Errors from Vecstim()

General issues of interest both for network and
individual cell parallelization.

Moderator: hines

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breakwave922

Errors from Vecstim()

Post by breakwave922 »

Dear all,

I've been stuck by this issue for at least two days. I got the following error message from my network model, when I used VecStim() to drive the synaptic event.

Code: Select all

40.000000 percent is done!
40.000000 percent is done!
40.000000 percent is done!
net_send td-t = -2.91038e-11 SelfEvent target=VecStim[27] 116666 flag=1
net_send td-t = -2.91038e-11 SelfEvent target=VecStim[27] 116666 flag=1
net_send td-t = -2.91038e-11 SelfEvent target=VecStim[27] 116666 flag=1
net_send td-t = -2.91038e-11 SelfEvent target=VecStim[27] 116666 flag=1
net_send td-t = -2.91038e-11 SelfEvent target=VecStim[27] 116666 flag=1
net_send td-t = -2.91038e-11 SelfEvent target=VecStim[27] 116666 flag=1
[d17B-12:03023] *** Process received signal ***
[d17B-12:03023] Signal: Aborted (6)
[d17B-12:03023] Signal code:  (-6)
[d17B-13:20988] *** Process received signal ***
[d17B-13:20988] Signal: Aborted (6)
[d17B-13:20988] Signal code:  (-6)
[d17B-13:20987] *** Process received signal ***
[d17B-13:20987] Signal: Aborted (6)
[d17B-13:20987] Signal code:  (-6)
[d17B-18:09972] *** Process received signal ***
[d17B-18:09972] Signal: Aborted (6)
[d17B-18:09972] Signal code:  (-6)
[d17B-18:09971] *** Process received signal ***
[d17B-18:09971] Signal: Aborted (6)
[d17B-18:09971] Signal code:  (-6)
[d17B-18:09973] *** Process received signal ***
[d17B-18:09973] Signal: Aborted (6)
[d17B-18:09973] Signal code:  (-6)
[d17B-12:03023] [ 0] /lib64/libpthread.so.0 [0x3baee0ebe0]
[d17B-12:03023] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x3bade30265]
[d17B-12:03023] [ 2] /lib64/libc.so.6(abort+0x110) [0x3bade31d10]
[d17B-12:03023] [ 3] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(nrn_net_send+0x10d) [0x2b56003fa3cd]
[d17B-12:03023] [ 4] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(artcell_net_send+0x143) [0x2b56003fc473]
[d17B-12:03023] [ 5] x86_64/.libs/libnrnmech.so [0x2aaab0c029da]
[d17B-12:03023] [ 6] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(_ZN9SelfEvent16call_net_receiveEP8NetCvode+0x33) [0x2b5600400a23]
[d17B-12:03023] [ 7] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(_ZN9SelfEvent7deliverEdP8NetCvodeP9NrnThread+0x12a) [0x2b56004009ba]
[d17B-12:03023] [ 8] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(_ZN8NetCvode13deliver_eventEdP9NrnThread+0x94) [0x2b5600408684]
[d17B-12:03023] [ 9] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(_ZN8NetCvode14deliver_eventsEdP9NrnThread+0x3a) [0x2b56004085ca]
[d17B-12:03023] [10] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(_ZN8NetCvode18deliver_net_eventsEP9NrnThread+0x12a) [0x2b56004084da]
[d17B-12:03023] [11] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(deliver_net_events+0x2e) [0x2b56003f044e]
[d17B-12:03023] [12] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrnoc.so.0 [0x2b5600128109]
[d17B-12:03023] [13] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrnoc.so.0(nrn_multithread_job+0x21a) [0x2b560013a07a]
[d17B-12:03023] [14] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrnoc.so.0(nrn_fixed_step_group+0x226) [0x2b5600128056]
[d17B-12:03023] [15] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(ncs2nrn_integrate+0x161) [0x2b56003fce91]
[d17B-12:03023] [16] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(_ZN3BBS12netpar_solveEd+0xde) [0x2b560043a91e]
[d17B-12:03023] [17] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0 [0x2b560041a05a]
[d17B-12:03023] [18] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrnoc.so.0(call_ob_proc+0x2ec) [0x2b5600142f3c]
