6 May
2020
6 May
'20
2:11 a.m.
Dear Nest Community,
Would anyone have insight into why I'm getting an UnknownModelName error?
I'm new to Nest and am using Nest 18.0 on Lubuntu Virtual Box (Windows 10
OS).
Thanks for any help.
Best Regards,
--Allen
**** Error Message--additional details attached ******
raise exceptionCls(commandname, message)
nest.ll_api.UnknownModelName: ('UnknownModelName in CopyModel_l_l_D:
/stdp_izh_bitwise_correct_connection is not a known model name. Please
check the modeldict for a list of available models.', 'UnknownModelName',
<SLILiteral: CopyModel_l_l_D>, ': /stdp_izh_bitwise_correct_connection is
not a known model name. Please check the modeldict for a list of available
models.')
********************************************************
6 May
6 May
8:33 a.m.
Hi Allen,
Several steps are required to add a model to NEST. The recommended way of adding a model
is to create your own NEST module outside the NEST source code tree. You will find an
example in examples/MyModule and more documentation at
https://nest.github.io/nest-simulator/extension_modules.
Placing code for custom models in the models directory in the NEST source code tree also
works, but makes it more difficult to move to newer versions of NEST or to share your
custom models with colleagues.
Briefly, in addition to adding the source code files to the models directory, you need to
1. add the files to models/CMakeLists.txt
2. #include the files in models/modelsmodule.cpp
3. add a line like
register_connection_model< StaticConnection >( "static_synapse" );
for each model. The template parameter is the model class, the string the name it will
have in NEST
4. recompile and reinstall NEST
Best,
Hans Ekkehard
On 6 May 2020, at 02:11, Allen Rabayda
<arabayda@masonlive.gmu.edu<mailto:arabayda@masonlive.gmu.edu>> wrote:
Dear Nest Community,
Would anyone have insight into why I'm getting an UnknownModelName error?
I'm new to Nest and am using Nest 18.0 on Lubuntu Virtual Box (Windows 10 OS).
Thanks for any help.
Best Regards,
--Allen
**** Error Message--additional details attached ******
raise exceptionCls(commandname, message)
nest.ll_api.UnknownModelName: ('UnknownModelName in CopyModel_l_l_D:
/stdp_izh_bitwise_correct_connection is not a known model name. Please check the modeldict
for a list of available models.', 'UnknownModelName', <SLILiteral:
CopyModel_l_l_D>, ': /stdp_izh_bitwise_correct_connection is not a known model
name. Please check the modeldict for a list of available models.')
********************************************************
<issue_UnknownModelName_4_May_2020>_______________________________________________
NEST Users mailing list --
users@nest-simulator.org<mailto:users@nest-simulator.org>
To unsubscribe send an email to
users-leave@nest-simulator.org<mailto:users-leave@nest-simulator.org>
--
Prof. Dr. Hans Ekkehard Plesser
Head, Data Science Section
Faculty of Science and Technology
Norwegian University of Life Sciences
PO Box 5003, 1432 Aas, Norway
Phone +47 6723 1560
Email hans.ekkehard.plesser(a)nmbu.no
Home http://arken.nmbu.no/~plesser
10:32 a.m.
Hi,
I just want to take the chance to advertise NESTML, a domain-specific language that you
can use to write custom neuron models for NEST in an easy syntax (without writing any C++
at all).
For more information, I will pass you the "sneak preview" link to the new NESTML
documentation: https://nestml-api-documentation.readthedocs.io/
If you decide to do your neuron modelling via NESTML, I would be happy to give you
additional pointers, on- or off-list.
With kind regards,
Charl
On Wed, May 6, 2020, at 08:33, Hans Ekkehard Plesser wrote:
Hi Allen,
Several steps are required to add a model to NEST. The recommended way of adding a model
is to create your own NEST module outside the NEST source code tree. You will find an
example in examples/MyModule and more documentation at
https://nest.github.io/nest-simulator/extension_modules.
Placing code for custom models in the models directory in the NEST source code tree also
works, but makes it more difficult to move to newer versions of NEST or to share your
custom models with colleagues.
Briefly, in addition to adding the source code files to the models directory, you need
to
1. add the files to models/CMakeLists.txt
2. #include the files in models/modelsmodule.cpp
3. add a line like
register_connection_model< StaticConnection >( "static_synapse" );
for each model. The template parameter is the model class, the string the name it will
have in NEST
4. recompile and reinstall NEST
Best,
Hans Ekkehard
On 6 May 2020, at 02:11, Allen Rabayda
<arabayda(a)masonlive.gmu.edu> wrote:
Dear Nest Community,
Would anyone have insight into why I'm getting an UnknownModelName error?
I'm new to Nest and am using Nest 18.0 on Lubuntu Virtual Box (Windows 10 OS).
Thanks for any help.
Best Regards,
--Allen
**** Error Message--additional details attached ******
raise exceptionCls(commandname, message)
nest.ll_api.UnknownModelName: ('UnknownModelName in CopyModel_l_l_D:
/stdp_izh_bitwise_correct_connection is not a known model name. Please check the modeldict
for a list of available models.', 'UnknownModelName', <SLILiteral:
CopyModel_l_l_D>, ': /stdp_izh_bitwise_correct_connection is not a known model
name. Please check the modeldict for a list of available models.')
********************************************************
<issue_UnknownModelName_4_May_2020>_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
--
Prof. Dr. Hans Ekkehard Plesser
Head, Data Science Section
Faculty of Science and Technology
Norwegian University of Life Sciences
PO Box 5003, 1432 Aas, Norway
Phone +47 6723 1560
Email hans.ekkehard.plesser(a)nmbu.no
Home http://arken.nmbu.no/~plesser
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
10:36 a.m.
Charl,
Is it like a .mod file in NEURON?
Thanks,
Itaru.
On Wed, May 6, 2020 at 5:32 PM Charl Linssen <nest-users(a)turingbirds.com> wrote:
>
> Hi,
>
> I just want to take the chance to advertise NESTML, a domain-specific language that
you can use to write custom neuron models for NEST in an easy syntax (without writing any
C++ at all).
>
> For more information, I will pass you the "sneak preview" link to the new
NESTML documentation: https://nestml-api-documentation.readthedocs.io/
>
> If you decide to do your neuron modelling via NESTML, I would be happy to give you
additional pointers, on- or off-list.
>
> With kind regards,
> Charl
>
>
> On Wed, May 6, 2020, at 08:33, Hans Ekkehard Plesser wrote:
>
>
> Hi Allen,
>
> Several steps are required to add a model to NEST. The recommended way of adding a
model is to create your own NEST module outside the NEST source code tree. You will find
an example in examples/MyModule and more documentation at
https://nest.github.io/nest-simulator/extension_modules.
>
> Placing code for custom models in the models directory in the NEST source code tree
also works, but makes it more difficult to move to newer versions of NEST or to share your
custom models with colleagues.
>
> Briefly, in addition to adding the source code files to the models directory, you
need to
>
> 1. add the files to models/CMakeLists.txt
> 2. #include the files in models/modelsmodule.cpp
> 3. add a line like
>
> register_connection_model< StaticConnection >( "static_synapse" );
>
> for each model. The template parameter is the model class, the string the name it
will have in NEST
> 4. recompile and reinstall NEST
>
> Best,
> Hans Ekkehard
>
>
>
> On 6 May 2020, at 02:11, Allen Rabayda <arabayda(a)masonlive.gmu.edu> wrote:
>
> Dear Nest Community,
>
> Would anyone have insight into why I'm getting an UnknownModelName error?
>
> I'm new to Nest and am using Nest 18.0 on Lubuntu Virtual Box (Windows 10 OS).
>
> Thanks for any help.
>
> Best Regards,
> --Allen
>
> **** Error Message--additional details attached ******
> raise exceptionCls(commandname, message)
> nest.ll_api.UnknownModelName: ('UnknownModelName in CopyModel_l_l_D:
/stdp_izh_bitwise_correct_connection is not a known model name. Please check the modeldict
for a list of available models.', 'UnknownModelName', <SLILiteral:
CopyModel_l_l_D>, ': /stdp_izh_bitwise_correct_connection is not a known model
name. Please check the modeldict for a list of available models.')
> ********************************************************
>
<issue_UnknownModelName_4_May_2020>_______________________________________________
> NEST Users mailing list -- users(a)nest-simulator.org
> To unsubscribe send an email to users-leave(a)nest-simulator.org
>
>
> --
>
> Prof. Dr. Hans Ekkehard Plesser
> Head, Data Science Section
>
> Faculty of Science and Technology
> Norwegian University of Life Sciences
> PO Box 5003, 1432 Aas, Norway
>
> Phone +47 6723 1560
> Email hans.ekkehard.plesser(a)nmbu.no
> Home http://arken.nmbu.no/~plesser
> _______________________________________________
> NEST Users mailing list -- users(a)nest-simulator.org
> To unsubscribe send an email to users-leave(a)nest-simulator.org
>
>
> _______________________________________________
> NEST Users mailing list -- users(a)nest-simulator.org
> To unsubscribe send an email to users-leave(a)nest-simulator.org
10:41 a.m.
Hi Itaru,
You are quite right, there are a lot of similarities between NMODL and NESTML.
Kind regards,
Charl
On Wed, May 6, 2020, at 10:36, Itaru Kitayama wrote:
> Charl,
> Is it like a .mod file in NEURON?
>
> Thanks,
> Itaru.
>
> On Wed, May 6, 2020 at 5:32 PM Charl Linssen <nest-users(a)turingbirds.com>
wrote:
> >
> > Hi,
> >
> > I just want to take the chance to advertise NESTML, a domain-specific language
that you can use to write custom neuron models for NEST in an easy syntax (without writing
any C++ at all).
> >
> > For more information, I will pass you the "sneak preview" link to the
new NESTML documentation: https://nestml-api-documentation.readthedocs.io/
> >
> > If you decide to do your neuron modelling via NESTML, I would be happy to give
you additional pointers, on- or off-list.
> >
> > With kind regards,
> > Charl
> >
> >
> > On Wed, May 6, 2020, at 08:33, Hans Ekkehard Plesser wrote:
> >
> >
> > Hi Allen,
> >
> > Several steps are required to add a model to NEST. The recommended way of adding
a model is to create your own NEST module outside the NEST source code tree. You will find
an example in examples/MyModule and more documentation at
https://nest.github.io/nest-simulator/extension_modules.
> >
> > Placing code for custom models in the models directory in the NEST source code
tree also works, but makes it more difficult to move to newer versions of NEST or to share
your custom models with colleagues.
> >
> > Briefly, in addition to adding the source code files to the models directory,
you need to
> >
> > 1. add the files to models/CMakeLists.txt
> > 2. #include the files in models/modelsmodule.cpp
> > 3. add a line like
> >
> > register_connection_model< StaticConnection >(
"static_synapse" );
> >
> > for each model. The template parameter is the model class, the string the
name it will have in NEST
> > 4. recompile and reinstall NEST
> >
> > Best,
> > Hans Ekkehard
> >
> >
> >
> > On 6 May 2020, at 02:11, Allen Rabayda <arabayda(a)masonlive.gmu.edu>
wrote:
> >
> > Dear Nest Community,
> >
> > Would anyone have insight into why I'm getting an UnknownModelName error?
> >
> > I'm new to Nest and am using Nest 18.0 on Lubuntu Virtual Box (Windows 10
OS).
> >
> > Thanks for any help.
> >
> > Best Regards,
> > --Allen
> >
> > **** Error Message--additional details attached ******
> > raise exceptionCls(commandname, message)
> > nest.ll_api.UnknownModelName: ('UnknownModelName in CopyModel_l_l_D:
/stdp_izh_bitwise_correct_connection is not a known model name. Please check the modeldict
for a list of available models.', 'UnknownModelName', <SLILiteral:
CopyModel_l_l_D>, ': /stdp_izh_bitwise_correct_connection is not a known model
name. Please check the modeldict for a list of available models.')
> > ********************************************************
> >
<issue_UnknownModelName_4_May_2020>_______________________________________________
> > NEST Users mailing list -- users(a)nest-simulator.org
> > To unsubscribe send an email to users-leave(a)nest-simulator.org
> >
> >
> > --
> >
> > Prof. Dr. Hans Ekkehard Plesser
> > Head, Data Science Section
> >
> > Faculty of Science and Technology
> > Norwegian University of Life Sciences
> > PO Box 5003, 1432 Aas, Norway
> >
> > Phone +47 6723 1560
> > Email hans.ekkehard.plesser(a)nmbu.no
> > Home http://arken.nmbu.no/~plesser
> > _______________________________________________
> > NEST Users mailing list -- users(a)nest-simulator.org
> > To unsubscribe send an email to users-leave(a)nest-simulator.org
> >
> >
> > _______________________________________________
> > NEST Users mailing list -- users(a)nest-simulator.org
> > To unsubscribe send an email to users-leave(a)nest-simulator.org
> _______________________________________________
> NEST Users mailing list -- users(a)nest-simulator.org
> To unsubscribe send an email to users-leave(a)nest-simulator.org
>
10:44 a.m.
Charl,
Thanks. I'll look forward to "The NEST Book." then.
On Wed, May 6, 2020 at 5:41 PM Charl Linssen <nest-users(a)turingbirds.com> wrote:
>
> Hi Itaru,
>
> You are quite right, there are a lot of similarities between NMODL and NESTML.
>
> Kind regards,
> Charl
>
>
> On Wed, May 6, 2020, at 10:36, Itaru Kitayama wrote:
> > Charl,
> > Is it like a .mod file in NEURON?
> >
> > Thanks,
> > Itaru.
> >
> > On Wed, May 6, 2020 at 5:32 PM Charl Linssen <nest-users(a)turingbirds.com>
wrote:
> > >
> > > Hi,
> > >
> > > I just want to take the chance to advertise NESTML, a domain-specific
language that you can use to write custom neuron models for NEST in an easy syntax
(without writing any C++ at all).
> > >
> > > For more information, I will pass you the "sneak preview" link to
the new NESTML documentation: https://nestml-api-documentation.readthedocs.io/
> > >
> > > If you decide to do your neuron modelling via NESTML, I would be happy to
give you additional pointers, on- or off-list.
> > >
> > > With kind regards,
> > > Charl
> > >
> > >
> > > On Wed, May 6, 2020, at 08:33, Hans Ekkehard Plesser wrote:
> > >
> > >
> > > Hi Allen,
> > >
> > > Several steps are required to add a model to NEST. The recommended way of
adding a model is to create your own NEST module outside the NEST source code tree. You
will find an example in examples/MyModule and more documentation at
https://nest.github.io/nest-simulator/extension_modules.
> > >
> > > Placing code for custom models in the models directory in the NEST source
code tree also works, but makes it more difficult to move to newer versions of NEST or to
share your custom models with colleagues.
> > >
> > > Briefly, in addition to adding the source code files to the models
directory, you need to
> > >
> > > 1. add the files to models/CMakeLists.txt
> > > 2. #include the files in models/modelsmodule.cpp
> > > 3. add a line like
> > >
> > > register_connection_model< StaticConnection >(
"static_synapse" );
> > >
> > > for each model. The template parameter is the model class, the string
the name it will have in NEST
> > > 4. recompile and reinstall NEST
> > >
> > > Best,
> > > Hans Ekkehard
> > >
> > >
> > >
> > > On 6 May 2020, at 02:11, Allen Rabayda <arabayda(a)masonlive.gmu.edu>
wrote:
> > >
> > > Dear Nest Community,
> > >
> > > Would anyone have insight into why I'm getting an UnknownModelName
error?
> > >
> > > I'm new to Nest and am using Nest 18.0 on Lubuntu Virtual Box
(Windows 10 OS).
> > >
> > > Thanks for any help.
> > >
> > > Best Regards,
> > > --Allen
> > >
> > > **** Error Message--additional details attached ******
> > > raise exceptionCls(commandname, message)
> > > nest.ll_api.UnknownModelName: ('UnknownModelName in CopyModel_l_l_D:
/stdp_izh_bitwise_correct_connection is not a known model name. Please check the modeldict
for a list of available models.', 'UnknownModelName', <SLILiteral:
CopyModel_l_l_D>, ': /stdp_izh_bitwise_correct_connection is not a known model
name. Please check the modeldict for a list of available models.')
> > > ********************************************************
> > >
<issue_UnknownModelName_4_May_2020>_______________________________________________
> > > NEST Users mailing list -- users(a)nest-simulator.org
> > > To unsubscribe send an email to users-leave(a)nest-simulator.org
> > >
> > >
> > > --
> > >
> > > Prof. Dr. Hans Ekkehard Plesser
> > > Head, Data Science Section
> > >
> > > Faculty of Science and Technology
> > > Norwegian University of Life Sciences
> > > PO Box 5003, 1432 Aas, Norway
> > >
> > > Phone +47 6723 1560
> > > Email hans.ekkehard.plesser(a)nmbu.no
> > > Home http://arken.nmbu.no/~plesser
> > > _______________________________________________
> > > NEST Users mailing list -- users(a)nest-simulator.org
> > > To unsubscribe send an email to users-leave(a)nest-simulator.org
> > >
> > >
> > > _______________________________________________
> > > NEST Users mailing list -- users(a)nest-simulator.org
> > > To unsubscribe send an email to users-leave(a)nest-simulator.org
> > _______________________________________________
> > NEST Users mailing list -- users(a)nest-simulator.org
> > To unsubscribe send an email to users-leave(a)nest-simulator.org
> >
> _______________________________________________
> NEST Users mailing list -- users(a)nest-simulator.org
> To unsubscribe send an email to users-leave(a)nest-simulator.org
10:48 a.m.
I think if a user is quite familiar with C++ as often the case with
neuroscientists, then writing a module
directly in C++ would give him/her a greater deal of freedom and
debugging opportunities.
On Wed, May 6, 2020 at 5:44 PM Itaru Kitayama <itaru.kitayama(a)gmail.com> wrote:
>
> Charl,
> Thanks. I'll look forward to "The NEST Book." then.
>
> On Wed, May 6, 2020 at 5:41 PM Charl Linssen <nest-users(a)turingbirds.com>
wrote:
> >
> > Hi Itaru,
> >
> > You are quite right, there are a lot of similarities between NMODL and NESTML.
> >
> > Kind regards,
> > Charl
> >
> >
> > On Wed, May 6, 2020, at 10:36, Itaru Kitayama wrote:
> > > Charl,
> > > Is it like a .mod file in NEURON?
> > >
> > > Thanks,
> > > Itaru.
> > >
> > > On Wed, May 6, 2020 at 5:32 PM Charl Linssen
<nest-users(a)turingbirds.com> wrote:
> > > >
> > > > Hi,
> > > >
> > > > I just want to take the chance to advertise NESTML, a domain-specific
language that you can use to write custom neuron models for NEST in an easy syntax
(without writing any C++ at all).
> > > >
> > > > For more information, I will pass you the "sneak preview"
link to the new NESTML documentation: https://nestml-api-documentation.readthedocs.io/
> > > >
> > > > If you decide to do your neuron modelling via NESTML, I would be happy
to give you additional pointers, on- or off-list.
> > > >
> > > > With kind regards,
> > > > Charl
> > > >
> > > >
> > > > On Wed, May 6, 2020, at 08:33, Hans Ekkehard Plesser wrote:
> > > >
> > > >
> > > > Hi Allen,
> > > >
> > > > Several steps are required to add a model to NEST. The recommended way
of adding a model is to create your own NEST module outside the NEST source code tree. You
will find an example in examples/MyModule and more documentation at
https://nest.github.io/nest-simulator/extension_modules.
