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Re: [moose-devel] Error in moose.connect method
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From: Saeed <sa...@gn...> - 2014-04-30 18:21:51
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Thank you Subhasis, It was very helpful.
I know that the code is under development and I should not expect
correct execution at this moment. But my problem is that I suggested to
some students to have performance analysis on the Moose for their class
project. Their deadline is quite close and I want to give them a small
model and a version of Moose that is work enough for applying
performance tests.
It would be my great pleasure if you could tell me which kind of test
cases you have used for testing the parallel execution. For example if
one of the snippets are suitable for these test, would be great. Also,
do you know any revision of the async13 which is working and suitable
for parallel test?
For example the last code of async13 has some missed files such as
boost, global.cpp, etc. I just added files from other branches and I do
not know are they correct version or not. By the way it compiled, but in
simulation the below errors occur:
bin: 101
Error: bin:101t: 1921.01 currTime_ 1920 dt_: 0.01
Simulated till 1930. Left: 70. 10 of simulation took: 0.016554 s
bin: 101
Error: bin:101t: 1931.01 currTime_ 1930 dt_: 0.01
Simulated till 1940. Left: 60. 10 of simulation took: 0.016555 s
bin: 101
Error: bin:101t: 1941.01 currTime_ 1940 dt_: 0.01
It can be possibly the result of changes which I made in the code.
Thank you very much in advance
On 30-04-2014 02:41, Subhasis Ray wrote:
> Hi,
> More specifically the error is due to incorrect field name, as the error
> message suggests. The field name is 'spikeOut' and the snippet had not been
> updated to reflect the change in naming.
>
> Please note that we have settled on some naming conventions for fields
> since async13 branch.
> In particular, all source fields are suffixed 'Out' unless the field name
> itself is output. Many of the old snippets and demos have been copied over
> to the async13 branch but not yet updated to follow the new naming
> convention and hence this error.
>
> You can check the available field names using moose.doc() function in
> Python which displays the class documentation and a list of fields, like
> this:
>
>>>> moose.doc('Compartment')
> If you want to display the documentation for a particular field, then
> append the field name with a dot as separator:
>
>>>> moose.doc('Compartment.Vm')
> I made some fixes to docstring generation, so please update before reading
> the docs.
>
> Best,
> - Subhasis
> ( ʃʊbʱaːʃɪʃ )
>
>
> On Tue, Apr 29, 2014 at 11:32 PM, Dilawar Singh <dil...@nc...>wrote:
>
>> Hi Saeed,
>>
>> We are in process of integrating 'hsolve' into async13 branch. Only
>> today, I
>> got some sanity check of hsolve working. I am not sure how long it
>> will take
>> to get hsolve properly integrated with python.
>>
>> For time being -- if you want to use async13 branch -- you can change
>> the
>> solver to 'ee' from 'hsolve'.
>>
>> I'll let you know as soon as hsolve is ready.
>>
>> Dilawar
>>
>> On Tue, Apr 29, 2014 at 02:58:28PM -0300, Saeed wrote:
>>> Sure, Sorry for the lack of information.
>>> As I found it happens in many of Demo files, for example at
>> "async13/Demos/snippets/testHsolve.py" the below error produces:
>>> =====================================
>>> on node 0, numNodes = 1, numCores = 12
>>> Info: Time to define moose classes:0
>>> Info: Time to initialize module:0.05
>>> Created 306 path=/n numData=1 isGlobal=0 baseType=Neutral
>>> Created 307 path=/n/compt numData=1 isGlobal=0 baseType=SymCompartment
>>> Created 308 path=/n/compt/Na numData=1 isGlobal=0 baseType=HHChannel
>>> Created 312 path=/n/compt/K numData=1 isGlobal=0 baseType=HHChannel
>>> Created 316 path=/n/compt/synInput numData=1 isGlobal=0 baseType=SpikeGen
>>> Created 317 path=/n[0]/shaft0 numData=1 isGlobal=0 baseType=SymCompartment
>>> Created 318 path=/n[0]/head0 numData=1 isGlobal=0 baseType=SymCompartment
>>> Created 319 path=/n[0]/head0[0]/gluR numData=1 isGlobal=0 baseType=SynChan
>>> Created 321 path=/n[0]/head0[0]/ca numData=1 isGlobal=0 baseType=CaConc
>>> 0: Shell::doAddMsg: Error: Failed to find field event on src: synInput
>>> Traceback (most recent call last):
>>> File "testHsolve.py", line 297, in <module>
>>> main()
>>> File "testHsolve.py", line 294, in main
>>> test_elec_alone()
>>> File "testHsolve.py", line 265, in test_elec_alone
>>> make_spiny_compt()
>>> File "testHsolve.py", line 243, in make_spiny_compt
>>> moose.connect( synInput, 'event', syn, 'addSpike', 'Single' )
>>> NameError: check field names and type compatibility.
>>>
>>> ======================================
>>>
>>> It seems that the finfoMap_ array at Cinfo.cpp:214 does not contains all
>> object names.
>>>
>>>
>>>> Upi
>>>> Dear Saeed,
>>>> Please give script snippet where this happens. Also you might wish
>>>> to look in Demos/snippets for examples of the correct use of the
>> function.
>>>> Best,
>>>> Upi
>>>> On Tuesday 29 April 2014 09:04 PM, Saeed Shariati wrote:
>>>>> Hi,
>>>>>
>>>>> At async13 branch, when it tries to use connect method, the below error
>>>>> throws away:
>>>>>
>>>>> 0: Shell::doAddMsg: Error: Failed to find field spike on src: cell_0
>>>>>
>>>>> It would be my please if you have a look at this.
>>>>>
>>>>> Bests,
>>>>> Saeed
>>>>>
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