[d17B-12:03023] [19] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrnoc.so.0(hoc_object_component+0x6c8) [0x2b5600142928]
[d17B-12:03023] [20] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrnoc.so.0(hoc_execute+0x5b) [0x2b560013c0ab]
[d17B-12:03023] [21] /share/sw/nrn/nrn-7.3/x86_64/lib/liboc.so.0 [0x2b5600910b5c]
[d17B-12:03023] [22] /share/sw/nrn/nrn-7.3/x86_64/lib/liboc.so.0(hoc_main1+0x151) [0x2b56009103b1]
[d17B-12:03023] [23] nrniv(ivocmain+0x612) [0x403c82]
[d17B-12:03023] [24] nrniv(main+0x7c) [0x40360c]
[d17B-12:03023] [25] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3bade1d994]
[d17B-12:03023] [26] nrniv(_ZNSt8ios_base4InitD1Ev+0x39) [0x403389]
[d17B-12:03023] *** End of error message ***
[d17B-13:20988] [ 0] /lib64/libpthread.so.0 [0x3baee0ebe0]
[d17B-13:20988] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x3bade30265]
[d17B-13:20988] [ 2] /lib64/libc.so.6(abort+0x110) [0x3bade31d10]
[d17B-13:20988] [ 3] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(nrn_net_send+0x10d) [0x2b4e6c2ba3cd]
[d17B-13:20988] [ 4] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(artcell_net_send+0x143) [0x2b4e6c2bc473]
[d17B-13:20988] [ 5] x86_64/.libs/libnrnmech.so [0x2aaab0dfd9da]
[d17B-13:20988] [ 6] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(_ZN9SelfEvent16call_net_receiveEP8NetCvode+0x33) [0x2b4e6c2c0a23]
[d17B-13:20988] [ 7] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(_ZN9SelfEvent7deliverEdP8NetCvodeP9NrnThread+0x12a) [0x2b4e6c2c09ba]
[d17B-13:20988] [ 8] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(_ZN8NetCvode13deliver_eventEdP9NrnThread+0x94) [0x2b4e6c2c8684]
[d17B-13:20988] [ 9] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(_ZN8NetCvode14deliver_eventsEdP9NrnThread+0x3a) [0x2b4e6c2c85ca]
[d17B-13:20988] [10] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(_ZN8NetCvode18deliver_net_eventsEP9NrnThread+0x12a) [0x2b4e6c2c84da]
[d17B-13:20987] [ 0] /lib64/libpthread.so.0 [0x3baee0ebe0]
[d17B-13:20987] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x3bade30265]
[d17B-13:20987] [ 2] /lib64/libc.so.6(abort+0x110) [0x3bade31d10]
[d17B-13:20987] [ 3] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(nrn_net_send+0x10d) [0x2af4950983cd]
[d17B-13:20987] [ 4] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(artcell_net_send+0x143) [0x2af49509a473]
[d17B-13:20987] [ 5] x86_64/.libs/libnrnmech.so [0x2aaaaf8c89da]
[d17B-13:20987] [ 6] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(_ZN9SelfEvent16call_net_receiveEP8NetCvode+0x33) [0x2af49509ea23]
[d17B-13:20987] [ 7] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(_ZN9SelfEvent7deliverEdP8NetCvodeP9NrnThread+0x12a) [0x2af49509e9ba]
[d17B-13:20987] [ 8] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(_ZN8NetCvode13deliver_eventEdP9NrnThread+0x94) [0x2af4950a6684]
[d17B-13:20987] [ 9] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(_ZN8NetCvode14deliver_eventsEdP9NrnThread+0x3a) [0x2af4950a65ca]
[d17B-13:20987] [10] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(_ZN8NetCvode18deliver_net_eventsEP9NrnThread+0x12a) [0x2af4950a64da]
[d17B-13:20987] [11] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(deliver_net_events+0x2e) [0x2af49508e44e]
[d17B-13:20987] [12] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrnoc.so.0 [0x2af494dc6109]
[d17B-13:20987] [13] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrnoc.so.0(nrn_multithread_job+0x21a) [0x2af494dd807a]
[d17B-13:20987] [14] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrnoc.so.0(nrn_fixed_step_group+0x226) [0x2af494dc6056]
[d17B-13:20987] [15] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(ncs2nrn_integrate+0x161) [0x2af49509ae91]
