26 Feb
2023
26 Feb
'23
3:23 p.m.
Hello,
For the following code, I receive a coredump (it throws and assertion from grid_layer.h)
(output at the end). When not connecting 'input' to 'layer_1', everything
works fine. It looks like it does not like to connect a layer to more than one target
layer.
Thanks a lot in advance!
import nest
pos = nest.spatial.grid(shape = [3,3] )
input = nest.Create('iaf_psc_alpha', positions=pos)
layer_0 = nest.Create('iaf_psc_alpha', positions=pos)
layer_1 = nest.Create('iaf_psc_alpha', positions=pos)
conn_neur = {'rule':'pairwise_bernoulli', 'use_on_source': True,
'mask': {'grid':{'shape':[3,3]}} }
nest.Connect(input, layer_0, conn_neur)
nest.Connect(input, layer_1, conn_neur)
nest.DumpLayerConnections(input, layer_0, 'static_synapse', 'conn.txt')
The output message is:
python3: /home/neurobit/src/nest_3.3_src/nestkernel/grid_layer.h:223:
nest::Position<D> nest::GridLayer<D>::lid_to_position(nest::index) const [with
int D = 2; nest::index = long unsigned int]: Assertion `lid < dims_[ 0 ]' failed.
[dcccluster:326996] *** Process received signal ***
[dcccluster:326996] Signal: Aborted (6)
[dcccluster:326996] Signal code: (-6)
[dcccluster:326996] [ 0] /lib64/libpthread.so.0(+0x12c20)[0x7fb317ec0c20]
[dcccluster:326996] [ 1] /lib64/libc.so.6(gsignal+0x10f)[0x7fb31739637f]
[dcccluster:326996] [ 2] /lib64/libc.so.6(abort+0x127)[0x7fb317380db5]
[dcccluster:326996] [ 3] /lib64/libc.so.6(+0x21c89)[0x7fb317380c89]
[dcccluster:326996] [ 4] /lib64/libc.so.6(+0x2fa76)[0x7fb31738ea76]
[dcccluster:326996] [ 5]
/home/neurobit/local/nest_3.3/lib64/python3.8/site-packages/nest/../../../nest/libnestkernel.so(+0x1d7783)[0x7fb2fcbf7783]
[dcccluster:326996] [ 6]
/home/neurobit/local/nest_3.3/lib64/python3.8/site-packages/nest/../../../nest/libnestkernel.so(_ZNK4nest9GridLayerILi2EE12get_positionEm+0xa)[0x7fb2fcbf779a]
[dcccluster:326996] [ 7]
/home/neurobit/local/nest_3.3/lib64/python3.8/site-packages/nest/../../../nest/libnestkernel.so(_ZN4nest5LayerILi2EE16dump_connectionsERSoSt10shared_ptrINS_14NodeCollectionEES3_INS_13AbstractLayerEERK5Token+0x525)[0x7fb2fcbfca75]
[dcccluster:326996] [ 8]
/home/neurobit/local/nest_3.3/lib64/python3.8/site-packages/nest/../../../nest/libnestkernel.so(_ZN4nest22dump_layer_connectionsERK5TokenSt10shared_ptrINS_14NodeCollectionEES5_R12lockPTRDatumISoXadL_ZN14SLIInterpreter11OstreamtypeEEEE+0x35c)[0x7fb2fcc1530c]
[dcccluster:326996] [ 9]
/home/neurobit/local/nest_3.3/lib64/python3.8/site-packages/nest/../../../nest/libnestkernel.so(_ZNK4nest10NestModule37DumpLayerConnections_os_g_g_lFunction7executeEP14SLIInterpreter+0xfc)[0x7fb2fcb491dc]
[dcccluster:326996] [10]
/home/neurobit/local/nest_3.3/lib64/python3.8/site-packages/nest/../../../nest/libsli.so(_ZN13FunctionDatum7executeEP14SLIInterpreter+0x2b)[0x7fb2f7c0975b]
[dcccluster:326996] [11]
/home/neurobit/local/nest_3.3/lib64/python3.8/site-packages/nest/../../../nest/libsli.so(_ZN14SLIInterpreter8execute_Em+0x1b2)[0x7fb2f7c06b32]
[dcccluster:326996] [12]
/home/neurobit/local/nest_3.3/lib64/python3.8/site-packages/nest/../../../nest/libsli.so(_ZN14SLIInterpreter7executeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x1ea)[0x7fb2f7c06e7a]
[dcccluster:326996] [13]
/home/neurobit/local/nest_3.3/lib64/python3.8/site-packages/nest/pynestkernel.so(+0x38669)[0x7fb2ff200669]