> > > >
> > > > Placing code for custom models in the models directory in the NEST
source code tree also works, but makes it more difficult to move to newer versions of NEST
or to share your custom models with colleagues.
> > > >
> > > > Briefly, in addition to adding the source code files to the models
directory, you need to
> > > >
> > > > 1. add the files to models/CMakeLists.txt
> > > > 2. #include the files in models/modelsmodule.cpp
> > > > 3. add a line like
> > > >
> > > > register_connection_model< StaticConnection >(
"static_synapse" );
> > > >
> > > > for each model. The template parameter is the model class, the
string the name it will have in NEST
> > > > 4. recompile and reinstall NEST
> > > >
> > > > Best,
> > > > Hans Ekkehard
> > > >
> > > >
> > > >
> > > > On 6 May 2020, at 02:11, Allen Rabayda
<arabayda(a)masonlive.gmu.edu> wrote:
> > > >
> > > > Dear Nest Community,
> > > >
> > > > Would anyone have insight into why I'm getting an
UnknownModelName error?
> > > >
> > > > I'm new to Nest and am using Nest 18.0 on Lubuntu Virtual Box
(Windows 10 OS).
> > > >
> > > > Thanks for any help.
> > > >
> > > > Best Regards,
> > > > --Allen
> > > >
> > > > **** Error Message--additional details attached ******
> > > > raise exceptionCls(commandname, message)
> > > > nest.ll_api.UnknownModelName: ('UnknownModelName in
CopyModel_l_l_D: /stdp_izh_bitwise_correct_connection is not a known model name. Please
check the modeldict for a list of available models.', 'UnknownModelName',
<SLILiteral: CopyModel_l_l_D>, ': /stdp_izh_bitwise_correct_connection is not a
known model name. Please check the modeldict for a list of available models.')
> > > > ********************************************************
> > > >
<issue_UnknownModelName_4_May_2020>_______________________________________________
> > > > NEST Users mailing list -- users(a)nest-simulator.org
> > > > To unsubscribe send an email to users-leave(a)nest-simulator.org
> > > >
> > > >
> > > > --
> > > >
> > > > Prof. Dr. Hans Ekkehard Plesser
> > > > Head, Data Science Section
> > > >
> > > > Faculty of Science and Technology
> > > > Norwegian University of Life Sciences
> > > > PO Box 5003, 1432 Aas, Norway
> > > >
> > > > Phone +47 6723 1560
> > > > Email hans.ekkehard.plesser(a)nmbu.no
> > > > Home http://arken.nmbu.no/~plesser
> > > > _______________________________________________
> > > > NEST Users mailing list -- users(a)nest-simulator.org
> > > > To unsubscribe send an email to users-leave(a)nest-simulator.org
> > > >
> > > >
> > > > _______________________________________________
> > > > NEST Users mailing list -- users(a)nest-simulator.org
> > > > To unsubscribe send an email to users-leave(a)nest-simulator.org
> > > _______________________________________________
> > > NEST Users mailing list -- users(a)nest-simulator.org
> > > To unsubscribe send an email to users-leave(a)nest-simulator.org
> > >
> > _______________________________________________
> > NEST Users mailing list -- users(a)nest-simulator.org
> > To unsubscribe send an email to users-leave(a)nest-simulator.org
20 May
20 May
4:34 a.m.
**** Error at bottom of email: #include [linkages appear missing w/ NEST
source directories:. ./libnestutil, ./nestkernal,, and ./sli ]****
Hans,
Thank you for your suggestions on May 6th. I've since built my own
module, 'My2Module' per your guidance and that on
https://nest.github.io/nest-simulator/extension_modules
<https://secure-web.cisco.com/1OkG_4Lw1yXYSv9Bo1mMO2W05lnXnEL03XeGcAPY__8APmBFD6LJj5zzZE42doCxkKRobTud5P4AT-oAs4WO_e4LtGvMBLDNRl2akKXbAPU8F8r9Rm4A-tpRybnnEUh062b56HNleUWk7QJ6N1WbDPtfI2tSIZfBrNSy7ZS4MsvzYfYHFlpG8GQQde5gApJecM5CFQEEP9CGymqYZ18LQ3zj1pcYeYG_L4XhXZhfL9be5WtSMrDZVy_ZeB0g3Qorb-lhDrLguvPgqUhCze8vfsqesaXfTpE3HtpsEMUcfd3Xc5vUP1KU6rRWzSAw8az7wM5CxmAlax7wYyP8eT_0bQAweIakbsUW3bXaCT9znQv15l-qoBLExOyTKQvbcyNiwLEBNflla-_MsLueEemTJ1NRiHSI7kGavYtpaKaeXtlSy7q0YU9lIMHnnS0AWr5keolzddt0U0uCpJmO2uL9FUA/https%3A%2F%2Fnest.github.io%2Fnest-simulator%2Fextension_modules>.
Unfortunately it appears the NEST source directories ./libnestutil,
./nestkernal,, and ./sli are not visible/linked to my2module.cpp
Is this non-linkage to be expected as it forces every "#include' in
my2module.cpp and my STDP model to have its absolute path included?
Below I show how I adapted/complied the example MyModule included on
github and the error message I get (bottom of email).
Thank you for any further suggestions.
Best Regards,
--Allen
---------CREATE MODULE: 1 directory copied, 4 files updated, 2 files
added------------
1. Make Module directory
/home/nest/work/nest-install/examples/MyModule copied/renamed to:
/home/nest/examples/My2Module
Two files with new STDP model added:
stdp_izh_bitwise_correct_connection.cpp
stdp_izh_bitwise_correct_connection.h
2. Updated "myModule.cpp"
name changed to "my2Module.cpp", references within updated
New STDP Model Listed by adding line:
#include "stdp_izh_bitwise_correct_connection.h"
New STDP Model Registered with model manager by adding line:
nest.kernel().model_manager.register_connection_model<STDPIzhBitwiseCorrectConnection<nest::TargetIdentifierPtrRport
>( "stdp_izh_bitwise_correct_connection"
);]
3. Updated "myModule.h"
name changed to "my2Module.h"
two absolute paths inserted (correct missing file error):
#include "/home/nest/work/nest-simulator-2.18.0/sli/slifunction.h"
#include "/home/nest/work/nest-simulator-2.18.0/sli/slimodule.h"
4. Updated "CMakeLists.txt"
SHORT_NAME renamed to "my2", references within updated
MODEL_SOURCE added:
stdp_izh_bitwise_correct_connection.cpp
stdp_izh_bitwise_correct_connection.h
5. Updated "mymodule-init.sli"
name changed to "my2module-init.sli", references within/across files above
updated
--------------------------------------------------------------
------------CMAKE Nest Build/Install (explicitly followed
instructions)---------
$ export NEST_INSTALL_DIR=/home/nest/work/nest-install
$ cd /home/nest/examples/My2Module
$ cd ..
$ mkdir mmb
$ cd mmb
$ cmake -Dwith-nest=${NEST_INSTALL_DIR}/bin/nest-config ../My2Module
$ make
**********************
***ERROR MSG***
make: *** No targets specified and no makefile found. Stop.
*********************
*********************
*** changed directory from ./mmb to ./My2Module then re-ran make*****
$ cd ~ examples/My2Module
$ make
***************'*******
***ERROR MSG****
Scanning dependencies of target my2module_module
[ 10%] Building CXX object CMakeFiles/my2module_module.dir/my2module.cpp.o
In file included from /home/nest/examples/My2Module/my2module.cpp:29:0:
/home/nest/examples/My2Module/drop_odd_spike_connection.h:27:10: fatal
error: connection.h: No such file or directory #include "connection.h"
**********************
*********************
On Wed, May 6, 2020 at 2:33 AM Hans Ekkehard Plesser <
hans.ekkehard.plesser(a)nmbu.no> wrote:
Hi Allen,
Several steps are required to add a model to NEST. The recommended way of
adding a model is to create your own NEST module outside the NEST source
code tree. You will find an example in examples/MyModule and more
documentation at https://nest.github.io/nest-simulator/extension_modules
<https://secure-web.cisco.com/1OkG_4Lw1yXYSv9Bo1mMO2W05lnXnEL03XeGcAPY__8APmBFD6LJj5zzZE42doCxkKRobTud5P4AT-oAs4WO_e4LtGvMBLDNRl2akKXbAPU8F8r9Rm4A-tpRybnnEUh062b56HNleUWk7QJ6N1WbDPtfI2tSIZfBrNSy7ZS4MsvzYfYHFlpG8GQQde5gApJecM5CFQEEP9CGymqYZ18LQ3zj1pcYeYG_L4XhXZhfL9be5WtSMrDZVy_ZeB0g3Qorb-lhDrLguvPgqUhCze8vfsqesaXfTpE3HtpsEMUcfd3Xc5vUP1KU6rRWzSAw8az7wM5CxmAlax7wYyP8eT_0bQAweIakbsUW3bXaCT9znQv15l-qoBLExOyTKQvbcyNiwLEBNflla-_MsLueEemTJ1NRiHSI7kGavYtpaKaeXtlSy7q0YU9lIMHnnS0AWr5keolzddt0U0uCpJmO2uL9FUA/https%3A%2F%2Fnest.github.io%2Fnest-simulator%2Fextension_modules>
.
Placing code for custom models in the models directory in the NEST source
code tree also works, but makes it more difficult to move to newer versions
of NEST or to share your custom models with colleagues.
Briefly, in addition to adding the source code files to the models
directory, you need to
1. add the files to models/CMakeLists.txt
2. #include the files in models/modelsmodule.cpp
3. add a line like
register_connection_model< StaticConnection >( "static_synapse" );
for each model. The template parameter is the model class, the string
the name it will have in NEST
4. recompile and reinstall NEST
Best,
Hans Ekkehard
On 6 May 2020, at 02:11, Allen Rabayda <arabayda(a)masonlive.gmu.edu> wrote:
Dear Nest Community,
Would anyone have insight into why I'm getting an UnknownModelName error?
I'm new to Nest and am using Nest 18.0 on Lubuntu Virtual Box (Windows
10 OS).
Thanks for any help.
Best Regards,
--Allen
**** Error Message--additional details attached ******
raise exceptionCls(commandname, message)
nest.ll_api.UnknownModelName: ('UnknownModelName in CopyModel_l_l_D:
/stdp_izh_bitwise_correct_connection is not a known model name. Please
check the modeldict for a list of available models.', 'UnknownModelName',
<SLILiteral: CopyModel_l_l_D>, ': /stdp_izh_bitwise_correct_connection is
not a known model name. Please check the modeldict for a list of available
models.')
********************************************************
<issue_UnknownModelName_4_May_2020>
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
--
Prof. Dr. Hans Ekkehard Plesser
Head, Data Science Section
Faculty of Science and Technology
Norwegian University of Life Sciences
PO Box 5003, 1432 Aas, Norway
Phone +47 6723 1560
Email hans.ekkehard.plesser(a)nmbu.no
Home http://arken.nmbu.no/~plesser
<http://secure-web.cisco.com/1NGU903Sz1mZbu-kUPO3tQjT8UGyiDXuL1fL2jQ0S4SkecW_uuWYlUr2l7vZeLiTlDo3I1xA_9Uf9v2N2p6tjNn25_ocHbrkd2JTx3GnGb-vebjXVovfSgdnKywi7KN485GJR_TQFVuJx5_MF6BXctVjmSoVYFiOG8Mu-TNlxK_xmGEWTPq3fhJXq122hpV7ruHShklc4kmqI33bXV1ZEU5eouIGhJ9nWmVo-NDeVaimFTzO6qmmGUU8EmR5e85dLtIrPmdtDprPb6mYTmwlmgj1lXqSapHgZL1zIn5I8o20lNXdX7P9nJVozEyOsAC9-TANbvcvJ4GMYG2gqDGBhlRa8QFDC9bpJFc6GW_bJhvI45kyeJj_P-qg6vmCiw6UCdxjNZSxzNTt4B7wtYDbj8F7EPJbVjtAeY5zLpAYyKQsL_mXRdL5yHAz35VHWlUwy/http%3A%2F%2Farken.nmbu.no%2F%7Eplesser>
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
9:08 a.m.
Hi Allen,
Below I show how I adapted/complied the example MyModule included on github and the
error message I get (bottom of email).
The steps look generally good.
two absolute paths inserted (correct missing file error):
#include "/home/nest/work/nest-simulator-2.18.0/sli/slifunction.h"
#include "/home/nest/work/nest-simulator-2.18.0/sli/slimodule.h"
You should not need the absolute paths, just the filenames should suffice.
$ cd mmb
$ cmake -Dwith-nest=${NEST_INSTALL_DIR}/bin/nest-config ../My2Module
$ make
Could you post the output of the cmake command?
And also the output of the following command
${NEST_INSTALL_DIR}/bin/nest-config --prefix --includes --libs --cflags
Best,
Hans Ekkehard
**********************
***ERROR MSG***
make: *** No targets specified and no makefile found. Stop.
*********************
*********************
*** changed directory from ./mmb to ./My2Module then re-ran make*****
$ cd ~ examples/My2Module
$ make
***************'*******
***ERROR MSG****
Scanning dependencies of target my2module_module
[ 10%] Building CXX object CMakeFiles/my2module_module.dir/my2module.cpp.o
In file included from /home/nest/examples/My2Module/my2module.cpp:29:0:
/home/nest/examples/My2Module/drop_odd_spike_connection.h:27:10: fatal error:
connection.h: No such file or directory #include "connection.h"
**********************
*********************
On Wed, May 6, 2020 at 2:33 AM Hans Ekkehard Plesser
<hans.ekkehard.plesser@nmbu.no<mailto:hans.ekkehard.plesser@nmbu.no>> wrote:
Hi Allen,
Several steps are required to add a model to NEST. The recommended way of adding a model
is to create your own NEST module outside the NEST source code tree. You will find an
example in examples/MyModule and more documentation at
https://nest.github.io/nest-simulator/extension_modules<https://secure-w…es>.
Placing code for custom models in the models directory in the NEST source code tree also
works, but makes it more difficult to move to newer versions of NEST or to share your
custom models with colleagues.
Briefly, in addition to adding the source code files to the models directory, you need to
1. add the files to models/CMakeLists.txt
2. #include the files in models/modelsmodule.cpp
3. add a line like
register_connection_model< StaticConnection >( "static_synapse" );
for each model. The template parameter is the model class, the string the name it will
have in NEST
4. recompile and reinstall NEST
Best,
Hans Ekkehard
On 6 May 2020, at 02:11, Allen Rabayda
<arabayda@masonlive.gmu.edu<mailto:arabayda@masonlive.gmu.edu>> wrote:
Dear Nest Community,
Would anyone have insight into why I'm getting an UnknownModelName error?
I'm new to Nest and am using Nest 18.0 on Lubuntu Virtual Box (Windows 10 OS).
Thanks for any help.
Best Regards,
--Allen
**** Error Message--additional details attached ******
raise exceptionCls(commandname, message)
nest.ll_api.UnknownModelName: ('UnknownModelName in CopyModel_l_l_D:
/stdp_izh_bitwise_correct_connection is not a known model name. Please check the modeldict
for a list of available models.', 'UnknownModelName', <SLILiteral:
CopyModel_l_l_D>, ': /stdp_izh_bitwise_correct_connection is not a known model
name. Please check the modeldict for a list of available models.')
********************************************************
<issue_UnknownModelName_4_May_2020>_______________________________________________
NEST Users mailing list --
users@nest-simulator.org<mailto:users@nest-simulator.org>
To unsubscribe send an email to
users-leave@nest-simulator.org<mailto:users-leave@nest-simulator.org>
--
Prof. Dr. Hans Ekkehard Plesser
Head, Data Science Section
Faculty of Science and Technology
Norwegian University of Life Sciences
PO Box 5003, 1432 Aas, Norway
Phone +47 6723 1560
Email hans.ekkehard.plesser@nmbu.no<http://nmbu.no/>
Home
http://arken.nmbu.no/~plesser<http://secure-web.cisco.com/1NGU903Sz1mZbu…
_______________________________________________
NEST Users mailing list --
users@nest-simulator.org<mailto:users@nest-simulator.org>
To unsubscribe send an email to
users-leave@nest-simulator.org<mailto:users-leave@nest-simulator.org>
_______________________________________________
NEST Users mailing list --
users@nest-simulator.org<mailto:users@nest-simulator.org>
To unsubscribe send an email to
users-leave@nest-simulator.org<mailto:users-leave@nest-simulator.org>
--
Prof. Dr. Hans Ekkehard Plesser
Head, Data Science Section
Faculty of Science and Technology
Norwegian University of Life Sciences
PO Box 5003, 1432 Aas, Norway
Phone +47 6723 1560
Email hans.ekkehard.plesser(a)nmbu.no
Home http://arken.nmbu.no/~plesser
9:47 a.m.
Hi,
Just to link these discussions: see also
https://github.com/nest/nest-simulator/issues/1331
Kind regards,
Charl
On Wed, May 20, 2020, at 09:08, Hans Ekkehard Plesser wrote:
Hi Allen,
Below I show how I adapted/complied the example
MyModule included on github and the error message I get (bottom of email).
The steps look generally good.
two absolute paths inserted (correct missing file
error):
#include "/home/nest/work/nest-simulator-2.18.0/sli/slifunction.h"
#include "/home/nest/work/nest-simulator-2.18.0/sli/slimodule.h"
You should not need the absolute paths, just the filenames should suffice.
$ cd mmb
$ cmake -Dwith-nest=${NEST_INSTALL_DIR}/bin/nest-config ../My2Module
$ make
Could you post the output of the cmake command?
And also the output of the following command
${NEST_INSTALL_DIR}/bin/nest-config --prefix --includes --libs --cflags
Best,
Hans Ekkehard
**********************
***ERROR MSG***
make: *** No targets specified and no makefile found. Stop.
*********************
*********************
*** changed directory from ./mmb to ./My2Module then re-ran make*****
$ cd ~ examples/My2Module
$ make
***************'*******
***ERROR MSG****
Scanning dependencies of target my2module_module
[ 10%] Building CXX object CMakeFiles/my2module_module.dir/my2module.cpp.o
In file included from /home/nest/examples/My2Module/my2module.cpp:29:0:
/home/nest/examples/My2Module/drop_odd_spike_connection.h:27:10: fatal error:
connection.h: No such file or directory #include "connection.h"
**********************
*********************
On Wed, May 6, 2020 at 2:33 AM Hans Ekkehard Plesser
<hans.ekkehard.plesser(a)nmbu.no> wrote:
--
Prof. Dr. Hans Ekkehard Plesser
Head, Data Science Section
Faculty of Science and Technology
Norwegian University of Life Sciences
PO Box 5003, 1432 Aas, Norway
Phone +47 6723 1560
Email hans.ekkehard.plesser(a)nmbu.no
Home http://arken.nmbu.no/~plesser
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
Hi Allen,
Several steps are required to add a model to NEST. The recommended way of adding a model
is to create your own NEST module outside the NEST source code tree. You will find an
example in examples/MyModule and more documentation at
https://nest.github.io/nest-simulator/extension_modules
<https://secure-web.cisco.com/1OkG_4Lw1yXYSv9Bo1mMO2W05lnXnEL03XeGcAPY__8APmBFD6LJj5zzZE42doCxkKRobTud5P4AT-oAs4WO_e4LtGvMBLDNRl2akKXbAPU8F8r9Rm4A-tpRybnnEUh062b56HNleUWk7QJ6N1WbDPtfI2tSIZfBrNSy7ZS4MsvzYfYHFlpG8GQQde5gApJecM5CFQEEP9CGymqYZ18LQ3zj1pcYeYG_L4XhXZhfL9be5WtSMrDZVy_ZeB0g3Qorb-lhDrLguvPgqUhCze8vfsqesaXfTpE3HtpsEMUcfd3Xc5vUP1KU6rRWzSAw8az7wM5CxmAlax7wYyP8eT_0bQAweIakbsUW3bXaCT9znQv15l-qoBLExOyTKQvbcyNiwLEBNflla-_MsLueEemTJ1NRiHSI7kGavYtpaKaeXtlSy7q0YU9lIMHnnS0AWr5keolzddt0U0uCpJmO2uL9FUA/https%3A%2F%2Fnest.github.io%2Fnest-simulator%2Fextension_modules>.