[d17B-13:20987] [16] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(_ZN3BBS12netpar_solveEd+0xde) [0x2af4950d891e]
[d17B-13:20987] [17] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0 [0x2af4950b805a]
[d17B-13:20987] [18] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrnoc.so.0(call_ob_proc+0x2ec) [0x2af494de0f3c]
[d17B-13:20987] [19] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrnoc.so.0(hoc_object_component+0x6c8) [0x2af494de0928]
[d17B-13:20987] [20] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrnoc.so.0(hoc_execute+0x5b) [0x2af494dda0ab]
[d17B-13:20987] [21] /share/sw/nrn/nrn-7.3/x86_64/lib/liboc.so.0 [0x2af4955aeb5c]
[d17B-13:20987] [22] /share/sw/nrn/nrn-7.3/x86_64/lib/liboc.so.0(hoc_main1+0x151) [0x2af4955ae3b1]
[d17B-13:20987] [23] nrniv(ivocmain+0x612) [0x403c82]
[d17B-13:20987] [24] nrniv(main+0x7c) [0x40360c]
[d17B-13:20987] [25] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3bade1d994]
[d17B-13:20987] [26] nrniv(_ZNSt8ios_base4InitD1Ev+0x39) [0x403389]
[d17B-13:20987] *** End of error message ***
[d17B-13:20988] [11] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(deliver_net_events+0x2e) [0x2b4e6c2b044e]
[d17B-13:20988] [12] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrnoc.so.0 [0x2b4e6bfe8109]
[d17B-13:20988] [13] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrnoc.so.0(nrn_multithread_job+0x21a) [0x2b4e6bffa07a]
[d17B-13:20988] [14] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrnoc.so.0(nrn_fixed_step_group+0x226) [0x2b4e6bfe8056]
[d17B-13:20988] [15] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(ncs2nrn_integrate+0x161) [0x2b4e6c2bce91]
[d17B-13:20988] [16] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(_ZN3BBS12netpar_solveEd+0xde) [0x2b4e6c2fa91e]
[d17B-13:20988] [17] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0 [0x2b4e6c2da05a]
[d17B-13:20988] [18] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrnoc.so.0(call_ob_proc+0x2ec) [0x2b4e6c002f3c]
[d17B-13:20988] [19] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrnoc.so.0(hoc_object_component+0x6c8) [0x2b4e6c002928]
[d17B-13:20988] [20] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrnoc.so.0(hoc_execute+0x5b) [0x2b4e6bffc0ab]
[d17B-13:20988] [21] /share/sw/nrn/nrn-7.3/x86_64/lib/liboc.so.0 [0x2b4e6c7d0b5c]
[d17B-13:20988] [22] /share/sw/nrn/nrn-7.3/x86_64/lib/liboc.so.0(hoc_main1+0x151) [0x2b4e6c7d03b1]
[d17B-13:20988] [23] nrniv(ivocmain+0x612) [0x403c82]
[d17B-13:20988] [24] nrniv(main+0x7c) [0x40360c]
[d17B-13:20988] [25] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3bade1d994]
[d17B-13:20988] [26] nrniv(_ZNSt8ios_base4InitD1Ev+0x39) [0x403389]
[d17B-13:20988] *** End of error message ***
[d17B-18:09972] [ 0] /lib64/libpthread.so.0 [0x3baee0ebe0]
[d17B-18:09972] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x3bade30265]
[d17B-18:09972] [ 2] /lib64/libc.so.6(abort+0x110) [0x3bade31d10]
[d17B-18:09972] [ 3] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(nrn_net_send+0x10d) [0x2b16ed5063cd]
[d17B-18:09972] [ 4] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(artcell_net_send+0x143) [0x2b16ed508473]
[d17B-18:09972] [ 5] x86_64/.libs/libnrnmech.so [0x2aaaaf8c89da]
[d17B-18:09972] [ 6] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(_ZN9SelfEvent16call_net_receiveEP8NetCvode+0x33) [0x2b16ed50ca23]
[d17B-18:09972] [ 7] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(_ZN9SelfEvent7deliverEdP8NetCvodeP9NrnThread+0x12a) [0x2b16ed50c9ba]
[d17B-18:09972] [ 8] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(_ZN8NetCvode13deliver_eventEdP9NrnThread+0x94) [0x2b16ed514684]
[d17B-18:09972] [ 9] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(_ZN8NetCvode14deliver_eventsEdP9NrnThread+0x3a) [0x2b16ed5145ca]
