/python3.8/site-packages/nest/../../../nest/libsli.so.3(_ZN9SLIModule7installERSoP14SLIInterpreter+0x59)[0x7f8c29a22369]
[dcccluster:979935] [10] /home/neurobit/local/nest_3.3/lib64/python3.8/site-packages/nest/../../../nest/libsli.so.3(_ZN14SLIInterpreter9addmoduleEP9SLIModule+0x44)[0x7f8c299c29f4]
[dcccluster:979935] [11] /home/neurobit/local/nest_3.3/lib64/python3.8/site-packages/nest/../../../nest/libnest.so.3(_Z11neststartupPiPPPcR14SLIInterpreterNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x13cc)[0x7f8c2b6d37ec]
[dcccluster:979935] [12] /home/neurobit/local/nest_3.3/lib64/python3.8/site-packages/nest/pynestkernel.so(+0x42475)[0x7f8c2b920475]
[dcccluster:979935] [13] /usr/lib64/libpython3.8.so.1.0(+0x1d8faf)[0x7f8c3a9dcfaf]
[dcccluster:979935] [14] /usr/lib64/libpython3.8.so.1.0(_PyEval_EvalFrameDefault+0x976)[0x7f8c3a9e5406]
[dcccluster:979935] [15] /usr/lib64/libpython3.8.so.1.0(_PyFunction_Vectorcall+0x1bf)[0x7f8c3a9a37af]
[dcccluster:979935] [16] /usr/lib64/libpython3.8.so.1.0(_PyEval_EvalFrameDefault+0x5da)[0x7f8c3a9e506a]
[dcccluster:979935] [17] /usr/lib64/libpython3.8.so.1.0(_PyEval_EvalCodeWithName+0x3e7)[0x7f8c3a9a23c7]
[dcccluster:979935] [18] /usr/lib64/libpython3.8.so.1.0(PyEval_EvalCode+0x23)[0x7f8c3a9a35a3]
[dcccluster:979935] [19] /usr/lib64/libpython3.8.so.1.0(+0x25114b)[0x7f8c3aa5514b]
[dcccluster:979935] [20] /usr/lib64/libpython3.8.so.1.0(+0x1667e0)[0x7f8c3a96a7e0]
[dcccluster:979935] [21] /usr/lib64/libpython3.8.so.1.0(PyVectorcall_Call+0x70)[0x7f8c3a96f390]
[dcccluster:979935] [22] /usr/lib64/libpython3.8.so.1.0(_PyEval_EvalFrameDefault+0x68d9)[0x7f8c3a9eb369]
[dcccluster:979935] [23] /usr/lib64/libpython3.8.so.1.0(_PyEval_EvalCodeWithName+0x3e7)[0x7f8c3a9a23c7]
[dcccluster:979935] [24] /usr/lib64/libpython3.8.so.1.0(_PyFunction_Vectorcall+0x422)[0x7f8c3a9a3a12]
[dcccluster:979935] [25] /usr/lib64/libpython3.8.so.1.0(_PyEval_EvalFrameDefault+0x54d9)[0x7f8c3a9e9f69]
[dcccluster:979935] [26] /usr/lib64/libpython3.8.so.1.0(_PyFunction_Vectorcall+0x1bf)[0x7f8c3a9a37af]
[dcccluster:979935] [27] /usr/lib64/libpython3.8.so.1.0(_PyEval_EvalFrameDefault+0x976)[0x7f8c3a9e5406]
[dcccluster:979935] [28] /usr/lib64/libpython3.8.so.1.0(_PyFunction_Vectorcall+0x1bf)[0x7f8c3a9a37af]
[dcccluster:979935] [29] /usr/lib64/libpython3.8.so.1.0(_PyEval_EvalFrameDefault+0x5da)[0x7f8c3a9e506a]
[dcccluster:979935] *** End of error message ***
Aborted (`core' generado)
- Rocky Linux 8.5
- NEST 3.3 (Installation from source)
- Problem also exists with current git
Could you try running nest directly as follows:
source <nest_install_dir>/bin/nest_vars.sh
nest
and see if that works? If that does not work, could you try
sli -c "statusdict info"
sli -c "statusdict /architecture get info"
and report the output? Could you also look at libnestutil/config.h in the build directory and post these lines corresponding to these (towards the end of the file):
/* Bit counts for Target members */
#define TARGET_BITS_SPLIT 0
#define TARGET_BITS_SPLIT_STANDARD 0
#define TARGET_BITS_SPLIT_HPC 1
Executing the "source ..." and "nest" command shows the same error:
nest: /home/neurobit/src/nest_3.3_src/nestkernel/model_manager.h:321: size_t nest::ModelManager::get_num_connection_models() const: Assertion `connection_models_[ 0 ].size() <= invalid_synindex' failed.