Placing code for custom models in the models directory in the NEST source code tree also
works, but makes it more difficult to move to newer versions of NEST or to share your
custom models with colleagues.
Briefly, in addition to adding the source code files to the models directory, you need
to
1. add the files to models/CMakeLists.txt
2. #include the files in models/modelsmodule.cpp
3. add a line like
register_connection_model< StaticConnection >( "static_synapse" );
for each model. The template parameter is the model class, the string the name it will
have in NEST
4. recompile and reinstall NEST
Best,
Hans Ekkehard
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org On 6 May 2020, at 02:11, Allen Rabayda
<arabayda(a)masonlive.gmu.edu> wrote:
Dear Nest Community,
Would anyone have insight into why I'm getting an UnknownModelName error?
I'm new to Nest and am using Nest 18.0 on Lubuntu Virtual Box (Windows 10 OS).
Thanks for any help.
Best Regards,
--Allen
**** Error Message--additional details attached ******
raise exceptionCls(commandname, message)
nest.ll_api.UnknownModelName: ('UnknownModelName in CopyModel_l_l_D:
/stdp_izh_bitwise_correct_connection is not a known model name. Please check the modeldict
for a list of available models.', 'UnknownModelName', <SLILiteral:
CopyModel_l_l_D>, ': /stdp_izh_bitwise_correct_connection is not a known model
name. Please check the modeldict for a list of available models.')
********************************************************
<issue_UnknownModelName_4_May_2020>_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
--
Prof. Dr. Hans Ekkehard Plesser
Head, Data Science Section
Faculty of Science and Technology
Norwegian University of Life Sciences
PO Box 5003, 1432 Aas, Norway
Phone +47 6723 1560
Email hans.ekkehard.plesser(a)nmbu.no
Home http://arken.nmbu.no/~plesser
<http://secure-web.cisco.com/1NGU903Sz1mZbu-kUPO3tQjT8UGyiDXuL1fL2jQ0S4SkecW_uuWYlUr2l7vZeLiTlDo3I1xA_9Uf9v2N2p6tjNn25_ocHbrkd2JTx3GnGb-vebjXVovfSgdnKywi7KN485GJR_TQFVuJx5_MF6BXctVjmSoVYFiOG8Mu-TNlxK_xmGEWTPq3fhJXq122hpV7ruHShklc4kmqI33bXV1ZEU5eouIGhJ9nWmVo-NDeVaimFTzO6qmmGUU8EmR5e85dLtIrPmdtDprPb6mYTmwlmgj1lXqSapHgZL1zIn5I8o20lNXdX7P9nJVozEyOsAC9-TANbvcvJ4GMYG2gqDGBhlRa8QFDC9bpJFc6GW_bJhvI45kyeJj_P-qg6vmCiw6UCdxjNZSxzNTt4B7wtYDbj8F7EPJbVjtAeY5zLpAYyKQsL_mXRdL5yHAz35VHWlUwy/http%3A%2F%2Farken.nmbu.no%2F%7Eplesser>
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
21 May
21 May
3:43 a.m.
Hans,
Below is the output from my 1) "cmake" and 2) "
{NEST_INSTALL_DIR}/bin/nest-config --prefix --includes --libs --cflags"
commands.
Thank you,
--Allen
Charl, I had not yet tried any of the processes on
https://github.com/nest/nest-simulator/issues/1331. Thank you,--Allen
*****************
1) CMAKE OUTPUT:
*****************
nest@nestvm:~/examples/My2Module$ cmake
-Dwith-nest=${NEST_INSTALL_DIR}/bin/nest-config ../My2Module
-------------------------------------------------------
my2module Configuration Summary
-------------------------------------------------------
C++ compiler : /usr/bin/c++
Build static libs : OFF
C++ compiler flags :
NEST compiler flags : -std=c++11 -O2 -Wall -fopenmp -pthread
-fdiagnostics-color=auto
NEST include dirs : -I/home/nest/work/nest-simulator-2.18.0/conngen
-I../nest-install/include/nest -I/usr/include -I/usr/include
-I/usr/local/include -I/usr/include
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include
-I/usr/lib/x86_64-linux-gnu/openmpi/include
NEST libraries flags : -L/home/nest/work/nest-install/lib -lconngen
-lnestutil -lnest -lrandom -lsli -lnestkernel -ltopology -fopenmp
/usr/lib/x86_64-linux-gnu/libltdl.so /usr/lib/x86_64-linux-gnu/libgsl.so
/usr/lib/x86_64-linux-gnu/libgslcblas.so /usr/local/lib/libneurosim.so
/usr/local/lib/libpyneurosim.so /usr/lib/x86_64-linux-gnu/libmusic.so
/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so
/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so
-------------------------------------------------------
You can now build and install 'my2module' using
make
make install
The library file libmy2module.so will be installed to
/home/nest/work/nest-install/lib/nest
Help files will be installed to
/home/nest/work/nest-install/share/doc/nest
The module can be loaded into NEST using
(my2module) Install (in SLI)
nest.Install('my2module') (in PyNEST)
The module will be installed into a non-default location!
Make sure to set the environment variables:
export
NEST_MODULE_PATH=/home/nest/work/nest-install/lib/nest:$NEST_MODULE_PATH
export SLI_PATH=/home/nest/work/nest-install/share/nest/sli:$SLI_PATH
-- Configuring done
-- Generating done
-- Build files have been written to: /home/nest/examples/My2Module
-----------------------------------------------------
*****************
2) "{NEST_INSTALL_DIR}/bin/nest-config --prefix --includes --libs
--cflags OUTPUT
*****************
nest@nestvm:~$ export NEST_INSTALL_DIR=/home/nest/work/nest-install
nest@nestvm:~$ {NEST_INSTALL_DIR}/bin/nest-config --prefix --includes
--libs --cflags
bash: {NEST_INSTALL_DIR}/bin/nest-config: No such file or directory
*****************
then added absolute path to produce output below
*****************
nest@nestvm:~$ /home/nest/work/nest-install/bin/nest-config --prefix
--includes --libs --cflags
/home/nest/work/nest-install
-I/home/nest/work/nest-simulator-2.18.0/conngen
-I../nest-install/include/nest -I/usr/include -I/usr/include
-I/usr/local/include -I/usr/include
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include
-I/usr/lib/x86_64-linux-gnu/openmpi/include
-L/home/nest/work/nest-install/lib -lconngen -lnestutil -lnest -lrandom
-lsli -lnestkernel -ltopology -fopenmp /usr/lib/x86_64-linux-gnu/libltdl.so
/usr/lib/x86_64-linux-gnu/libgsl.so
/usr/lib/x86_64-linux-gnu/libgslcblas.so /usr/local/lib/libneurosim.so
/usr/local/lib/libpyneurosim.so /usr/lib/x86_64-linux-gnu/libmusic.so
/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so
/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so
-std=c++11 -O2 -Wall -fopenmp -pthread -fdiagnostics-color=auto
*****************
END
*****************
On Wed, May 20, 2020 at 3:47 AM Charl Linssen <nest-users(a)turingbirds.com>
wrote:
Hi,
Just to link these discussions: see also
https://github.com/nest/nest-simulator/issues/1331
<https://secure-web.cisco.com/1ZSoZdO3QZUbfIeZPV6mH8fc-L_98EQC-isgNAmExSsl2H_Oi0LgBa4frA2RXkdjulu42MXUyOLYK8ArGIwNN5oU8H3uCIXd89DNyy9Md14DgaXhd_RWdV3YyvPFZfzFvXxJi9xoTlFhYp6TfLwR2FadlUfia_3Zq2WqdTuICTOubyuuSwkK3J23DUOqSel74ebZbeHmon3iJ9xXtAgRkNUIX-3fzaz6VFhMICLU6I2MH_dZtS73je0f4r9arPTT67jZNDMOZIP9MBRJz0LSqziL2R1aGL4UZkNfepzpVrhyZEZPm-YGztMjq0cIXKDb1y3ZL4fYtDgS_LXtwk5telmBaODPj_-Bzd7FC3I0cF2R7H-58WGxeFXxO5mlDGILKkY-fmwBrkRV0sbqoBLjUhblSX97Ih4A84ptDwpf13e1viia0WkPDS6pmBsRDm00klFx8oSSmSugzb-CIgmbi7g/https%3A%2F%2Fgithub.com%2Fnest%2Fnest-simulator%2Fissues%2F1331>
Kind regards,
Charl
On Wed, May 20, 2020, at 09:08, Hans Ekkehard Plesser wrote:
Hi Allen,
Below I show how I adapted/complied the example MyModule included on
github and the error message I get (bottom of email).
The steps look generally good.
two absolute paths inserted (correct missing file error):
#include "/home/nest/work/nest-simulator-2.18.0/sli/slifunction.h"
#include "/home/nest/work/nest-simulator-2.18.0/sli/slimodule.h"
You should not need the absolute paths, just the filenames should suffice.
$ cd mmb
$ cmake -Dwith-nest=${NEST_INSTALL_DIR}/bin/nest-config ../My2Module
$ make
Could you post the output of the cmake command?
And also the output of the following command
${NEST_INSTALL_DIR}/bin/nest-config --prefix --includes --libs --cflags
Best,
Hans Ekkehard
**********************
***ERROR MSG***
make: *** No targets specified and no makefile found. Stop.
*********************
*********************
*** changed directory from ./mmb to ./My2Module then re-ran make*****
$ cd ~ examples/My2Module
$ make
***************'*******
***ERROR MSG****
Scanning dependencies of target my2module_module
[ 10%] Building CXX object CMakeFiles/my2module_module.dir/my2module.cpp.o
In file included from /home/nest/examples/My2Module/my2module.cpp:29:0:
/home/nest/examples/My2Module/drop_odd_spike_connection.h:27:10: fatal
error: connection.h: No such file or directory #include "connection.h"
**********************
*********************
On Wed, May 6, 2020 at 2:33 AM Hans Ekkehard Plesser <
hans.ekkehard.plesser(a)nmbu.no> wrote:
Hi Allen,
Several steps are required to add a model to NEST. The recommended way of
adding a model is to create your own NEST module outside the NEST source
code tree. You will find an example in examples/MyModule and more
documentation at https://nest.github.io/nest-simulator/extension_modules
<https://secure-web.cisco.com/1OkG_4Lw1yXYSv9Bo1mMO2W05lnXnEL03XeGcAPY__8APmBFD6LJj5zzZE42doCxkKRobTud5P4AT-oAs4WO_e4LtGvMBLDNRl2akKXbAPU8F8r9Rm4A-tpRybnnEUh062b56HNleUWk7QJ6N1WbDPtfI2tSIZfBrNSy7ZS4MsvzYfYHFlpG8GQQde5gApJecM5CFQEEP9CGymqYZ18LQ3zj1pcYeYG_L4XhXZhfL9be5WtSMrDZVy_ZeB0g3Qorb-lhDrLguvPgqUhCze8vfsqesaXfTpE3HtpsEMUcfd3Xc5vUP1KU6rRWzSAw8az7wM5CxmAlax7wYyP8eT_0bQAweIakbsUW3bXaCT9znQv15l-qoBLExOyTKQvbcyNiwLEBNflla-_MsLueEemTJ1NRiHSI7kGavYtpaKaeXtlSy7q0YU9lIMHnnS0AWr5keolzddt0U0uCpJmO2uL9FUA/https%3A%2F%2Fnest.github.io%2Fnest-simulator%2Fextension_modules>
.
Placing code for custom models in the models directory in the NEST source
code tree also works, but makes it more difficult to move to newer versions
of NEST or to share your custom models with colleagues.
Briefly, in addition to adding the source code files to the models
directory, you need to
1. add the files to models/CMakeLists.txt
2. #include the files in models/modelsmodule.cpp
3. add a line like
register_connection_model< StaticConnection >( "static_synapse" );
for each model. The template parameter is the model class, the string
the name it will have in NEST
4. recompile and reinstall NEST
Best,
Hans Ekkehard
On 6 May 2020, at 02:11, Allen Rabayda <arabayda(a)masonlive.gmu.edu> wrote:
Dear Nest Community,
Would anyone have insight into why I'm getting an UnknownModelName error?
I'm new to Nest and am using Nest 18.0 on Lubuntu Virtual Box (Windows
10 OS).
Thanks for any help.
Best Regards,
--Allen
**** Error Message--additional details attached ******
raise exceptionCls(commandname, message)
nest.ll_api.UnknownModelName: ('UnknownModelName in CopyModel_l_l_D:
/stdp_izh_bitwise_correct_connection is not a known model name. Please
check the modeldict for a list of available models.', 'UnknownModelName',
<SLILiteral: CopyModel_l_l_D>, ': /stdp_izh_bitwise_correct_connection is
not a known model name. Please check the modeldict for a list of available
models.')
********************************************************
<issue_UnknownModelName_4_May_2020>
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--
Prof. Dr. Hans Ekkehard Plesser
Head, Data Science Section
Faculty of Science and Technology
Norwegian University of Life Sciences
PO Box 5003, 1432 Aas, Norway
Phone +47 6723 1560
Email hans.ekkehard.plesser(a)nmbu.no
<http://secure-web.cisco.com/1MZeV7tfgcKPl9mXCQjzVk-ZMtF_D1dr2oegLAsr1g2yZXyJkwQ_rSsb41hEW4mO0ZvHwDBhj_2L9V6ZMcZTq098bn9WovzUkjNZNECtSpRPo0z0Ga9Hd2G7f-qQsvOfsx9Ej-n1vtYfMsCOryF5XixOvhsLOjY1FEl_-oHafe_SBeBc_A43IttVqF206MWU_08dMBcllR9Qh7vGwZ031Fas5zLTCSkJwKccFSlfXTySAX9tz7WslqCBmQAPpqqMeVw6UAahNnAMDbGQpuVFDCQbQeNJ2wKagzlaGd4jM2aNU5K0SkhKgKIyvDnZneQXkNvrZv8IXuN468sOxGd3J0xoCcWIV9kUXczRmYjvb02Uf4m4k7QnT6q7rAmJrXfGCef_BA1gV7KaKqVnFg2PJiUKR1b-y6eQEEUM6yEnyPO55VJb9zQL5lZ_fzDDkgnVzD8zzOnwWi7Ce613KVhVsfg/http%3A%2F%2Fnmbu.no%2F>
Home http://arken.nmbu.no/~plesser
<http://secure-web.cisco.com/1NGU903Sz1mZbu-kUPO3tQjT8UGyiDXuL1fL2jQ0S4SkecW_uuWYlUr2l7vZeLiTlDo3I1xA_9Uf9v2N2p6tjNn25_ocHbrkd2JTx3GnGb-vebjXVovfSgdnKywi7KN485GJR_TQFVuJx5_MF6BXctVjmSoVYFiOG8Mu-TNlxK_xmGEWTPq3fhJXq122hpV7ruHShklc4kmqI33bXV1ZEU5eouIGhJ9nWmVo-NDeVaimFTzO6qmmGUU8EmR5e85dLtIrPmdtDprPb6mYTmwlmgj1lXqSapHgZL1zIn5I8o20lNXdX7P9nJVozEyOsAC9-TANbvcvJ4GMYG2gqDGBhlRa8QFDC9bpJFc6GW_bJhvI45kyeJj_P-qg6vmCiw6UCdxjNZSxzNTt4B7wtYDbj8F7EPJbVjtAeY5zLpAYyKQsL_mXRdL5yHAz35VHWlUwy/http%3A%2F%2Farken.nmbu.no%2F%7Eplesser>
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To unsubscribe send an email to users-leave(a)nest-simulator.org
--
Prof. Dr. Hans Ekkehard Plesser
Head, Data Science Section
Faculty of Science and Technology
Norwegian University of Life Sciences
PO Box 5003, 1432 Aas, Norway
Phone +47 6723 1560
Email hans.ekkehard.plesser(a)nmbu.no
Home http://arken.nmbu.no/~plesser
<http://secure-web.cisco.com/1G6J2sOXzgU3M6MYhCfcsAvmUBCRyztw33VeGZy-N4aj72uLz4RVh1d-M55er4bhLnienY6JyzqkvunMi1Lxw6dLUQF2HUD_knrsf4vGBWYQioD3UaCVnQ14k4zKKcb5kRg0PJ_S9m5wq1PFMkqpKeCVmpGtYZt3LstFLkK1x5gBm59H347Qs253gwWNMTI0zK6C5J1dA9dV8zSDg6wBNavm1zTkUidJj_JVRbVjNyQepzl_ZnlVJSPHy-5VgNFP0kt0_77u_kfb_yTkJ_5_1b1WucfONFQhv7N8sA1dJ9RuC9tkiUei-RNt68UgPr1_POzOd80XLLwvNwLTHgrsPl4GIFOIuWXgOdSxJtSi-V-8TyHwblSSD7k7_m3s8UfUe15BpkgH9rKHnZXWG8rYou9Y2avsV4_jPIQas2ll8Owla0EJCmXjnyj92VlaLFjsUs3PvUo7N81Y95ON3-P4vBg/http%3A%2F%2Farken.nmbu.no%2F%7Eplesser>
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10:13 p.m.
Hans,
Below is the output from my 1) "cmake" and 2) "
{NEST_INSTALL_DIR}/bin/nest-config --prefix --includes --libs --cflags"
commands.
Thank you,
--Allen
Charl, I had not yet tried any of the processes on
https://github.com/nest/nest-simulator/issues/1331. Thank you,--Allen
*****************
1) CMAKE OUTPUT:
*****************
nest@nestvm:~/examples/My2Module$ cmake
-Dwith-nest=${NEST_INSTALL_DIR}/bin/nest-config ../My2Module
-------------------------------------------------------
my2module Configuration Summary
-------------------------------------------------------
C++ compiler : /usr/bin/c++
Build static libs : OFF
C++ compiler flags :
NEST compiler flags : -std=c++11 -O2 -Wall -fopenmp -pthread
-fdiagnostics-color=auto
NEST include dirs : -I/home/nest/work/nest-simulator-2.18.0/conngen
-I../nest-install/include/nest -I/usr/include -I/usr/include
-I/usr/local/include -I/usr/include
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include
-I/usr/lib/x86_64-linux-gnu/openmpi/include
NEST libraries flags : -L/home/nest/work/nest-install/lib -lconngen
-lnestutil -lnest -lrandom -lsli -lnestkernel -ltopology -fopenmp
/usr/lib/x86_64-linux-gnu/libltdl.so /usr/lib/x86_64-linux-gnu/libgsl.so
/usr/lib/x86_64-linux-gnu/libgslcblas.so /usr/local/lib/libneurosim.so
/usr/local/lib/libpyneurosim.so /usr/lib/x86_64-linux-gnu/libmusic.so
/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so
/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so
-------------------------------------------------------
You can now build and install 'my2module' using
make
make install
The library file libmy2module.so will be installed to
/home/nest/work/nest-install/lib/nest
Help files will be installed to
/home/nest/work/nest-install/share/doc/nest
The module can be loaded into NEST using
(my2module) Install (in SLI)
nest.Install('my2module') (in PyNEST)
The module will be installed into a non-default location!