[d17B-18:09972] [10] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(_ZN8NetCvode18deliver_net_eventsEP9NrnThread+0x12a) [0x2b16ed5144da]
[d17B-18:09972] [11] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(deliver_net_events+0x2e) [0x2b16ed4fc44e]
[d17B-18:09972] [12] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrnoc.so.0 [0x2b16ed234109]
[d17B-18:09972] [13] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrnoc.so.0(nrn_multithread_job+0x21a) [0x2b16ed24607a]
[d17B-18:09972] [14] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrnoc.so.0(nrn_fixed_step_group+0x226) [0x2b16ed234056]
[d17B-18:09972] [15] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(ncs2nrn_integrate+0x161) [0x2b16ed508e91]
[d17B-18:09972] [16] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(_ZN3BBS12netpar_solveEd+0xde) [0x2b16ed54691e]
[d17B-18:09972] [17] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0 [0x2b16ed52605a]
[d17B-18:09972] [18] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrnoc.so.0(call_ob_proc+0x2ec) [0x2b16ed24ef3c]
[d17B-18:09972] [19] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrnoc.so.0(hoc_object_component+0x6c8) [0x2b16ed24e928]
[d17B-18:09972] [20] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrnoc.so.0(hoc_execute+0x5b) [0x2b16ed2480ab]
[d17B-18:09972] [21] /share/sw/nrn/nrn-7.3/x86_64/lib/liboc.so.0 [0x2b16eda1cb5c]
[d17B-18:09972] [22] /share/sw/nrn/nrn-7.3/x86_64/lib/liboc.so.0(hoc_main1+0x151) [0x2b16eda1c3b1]
[d17B-18:09972] [23] nrniv(ivocmain+0x612) [0x403c82]
[d17B-18:09972] [24] nrniv(main+0x7c) [0x40360c]
[d17B-18:09972] [25] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3bade1d994]
[d17B-18:09972] [26] nrniv(_ZNSt8ios_base4InitD1Ev+0x39) [0x403389]
[d17B-18:09972] *** End of error message ***
[d17B-18:09971] [ 0] /lib64/libpthread.so.0 [0x3baee0ebe0]
[d17B-18:09971] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x3bade30265]
[d17B-18:09971] [ 2] /lib64/libc.so.6(abort+0x110) [0x3bade31d10]
[d17B-18:09971] [ 3] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(nrn_net_send+0x10d) [0x2b8958bcc3cd]
[d17B-18:09971] [ 4] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(artcell_net_send+0x143) [0x2b8958bce473]
[d17B-18:09971] [ 5] x86_64/.libs/libnrnmech.so [0x2aaaafa459da]
[d17B-18:09971] [ 6] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(_ZN9SelfEvent16call_net_receiveEP8NetCvode+0x33) [0x2b8958bd2a23]
[d17B-18:09971] [ 7] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(_ZN9SelfEvent7deliverEdP8NetCvodeP9NrnThread+0x12a) [0x2b8958bd29ba]
[d17B-18:09971] [ 8] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(_ZN8NetCvode13deliver_eventEdP9NrnThread+0x94) [0x2b8958bda684]
[d17B-18:09971] [ 9] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(_ZN8NetCvode14deliver_eventsEdP9NrnThread+0x3a) [0x2b8958bda5ca]
[d17B-18:09971] [10] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(_ZN8NetCvode18deliver_net_eventsEP9NrnThread+0x12a) [0x2b8958bda4da]
[d17B-18:09971] [11] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(deliver_net_events+0x2e) [0x2b8958bc244e]
[d17B-18:09971] [12] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrnoc.so.0 [0x2b89588fa109]
[d17B-18:09971] [13] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrnoc.so.0(nrn_multithread_job+0x21a) [0x2b895890c07a]
[d17B-18:09971] [14] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrnoc.so.0(nrn_fixed_step_group+0x226) [0x2b89588fa056]
[d17B-18:09971] [15] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(ncs2nrn_integrate+0x161) [0x2b8958bcee91]
[d17B-18:09971] [16] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(_ZN3BBS12netpar_solveEd+0xde) [0x2b8958c0c91e]