[dcccluster:326996] [14] /lib64/libpython3.8.so.1.0(+0x173db8)[0x7fb31846adb8]
[dcccluster:326996] [15]
/lib64/libpython3.8.so.1.0(_PyEval_EvalFrameDefault+0x976)[0x7fb3184d8406]
[dcccluster:326996] [16]
/lib64/libpython3.8.so.1.0(_PyFunction_Vectorcall+0x1bf)[0x7fb3184967af]
[dcccluster:326996] [17]
/lib64/libpython3.8.so.1.0(_PyEval_EvalFrameDefault+0x5da)[0x7fb3184d806a]
[dcccluster:326996] [18]
/lib64/libpython3.8.so.1.0(_PyEval_EvalCodeWithName+0x3e7)[0x7fb3184953c7]
[dcccluster:326996] [19]
/lib64/libpython3.8.so.1.0(_PyFunction_Vectorcall+0x422)[0x7fb318496a12]
[dcccluster:326996] [20]
/lib64/libpython3.8.so.1.0(_PyEval_EvalFrameDefault+0x5da)[0x7fb3184d806a]
[dcccluster:326996] [21]
/lib64/libpython3.8.so.1.0(_PyFunction_Vectorcall+0x1bf)[0x7fb3184967af]
[dcccluster:326996] [22]
/lib64/libpython3.8.so.1.0(_PyEval_EvalFrameDefault+0x54d9)[0x7fb3184dcf69]
[dcccluster:326996] [23]
/lib64/libpython3.8.so.1.0(_PyEval_EvalCodeWithName+0x3e7)[0x7fb3184953c7]
[dcccluster:326996] [24] /lib64/libpython3.8.so.1.0(PyEval_EvalCode+0x23)[0x7fb3184965a3]
[dcccluster:326996] [25] /lib64/libpython3.8.so.1.0(+0x22b09a)[0x7fb31852209a]
[dcccluster:326996] [26] /lib64/libpython3.8.so.1.0(+0x250fa2)[0x7fb318547fa2]
[dcccluster:326996] [27] /lib64/libpython3.8.so.1.0(+0x10312c)[0x7fb3183fa12c]
[dcccluster:326996] [28]
/lib64/libpython3.8.so.1.0(PyRun_SimpleFileExFlags+0x369)[0x7fb318400fe3]
[dcccluster:326996] [29] /lib64/libpython3.8.so.1.0(Py_RunMain+0x2ef)[0x7fb318549b6f]
[dcccluster:326996] *** End of error message ***
1 Mar
1 Mar
9:48 a.m.
Hi Xavier,
The code runs fine for me with NEST 3.3, and I have not been able to reproduce the error.
Could you provide some more details about the environment you use? For example, is NEST
installed from a pre-built package or from source? With or without MPI? Which OS / system?
Etc.
Best,
Nicolai
________________________________
From: Xavier Otazu <xotazu(a)cvc.uab.cat>
Sent: 26 February 2023 19:23
To: users(a)nest-simulator.org <users(a)nest-simulator.org>
Subject: [NEST Users] Coredump with DumpLayerConnections
[Some people who received this message don't often get email from xotazu(a)cvc.uab.cat.
Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ]
Hello,
For the following code, I receive a coredump (it throws and assertion from grid_layer.h)
(output at the end). When not connecting 'input' to 'layer_1', everything
works fine. It looks like it does not like to connect a layer to more than one target
layer.
Thanks a lot in advance!
import nest
pos = nest.spatial.grid(shape = [3,3] )
input = nest.Create('iaf_psc_alpha', positions=pos)
layer_0 = nest.Create('iaf_psc_alpha', positions=pos)
layer_1 = nest.Create('iaf_psc_alpha', positions=pos)
conn_neur = {'rule':'pairwise_bernoulli', 'use_on_source': True,
'mask': {'grid':{'shape':[3,3]}} }
nest.Connect(input, layer_0, conn_neur)
nest.Connect(input, layer_1, conn_neur)
nest.DumpLayerConnections(input, layer_0, 'static_synapse', 'conn.txt')
The output message is:
python3: /home/neurobit/src/nest_3.3_src/nestkernel/grid_layer.h:223:
nest::Position<D> nest::GridLayer<D>::lid_to_position(nest::index) const [with
int D = 2; nest::index = long unsigned int]: Assertion `lid < dims_[ 0 ]' failed.