Make sure to set the environment variables:
export
NEST_MODULE_PATH=/home/nest/work/nest-install/lib/nest:$NEST_MODULE_PATH
export SLI_PATH=/home/nest/work/nest-install/share/nest/sli:$SLI_PATH
-- Configuring done
-- Generating done
-- Build files have been written to: /home/nest/examples/My2Module
-----------------------------------------------------
*****************
2) "{NEST_INSTALL_DIR}/bin/nest-config --prefix --includes --libs
--cflags OUTPUT
*****************
nest@nestvm:~$ export NEST_INSTALL_DIR=/home/nest/work/nest-install
nest@nestvm:~$ {NEST_INSTALL_DIR}/bin/nest-config --prefix --includes
--libs --cflags
bash: {NEST_INSTALL_DIR}/bin/nest-config: No such file or directory
*****************
then added absolute path to produce output below
*****************
nest@nestvm:~$ /home/nest/work/nest-install/bin/nest-config --prefix
--includes --libs --cflags
/home/nest/work/nest-install
-I/home/nest/work/nest-simulator-2.18.0/conngen
-I../nest-install/include/nest -I/usr/include -I/usr/include
-I/usr/local/include -I/usr/include
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include
-I/usr/lib/x86_64-linux-gnu/openmpi/include
-L/home/nest/work/nest-install/lib -lconngen -lnestutil -lnest -lrandom
-lsli -lnestkernel -ltopology -fopenmp /usr/lib/x86_64-linux-gnu/libltdl.so
/usr/lib/x86_64-linux-gnu/libgsl.so
/usr/lib/x86_64-linux-gnu/libgslcblas.so /usr/local/lib/libneurosim.so
/usr/local/lib/libpyneurosim.so /usr/lib/x86_64-linux-gnu/libmusic.so
/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so
/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so
-std=c++11 -O2 -Wall -fopenmp -pthread -fdiagnostics-color=auto
*****************
END
*****************
On Wed, May 20, 2020 at 3:08 AM Hans Ekkehard Plesser <
hans.ekkehard.plesser(a)nmbu.no> wrote:
Hi Allen,
Below I show how I adapted/complied the example MyModule included on
github and the error message I get (bottom of email).
The steps look generally good.
two absolute paths inserted (correct missing file error):
#include "/home/nest/work/nest-simulator-2.18.0/sli/slifunction.h"
#include "/home/nest/work/nest-simulator-2.18.0/sli/slimodule.h"
You should not need the absolute paths, just the filenames should suffice.
$ cd mmb
$ cmake -Dwith-nest=${NEST_INSTALL_DIR}/bin/nest-config ../My2Module
$ make
Could you post the output of the cmake command?
And also the output of the following command
${NEST_INSTALL_DIR}/bin/nest-config --prefix --includes --libs --cflags
Best,
Hans Ekkehard
**********************
***ERROR MSG***
make: *** No targets specified and no makefile found. Stop.
*********************
*********************
*** changed directory from ./mmb to ./My2Module then re-ran make*****
$ cd ~ examples/My2Module
$ make
***************'*******
***ERROR MSG****
Scanning dependencies of target my2module_module
[ 10%] Building CXX object CMakeFiles/my2module_module.dir/my2module.cpp.o
In file included from /home/nest/examples/My2Module/my2module.cpp:29:0:
/home/nest/examples/My2Module/drop_odd_spike_connection.h:27:10: fatal
error: connection.h: No such file or directory #include "connection.h"
**********************
*********************
On Wed, May 6, 2020 at 2:33 AM Hans Ekkehard Plesser <
hans.ekkehard.plesser(a)nmbu.no> wrote:
Hi Allen,
Several steps are required to add a model to NEST. The recommended way of
adding a model is to create your own NEST module outside the NEST source
code tree. You will find an example in examples/MyModule and more
documentation at https://nest.github.io/nest-simulator/extension_modules
<https://secure-web.cisco.com/1OkG_4Lw1yXYSv9Bo1mMO2W05lnXnEL03XeGcAPY__8APmBFD6LJj5zzZE42doCxkKRobTud5P4AT-oAs4WO_e4LtGvMBLDNRl2akKXbAPU8F8r9Rm4A-tpRybnnEUh062b56HNleUWk7QJ6N1WbDPtfI2tSIZfBrNSy7ZS4MsvzYfYHFlpG8GQQde5gApJecM5CFQEEP9CGymqYZ18LQ3zj1pcYeYG_L4XhXZhfL9be5WtSMrDZVy_ZeB0g3Qorb-lhDrLguvPgqUhCze8vfsqesaXfTpE3HtpsEMUcfd3Xc5vUP1KU6rRWzSAw8az7wM5CxmAlax7wYyP8eT_0bQAweIakbsUW3bXaCT9znQv15l-qoBLExOyTKQvbcyNiwLEBNflla-_MsLueEemTJ1NRiHSI7kGavYtpaKaeXtlSy7q0YU9lIMHnnS0AWr5keolzddt0U0uCpJmO2uL9FUA/https%3A%2F%2Fnest.github.io%2Fnest-simulator%2Fextension_modules>
.
Placing code for custom models in the models directory in the NEST source
code tree also works, but makes it more difficult to move to newer versions
of NEST or to share your custom models with colleagues.
Briefly, in addition to adding the source code files to the models
directory, you need to
1. add the files to models/CMakeLists.txt
2. #include the files in models/modelsmodule.cpp
3. add a line like
register_connection_model< StaticConnection >( "static_synapse" );
for each model. The template parameter is the model class, the string
the name it will have in NEST
4. recompile and reinstall NEST
Best,
Hans Ekkehard
On 6 May 2020, at 02:11, Allen Rabayda <arabayda(a)masonlive.gmu.edu>
wrote:
Dear Nest Community,
Would anyone have insight into why I'm getting an UnknownModelName
error?
I'm new to Nest and am using Nest 18.0 on Lubuntu Virtual Box (Windows
10 OS).
Thanks for any help.
Best Regards,
--Allen
**** Error Message--additional details attached ******
raise exceptionCls(commandname, message)
nest.ll_api.UnknownModelName: ('UnknownModelName in CopyModel_l_l_D:
/stdp_izh_bitwise_correct_connection is not a known model name. Please
check the modeldict for a list of available models.', 'UnknownModelName',
<SLILiteral: CopyModel_l_l_D>, ': /stdp_izh_bitwise_correct_connection is
not a known model name. Please check the modeldict for a list of available
models.')
********************************************************
<issue_UnknownModelName_4_May_2020>
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--
Prof. Dr. Hans Ekkehard Plesser
Head, Data Science Section
Faculty of Science and Technology
Norwegian University of Life Sciences
PO Box 5003, 1432 Aas, Norway
Phone +47 6723 1560
Email hans.ekkehard.plesser(a)nmbu.no
<http://secure-web.cisco.com/1oGxjTBn6G3zlyNTvv_hoyiXx9VwKKhVYGsnt8WkKZtjey0jolrbMkgNX8nwZ1_mVOfMZGiux9uomyEPFv1tB5lZkHqSDndkoq7WT3154Yx4mGDr8Arv_7jWQmncdw7br50zI6WljWy5IK7VdXa7cWJJMsib-PBr0HtFYGs5gbgToIMYR4w5rKqurTb-v0rgSNtJsrdJncRz5eqmnGWYbcKnShFCDiXti1pbbYmie86yWljTQbF0AtIphD_zoqJhi-TJYrXXjeVGyc2k_WQiq9cNQvbZlxfWAY8GM2CJWq_YnFnAj_wgKoFCuxVcs6gPmu6B-M8f9ZylTFcZTKA4SjnK6SJPiDig8sJf7qhGQW0aB1CMf88nIeQJFd5NE_nXYNkveMYHT2So_RNGY06D7hdDTA1VoxJgrV-JxlTvip1uelk7bGF8CPbWbPaNV-TAvtps_fwU_5vhhGiNNNPML6Q/http%3A%2F%2Fnmbu.no%2F>
Home http://arken.nmbu.no/~plesser
<http://secure-web.cisco.com/1NGU903Sz1mZbu-kUPO3tQjT8UGyiDXuL1fL2jQ0S4SkecW_uuWYlUr2l7vZeLiTlDo3I1xA_9Uf9v2N2p6tjNn25_ocHbrkd2JTx3GnGb-vebjXVovfSgdnKywi7KN485GJR_TQFVuJx5_MF6BXctVjmSoVYFiOG8Mu-TNlxK_xmGEWTPq3fhJXq122hpV7ruHShklc4kmqI33bXV1ZEU5eouIGhJ9nWmVo-NDeVaimFTzO6qmmGUU8EmR5e85dLtIrPmdtDprPb6mYTmwlmgj1lXqSapHgZL1zIn5I8o20lNXdX7P9nJVozEyOsAC9-TANbvcvJ4GMYG2gqDGBhlRa8QFDC9bpJFc6GW_bJhvI45kyeJj_P-qg6vmCiw6UCdxjNZSxzNTt4B7wtYDbj8F7EPJbVjtAeY5zLpAYyKQsL_mXRdL5yHAz35VHWlUwy/http%3A%2F%2Farken.nmbu.no%2F%7Eplesser>
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--
Prof. Dr. Hans Ekkehard Plesser
Head, Data Science Section
Faculty of Science and Technology
Norwegian University of Life Sciences
PO Box 5003, 1432 Aas, Norway
Phone +47 6723 1560
Email hans.ekkehard.plesser(a)nmbu.no
Home http://arken.nmbu.no/~plesser
<http://secure-web.cisco.com/1Yaz1kjc6VGnCjQQ1iYz5UzgeB8gnIvsxcPfiFurdqrnLLEWwnAKf1OZf_fQ2tyFo0TCRgdCgP6hn0zGKQEBdzOBDzQKjHGM9AI7d7tpeDLOm-jgCdjaiHVa1soloQe1uDkeWcKDWx4uEqNa7RanMBiY5pcihXtfkEJsP_kJi-fNMVAJUzp4PU1Q3vI-u039bL3kxazbvIqYnR5TY-jdwqAJktCuCdh8VCMEX6hNO62dDiD8Nmhpa-btsTr-jjlPsCPaNjkA7aZ08WxrEyinmMYfdOB1b38lthuLD3HSlT9yy483Jt2iLUip3GwCXeIW0c21Mqdg9KLcj65O5lAIsslHkqdpNmNjRP0K9tAMp8xrCg4JdGkK6YLINQvz65xkso4plOFxA9laXV0PUAaHgbylgRD34SSBj2I3lSM43Kofs0nQX3UWMtgmCbwFQ45EHMLfxEHKMAWZVUbLgujnSYw/http%3A%2F%2Farken.nmbu.no%2F%7Eplesser>
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22 May
22 May
2:24 p.m.
Hi Allen,
Thanks. It looks like a relative path has ended up in your nest-config file where it
should have been an absolute path. Could you open file
nest-install/bin/nest-config
and go to roughly line 55, where you should find something like
--includes)
echo " -I/home/nest/work/nest-simulator-2.18.0/conngen
-I../nest-install/include/nest -I/usr/include -I/usr/include -I/usr/local/include
-I/usr/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include
-I/usr/lib/x86_64-linux-gnu/openmpi/include"
;;
Please replace within
-I../nest-install/include/nest
the .. with the absolute path. Then run cmake and make again in the My2Module build
directory. You may want to delete anything in that build directory first to avoid old
Cmake cached data.
Best,
Hans Ekkehard
On 21 May 2020, at 22:13, Allen Rabayda
<arabayda@masonlive.gmu.edu<mailto:arabayda@masonlive.gmu.edu>> wrote:
Hans,
Below is the output from my 1) "cmake" and 2)
"{NEST_INSTALL_DIR}/bin/nest-config --prefix --includes --libs --cflags"
commands.
Thank you,
--Allen
Charl, I had not yet tried any of the processes on
https://github.com/nest/nest-simulator/issues/1331. Thank you,--Allen
*****************
1) CMAKE OUTPUT:
*****************
nest@nestvm:~/examples/My2Module$ cmake -Dwith-nest=${NEST_INSTALL_DIR}/bin/nest-config
../My2Module
-------------------------------------------------------
my2module Configuration Summary
-------------------------------------------------------
C++ compiler : /usr/bin/c++
Build static libs : OFF
C++ compiler flags :
NEST compiler flags : -std=c++11 -O2 -Wall -fopenmp -pthread -fdiagnostics-color=auto
NEST include dirs : -I/home/nest/work/nest-simulator-2.18.0/conngen
-I../nest-install/include/nest -I/usr/include -I/usr/include -I/usr/local/include
-I/usr/include -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include
-I/usr/lib/x86_64-linux-gnu/openmpi/include
NEST libraries flags : -L/home/nest/work/nest-install/lib -lconngen -lnestutil -lnest
-lrandom -lsli -lnestkernel -ltopology -fopenmp /usr/lib/x86_64-linux-gnu/libltdl.so
/usr/lib/x86_64-linux-gnu/libgsl.so /usr/lib/x86_64-linux-gnu/libgslcblas.so
/usr/local/lib/libneurosim.so /usr/local/lib/libpyneurosim.so
/usr/lib/x86_64-linux-gnu/libmusic.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so
/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so
-------------------------------------------------------
You can now build and install 'my2module' using
make
make install
The library file libmy2module.so will be installed to
/home/nest/work/nest-install/lib/nest
Help files will be installed to
/home/nest/work/nest-install/share/doc/nest
The module can be loaded into NEST using
(my2module) Install (in SLI)
nest.Install('my2module') (in PyNEST)
The module will be installed into a non-default location!
Make sure to set the environment variables:
export NEST_MODULE_PATH=/home/nest/work/nest-install/lib/nest:$NEST_MODULE_PATH
export SLI_PATH=/home/nest/work/nest-install/share/nest/sli:$SLI_PATH
-- Configuring done
-- Generating done
-- Build files have been written to: /home/nest/examples/My2Module
-----------------------------------------------------
*****************
2) "{NEST_INSTALL_DIR}/bin/nest-config --prefix --includes --libs --cflags OUTPUT
*****************
nest@nestvm:~$ export NEST_INSTALL_DIR=/home/nest/work/nest-install
nest@nestvm:~$ {NEST_INSTALL_DIR}/bin/nest-config --prefix --includes --libs --cflags
bash: {NEST_INSTALL_DIR}/bin/nest-config: No such file or directory
*****************
then added absolute path to produce output below
*****************
nest@nestvm:~$ /home/nest/work/nest-install/bin/nest-config --prefix --includes --libs
--cflags
/home/nest/work/nest-install
-I/home/nest/work/nest-simulator-2.18.0/conngen -I../nest-install/include/nest
-I/usr/include -I/usr/include -I/usr/local/include -I/usr/include
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include
-I/usr/lib/x86_64-linux-gnu/openmpi/include
-L/home/nest/work/nest-install/lib -lconngen -lnestutil -lnest -lrandom -lsli -lnestkernel
-ltopology -fopenmp /usr/lib/x86_64-linux-gnu/libltdl.so
/usr/lib/x86_64-linux-gnu/libgsl.so /usr/lib/x86_64-linux-gnu/libgslcblas.so
/usr/local/lib/libneurosim.so /usr/local/lib/libpyneurosim.so
/usr/lib/x86_64-linux-gnu/libmusic.so /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so
/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so
-std=c++11 -O2 -Wall -fopenmp -pthread -fdiagnostics-color=auto
*****************
END
*****************
On Wed, May 20, 2020 at 3:08 AM Hans Ekkehard Plesser
<hans.ekkehard.plesser@nmbu.no<mailto:hans.ekkehard.plesser@nmbu.no>> wrote:
Hi Allen,
Below I show how I adapted/complied the example MyModule included on github and the
error message I get (bottom of email).
The steps look generally good.
two absolute paths inserted (correct missing file error):
#include "/home/nest/work/nest-simulator-2.18.0/sli/slifunction.h"
#include "/home/nest/work/nest-simulator-2.18.0/sli/slimodule.h"
You should not need the absolute paths, just the filenames should suffice.
$ cd mmb
$ cmake -Dwith-nest=${NEST_INSTALL_DIR}/bin/nest-config ../My2Module
$ make
Could you post the output of the cmake command?
And also the output of the following command
${NEST_INSTALL_DIR}/bin/nest-config --prefix --includes --libs --cflags
Best,
Hans Ekkehard
**********************
***ERROR MSG***
make: *** No targets specified and no makefile found. Stop.
*********************
*********************
*** changed directory from ./mmb to ./My2Module then re-ran make*****
$ cd ~ examples/My2Module
$ make
***************'*******
***ERROR MSG****
Scanning dependencies of target my2module_module
[ 10%] Building CXX object CMakeFiles/my2module_module.dir/my2module.cpp.o
In file included from /home/nest/examples/My2Module/my2module.cpp:29:0:
/home/nest/examples/My2Module/drop_odd_spike_connection.h:27:10: fatal error:
connection.h: No such file or directory #include "connection.h"
**********************
*********************
On Wed, May 6, 2020 at 2:33 AM Hans Ekkehard Plesser
<hans.ekkehard.plesser@nmbu.no<mailto:hans.ekkehard.plesser@nmbu.no>> wrote:
Hi Allen,
Several steps are required to add a model to NEST. The recommended way of adding a model
is to create your own NEST module outside the NEST source code tree. You will find an
example in examples/MyModule and more documentation at
https://nest.github.io/nest-simulator/extension_modules<https://secure-w…es>.
Placing code for custom models in the models directory in the NEST source code tree also
works, but makes it more difficult to move to newer versions of NEST or to share your
custom models with colleagues.
Briefly, in addition to adding the source code files to the models directory, you need to
1. add the files to models/CMakeLists.txt
2. #include the files in models/modelsmodule.cpp
3. add a line like
register_connection_model< StaticConnection >( "static_synapse" );
for each model. The template parameter is the model class, the string the name it will
have in NEST
4. recompile and reinstall NEST
Best,
Hans Ekkehard
On 6 May 2020, at 02:11, Allen Rabayda
<arabayda@masonlive.gmu.edu<mailto:arabayda@masonlive.gmu.edu>> wrote:
Dear Nest Community,
Would anyone have insight into why I'm getting an UnknownModelName error?
I'm new to Nest and am using Nest 18.0 on Lubuntu Virtual Box (Windows 10 OS).
Thanks for any help.
Best Regards,
--Allen
**** Error Message--additional details attached ******
raise exceptionCls(commandname, message)
nest.ll_api.UnknownModelName: ('UnknownModelName in CopyModel_l_l_D:
/stdp_izh_bitwise_correct_connection is not a known model name. Please check the modeldict
for a list of available models.', 'UnknownModelName', <SLILiteral:
CopyModel_l_l_D>, ': /stdp_izh_bitwise_correct_connection is not a known model
name. Please check the modeldict for a list of available models.')