[d17B-18:09971] [17] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0 [0x2b8958bec05a]
[d17B-18:09971] [18] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrnoc.so.0(call_ob_proc+0x2ec) [0x2b8958914f3c]
[d17B-18:09971] [19] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrnoc.so.0(hoc_object_component+0x6c8) [0x2b8958914928]
[d17B-18:09971] [20] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrnoc.so.0(hoc_execute+0x5b) [0x2b895890e0ab]
[d17B-18:09971] [21] /share/sw/nrn/nrn-7.3/x86_64/lib/liboc.so.0 [0x2b89590e2b5c]
[d17B-18:09971] [22] /share/sw/nrn/nrn-7.3/x86_64/lib/liboc.so.0(hoc_main1+0x151) [0x2b89590e23b1]
[d17B-18:09971] [23] nrniv(ivocmain+0x612) [0x403c82]
[d17B-18:09971] [24] nrniv(main+0x7c) [0x40360c]
[d17B-18:09971] [25] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3bade1d994]
[d17B-18:09971] [26] nrniv(_ZNSt8ios_base4InitD1Ev+0x39) [0x403389]
[d17B-18:09971] *** End of error message ***
[d17B-18:09973] [ 0] /lib64/libpthread.so.0 [0x3baee0ebe0]
[d17B-18:09973] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x3bade30265]
[d17B-18:09973] [ 2] /lib64/libc.so.6(abort+0x110) [0x3bade31d10]
[d17B-18:09973] [ 3] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(nrn_net_send+0x10d) [0x2b95293293cd]
[d17B-18:09973] [ 4] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(artcell_net_send+0x143) [0x2b952932b473]
[d17B-18:09973] [ 5] x86_64/.libs/libnrnmech.so [0x2aaab0c569da]
[d17B-18:09973] [ 6] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(_ZN9SelfEvent16call_net_receiveEP8NetCvode+0x33) [0x2b952932fa23]
[d17B-18:09973] [ 7] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(_ZN9SelfEvent7deliverEdP8NetCvodeP9NrnThread+0x12a) [0x2b952932f9ba]
[d17B-18:09973] [ 8] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(_ZN8NetCvode13deliver_eventEdP9NrnThread+0x94) [0x2b9529337684]
[d17B-18:09973] [ 9] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(_ZN8NetCvode14deliver_eventsEdP9NrnThread+0x3a) [0x2b95293375ca]
[d17B-18:09973] [10] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(_ZN8NetCvode18deliver_net_eventsEP9NrnThread+0x12a) [0x2b95293374da]
[d17B-18:09973] [11] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(deliver_net_events+0x2e) [0x2b952931f44e]
[d17B-18:09973] [12] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrnoc.so.0 [0x2b9529057109]
[d17B-18:09973] [13] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrnoc.so.0(nrn_multithread_job+0x21a) [0x2b952906907a]
[d17B-18:09973] [14] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrnoc.so.0(nrn_fixed_step_group+0x226) [0x2b9529057056]
[d17B-18:09973] [15] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(ncs2nrn_integrate+0x161) [0x2b952932be91]
[d17B-18:09973] [16] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0(_ZN3BBS12netpar_solveEd+0xde) [0x2b952936991e]
[d17B-18:09973] [17] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrniv.so.0 [0x2b952934905a]
[d17B-18:09973] [18] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrnoc.so.0(call_ob_proc+0x2ec) [0x2b9529071f3c]
[d17B-18:09973] [19] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrnoc.so.0(hoc_object_component+0x6c8) [0x2b9529071928]
[d17B-18:09973] [20] /share/sw/nrn/nrn-7.3/x86_64/lib/libnrnoc.so.0(hoc_execute+0x5b) [0x2b952906b0ab]
[d17B-18:09973] [21] /share/sw/nrn/nrn-7.3/x86_64/lib/liboc.so.0 [0x2b952983fb5c]
[d17B-18:09973] [22] /share/sw/nrn/nrn-7.3/x86_64/lib/liboc.so.0(hoc_main1+0x151) [0x2b952983f3b1]
[d17B-18:09973] [23] nrniv(ivocmain+0x612) [0x403c82]
[d17B-18:09973] [24] nrniv(main+0x7c) [0x40360c]
[d17B-18:09973] [25] /lib64/libc.so.6(__libc_start_main+0xf4) [0x3bade1d994]
[d17B-18:09973] [26] nrniv(_ZNSt8ios_base4InitD1Ev+0x39) [0x403389]
[d17B-18:09973] *** End of error message ***