[dcccluster:326996] *** Process received signal ***
[dcccluster:326996] Signal: Aborted (6)
[dcccluster:326996] Signal code: (-6)
[dcccluster:326996] [ 0] /lib64/libpthread.so.0(+0x12c20)[0x7fb317ec0c20]
[dcccluster:326996] [ 1] /lib64/libc.so.6(gsignal+0x10f)[0x7fb31739637f]
[dcccluster:326996] [ 2] /lib64/libc.so.6(abort+0x127)[0x7fb317380db5]
[dcccluster:326996] [ 3] /lib64/libc.so.6(+0x21c89)[0x7fb317380c89]
[dcccluster:326996] [ 4] /lib64/libc.so.6(+0x2fa76)[0x7fb31738ea76]
[dcccluster:326996] [ 5]
/home/neurobit/local/nest_3.3/lib64/python3.8/site-packages/nest/../../../nest/libnestkernel.so(+0x1d7783)[0x7fb2fcbf7783]
[dcccluster:326996] [ 6]
/home/neurobit/local/nest_3.3/lib64/python3.8/site-packages/nest/../../../nest/libnestkernel.so(_ZNK4nest9GridLayerILi2EE12get_positionEm+0xa)[0x7fb2fcbf779a]
[dcccluster:326996] [ 7]
/home/neurobit/local/nest_3.3/lib64/python3.8/site-packages/nest/../../../nest/libnestkernel.so(_ZN4nest5LayerILi2EE16dump_connectionsERSoSt10shared_ptrINS_14NodeCollectionEES3_INS_13AbstractLayerEERK5Token+0x525)[0x7fb2fcbfca75]
[dcccluster:326996] [ 8]
/home/neurobit/local/nest_3.3/lib64/python3.8/site-packages/nest/../../../nest/libnestkernel.so(_ZN4nest22dump_layer_connectionsERK5TokenSt10shared_ptrINS_14NodeCollectionEES5_R12lockPTRDatumISoXadL_ZN14SLIInterpreter11OstreamtypeEEEE+0x35c)[0x7fb2fcc1530c]
[dcccluster:326996] [ 9]
/home/neurobit/local/nest_3.3/lib64/python3.8/site-packages/nest/../../../nest/libnestkernel.so(_ZNK4nest10NestModule37DumpLayerConnections_os_g_g_lFunction7executeEP14SLIInterpreter+0xfc)[0x7fb2fcb491dc]
[dcccluster:326996] [10]
/home/neurobit/local/nest_3.3/lib64/python3.8/site-packages/nest/../../../nest/libsli.so(_ZN13FunctionDatum7executeEP14SLIInterpreter+0x2b)[0x7fb2f7c0975b]
[dcccluster:326996] [11]
/home/neurobit/local/nest_3.3/lib64/python3.8/site-packages/nest/../../../nest/libsli.so(_ZN14SLIInterpreter8execute_Em+0x1b2)[0x7fb2f7c06b32]
[dcccluster:326996] [12]
/home/neurobit/local/nest_3.3/lib64/python3.8/site-packages/nest/../../../nest/libsli.so(_ZN14SLIInterpreter7executeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x1ea)[0x7fb2f7c06e7a]
[dcccluster:326996] [13]
/home/neurobit/local/nest_3.3/lib64/python3.8/site-packages/nest/pynestkernel.so(+0x38669)[0x7fb2ff200669]
[dcccluster:326996] [14] /lib64/libpython3.8.so.1.0(+0x173db8)[0x7fb31846adb8]
[dcccluster:326996] [15]
/lib64/libpython3.8.so.1.0(_PyEval_EvalFrameDefault+0x976)[0x7fb3184d8406]
[dcccluster:326996] [16]
/lib64/libpython3.8.so.1.0(_PyFunction_Vectorcall+0x1bf)[0x7fb3184967af]
[dcccluster:326996] [17]
/lib64/libpython3.8.so.1.0(_PyEval_EvalFrameDefault+0x5da)[0x7fb3184d806a]
[dcccluster:326996] [18]
/lib64/libpython3.8.so.1.0(_PyEval_EvalCodeWithName+0x3e7)[0x7fb3184953c7]
[dcccluster:326996] [19]
/lib64/libpython3.8.so.1.0(_PyFunction_Vectorcall+0x422)[0x7fb318496a12]
[dcccluster:326996] [20]
/lib64/libpython3.8.so.1.0(_PyEval_EvalFrameDefault+0x5da)[0x7fb3184d806a]
[dcccluster:326996] [21]
/lib64/libpython3.8.so.1.0(_PyFunction_Vectorcall+0x1bf)[0x7fb3184967af]
[dcccluster:326996] [22]
/lib64/libpython3.8.so.1.0(_PyEval_EvalFrameDefault+0x54d9)[0x7fb3184dcf69]
[dcccluster:326996] [23]
/lib64/libpython3.8.so.1.0(_PyEval_EvalCodeWithName+0x3e7)[0x7fb3184953c7]
[dcccluster:326996] [24] /lib64/libpython3.8.so.1.0(PyEval_EvalCode+0x23)[0x7fb3184965a3]
[dcccluster:326996] [25] /lib64/libpython3.8.so.1.0(+0x22b09a)[0x7fb31852209a]
[dcccluster:326996] [26] /lib64/libpython3.8.so.1.0(+0x250fa2)[0x7fb318547fa2]
[dcccluster:326996] [27] /lib64/libpython3.8.so.1.0(+0x10312c)[0x7fb3183fa12c]
[dcccluster:326996] [28]
/lib64/libpython3.8.so.1.0(PyRun_SimpleFileExFlags+0x369)[0x7fb318400fe3]
[dcccluster:326996] [29] /lib64/libpython3.8.so.1.0(Py_RunMain+0x2ef)[0x7fb318549b6f]
[dcccluster:326996] *** End of error message ***
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2 Mar
2 Mar
8:07 a.m.