********************************************************
<issue_UnknownModelName_4_May_2020>_______________________________________________
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users@nest-simulator.org<mailto:users@nest-simulator.org>
To unsubscribe send an email to
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--
Prof. Dr. Hans Ekkehard Plesser
Head, Data Science Section
Faculty of Science and Technology
Norwegian University of Life Sciences
PO Box 5003, 1432 Aas, Norway
Phone +47 6723 1560
Email
hans.ekkehard.plesser@nmbu.no<http://secure-web.cisco.com/1oGxjTBn6G3zlyNTvv_hoyiXx9VwKKhVYGsnt8WkKZtjey0jolrbMkgNX8nwZ1_mVOfMZGiux9uomyEPFv1tB5lZkHqSDndkoq7WT3154Yx4mGDr8Arv_7jWQmncdw7br50zI6WljWy5IK7VdXa7cWJJMsib-PBr0HtFYGs5gbgToIMYR4w5rKqurTb-v0rgSNtJsrdJncRz5eqmnGWYbcKnShFCDiXti1pbbYmie86yWljTQbF0AtIphD_zoqJhi-TJYrXXjeVGyc2k_WQiq9cNQvbZlxfWAY8GM2CJWq_YnFnAj_wgKoFCuxVcs6gPmu6B-M8f9ZylTFcZTKA4SjnK6SJPiDig8sJf7qhGQW0aB1CMf88nIeQJFd5NE_nXYNkveMYHT2So_RNGY06D7hdDTA1VoxJgrV-JxlTvip1uelk7bGF8CPbWbPaNV-TAvtps_fwU_5vhhGiNNNPML6Q/http%3A%2F%2Fnmbu.no%2F>
Home
http://arken.nmbu.no/~plesser<http://secure-web.cisco.com/1NGU903Sz1mZbu…
_______________________________________________
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users@nest-simulator.org<mailto:users@nest-simulator.org>
To unsubscribe send an email to
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--
Prof. Dr. Hans Ekkehard Plesser
Head, Data Science Section
Faculty of Science and Technology
Norwegian University of Life Sciences
PO Box 5003, 1432 Aas, Norway
Phone +47 6723 1560
Email hans.ekkehard.plesser@nmbu.no<http://nmbu.no/>
Home
http://arken.nmbu.no/~plesser<http://secure-web.cisco.com/1Yaz1kjc6VGnCj…
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users@nest-simulator.org<mailto:users@nest-simulator.org>
To unsubscribe send an email to
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--
Prof. Dr. Hans Ekkehard Plesser
Head, Data Science Section
Faculty of Science and Technology
Norwegian University of Life Sciences
PO Box 5003, 1432 Aas, Norway
Phone +47 6723 1560
Email hans.ekkehard.plesser(a)nmbu.no
Home http://arken.nmbu.no/~plesser
4 Jun
4 Jun
3:49 a.m.
Hans,
Hello again. I updated the nest-config file as you recommended and it
appeared to correct the error at hand, however uncovered several more (ref:
error message below).
I've created my own module, modified/updated custom synapse files
(itemized my actions below and attached for ref), and attempted to
re-compile but have error that states "connection" was not declared (ref:
Error message below)
Thank you once again for any additional suggestions.
Best Regards,
--Allen
**** ERROR AS OF 3-Jun-2020 *****
Scanning dependencies of target my2module_module
[ 12%] Building CXX object CMakeFiles/my2module_module.dir/my2module.cpp.o
In file included from /home/nest/examples/My2Module/my2module.cpp:33:0:
/home/nest/examples/My2Module/stdp_izh_connection.h: In member function
‘void nest::STDPIzhConnection<targetidentifierT>::send(nest::Event&,
nest::thread, const CommonPropertiesType&)’:
/home/nest/examples/My2Module/stdp_izh_connection.h:264:5: error: ‘class
nest::Event’ has no member named ‘set_multiplicity’
e.set_multiplicity( -1 );
^~~~~~~~~~~~~~~~
/home/nest/examples/My2Module/stdp_izh_connection.h:265:5: error: ‘class
nest::Event’ has no member named ‘set_delay’; did you mean ‘set_sender’?
e.set_delay( get_delay_steps() );
^~~~~~~~~
set_sender
/home/nest/examples/My2Module/my2module.cpp: In member function ‘virtual
void mynest::My2Module::init(SLIInterpreter*)’:
/home/nest/examples/My2Module/my2module.cpp:137:7: error: expected
primary-expression before ‘.’ token
nest.kernel().model_manager.register_connection_model<
STDPIzhConnection< nest::TargetIdentifierPtrRport > >(
^
/home/nest/examples/My2Module/my2module.cpp:137:58: error:
‘STDPIzhConnection’ was not declared in this scope
nest.kernel().model_manager.register_connection_model<
STDPIzhConnection< nest::TargetIdentifierPtrRport > >(
^~~~~~~~~~~~~~~~~
/home/nest/examples/My2Module/my2module.cpp:137:58: note: suggested
alternative:
In file included from /home/nest/examples/My2Module/my2module.cpp:33:0:
/home/nest/examples/My2Module/stdp_izh_connection.h:99:7: note:
‘nest::STDPIzhConnection’
class STDPIzhConnection: public nest::Connection< targetidentifierT >
^~~~~~~~~~~~~~~~~
/home/nest/examples/My2Module/my2module.cpp:137:108: error: expected
primary-expression before ‘>’ token
nest.kernel().model_manager.register_connection_model<
STDPIzhConnection< nest::TargetIdentifierPtrRport > >(
^
/home/nest/examples/My2Module/my2module.cpp:137:110: error: expected
primary-expression before ‘>’ token
nest.kernel().model_manager.register_connection_model<
STDPIzhConnection< nest::TargetIdentifierPtrRport > >(
^
CMakeFiles/my2module_module.dir/build.make:62: recipe for target
'CMakeFiles/my2module_module.dir/my2module.cpp.o' failed
make[2]: *** [CMakeFiles/my2module_module.dir/my2module.cpp.o] Error 1
CMakeFiles/Makefile2:67: recipe for target
'CMakeFiles/my2module_module.dir/all' failed
make[1]: *** [CMakeFiles/my2module_module.dir/all] Error 2
Makefile:151: recipe for target 'all' failed
make: *** [all] Error 2
***************************************************************
***** STEPS I TAKE TO RE-COMPILE ****************
export NEST_INSTALL_DIR=/home/nest/work/nest-install
cd /home/nest/examples/My2Module
cd ..
rmr -r /home/nest/examples/mmb
mkdir mmb
cd mmb
cmake -Dwith-nest=${NEST_INSTALL_DIR}/bin/nest-config ../My2Module
make
make install
***************************************************************
****** Modifications I Made to Custom Synapse Model **************
- added "stdp_izh_connection.h" "stdp_izh_connection.cpp" files to
/home/nest/examples/My2Module
- added filenames above to "set( models_sources..." section in
"/home/nest/examples/My2Module/Cmakelist.txt
- added "#include filenames above"
to /home/nest/examples/My2Module/my2module.cpp
- added "kernel().model_manager.register_connection_model<
STDPIzhConnection >( "stdp_izh_connection" )"
to /home/nest/examples/My2Module/my2module.cpp
- updated "stdp_izh_connection.h" & "stdp_izh_connection.cpp"
files per
the following references/samples:
--https://nest.github.io/nest-simulator/synapse_models
-- https://nest.github.io/nest-simulator/model_conversion_5g
--https://nest.github.io/nest-simulator/extension_modules
--
https://github.com/nest/nest-simulator/blob/master/examples/MyModule/drop_o…
--
https://github.com/nest/nest-simulator/blob/master/models/stdp_connection_h…
******************************************************************
On Fri, May 22, 2020 at 8:24 AM Hans Ekkehard Plesser <
hans.ekkehard.plesser(a)nmbu.no> wrote:
Hi Allen,
Thanks. It looks like a relative path has ended up in your nest-config
file where it should have been an absolute path. Could you open file
nest-install/bin/nest-config
and go to roughly line 55, where you should find something like
--includes)
echo " -I/home/nest/work/nest-simulator-2.18.0/conngen
-I../nest-install/include/nest -I/usr/include -I/usr/include
-I/usr/local/include -I/usr/include
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include
-I/usr/lib/x86_64-linux-gnu/openmpi/include"
;;
Please replace within
-I../nest-install/include/nest
the .. with the absolute path. Then run cmake and make again in the
My2Module build directory. You may want to delete anything in that build
directory first to avoid old Cmake cached data.
Best,
Hans Ekkehard
On 21 May 2020, at 22:13, Allen Rabayda <arabayda(a)masonlive.gmu.edu>
wrote:
Hans,
Below is the output from my 1) "cmake" and 2) "
{NEST_INSTALL_DIR}/bin/nest-config --prefix --includes --libs --cflags"
commands.
Thank you,
--Allen
Charl, I had not yet tried any of the processes on
https://github.com/nest/nest-simulator/issues/1331
<https://secure-web.cisco.com/1pvWX8gcr0ktPCO_pJ-XSV7OsLHFiWmE4gqVEtVzPY62QxY1eQ-8GQWP65ZAm2UnzB305znKhGBeGwk3pBCBzl8VOR2DbwaEVtwB6IqqgcUZ00aQ3KCz0pZCavFLjDbhwHT4dDzuJDzmZfXfPOh43poIG8N04bRnb8yWGChAfBw_d6FveE9QCARl1P7RLbZx2JO3Jutn_6NeHuvQ0US81N-LR2KHLRq2OP2zVHL989CZBuJHc2L7rHt8e95I7GsWuJ3nWlu8gts8AL8Q0aGjxo0Kzn1ZZbaQDJeBZkM7a8aQGjOjHfq24TEYMImyCtMnNUrAJciz44-6tObOUK8QDbtLQq6fszadM72YPHar9u1kjbVNXqRfAN6N6YNs3faASL0TwqOGptnApRBX2ImM9ySgQBFW48w8-871pKl3Dw83zEcxHGZ9dvmzsLptIVDNL/https%3A%2F%2Fgithub.com%2Fnest%2Fnest-simulator%2Fissues%2F1331>.
Thank you,--Allen
*****************
1) CMAKE OUTPUT:
*****************
nest@nestvm:~/examples/My2Module$ cmake
-Dwith-nest=${NEST_INSTALL_DIR}/bin/nest-config ../My2Module
-------------------------------------------------------
my2module Configuration Summary
-------------------------------------------------------
C++ compiler : /usr/bin/c++
Build static libs : OFF
C++ compiler flags :
NEST compiler flags : -std=c++11 -O2 -Wall -fopenmp -pthread
-fdiagnostics-color=auto
NEST include dirs : -I/home/nest/work/nest-simulator-2.18.0/conngen
-I../nest-install/include/nest -I/usr/include -I/usr/include
-I/usr/local/include -I/usr/include
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include
-I/usr/lib/x86_64-linux-gnu/openmpi/include
NEST libraries flags : -L/home/nest/work/nest-install/lib -lconngen
-lnestutil -lnest -lrandom -lsli -lnestkernel -ltopology -fopenmp
/usr/lib/x86_64-linux-gnu/libltdl.so /usr/lib/x86_64-linux-gnu/libgsl.so
/usr/lib/x86_64-linux-gnu/libgslcblas.so /usr/local/lib/libneurosim.so
/usr/local/lib/libpyneurosim.so /usr/lib/x86_64-linux-gnu/libmusic.so
/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so
/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so
-------------------------------------------------------
You can now build and install 'my2module' using
make
make install
The library file libmy2module.so will be installed to
/home/nest/work/nest-install/lib/nest
Help files will be installed to
/home/nest/work/nest-install/share/doc/nest
The module can be loaded into NEST using
(my2module) Install (in SLI)
nest.Install('my2module') (in PyNEST)
The module will be installed into a non-default location!
Make sure to set the environment variables:
export
NEST_MODULE_PATH=/home/nest/work/nest-install/lib/nest:$NEST_MODULE_PATH
export SLI_PATH=/home/nest/work/nest-install/share/nest/sli:$SLI_PATH
-- Configuring done
-- Generating done
-- Build files have been written to: /home/nest/examples/My2Module
-----------------------------------------------------
*****************
2) "{NEST_INSTALL_DIR}/bin/nest-config --prefix --includes --libs --cflags OUTPUT
*****************
nest@nestvm:~$ export NEST_INSTALL_DIR=/home/nest/work/nest-install
nest@nestvm:~$ {NEST_INSTALL_DIR}/bin/nest-config --prefix --includes
--libs --cflags
bash: {NEST_INSTALL_DIR}/bin/nest-config: No such file or directory
*****************
then added absolute path to produce output below
*****************
nest@nestvm:~$ /home/nest/work/nest-install/bin/nest-config --prefix
--includes --libs --cflags
/home/nest/work/nest-install
-I/home/nest/work/nest-simulator-2.18.0/conngen
-I../nest-install/include/nest -I/usr/include -I/usr/include
-I/usr/local/include -I/usr/include
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include
-I/usr/lib/x86_64-linux-gnu/openmpi/include
-L/home/nest/work/nest-install/lib -lconngen -lnestutil -lnest -lrandom
-lsli -lnestkernel -ltopology -fopenmp /usr/lib/x86_64-linux-gnu/libltdl.so
/usr/lib/x86_64-linux-gnu/libgsl.so
/usr/lib/x86_64-linux-gnu/libgslcblas.so /usr/local/lib/libneurosim.so
/usr/local/lib/libpyneurosim.so /usr/lib/x86_64-linux-gnu/libmusic.so
/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so
/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so
-std=c++11 -O2 -Wall -fopenmp -pthread -fdiagnostics-color=auto
*****************
END
*****************
On Wed, May 20, 2020 at 3:08 AM Hans Ekkehard Plesser <
hans.ekkehard.plesser(a)nmbu.no> wrote:
Hi Allen,
Below I show how I adapted/complied the example MyModule included on
github and the error message I get (bottom of email).
The steps look generally good.
two absolute paths inserted (correct missing file error):
#include "/home/nest/work/nest-simulator-2.18.0/sli/slifunction.h"
#include "/home/nest/work/nest-simulator-2.18.0/sli/slimodule.h"
You should not need the absolute paths, just the filenames should suffice.
$ cd mmb
$ cmake -Dwith-nest=${NEST_INSTALL_DIR}/bin/nest-config ../My2Module
$ make
Could you post the output of the cmake command?
And also the output of the following command
${NEST_INSTALL_DIR}/bin/nest-config --prefix --includes --libs --cflags
Best,
Hans Ekkehard
**********************
***ERROR MSG***
make: *** No targets specified and no makefile found. Stop.
*********************
*********************
*** changed directory from ./mmb to ./My2Module then re-ran make*****
$ cd ~ examples/My2Module
$ make
***************'*******
***ERROR MSG****
Scanning dependencies of target my2module_module
[ 10%] Building CXX object CMakeFiles/my2module_module.dir/my2module.cpp.o
In file included from /home/nest/examples/My2Module/my2module.cpp:29:0:
/home/nest/examples/My2Module/drop_odd_spike_connection.h:27:10: fatal
error: connection.h: No such file or directory #include "connection.h"
**********************
*********************
On Wed, May 6, 2020 at 2:33 AM Hans Ekkehard Plesser <
hans.ekkehard.plesser(a)nmbu.no> wrote:
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
To unsubscribe send an email to users-leave(a)nest-simulator.org
--
Prof. Dr. Hans Ekkehard Plesser
Head, Data Science Section
Faculty of Science and Technology
Norwegian University of Life Sciences
PO Box 5003, 1432 Aas, Norway
Phone +47 6723 1560
Email hans.ekkehard.plesser(a)nmbu.no
Home http://arken.nmbu.no/~plesser
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Hi Allen,
Several steps are required to add a model to NEST. The recommended way
of adding a model is to create your own NEST module outside the NEST source
code tree. You will find an example in examples/MyModule and more
documentation at https://nest.github.io/nest-simulator/extension_modules
<https://secure-web.cisco.com/1OkG_4Lw1yXYSv9Bo1mMO2W05lnXnEL03XeGcAPY__8APmBFD6LJj5zzZE42doCxkKRobTud5P4AT-oAs4WO_e4LtGvMBLDNRl2akKXbAPU8F8r9Rm4A-tpRybnnEUh062b56HNleUWk7QJ6N1WbDPtfI2tSIZfBrNSy7ZS4MsvzYfYHFlpG8GQQde5gApJecM5CFQEEP9CGymqYZ18LQ3zj1pcYeYG_L4XhXZhfL9be5WtSMrDZVy_ZeB0g3Qorb-lhDrLguvPgqUhCze8vfsqesaXfTpE3HtpsEMUcfd3Xc5vUP1KU6rRWzSAw8az7wM5CxmAlax7wYyP8eT_0bQAweIakbsUW3bXaCT9znQv15l-qoBLExOyTKQvbcyNiwLEBNflla-_MsLueEemTJ1NRiHSI7kGavYtpaKaeXtlSy7q0YU9lIMHnnS0AWr5keolzddt0U0uCpJmO2uL9FUA/https%3A%2F%2Fnest.github.io%2Fnest-simulator%2Fextension_modules>
.
Placing code for custom models in the models directory in the NEST
source code tree also works, but makes it more difficult to move to newer
versions of NEST or to share your custom models with colleagues.
Briefly, in addition to adding the source code files to the models
directory, you need to
1. add the files to models/CMakeLists.txt
2. #include the files in models/modelsmodule.cpp
3. add a line like
register_connection_model< StaticConnection >( "static_synapse" );
for each model. The template parameter is the model class, the
string the name it will have in NEST
4. recompile and reinstall NEST
Best,
Hans Ekkehard
On 6 May 2020, at 02:11, Allen Rabayda <arabayda(a)masonlive.gmu.edu>
wrote:
Dear Nest Community,
Would anyone have insight into why I'm getting an UnknownModelName
error?
I'm new to Nest and am using Nest 18.0 on Lubuntu Virtual Box (Windows
10 OS).
Thanks for any help.
Best Regards,
--Allen
**** Error Message--additional details attached ******
raise exceptionCls(commandname, message)
nest.ll_api.UnknownModelName: ('UnknownModelName in CopyModel_l_l_D:
/stdp_izh_bitwise_correct_connection is not a known model name. Please
check the modeldict for a list of available models.', 'UnknownModelName',
<SLILiteral: CopyModel_l_l_D>, ': /stdp_izh_bitwise_correct_connection is
not a known model name. Please check the modeldict for a list of available
models.')
********************************************************
<issue_UnknownModelName_4_May_2020>
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--
Prof. Dr. Hans Ekkehard Plesser
Head, Data Science Section
Faculty of Science and Technology
Norwegian University of Life Sciences
PO Box 5003, 1432 Aas, Norway
Phone +47 6723 1560
Email hans.ekkehard.plesser(a)nmbu.no
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--
Prof. Dr. Hans Ekkehard Plesser
Head, Data Science Section
Faculty of Science and Technology
Norwegian University of Life Sciences
PO Box 5003, 1432 Aas, Norway
Phone +47 6723 1560
Email hans.ekkehard.plesser(a)nmbu.no
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16 Jun
16 Jun
3:12 a.m.
Hans and Nest User Community,
I was wondering if you had any advice for my errors when I
compile/register the custom Synapse Model, stdp_izh_connection.h/.cpp as I
can compile/install without issue using the example custom models
like pif_psc_alpha and drop_odd_synapse alone.
Two quick questions.