[dcccluster:1177271] *** Process received signal ***
[dcccluster:1177271] Signal: Aborted (6)
[dcccluster:1177271] Signal code: (-6)
[dcccluster:1177271] [ 0] /lib64/libpthread.so.0(+0x12c20)[0x7f34fe352c20]
[dcccluster:1177271] [ 1] /lib64/libc.so.6(gsignal+0x10f)[0x7f34fd63837f]
[dcccluster:1177271] [ 2] /lib64/libc.so.6(abort+0x127)[0x7f34fd622db5]
[dcccluster:1177271] [ 3] /lib64/libc.so.6(+0x21c89)[0x7f34fd622c89]
[dcccluster:1177271] [ 4] /lib64/libc.so.6(+0x2fa76)[0x7f34fd630a76]
[dcccluster:1177271] [ 5] /home/neurobit/local/nest_3.3/bin/../lib64/nest/libnestkernel.so(+0x187722)[0x7f34ffddc722]
[dcccluster:1177271] [ 6] /home/neurobit/local/nest_3.3/bin/../lib64/nest/libnestkernel.so(_ZN4nest12ModelManager26register_connection_model_EPNS_14ConnectorModelE+0x32d)[0x7f34ffd720ed]
[dcccluster:1177271] [ 7] /home/neurobit/local/nest_3.3/bin/../lib64/nest/libmodels.so(_ZN4nest12ModelManager25register_connection_modelINS_24vogels_sprekeler_synapseEEEvRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEENS_28RegisterConnectionModelFlagsE+0x171)[0x7f35005a93b1]
[dcccluster:1177271] [ 8] /home/neurobit/local/nest_3.3/bin/../lib64/nest/libmodels.so(_ZN4nest12ModelsModule4initEP14SLIInterpreter+0x2c14)[0x7f35004fc7e4]
[dcccluster:1177271] [ 9] /home/neurobit/local/nest_3.3/bin/../lib64/nest/libsli.so(_ZN9SLIModule7installERSoP14SLIInterpreter+0x59)[0x7f34ff1ba149]
[dcccluster:1177271] [10] /home/neurobit/local/nest_3.3/bin/../lib64/nest/libsli.so(_ZN14SLIInterpreter9addmoduleEP9SLIModule+0x44)[0x7f34ff15a7d4]
[dcccluster:1177271] [11] nest[0x4119a0]
[dcccluster:1177271] [12] nest[0x41020d]
[dcccluster:1177271] [13] /lib64/libc.so.6(__libc_start_main+0xf3)[0x7f34fd624493]
[dcccluster:1177271] [14] nest[0x41053e]
[dcccluster:1177271] *** End of error message ***
Aborted (`core' generado)
Executing sli -c "statusdict info" shows:
Jul 05 15:40:48 CopyFile [Error]:
Could not open source file.
Error in nest resource file: /BadIO in CopyFile_
--------------------------------------------------
Name Type Value
--------------------------------------------------
architecture dictionarytype <dictionarytype>
argv arraytype <arraytype>
built stringtype Jun 23 2022 21:46:14
environment dictionarytype <dictionarytype>
exitcode integertype 0
exitcodes dictionarytype <dictionarytype>
files arraytype <arraytype>
have_gsl booltype true
have_libneurosim booltype false
have_mpi booltype true
have_music booltype true
have_sionlib booltype true
host stringtype x86_64-pc-linux
hostcpu stringtype x86_64
hostos stringtype linux
hostvendor stringtype pc
interactive booltype false
is_mpi booltype false
ndebug booltype false
platform stringtype default
prefix stringtype /home/neurobit/local/nest_3.3
prgdatadir stringtype /home/neurobit/local/nest_3.3/share/nest
prgdocdir stringtype /home/neurobit/local/nest_3.3/share/doc/nest
threading stringtype openmp
userargs arraytype <arraytype>
version stringtype 3.3
--------------------------------------------------
Total number of entries: 26
Executing sli -c "statusdict /architecture get info" shows:
--------------------------------------------------
Name Type Value
--------------------------------------------------
ArrayDatum integertype 48
Dictionary integertype 56
DictionaryDatum integertype 56
double integertype 8
have_long_long booltype true
int integertype 4
IntegerDatum integertype 40
long integertype 8
long_long integertype 8
Token integertype 16
TokenArray integertype 16
TokenArrayObj integertype 40
TokenMap integertype 48
void_ptr integertype 8
--------------------------------------------------
Total number of entries: 14
The last lines of the libnestutil/config.h file are
/* Bit counts for Target members */
#define TARGET_BITS_SPLIT 1
#define TARGET_BITS_SPLIT_STANDARD 0
#define TARGET_BITS_SPLIT_HPC 1
/* Whether to enable detailed NEST internal timers */
/* #undef TIMER_DETAILED */
#endif // #ifndef CONFIG_H
Did you configure NEST with the CMake option -Dtarget-bits-split=hpc? That likely explains the effect. Could you configure and build NEST again without this option and try again?
With hpc, NEST only uses 6 bits to encode up to 64 synapse model IDs, but NEST by default comes with 74 synapse models (because most synapse models come in plain, _lbl and _hpc variants). In the standard configuration, 9 bits are available for up to 512 synapse model IDs. The hpc setting should only be required in extreme cases (>= 2^18 MPI processes or more than 512 threads per process).
We clearly need to handle this situation better, but I'd appreciate your feedback on whether my suggestion fixes the problem first.
You are right! Initially I compiled NEST with -Dtarget-bits-split=hpc
Now I have deactivated this option, compiled and reinstalled NEST. Now it works correctly. I can "import nest" from python and no error appear.
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