Nicolay,
I avoid the problem by copying the synapse model to a new one. That is, the following code
works fine for me. It is a bit convoluted to perform a copy and a rename for every
connection.
Thanks a lot in advance!
Xavier
-----
import nest
pos = nest.spatial.grid(shape = [3,3] )
input = nest.Create('iaf_psc_alpha', positions=pos)
layer_0 = nest.Create('iaf_psc_alpha', positions=pos)
layer_1 = nest.Create('iaf_psc_alpha', positions=pos)
conn_neur = {'rule':'pairwise_bernoulli', 'use_on_source': True,
'mask': {'grid':{'shape':[3,3]}} }
nest.CopyModel('static_synapse', 'syn_1_model')
syn_0 = {'synapse_model': 'static_synapse'}
syn_1 = {'synapse_model': 'syn_1_model'}
nest.Connect(input, layer_0, conn_neur, syn_0)
nest.Connect(input, layer_1, conn_neur, syn_1)
nest.DumpLayerConnections(input, layer_0, 'static_synapse', 'conn.txt')
nest.DumpLayerConnections(input, layer_1, 'syn_1_model', 'conn.txt')
7 Mar
7 Mar
12:39 p.m.
Hi Xavier,
Thanks for the update, and it is great that you found a temporary workaround. I have been
able to reproduce the bug but not locate it yet. I have created an issue for the bug here:
https://github.com/nest/nest-simulator/issues/2629
Best,
Nicolai
________________________________
From: Xavier Otazu <xotazu(a)cvc.uab.cat>
Sent: 02 March 2023 12:07
To: users(a)nest-simulator.org <users(a)nest-simulator.org>
Subject: [NEST Users] Re: Coredump with DumpLayerConnections
[You don't often get email from xotazu(a)cvc.uab.cat. Learn why this is important at
https://aka.ms/LearnAboutSenderIdentification ]
Nicolay,
I avoid the problem by copying the synapse model to a new one. That is, the following code
works fine for me. It is a bit convoluted to perform a copy and a rename for every
connection.
Thanks a lot in advance!
Xavier
-----
import nest
pos = nest.spatial.grid(shape = [3,3] )
input = nest.Create('iaf_psc_alpha', positions=pos)
layer_0 = nest.Create('iaf_psc_alpha', positions=pos)
layer_1 = nest.Create('iaf_psc_alpha', positions=pos)
conn_neur = {'rule':'pairwise_bernoulli', 'use_on_source': True,
'mask': {'grid':{'shape':[3,3]}} }
nest.CopyModel('static_synapse', 'syn_1_model')
syn_0 = {'synapse_model': 'static_synapse'}
syn_1 = {'synapse_model': 'syn_1_model'}
nest.Connect(input, layer_0, conn_neur, syn_0)
nest.Connect(input, layer_1, conn_neur, syn_1)
nest.DumpLayerConnections(input, layer_0, 'static_synapse', 'conn.txt')
nest.DumpLayerConnections(input, layer_1, 'syn_1_model', 'conn.txt')
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13 Mar
13 Mar
7:06 a.m.
Hi Nicolay,
I've read on the github issue that it works for you in NEST 3.3 and Python 3.9 ... it
is curious, because it fails for me (I am using Python 3.8). Anyway, I'll wait for the
corrected 3.4 version :-)
Best,
Xavier
1 Mar
1 Mar
11:49 a.m.
Hello Nicolai,
It was compiled with MPI (music and sionlib) from source. My python is 3.8.12
Xavier.
426
days inactive
441
days old
5 comments
2 participants
participants (2)
-
Nicolai Haug -
Xavier Otazu