#1 Which synapse model registration statement should I use in
"my2module.cpp":
-
nest::kernel().model_manager.register_connection_model<STDPIzhConnection<targetidentifierT
>( "stdp_izh_connection" );
-
nest::kernel().model_manager.register_connection_model<
STDPIzhConnection< nest::TargetIdentifierPtrRport >
>("stdp_izh_connection"
);
- nest::kernel().model_manager.register_prototype_connection<
STDPIzhConnection< nest::TargetIdentifierPtrRport >
>("stdp_izh_connection"
);
- nest::kernel().model_manager.register_prototype_connection<
STDPIzhConnection>(net_, "stdp_izh_connection" );
#2 Which argument, "targetidentifierT" or "TargetIdentifierPtrRport",
should I use:
- in "my2module.cpp" model registration?
- and in my synapse model, "stdp_izh_connection.h", templates?
I've included one of my error messages below for reference. I received
similar error messages for each of the registration statements used above.
Thank you for any advice you may offer.
Best Regards,
--Allen
********* Background on the Custom Synapse Model********
- stdp_izh_connection.h/.cpp has been updated for nest 5g kernel per
https://nest.github.io/nest-simulator/model_conversion_5g
- stdp_izh_connection.h/.cpp has reformatted using
https://github.com/nest/nest-simulator/blob/master/models/stdp_connection_h…
as an example.
*********************************************************************
*********** Nest Compile Errors when including:
stdp_izh_connection.h/.cpp***********
[ 10%] Building CXX object CMakeFiles/my2module_module.dir/my2module.cpp.o
In file included from /home/nest/examples/My2Module/my2module.cpp:33:0:
/home/nest/examples/My2Module/stdp_izh_connection.h: In member function
‘void nest::STDPIzhConnection<targetidentifierT>::send(nest::Event&,
nest::thread, const nest::STDPIzhCommonProperties&)’:
/home/nest/examples/My2Module/stdp_izh_connection.h:305:5: error: ‘class
nest::Event’ has no member named ‘set_multiplicity’
e.set_multiplicity( -1 );
^~~~~~~~~~~~~~~~
/home/nest/examples/My2Module/stdp_izh_connection.h:306:5: error: ‘class
nest::Event’ has no member named ‘set_delay’; did you mean ‘set_sender’?
e.set_delay( ConnectionBase::get_delay_steps() ); // ConnectionBase not
used in sample
^~~~~~~~~
set_sender
/home/nest/examples/My2Module/stdp_izh_connection.h:309:18: error:
‘t_spike’ was not declared in this scope
t_lastspike_ = t_spike; // added per ref:
https://nest.github.io/nest-simulator/model_conversion_5g
^~~~~~~
/home/nest/examples/My2Module/stdp_izh_connection.h:309:18: note: suggested
alternative:
In file included from /home/nest/work/nest-install/include/nest/node.h:37:0,
from
/home/nest/work/nest-install/include/nest/common_synapse_properties.h:29,
from
/home/nest/work/nest-install/include/nest/connection.h:27,
from
/home/nest/examples/My2Module/drop_odd_spike_connection.h:27,
from /home/nest/examples/My2Module/my2module.cpp:29:
/home/nest/work/nest-install/include/nest/nest_names.h:424:19: note:
‘nest::names::t_spike’
extern const Name t_spike;
^~~~~~~
/home/nest/examples/My2Module/my2module.cpp: In member function ‘virtual
void mynest::My2Module::init(SLIInterpreter*)’:
/home/nest/examples/My2Module/my2module.cpp:142:59: error:
‘STDPIzhConnection’ was not declared in this scope
nest::kernel().model_manager.register_connection_model<
STDPIzhConnection< targetidentifierT > >(
^~~~~~~~~~~~~~~~~
/home/nest/examples/My2Module/my2module.cpp:142:59: note: suggested
alternative:
In file included from /home/nest/examples/My2Module/my2module.cpp:33:0:
/home/nest/examples/My2Module/stdp_izh_connection.h:114:7: note:
‘nest::STDPIzhConnection’
class STDPIzhConnection: public nest::Connection< targetidentifierT >
^~~~~~~~~~~~~~~~~
/home/nest/examples/My2Module/my2module.cpp:142:78: error:
‘targetidentifierT’ was not declared in this scope
nest::kernel().model_manager.register_connection_model<
STDPIzhConnection< targetidentifierT > >(
^~~~~~~~~~~~~~~~~
/home/nest/examples/My2Module/my2module.cpp:143:27: warning: comparison
with string literal results in unspecified behavior [-Waddress]
"stdp_izh_connection" );
^
/home/nest/examples/My2Module/my2module.cpp:142:98: error: invalid operands
of types ‘<unresolved overloaded function type>’ and ‘const char [20]’ to
binary ‘operator>’
nest::kernel().model_manager.register_connection_model<
STDPIzhConnection< targetidentifierT > >(
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
"stdp_izh_connection" );
~~~~~~~~~~~~~~~~~~~~~~~
CMakeFiles/my2module_module.dir/build.make:62: recipe for target
'CMakeFiles/my2module_module.dir/my2module.cpp.o' failed
make[2]: *** [CMakeFiles/my2module_module.dir/my2module.cpp.o] Error 1
CMakeFiles/Makefile2:67: recipe for target
'CMakeFiles/my2module_module.dir/all' failed
make[1]: *** [CMakeFiles/my2module_module.dir/all] Error 2
Makefile:151: recipe for target 'all' failed
make: *** [all] Error 2
On Fri, May 22, 2020 at 8:24 AM Hans Ekkehard Plesser <
hans.ekkehard.plesser(a)nmbu.no> wrote:
Hi Allen,
Thanks. It looks like a relative path has ended up in your nest-config
file where it should have been an absolute path. Could you open file
nest-install/bin/nest-config
and go to roughly line 55, where you should find something like
--includes)
echo " -I/home/nest/work/nest-simulator-2.18.0/conngen
-I../nest-install/include/nest -I/usr/include -I/usr/include
-I/usr/local/include -I/usr/include
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include
-I/usr/lib/x86_64-linux-gnu/openmpi/include"
;;
Please replace within
-I../nest-install/include/nest
the .. with the absolute path. Then run cmake and make again in the
My2Module build directory. You may want to delete anything in that build
directory first to avoid old Cmake cached data.
Best,
Hans Ekkehard
On 21 May 2020, at 22:13, Allen Rabayda <arabayda(a)masonlive.gmu.edu>
wrote:
Hans,
Below is the output from my 1) "cmake" and 2) "
{NEST_INSTALL_DIR}/bin/nest-config --prefix --includes --libs --cflags"
commands.
Thank you,
--Allen
Charl, I had not yet tried any of the processes on
https://github.com/nest/nest-simulator/issues/1331
<https://secure-web.cisco.com/1pvWX8gcr0ktPCO_pJ-XSV7OsLHFiWmE4gqVEtVzPY62QxY1eQ-8GQWP65ZAm2UnzB305znKhGBeGwk3pBCBzl8VOR2DbwaEVtwB6IqqgcUZ00aQ3KCz0pZCavFLjDbhwHT4dDzuJDzmZfXfPOh43poIG8N04bRnb8yWGChAfBw_d6FveE9QCARl1P7RLbZx2JO3Jutn_6NeHuvQ0US81N-LR2KHLRq2OP2zVHL989CZBuJHc2L7rHt8e95I7GsWuJ3nWlu8gts8AL8Q0aGjxo0Kzn1ZZbaQDJeBZkM7a8aQGjOjHfq24TEYMImyCtMnNUrAJciz44-6tObOUK8QDbtLQq6fszadM72YPHar9u1kjbVNXqRfAN6N6YNs3faASL0TwqOGptnApRBX2ImM9ySgQBFW48w8-871pKl3Dw83zEcxHGZ9dvmzsLptIVDNL/https%3A%2F%2Fgithub.com%2Fnest%2Fnest-simulator%2Fissues%2F1331>.
Thank you,--Allen
*****************
1) CMAKE OUTPUT:
*****************
nest@nestvm:~/examples/My2Module$ cmake
-Dwith-nest=${NEST_INSTALL_DIR}/bin/nest-config ../My2Module
-------------------------------------------------------
my2module Configuration Summary
-------------------------------------------------------
C++ compiler : /usr/bin/c++
Build static libs : OFF
C++ compiler flags :
NEST compiler flags : -std=c++11 -O2 -Wall -fopenmp -pthread
-fdiagnostics-color=auto
NEST include dirs : -I/home/nest/work/nest-simulator-2.18.0/conngen
-I../nest-install/include/nest -I/usr/include -I/usr/include
-I/usr/local/include -I/usr/include
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include
-I/usr/lib/x86_64-linux-gnu/openmpi/include
NEST libraries flags : -L/home/nest/work/nest-install/lib -lconngen
-lnestutil -lnest -lrandom -lsli -lnestkernel -ltopology -fopenmp
/usr/lib/x86_64-linux-gnu/libltdl.so /usr/lib/x86_64-linux-gnu/libgsl.so
/usr/lib/x86_64-linux-gnu/libgslcblas.so /usr/local/lib/libneurosim.so
/usr/local/lib/libpyneurosim.so /usr/lib/x86_64-linux-gnu/libmusic.so
/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so
/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so
-------------------------------------------------------
You can now build and install 'my2module' using
make
make install
The library file libmy2module.so will be installed to
/home/nest/work/nest-install/lib/nest
Help files will be installed to
/home/nest/work/nest-install/share/doc/nest
The module can be loaded into NEST using
(my2module) Install (in SLI)
nest.Install('my2module') (in PyNEST)
The module will be installed into a non-default location!
Make sure to set the environment variables:
export
NEST_MODULE_PATH=/home/nest/work/nest-install/lib/nest:$NEST_MODULE_PATH
export SLI_PATH=/home/nest/work/nest-install/share/nest/sli:$SLI_PATH
-- Configuring done
-- Generating done
-- Build files have been written to: /home/nest/examples/My2Module
-----------------------------------------------------
*****************
2) "{NEST_INSTALL_DIR}/bin/nest-config --prefix --includes --libs --cflags OUTPUT
*****************
nest@nestvm:~$ export NEST_INSTALL_DIR=/home/nest/work/nest-install
nest@nestvm:~$ {NEST_INSTALL_DIR}/bin/nest-config --prefix --includes
--libs --cflags
bash: {NEST_INSTALL_DIR}/bin/nest-config: No such file or directory
*****************
then added absolute path to produce output below
*****************
nest@nestvm:~$ /home/nest/work/nest-install/bin/nest-config --prefix
--includes --libs --cflags
/home/nest/work/nest-install
-I/home/nest/work/nest-simulator-2.18.0/conngen
-I../nest-install/include/nest -I/usr/include -I/usr/include
-I/usr/local/include -I/usr/include
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include
-I/usr/lib/x86_64-linux-gnu/openmpi/include
-L/home/nest/work/nest-install/lib -lconngen -lnestutil -lnest -lrandom
-lsli -lnestkernel -ltopology -fopenmp /usr/lib/x86_64-linux-gnu/libltdl.so
/usr/lib/x86_64-linux-gnu/libgsl.so
/usr/lib/x86_64-linux-gnu/libgslcblas.so /usr/local/lib/libneurosim.so
/usr/local/lib/libpyneurosim.so /usr/lib/x86_64-linux-gnu/libmusic.so
/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so
/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so
-std=c++11 -O2 -Wall -fopenmp -pthread -fdiagnostics-color=auto
*****************
END
*****************
On Wed, May 20, 2020 at 3:08 AM Hans Ekkehard Plesser <
hans.ekkehard.plesser(a)nmbu.no> wrote:
Hi Allen,
Below I show how I adapted/complied the example MyModule included on
github and the error message I get (bottom of email).
The steps look generally good.
two absolute paths inserted (correct missing file error):
#include "/home/nest/work/nest-simulator-2.18.0/sli/slifunction.h"
#include "/home/nest/work/nest-simulator-2.18.0/sli/slimodule.h"
You should not need the absolute paths, just the filenames should suffice.
$ cd mmb
$ cmake -Dwith-nest=${NEST_INSTALL_DIR}/bin/nest-config ../My2Module
$ make
Could you post the output of the cmake command?
And also the output of the following command
${NEST_INSTALL_DIR}/bin/nest-config --prefix --includes --libs --cflags
Best,
Hans Ekkehard
**********************
***ERROR MSG***
make: *** No targets specified and no makefile found. Stop.
*********************
*********************
*** changed directory from ./mmb to ./My2Module then re-ran make*****
$ cd ~ examples/My2Module
$ make
***************'*******
***ERROR MSG****
Scanning dependencies of target my2module_module
[ 10%] Building CXX object CMakeFiles/my2module_module.dir/my2module.cpp.o
In file included from /home/nest/examples/My2Module/my2module.cpp:29:0:
/home/nest/examples/My2Module/drop_odd_spike_connection.h:27:10: fatal
error: connection.h: No such file or directory #include "connection.h"
**********************
*********************
On Wed, May 6, 2020 at 2:33 AM Hans Ekkehard Plesser <
hans.ekkehard.plesser(a)nmbu.no> wrote:
_______________________________________________
NEST Users mailing list -- users(a)nest-simulator.org
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--
Prof. Dr. Hans Ekkehard Plesser
Head, Data Science Section
Faculty of Science and Technology
Norwegian University of Life Sciences
PO Box 5003, 1432 Aas, Norway
Phone +47 6723 1560
Email hans.ekkehard.plesser(a)nmbu.no
Home http://arken.nmbu.no/~plesser
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Hi Allen,
Several steps are required to add a model to NEST. The recommended way
of adding a model is to create your own NEST module outside the NEST source
code tree. You will find an example in examples/MyModule and more
documentation at https://nest.github.io/nest-simulator/extension_modules
<https://secure-web.cisco.com/1OkG_4Lw1yXYSv9Bo1mMO2W05lnXnEL03XeGcAPY__8APmBFD6LJj5zzZE42doCxkKRobTud5P4AT-oAs4WO_e4LtGvMBLDNRl2akKXbAPU8F8r9Rm4A-tpRybnnEUh062b56HNleUWk7QJ6N1WbDPtfI2tSIZfBrNSy7ZS4MsvzYfYHFlpG8GQQde5gApJecM5CFQEEP9CGymqYZ18LQ3zj1pcYeYG_L4XhXZhfL9be5WtSMrDZVy_ZeB0g3Qorb-lhDrLguvPgqUhCze8vfsqesaXfTpE3HtpsEMUcfd3Xc5vUP1KU6rRWzSAw8az7wM5CxmAlax7wYyP8eT_0bQAweIakbsUW3bXaCT9znQv15l-qoBLExOyTKQvbcyNiwLEBNflla-_MsLueEemTJ1NRiHSI7kGavYtpaKaeXtlSy7q0YU9lIMHnnS0AWr5keolzddt0U0uCpJmO2uL9FUA/https%3A%2F%2Fnest.github.io%2Fnest-simulator%2Fextension_modules>
.
Placing code for custom models in the models directory in the NEST
source code tree also works, but makes it more difficult to move to newer
versions of NEST or to share your custom models with colleagues.
Briefly, in addition to adding the source code files to the models
directory, you need to
1. add the files to models/CMakeLists.txt
2. #include the files in models/modelsmodule.cpp
3. add a line like
register_connection_model< StaticConnection >( "static_synapse" );
for each model. The template parameter is the model class, the
string the name it will have in NEST
4. recompile and reinstall NEST
Best,
Hans Ekkehard
On 6 May 2020, at 02:11, Allen Rabayda <arabayda(a)masonlive.gmu.edu>
wrote:
Dear Nest Community,
Would anyone have insight into why I'm getting an UnknownModelName
error?
I'm new to Nest and am using Nest 18.0 on Lubuntu Virtual Box (Windows
10 OS).
Thanks for any help.
Best Regards,
--Allen
**** Error Message--additional details attached ******
raise exceptionCls(commandname, message)
nest.ll_api.UnknownModelName: ('UnknownModelName in CopyModel_l_l_D:
/stdp_izh_bitwise_correct_connection is not a known model name. Please
check the modeldict for a list of available models.', 'UnknownModelName',
<SLILiteral: CopyModel_l_l_D>, ': /stdp_izh_bitwise_correct_connection is
not a known model name. Please check the modeldict for a list of available
models.')
********************************************************
<issue_UnknownModelName_4_May_2020>
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--
Prof. Dr. Hans Ekkehard Plesser
Head, Data Science Section
Faculty of Science and Technology
Norwegian University of Life Sciences
PO Box 5003, 1432 Aas, Norway
Phone +47 6723 1560
Email hans.ekkehard.plesser(a)nmbu.no
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--
Prof. Dr. Hans Ekkehard Plesser
Head, Data Science Section
Faculty of Science and Technology
Norwegian University of Life Sciences
PO Box 5003, 1432 Aas, Norway
Phone +47 6723 1560
Email hans.ekkehard.plesser(a)nmbu.no
<http://secure-web.cisco.com/1iP5XxSIgK1wF5QUFextVYBJcuhTvD7uZziUM9b_0s3CJyt4coQ-JaojYPcWkHY6GfIgOzSAlr4NFfZhr8Z172zC5SaCAWrN7Zz9ApSd4f6eA5bPremYXBOqAH_0MM6CCSJR7eDvRFU9Qd1y6vawZ91iPX2y5qaoU-0SyZyHI2UD7rp6FmPOi7PWHBHk9gXb6fp6qP1wbpMV8lwrvMGDglP_bw3HnLWIpw2DZKS0sDuzdrn7ECQmCzGHhIivmcUOsZgWNtnuP6A2WrPlnyAaeLuxwfQ4BYv7288-Qq4k9w4w5jGWOpMHFPs837kFW4zLht7l_9Dz4nsqCl8dSn1RmhHmeHEd412A_NctYEoizC86CDJutdeZ0jhh6K2HEDCT5snwo68iJAPnc20uucORO3mJinauyJ5801Fqj5-1zqMAIXt2rvrHJBTIrMSgG_dzU0jtP9ZS2AYhy13V_mxMYvA/http%3A%2F%2Fnmbu.no%2F>
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24 Jun
24 Jun
10:59 a.m.
Hi!
Just a quick heads up: I am currently working on a refactoring of the
example module, which might make things a bit easier in the future.
I'm expecting this to go live by the end of this week and will send
another mail to this list once I'm done.
Cheers,
Jochen!
On 16.06.20 03:12, Allen Rabayda wrote:
Hans and Nest User Community,
I was wondering if you had any advice for my errors when I
compile/register the custom Synapse Model, stdp_izh_connection.h/.cpp as
I can compile/install without issue using the example custom models
like pif_psc_alpha and drop_odd_synapse alone.
Two quick questions.
#1 Which synapse model registration statement should I use in
"my2module.cpp":
-
nest::kernel().model_manager.register_connection_model<STDPIzhConnection<targetidentifierT
--
Dr. Jochen Martin Eppler
Phone: +49(2461)61-96653
----------------------------------
Simulation Laboratory Neuroscience
Jülich Supercomputing Centre
Institute for Advanced Simulation
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Volker Rieke
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
>( "stdp_izh_connection" );
-
nest::kernel().model_manager.register_connection_model<
STDPIzhConnection< nest::TargetIdentifierPtrRport >
("stdp_izh_connection" );
-
nest::kernel().model_manager.register_prototype_connection<
STDPIzhConnection< nest::TargetIdentifierPtrRport >
("stdp_izh_connection" );
-
nest::kernel().model_manager.register_prototype_connection<
STDPIzhConnection>(net_, "stdp_izh_connection" );
#2 Which argument, "targetidentifierT" or
"TargetIdentifierPtrRport",
should I use:
- in "my2module.cpp" model registration?