Let me first describe my network model a little first. I have around 300 cells, and some of them was driven by the synaptic events, with event times were scripted in the .txt files. For those cells, I created a synapse first, and then used VecStim() to drive the synaptic events through the synapses. The event times in each text file were randomly generated by Matlab, and sorted in sequences. The network usually works. Because I need to change the time information sometimes, there is always possibilities that the network model didn't work with specific groups of event times and showed the above errors. Initially I suspected my generated event times file had some error inside, like negative times, but then I ruled my doubts out.

I was referred to the thread http://www.neuron.yale.edu/phpbb/viewto ... f=2&t=2147, but it didn't solve my problem. I don't know whether this is because of my paralleled code or not. So I post my question here.

Thanks in advance.
ted
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Re: Errors from Vecstim()

Post by ted »

First, an important question: does your program execute properly when executed serially, that is, on a single processor and not under mpiexec?
breakwave922

Re: Errors from Vecstim()

Post by breakwave922 »

ted wrote:First, an important question: does your program execute properly when executed serially, that is, on a single processor and not under mpiexec?
Hi, Ted,
Thanks for you time and reply. Yes, my program is under mpiexec. I didn't try the program on a single processor. One reason is, the program works fine for several sets of input event-time txt files, only for some input files, it fails. Another reason is, if the event-txt files doesn't work, doesn't mean it's not working immediately once the simulation started, but instead, it's showing the errors at around 40% of whole simulation. If I run it on a single processor, it'll take a very long time to run.
I can send you the code for more discussing and check.
Thanks.
ted
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Re: Errors from Vecstim()

Post by ted »

If I run it on a single processor, it'll take a very long time to run.
It'll run just as slow on a serial processor if I do it.

By the way, do you have a serial implementation of your program, and do you know if it can handle the same data that gags your parallel implementation? And if you feed it data that doesn't gag your parallel implementation, do the two versions of your program produce the same results?
breakwave922

Re: Errors from Vecstim()

Post by breakwave922 »

Hi, Ted,

I don't have the serial implementation of the program. But I will try to run it on single processor to see how it works.
ted
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Re: Errors from Vecstim()

Post by ted »

breakwave922 wrote:I don't have the serial implementation of the program.
Does one exist, and is it known to produce the same results as the parallel implementation does (when fed a data set that doesn't break the parallel implementation, that is).
breakwave922

Re: Errors from Vecstim()

Post by breakwave922 »

ted wrote:
breakwave922 wrote:I don't have the serial implementation of the program.
Does one exist, and is it known to produce the same results as the parallel implementation does (when fed a data set that doesn't break the parallel implementation, that is).
Hi, Ted,

I just tried on one processor, with the same data set that gags the parallel implementation, unfortunately, it's still showing the same error(shown below). So maybe this is not caused by the paralleled codes, but only because of the inappropriate way of using VecStim()?

Code: Select all

net_send td-t = -1.45519e-11 SelfEvent target=VecStim[14] 62858.7 flag=1
ted
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Re: Errors from Vecstim()

Post by ted »

breakwave922 wrote:I just tried on one processor, with the same data set that gags the parallel implementation, unfortunately, it's still showing the same error(shown below). So maybe this is not caused by the paralleled codes, but only because of the inappropriate way of using VecStim()
Or maybe you found a bug in NEURON's event delivery system. Can you look on your PC or Mac or whatever in
nrn/share/examples/nrniv/netcon
for these three files
vecevent.hoc
vecevent.mod
vecevent.ses
If you find them, copy them into a new empty directory, compile vecevent.mod, and use NEURON to launch vecevent.hoc
Click on the RunControl panel's Init & Run button and tell me if the "SpikePlot" window shows a spike raster, or if you get an error message.

Also please tell me what version of NEURON you're running (first line printed by the hoc interpreter when NEURON starts).

And hope that tomorrow's blizzard in Connecticut doesn't knock out my power and internet access, so I can read what you found out.
breakwave922

Re: Errors from Vecstim()

Post by breakwave922 »

Hi, Ted,

I run the simulation by using our university's multi-core compute servers, not running on my office PC, so I'm a little confused by what to check. I checked my office PC, in nrn/share/examples/nrniv/netcon, and it didn't give me error information and showed a spike raster in Spikeplot. But this doesn't mean anything, right? Because I didn't use those files in my simulation. BTW, the vecevent.mod file that I use in simulation is updated following this link http://www.neuron.yale.edu/phpbb/viewto ... f=2&t=2147,so it's different than in nrn/share/examples/nrniv/netcon. Do I need to check if I replace it in my simulation with the old one, what will happen?
All the Neuron version that I use is Neuron7.3.
Thanks for you time. Wish you all well in those winter storm days.
breakwave922

Re: Errors from Vecstim()

Post by breakwave922 »

Hi, Ted,

I just tried the old version of vecevent.mod, it gave me the same error when 21% of the simulation is done.
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