- and in my synapse model, "stdp_izh_connection.h", templates?
I've included one of my error messages below for reference. I
received similar error messages for each of the registration statements
used above.
Thank you for any advice you may offer.
Best Regards,
--Allen
********* Background on the Custom Synapse Model********
- stdp_izh_connection.h/.cpp has been updated for nest 5g kernel per
https://nest.github.io/nest-simulator/model_conversion_5g
- stdp_izh_connection.h/.cpp has reformatted using
https://github.com/nest/nest-simulator/blob/master/models/stdp_connection_h…
as an example.
*********************************************************************
*********** Nest Compile Errors when including:
stdp_izh_connection.h/.cpp***********
[ 10%] Building CXX object CMakeFiles/my2module_module.dir/my2module.cpp.o
In file included from /home/nest/examples/My2Module/my2module.cpp:33:0:
/home/nest/examples/My2Module/stdp_izh_connection.h: In member function
‘void nest::STDPIzhConnection<targetidentifierT>::send(nest::Event&,
nest::thread, const nest::STDPIzhCommonProperties&)’:
/home/nest/examples/My2Module/stdp_izh_connection.h:305:5: error: ‘class
nest::Event’ has no member named ‘set_multiplicity’
e.set_multiplicity( -1 );
^~~~~~~~~~~~~~~~
/home/nest/examples/My2Module/stdp_izh_connection.h:306:5: error: ‘class
nest::Event’ has no member named ‘set_delay’; did you mean ‘set_sender’?
e.set_delay( ConnectionBase::get_delay_steps() ); // ConnectionBase
not used in sample
^~~~~~~~~
set_sender
/home/nest/examples/My2Module/stdp_izh_connection.h:309:18: error:
‘t_spike’ was not declared in this scope
t_lastspike_ = t_spike; // added per ref:
https://nest.github.io/nest-simulator/model_conversion_5g
^~~~~~~
/home/nest/examples/My2Module/stdp_izh_connection.h:309:18: note:
suggested alternative:
In file included from /home/nest/work/nest-install/include/nest/node.h:37:0,
from
/home/nest/work/nest-install/include/nest/common_synapse_properties.h:29,
from
/home/nest/work/nest-install/include/nest/connection.h:27,
from
/home/nest/examples/My2Module/drop_odd_spike_connection.h:27,
from /home/nest/examples/My2Module/my2module.cpp:29:
/home/nest/work/nest-install/include/nest/nest_names.h:424:19: note:
‘nest::names::t_spike’
extern const Name t_spike;
^~~~~~~
/home/nest/examples/My2Module/my2module.cpp: In member function ‘virtual
void mynest::My2Module::init(SLIInterpreter*)’:
/home/nest/examples/My2Module/my2module.cpp:142:59: error:
‘STDPIzhConnection’ was not declared in this scope
nest::kernel().model_manager.register_connection_model<
STDPIzhConnection< targetidentifierT > >(
^~~~~~~~~~~~~~~~~
/home/nest/examples/My2Module/my2module.cpp:142:59: note: suggested
alternative:
In file included from /home/nest/examples/My2Module/my2module.cpp:33:0:
/home/nest/examples/My2Module/stdp_izh_connection.h:114:7: note:
‘nest::STDPIzhConnection’
class STDPIzhConnection: public nest::Connection< targetidentifierT >
^~~~~~~~~~~~~~~~~
/home/nest/examples/My2Module/my2module.cpp:142:78: error:
‘targetidentifierT’ was not declared in this scope
nest::kernel().model_manager.register_connection_model<
STDPIzhConnection< targetidentifierT > >(
^~~~~~~~~~~~~~~~~
/home/nest/examples/My2Module/my2module.cpp:143:27: warning: comparison
with string literal results in unspecified behavior [-Waddress]
"stdp_izh_connection" );
^
/home/nest/examples/My2Module/my2module.cpp:142:98: error: invalid
operands of types ‘<unresolved overloaded function type>’ and ‘const
char [20]’ to binary ‘operator>’
nest::kernel().model_manager.register_connection_model<
STDPIzhConnection< targetidentifierT > >(
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
"stdp_izh_connection" );
~~~~~~~~~~~~~~~~~~~~~~~
CMakeFiles/my2module_module.dir/build.make:62: recipe for target
'CMakeFiles/my2module_module.dir/my2module.cpp.o' failed
make[2]: *** [CMakeFiles/my2module_module.dir/my2module.cpp.o] Error 1
CMakeFiles/Makefile2:67: recipe for target
'CMakeFiles/my2module_module.dir/all' failed
make[1]: *** [CMakeFiles/my2module_module.dir/all] Error 2
Makefile:151: recipe for target 'all' failed
make: *** [all] Error 2
On Fri, May 22, 2020 at 8:24 AM Hans Ekkehard Plesser
<hans.ekkehard.plesser(a)nmbu.no <mailto:hans.ekkehard.plesser@nmbu.no>>
wrote:
Hi Allen,
Thanks. It looks like a relative path has ended up in your
nest-config file where it should have been an absolute path. Could
you open file
nest-install/bin/nest-config
and go to roughly line 55, where you should find something like
--includes)
echo " -I/home/nest/work/nest-simulator-2.18.0/conngen
-I../nest-install/include/nest -I/usr/include -I/usr/include
-I/usr/local/include -I/usr/include
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include
-I/usr/lib/x86_64-linux-gnu/openmpi/include"
;;
Please replace within
-I../nest-install/include/nest
the .. with the absolute path. Then run cmake and make again in the
My2Module build directory. You may want to delete anything in that
build directory first to avoid old Cmake cached data.
Best,
Hans Ekkehard
On 21 May 2020, at 22:13, Allen Rabayda
<arabayda(a)masonlive.gmu.edu <mailto:arabayda@masonlive.gmu.edu>>
wrote:
Hans,
Below is the output from my 1) "cmake" and 2)
"{NEST_INSTALL_DIR}/bin/nest-config --prefix --includes --libs
--cflags" commands.
Thank you,
--Allen
Charl, I had not yet tried any of the processes on
https://github.com/nest/nest-simulator/issues/1331
<https://secure-web.cisco.com/1pvWX8gcr0ktPCO_pJ-XSV7OsLHFiWmE4gqVEtVzPY62QxY1eQ-8GQWP65ZAm2UnzB305znKhGBeGwk3pBCBzl8VOR2DbwaEVtwB6IqqgcUZ00aQ3KCz0pZCavFLjDbhwHT4dDzuJDzmZfXfPOh43poIG8N04bRnb8yWGChAfBw_d6FveE9QCARl1P7RLbZx2JO3Jutn_6NeHuvQ0US81N-LR2KHLRq2OP2zVHL989CZBuJHc2L7rHt8e95I7GsWuJ3nWlu8gts8AL8Q0aGjxo0Kzn1ZZbaQDJeBZkM7a8aQGjOjHfq24TEYMImyCtMnNUrAJciz44-6tObOUK8QDbtLQq6fszadM72YPHar9u1kjbVNXqRfAN6N6YNs3faASL0TwqOGptnApRBX2ImM9ySgQBFW48w8-871pKl3Dw83zEcxHGZ9dvmzsLptIVDNL/https%3A%2F%2Fgithub.com%2Fnest%2Fnest-simulator%2Fissues%2F1331>.
Thank you,--Allen
*****************
1) CMAKE OUTPUT:
*****************
nest@nestvm:~/examples/My2Module$ cmake
-Dwith-nest=${NEST_INSTALL_DIR}/bin/nest-config ../My2Module
-------------------------------------------------------
my2module Configuration Summary
-------------------------------------------------------
C++ compiler : /usr/bin/c++
Build static libs : OFF
C++ compiler flags :
NEST compiler flags : -std=c++11 -O2 -Wall -fopenmp -pthread
-fdiagnostics-color=auto
NEST include dirs :
-I/home/nest/work/nest-simulator-2.18.0/conngen
-I../nest-install/include/nest -I/usr/include -I/usr/include
-I/usr/local/include -I/usr/include
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include
-I/usr/lib/x86_64-linux-gnu/openmpi/include
NEST libraries flags : -L/home/nest/work/nest-install/lib
-lconngen -lnestutil -lnest -lrandom -lsli -lnestkernel -ltopology
-fopenmp /usr/lib/x86_64-linux-gnu/libltdl.so
/usr/lib/x86_64-linux-gnu/libgsl.so
/usr/lib/x86_64-linux-gnu/libgslcblas.so
/usr/local/lib/libneurosim.so /usr/local/lib/libpyneurosim.so
/usr/lib/x86_64-linux-gnu/libmusic.so
/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so
/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so
-------------------------------------------------------
You can now build and install 'my2module' using
make
make install
The library file libmy2module.so will be installed to
/home/nest/work/nest-install/lib/nest
Help files will be installed to
/home/nest/work/nest-install/share/doc/nest
The module can be loaded into NEST using
(my2module) Install (in SLI)
nest.Install('my2module') (in PyNEST)
The module will be installed into a non-default location!
Make sure to set the environment variables:
export
NEST_MODULE_PATH=/home/nest/work/nest-install/lib/nest:$NEST_MODULE_PATH
export
SLI_PATH=/home/nest/work/nest-install/share/nest/sli:$SLI_PATH
-- Configuring done
-- Generating done
-- Build files have been written to: /home/nest/examples/My2Module
-----------------------------------------------------
*****************
2) "{NEST_INSTALL_DIR}/bin/nest-config --prefix --includes --libs
--cflags OUTPUT
*****************
nest@nestvm:~$ export NEST_INSTALL_DIR=/home/nest/work/nest-install
nest@nestvm:~$ {NEST_INSTALL_DIR}/bin/nest-config --prefix
--includes --libs --cflags
bash: {NEST_INSTALL_DIR}/bin/nest-config: No such file or directory
*****************
then added absolute path to produce output below
*****************
nest@nestvm:~$ /home/nest/work/nest-install/bin/nest-config
--prefix --includes --libs --cflags
/home/nest/work/nest-install
-I/home/nest/work/nest-simulator-2.18.0/conngen
-I../nest-install/include/nest -I/usr/include -I/usr/include
-I/usr/local/include -I/usr/include
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include
-I/usr/lib/x86_64-linux-gnu/openmpi/include
-L/home/nest/work/nest-install/lib -lconngen -lnestutil -lnest
-lrandom -lsli -lnestkernel -ltopology -fopenmp
/usr/lib/x86_64-linux-gnu/libltdl.so
/usr/lib/x86_64-linux-gnu/libgsl.so
/usr/lib/x86_64-linux-gnu/libgslcblas.so
/usr/local/lib/libneurosim.so /usr/local/lib/libpyneurosim.so
/usr/lib/x86_64-linux-gnu/libmusic.so
/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so
/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so
-std=c++11 -O2 -Wall -fopenmp -pthread -fdiagnostics-color=auto
*****************
END
*****************
On Wed, May 20, 2020 at 3:08 AM Hans Ekkehard Plesser
<hans.ekkehard.plesser(a)nmbu.no
<mailto:hans.ekkehard.plesser@nmbu.no>> wrote:
Hi Allen,
--
Prof. Dr. Hans Ekkehard Plesser
Head, Data Science Section
Faculty of Science and Technology
Norwegian Universityof Life Sciences
PO Box 5003, 1432Aas, Norway
Phone +47 6723 1560
Emailhans.ekkehard.plesser(a)nmbu.no <http://nmbu.no>
Homehttp://arken.nmbu.no/~plesser
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Below I show how I adapted/complied the
example MyModule
included on github and the error message I get (bottom of email).
The steps look generally good.
two absolute paths inserted (correct
missing file error):
#include
"/home/nest/work/nest-simulator-2.18.0/sli/slifunction.h"
#include "/home/nest/work/nest-simulator-2.18.0/sli/slimodule.h"
You should not need the absolute paths, just the filenames
should suffice.
$ cd mmb
$ cmake -Dwith-nest=${NEST_INSTALL_DIR}/bin/nest-config
../My2Module
$ make
Could you post the output of the cmake command?
And also the output of the following command
${NEST_INSTALL_DIR}/bin/nest-config --prefix --includes --libs
--cflags
Best,
Hans Ekkehard
**********************
***ERROR MSG***
make: *** No targets specified and no makefile found. Stop.
*********************
*********************
*** changed directory from ./mmb to ./My2Module then re-ran
make*****
$ cd ~ examples/My2Module
$ make
***************'*******
***ERROR MSG****
Scanning dependencies of target my2module_module
[ 10%] Building CXX object
CMakeFiles/my2module_module.dir/my2module.cpp.o
In file included from
/home/nest/examples/My2Module/my2module.cpp:29:0:
/home/nest/examples/My2Module/drop_odd_spike_connection.h:27:10:
fatal error: connection.h: No such file or directory #include
"connection.h"
**********************
*********************
On Wed, May 6, 2020 at 2:33 AM Hans Ekkehard Plesser
<hans.ekkehard.plesser(a)nmbu.no
<mailto:hans.ekkehard.plesser@nmbu.no>> wrote:
Hi Allen,
Several steps are required to add a model to NEST. The
recommended way of adding a model is to create your own
NEST module outside the NEST source code tree. You will
find an example in examples/MyModule and more
documentation at
https://nest.github.io/nest-simulator/extension_modules
<https://secure-web.cisco.com/1OkG_4Lw1yXYSv9Bo1mMO2W05lnXnEL03XeGcAPY__8APmBFD6LJj5zzZE42doCxkKRobTud5P4AT-oAs4WO_e4LtGvMBLDNRl2akKXbAPU8F8r9Rm4A-tpRybnnEUh062b56HNleUWk7QJ6N1WbDPtfI2tSIZfBrNSy7ZS4MsvzYfYHFlpG8GQQde5gApJecM5CFQEEP9CGymqYZ18LQ3zj1pcYeYG_L4XhXZhfL9be5WtSMrDZVy_ZeB0g3Qorb-lhDrLguvPgqUhCze8vfsqesaXfTpE3HtpsEMUcfd3Xc5vUP1KU6rRWzSAw8az7wM5CxmAlax7wYyP8eT_0bQAweIakbsUW3bXaCT9znQv15l-qoBLExOyTKQvbcyNiwLEBNflla-_MsLueEemTJ1NRiHSI7kGavYtpaKaeXtlSy7q0YU9lIMHnnS0AWr5keolzddt0U0uCpJmO2uL9FUA/https%3A%2F%2Fnest.github.io%2Fnest-simulator%2Fextension_modules>.
Placing code for custom models in the models directory in
the NEST source code tree also works, but makes it more
difficult to move to newer versions of NEST or to share
your custom models with colleagues.
Briefly, in addition to adding the source code files to
the models directory, you need to
1. add the files to models/CMakeLists.txt
2. #include the files in models/modelsmodule.cpp
3. add a line like
register_connection_model< StaticConnection >(
"static_synapse" );
for each model. The template parameter is the model
class, the string the name it will have in NEST
4. recompile and reinstall NEST
Best,
Hans Ekkehard
--
Prof. Dr. Hans Ekkehard Plesser
Head, Data Science Section
Faculty of Science and Technology
Norwegian Universityof Life Sciences
PO Box 5003, 1432Aas, Norway
Phone +47 6723 1560
Emailhans.ekkehard.plesser(a)nmbu.no
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<mailto:users-leave@nest-simulator.org> On 6 May 2020, at 02:11, Allen
Rabayda
<arabayda(a)masonlive.gmu.edu
<mailto:arabayda@masonlive.gmu.edu>> wrote:
Dear Nest Community,
Would anyone have insight into why I'm getting an
UnknownModelName error?
I'm new to Nest and am using Nest 18.0 on Lubuntu
Virtual Box (Windows 10 OS).
Thanks for any help.
Best Regards,
--Allen
**** Error Message--additional details attached ******
raise exceptionCls(commandname, message)
nest.ll_api.UnknownModelName: ('UnknownModelName in
CopyModel_l_l_D: /stdp_izh_bitwise_correct_connection is
not a known model name. Please check the modeldict for a
list of available models.', 'UnknownModelName',
<SLILiteral: CopyModel_l_l_D>, ':
/stdp_izh_bitwise_correct_connection is not a known
model name. Please check the modeldict for a list of
available models.')
********************************************************
<issue_UnknownModelName_4_May_2020>_______________________________________________
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--
Prof. Dr. Hans Ekkehard Plesser
Head, Data Science Section
Faculty of Science and Technology
Norwegian Universityof Life Sciences
PO Box 5003, 1432Aas, Norway
Phone +47 6723 1560
Emailhans.ekkehard.plesser(a)nmbu.no
<http://secure-web.cisco.com/1oGxjTBn6G3zlyNTvv_hoyiXx9VwKKhVYGsnt8WkKZtjey0jolrbMkgNX8nwZ1_mVOfMZGiux9uomyEPFv1tB5lZkHqSDndkoq7WT3154Yx4mGDr8Arv_7jWQmncdw7br50zI6WljWy5IK7VdXa7cWJJMsib-PBr0HtFYGs5gbgToIMYR4w5rKqurTb-v0rgSNtJsrdJncRz5eqmnGWYbcKnShFCDiXti1pbbYmie86yWljTQbF0AtIphD_zoqJhi-TJYrXXjeVGyc2k_WQiq9cNQvbZlxfWAY8GM2CJWq_YnFnAj_wgKoFCuxVcs6gPmu6B-M8f9ZylTFcZTKA4SjnK6SJPiDig8sJf7qhGQW0aB1CMf88nIeQJFd5NE_nXYNkveMYHT2So_RNGY06D7hdDTA1VoxJgrV-JxlTvip1uelk7bGF8CPbWbPaNV-TAvtps_fwU_5vhhGiNNNPML6Q/http%3A%2F%2Fnmbu.no%2F>
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27 Jun
27 Jun
5:05 p.m.
Jochen,
Thank you. Looking forward to using it. Will watch for your next email.
Best Regards,
--Allen
On Wed, Jun 24, 2020 at 4:59 AM Jochen Martin Eppler <j.eppler(a)fz-juelich.de>
wrote:
Hi!
Just a quick heads up: I am currently working on a refactoring of the
example module, which might make things a bit easier in the future.
I'm expecting this to go live by the end of this week and will send
another mail to this list once I'm done.
Cheers,
Jochen!
On 16.06.20 03:12, Allen Rabayda wrote:
https://secure-web.cisco.com/1VdennQVusYlBHKK3H6dHSFKR8Vx1UWLhPZEEF2FsPX0XI…
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include
> -I/usr/lib/x86_64-linux-gnu/openmpi/include"
> ;;
> Please replace within
> -I../nest-install/include/nest
> the .. with the absolute path.
Then run cmake and make again in the
> My2Module build directory. You may want to delete anything in that
> build directory first to avoid old Cmake cached data.
> Best,
> Hans Ekkehard
>> On 21 May 2020, at 22:13,
Allen Rabayda
>> <arabayda(a)masonlive.gmu.edu
<mailto:arabayda@masonlive.gmu.edu>>
>> wrote:
>>> Homehttp://
secure-web.cisco.com/1GxBrTIvidKyg8bDi2P5i7i22ns5X8VwghGHrD4rONPwtdTt4RHOt6…
>>>
>>> _______________________________________________
>>> NEST Users mailing list -- users(a)nest-simulator.org
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>>> users-leave(a)nest-simulator.org
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>>>
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>>> NEST Users mailing list -- users(a)nest-simulator.org
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>> Homehttp://
secure-web.cisco.com/1GxBrTIvidKyg8bDi2P5i7i22ns5X8VwghGHrD4rONPwtdTt4RHOt6…
> --
> Prof. Dr. Hans Ekkehard Plesser
> Head, Data Science Section
> Faculty of Science and
Technology
> Norwegian Universityof Life Sciences
> PO Box 5003, 1432Aas, Norway
> Phone +47 6723 1560
> Emailhans.ekkehard.plesser(a)nmbu.no <
http://secure-web.cisco.com/1EamN3fdQ-N495adJ-vlyTRgr6Kv7x5i-dOJ23TU7UShcTn…
> Homehttp://
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> <mailto:users-leave@nest-simulator.org>
> _______________________________________________
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> To unsubscribe send an email to users-leave(a)nest-simulator.org
--
Dr. Jochen Martin Eppler
Phone: +49(2461)61-96653
----------------------------------
Simulation Laboratory Neuroscience
Jülich Supercomputing Centre
Institute for Advanced Simulation
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Volker Rieke
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
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Hans and Nest User Community,
I was wondering if you had any advice for my errors when I
compile/register the custom Synapse Model, stdp_izh_connection.h/.cpp as
I can compile/install without issue using the example custom models
like pif_psc_alpha and drop_odd_synapse alone.
Two quick questions.
#1 Which synapse model registration statement should I use in
"my2module.cpp":
-
nest::kernel().model_manager.register_connection_model<STDPIzhConnection<targetidentifierT
>(
"stdp_izh_connection" );
-
nest::kernel().model_manager.register_connection_model<
STDPIzhConnection< nest::TargetIdentifierPtrRport
("stdp_izh_connection" );
-
nest::kernel().model_manager.register_prototype_connection<
STDPIzhConnection< nest::TargetIdentifierPtrRport
("stdp_izh_connection" );
-
nest::kernel().model_manager.register_prototype_connection<
STDPIzhConnection>(net_, "stdp_izh_connection" );
#2 Which argument, "targetidentifierT" or
"TargetIdentifierPtrRport",
should I use:
- in "my2module.cpp" model registration?
- and in my synapse model, "stdp_izh_connection.h", templates?
I've included one of my error messages below for reference. I
received similar error messages for each of the registration statements
used above.
Thank you for any advice you may offer.
Best Regards,
--Allen
********* Background on the Custom Synapse Model********
- stdp_izh_connection.h/.cpp has been updated for nest 5g kernel per
- stdp_izh_connection.h/.cpp has reformatted
using
https://secure-web.cisco.com/1lwxXr_h6qWHk3vUFEx9s3nM4-jO0JT_jD9S9iNMcA6K0M…
as an example.
*********************************************************************
*********** Nest Compile Errors when including:
stdp_izh_connection.h/.cpp***********
[ 10%] Building CXX object
CMakeFiles/my2module_module.dir/my2module.cpp.o
In file included from
/home/nest/examples/My2Module/my2module.cpp:33:0:
/home/nest/examples/My2Module/stdp_izh_connection.h: In member function
‘void nest::STDPIzhConnection<targetidentifierT>::send(nest::Event&,
nest::thread, const nest::STDPIzhCommonProperties&)’:
/home/nest/examples/My2Module/stdp_izh_connection.h:305:5: error: ‘class
nest::Event’ has no member named ‘set_multiplicity’
e.set_multiplicity( -1 );
^~~~~~~~~~~~~~~~
/home/nest/examples/My2Module/stdp_izh_connection.h:306:5: error: ‘class
nest::Event’ has no member named ‘set_delay’; did you mean ‘set_sender’?
e.set_delay( ConnectionBase::get_delay_steps() ); // ConnectionBase
not used in sample
^~~~~~~~~
set_sender
/home/nest/examples/My2Module/stdp_izh_connection.h:309:18: error:
‘t_spike’ was not declared in this scope
t_lastspike_ = t_spike; // added per ref:
https://secure-web.cisco.com/1VdennQVusYlBHKK3H6dHSFKR8Vx1UWLhPZEEF2FsPX0XI…
^~~~~~~
/home/nest/examples/My2Module/stdp_izh_connection.h:309:18: note:
suggested alternative:
In file included from
/home/nest/work/nest-install/include/nest/node.h:37:0,
from
/home/nest/work/nest-install/include/nest/common_synapse_properties.h:29,
from
/home/nest/work/nest-install/include/nest/connection.h:27,
from
/home/nest/examples/My2Module/drop_odd_spike_connection.h:27,
from /home/nest/examples/My2Module/my2module.cpp:29:
/home/nest/work/nest-install/include/nest/nest_names.h:424:19: note:
‘nest::names::t_spike’
extern const Name t_spike;
^~~~~~~
/home/nest/examples/My2Module/my2module.cpp: In member function ‘virtual
void mynest::My2Module::init(SLIInterpreter*)’:
/home/nest/examples/My2Module/my2module.cpp:142:59: error:
‘STDPIzhConnection’ was not declared in this scope
nest::kernel().model_manager.register_connection_model<
STDPIzhConnection< targetidentifierT > >(
^~~~~~~~~~~~~~~~~
/home/nest/examples/My2Module/my2module.cpp:142:59: note: suggested
alternative:
In file included from /home/nest/examples/My2Module/my2module.cpp:33:0:
/home/nest/examples/My2Module/stdp_izh_connection.h:114:7: note:
‘nest::STDPIzhConnection’
class STDPIzhConnection: public nest::Connection< targetidentifierT ^~~~~~~~~~~~~~~~~
/home/nest/examples/My2Module/my2module.cpp:142:78: error:
‘targetidentifierT’ was not declared in this scope
nest::kernel().model_manager.register_connection_model<
STDPIzhConnection< targetidentifierT > >(
^~~~~~~~~~~~~~~~~
/home/nest/examples/My2Module/my2module.cpp:143:27: warning: comparison
with string literal results in unspecified behavior [-Waddress]
"stdp_izh_connection" );
^
/home/nest/examples/My2Module/my2module.cpp:142:98: error: invalid
operands of types ‘<unresolved overloaded function type>’ and ‘const
char [20]’ to binary ‘operator>’
nest::kernel().model_manager.register_connection_model<
STDPIzhConnection< targetidentifierT > >(
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~
"stdp_izh_connection" );
~~~~~~~~~~~~~~~~~~~~~~~
CMakeFiles/my2module_module.dir/build.make:62: recipe for target
'CMakeFiles/my2module_module.dir/my2module.cpp.o' failed
make[2]: *** [CMakeFiles/my2module_module.dir/my2module.cpp.o] Error 1
CMakeFiles/Makefile2:67: recipe for target
'CMakeFiles/my2module_module.dir/all' failed
make[1]: *** [CMakeFiles/my2module_module.dir/all] Error 2
Makefile:151: recipe for target 'all' failed
make: *** [all] Error 2
On Fri, May 22, 2020 at 8:24 AM Hans Ekkehard Plesser
<hans.ekkehard.plesser(a)nmbu.no <mailto:hans.ekkehard.plesser@nmbu.no>>
wrote:
Hi Allen,
Thanks. It looks like a relative path has ended up in your
nest-config file where it should have been an absolute path. Could
you open file
nest-install/bin/nest-config
and go to roughly line 55, where you should find something like
--includes)
echo " -I/home/nest/work/nest-simulator-2.18.0/conngen
-I../nest-install/include/nest -I/usr/include -I/usr/include
-I/usr/local/include -I/usr/include
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent
>
>> Hans,
>> Below is the output from my 1) "cmake" and 2)
>> "{NEST_INSTALL_DIR}/bin/nest-config --prefix --includes --libs
>> --cflags" commands.
>> Thank you,
>> --Allen
>
>> Charl, I had not yet
tried any of the processes on
>
https://secure-web.cisco.com/1MLBFo3x6JJko67my3nTeNwTgT3_lFTJxBACoNQGKpE8Se…
> <
https://secure-web.cisco.com/1pvWX8gcr0ktPCO_pJ-XSV7OsLHFiWmE4gqVEtVzPY62Qx…
.
> Thank you,--Allen
>
>
> *****************
> 1) CMAKE OUTPUT:
> *****************
>
> nest@nestvm:~/examples/My2Module$ cmake
> -Dwith-nest=${NEST_INSTALL_DIR}/bin/nest-config ../My2Module
>
> -------------------------------------------------------
> my2module Configuration Summary
> -------------------------------------------------------
>
> C++ compiler : /usr/bin/c++
> Build static libs : OFF
> C++ compiler flags :
> NEST compiler flags : -std=c++11 -O2 -Wall -fopenmp -pthread
> -fdiagnostics-color=auto
> NEST include dirs :
> -I/home/nest/work/nest-simulator-2.18.0/conngen
> -I../nest-install/include/nest -I/usr/include -I/usr/include
> -I/usr/local/include -I/usr/include
> -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi
>
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent
>
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include
>> -I/usr/lib/x86_64-linux-gnu/openmpi/include
>> NEST libraries flags : -L/home/nest/work/nest-install/lib
>> -lconngen -lnestutil -lnest -lrandom -lsli -lnestkernel -ltopology
>> -fopenmp /usr/lib/x86_64-linux-gnu/libltdl.so
>> /usr/lib/x86_64-linux-gnu/libgsl.so
>> /usr/lib/x86_64-linux-gnu/libgslcblas.so
>> /usr/local/lib/libneurosim.so /usr/local/lib/libpyneurosim.so
>> /usr/lib/x86_64-linux-gnu/libmusic.so
>> /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so
>> /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so
>
>>
-------------------------------------------------------
>
>> You can now build and
install 'my2module' using
>> make
>> make install
>
>> The library file
libmy2module.so will be installed to
>> /home/nest/work/nest-install/lib/nest
>> Help files will be installed to
>> /home/nest/work/nest-install/share/doc/nest
>
>> The module can be loaded
into NEST using
>> (my2module) Install (in SLI)
>> nest.Install('my2module') (in PyNEST)
>
>> The module will be
installed into a non-default location!
>> Make sure to set the environment variables:
>> export
>
NEST_MODULE_PATH=/home/nest/work/nest-install/lib/nest:$NEST_MODULE_PATH
>> export
>> SLI_PATH=/home/nest/work/nest-install/share/nest/sli:$SLI_PATH
>
>> -- Configuring done
>> -- Generating done
>> -- Build files have been written to: /home/nest/examples/My2Module
>> -----------------------------------------------------
>
>> *****************
>> 2) "{NEST_INSTALL_DIR}/bin/nest-config --prefix --includes --libs
>> --cflags OUTPUT
>> *****************
>
>> nest@nestvm:~$ export
NEST_INSTALL_DIR=/home/nest/work/nest-install
>> nest@nestvm:~$ {NEST_INSTALL_DIR}/bin/nest-config --prefix
>> --includes --libs --cflags
>> bash: {NEST_INSTALL_DIR}/bin/nest-config: No such file or directory
>> *****************
>> then added absolute path to produce output below
>> *****************
>> nest@nestvm:~$ /home/nest/work/nest-install/bin/nest-config
>> --prefix --includes --libs --cflags
>> /home/nest/work/nest-install
>> -I/home/nest/work/nest-simulator-2.18.0/conngen
>> -I../nest-install/include/nest -I/usr/include -I/usr/include
>> -I/usr/local/include -I/usr/include
>> -I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi
>
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent
>
-I/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include
>> -I/usr/lib/x86_64-linux-gnu/openmpi/include
>> -L/home/nest/work/nest-install/lib -lconngen -lnestutil -lnest
>> -lrandom -lsli -lnestkernel -ltopology -fopenmp
>> /usr/lib/x86_64-linux-gnu/libltdl.so
>> /usr/lib/x86_64-linux-gnu/libgsl.so
>> /usr/lib/x86_64-linux-gnu/libgslcblas.so
>> /usr/local/lib/libneurosim.so /usr/local/lib/libpyneurosim.so
>> /usr/lib/x86_64-linux-gnu/libmusic.so
>> /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so
>> /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so
>> -std=c++11 -O2 -Wall -fopenmp -pthread -fdiagnostics-color=auto
>> *****************
>> END
>> *****************
>
>> On Wed, May 20, 2020 at
3:08 AM Hans Ekkehard Plesser
>> <hans.ekkehard.plesser(a)nmbu.no
>> <mailto:hans.ekkehard.plesser@nmbu.no>> wrote:
>
>
>> Hi Allen,
>
>>> Below I show
how I adapted/complied the example MyModule
>>> included on github and the error message I get (bottom of
email).
>
>> The steps look
generally good.
>
>>> two absolute
paths inserted (correct missing file error):
>>> #include
>>> "/home/nest/work/nest-simulator-2.18.0/sli/slifunction.h"
>>> #include
"/home/nest/work/nest-simulator-2.18.0/sli/slimodule.h"
>
>> You should not need
the absolute paths, just the filenames
>> should suffice.
>
>>> $ cd mmb
>>> $ cmake -Dwith-nest=${NEST_INSTALL_DIR}/bin/nest-config
>>> ../My2Module
>>> $ make
>
>> Could you post the
output of the cmake command?
>
>> And also the output
of the following command
>
>>
${NEST_INSTALL_DIR}/bin/nest-config --prefix --includes --libs
>> --cflags
>
>> Best,
>> Hans Ekkehard
>
>>>
>>> **********************
>>> ***ERROR MSG***
>>> make: *** No targets specified and no makefile found. Stop.
>>> *********************
>>> *********************
>>>
>>> *** changed directory from ./mmb to ./My2Module then re-ran
>>> make*****
>>>
>>> $ cd ~ examples/My2Module
>>> $ make
>>>
>>> ***************'*******
>>> ***ERROR MSG****
>>> Scanning dependencies of target my2module_module
>>> [ 10%] Building CXX object
>>> CMakeFiles/my2module_module.dir/my2module.cpp.o
>>> In file included from
>>> /home/nest/examples/My2Module/my2module.cpp:29:0:
>>>
/home/nest/examples/My2Module/drop_odd_spike_connection.h:27:10:
>> fatal error: connection.h: No
such file or directory #include
>> "connection.h"
>> **********************
>> *********************
>>
>>
>> On Wed, May 6, 2020 at 2:33 AM Hans Ekkehard Plesser
>> <hans.ekkehard.plesser(a)nmbu.no
>> <mailto:hans.ekkehard.plesser@nmbu.no>> wrote:
>>
>>
>> Hi Allen,
>>
>> Several steps are required to add a model to NEST. The
>> recommended way of adding a model is to create your own
>> NEST module outside the NEST source code tree. You will
>> find an example in examples/MyModule and more
>> documentation at
>>
https://secure-web.cisco.com/11nUY061zM84Rywlc6PRfWD_B9ZVp7ehPlNtXWQvY1m9V_…
>> <
https://secure-web.cisco.com/1OkG_4Lw1yXYSv9Bo1mMO2W05lnXnEL03XeGcAPY__8APm…
.
>>
>> Placing code for custom models in the models directory in
>> the NEST source code tree also works, but makes it more
>> difficult to move to newer versions of NEST or to share
>> your custom models with colleagues.
>>
>> Briefly, in addition to adding the source code files to
>> the models directory, you need to
>>
>> 1. add the files to models/CMakeLists.txt
>> 2. #include the files in models/modelsmodule.cpp
>> 3. add a line like
>>
>> register_connection_model< StaticConnection >(
"static_synapse" );
>>
>> for each model. The template parameter is the model
>> class, the string the name it will have in NEST
>> 4. recompile and reinstall NEST
>>
>> Best,
>> Hans Ekkehard
>>
>>
>>
>>> On 6 May 2020, at 02:11, Allen Rabayda
>>> <arabayda(a)masonlive.gmu.edu
>>> <mailto:arabayda@masonlive.gmu.edu>> wrote:
>>>
>>> Dear Nest Community,
>>>
>>> Would anyone have insight into why I'm getting an
>>> UnknownModelName error?
>>>
>>> I'm new to Nest and am using Nest 18.0 on Lubuntu
>>> Virtual Box (Windows 10 OS).
>>>
>>> Thanks for any help.
>>>
>>> Best Regards,
>>> --Allen
>>>
>>> **** Error Message--additional details attached ******
>>> raise exceptionCls(commandname, message)
>>> nest.ll_api.UnknownModelName: ('UnknownModelName in
>>> CopyModel_l_l_D: /stdp_izh_bitwise_correct_connection is
>>> not a known model name. Please check the modeldict for a
>>> list of available models.', 'UnknownModelName',
>>> <SLILiteral: CopyModel_l_l_D>, ':
>>> /stdp_izh_bitwise_correct_connection is not a known
>>> model name. Please check the modeldict for a list of
>>> available models.')
>>> ********************************************************
>>>
<issue_UnknownModelName_4_May_2020>_______________________________________________
>>>> NEST Users mailing list -- users(a)nest-simulator.org
>>>> <mailto:users@nest-simulator.org>
>>>> To unsubscribe send an email to
>>>> users-leave(a)nest-simulator.org
>>>> <mailto:users-leave@nest-simulator.org>
>>>
>>> --
>>>
>>> Prof. Dr. Hans Ekkehard Plesser
>>> Head, Data Science Section
>>>
>>> Faculty of Science and Technology
>>> Norwegian Universityof Life Sciences
>>> PO Box 5003, 1432Aas, Norway
>>>
>>> Phone +47 6723 1560
>>> Emailhans.ekkehard.plesser(a)nmbu.no
>> <
http://secure-web.cisco.com/1oGxjTBn6G3zlyNTvv_hoyiXx9VwKKhVYGsnt8WkKZtjey0…
>> <
http://secure-web.cisco.com/1NGU903Sz1mZbu-kUPO3tQjT8UGyiDXuL1fL2jQ0S4SkecW…
>
>> --
>
>> Prof. Dr. Hans
Ekkehard Plesser
>> Head, Data Science Section
>
>> Faculty of Science
and Technology
>> Norwegian Universityof Life Sciences
>> PO Box 5003, 1432Aas, Norway
>
>> Phone +47 6723 1560
>> Emailhans.ekkehard.plesser(a)nmbu.no
> <
http://secure-web.cisco.com/1iP5XxSIgK1wF5QUFextVYBJcuhTvD7uZziUM9b_0s3CJyt…
> <
http://secure-web.cisco.com/1Yaz1kjc6VGnCjQQ1iYz5UzgeB8gnIvsxcPfiFurdqrnLLE…
>
>> _______________________________________________
>> NEST Users mailing list -- users(a)nest-simulator.org
>> <mailto:users@nest-simulator.org>
>> To unsubscribe send an email to users-leave(a)nest-simulator.org
>> <mailto:users-leave@nest-simulator.org>
>
>>
_______________________________________________
>> NEST Users mailing list -- users(a)nest-simulator.org
>> <mailto:users@nest-simulator.org>
>> To unsubscribe send an email to users-leave(a)nest-simulator.org
>> <mailto:users-leave@nest-simulator.org>
<
http://secure-web.cisco.com/1nd3Dn41NSvMCZuqSxusD7gKebEdh81Q4sSm7WqGfmTpD98…
1603
days inactive
1655
days old
16 comments
5 participants
participants (5)
-
Allen Rabayda -
Charl Linssen -
Hans Ekkehard Plesser -
Itaru Kitayama -
Jochen Martin Eppler