Segmentation Violation 7.3

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Martenzi
Posts: 34
Joined: Thu Feb 28, 2013 4:17 am

Segmentation Violation 7.3

Post by Martenzi » Sun Jun 09, 2013 1:34 am

Im getting a segmentation violation with neuron 7.3 under windows 7. I loaded the cell and biophysics from "Branco et al. 2010" in ModelDB. I get this when I hit Init.

Where should I start the troubleshooting?

Martenzi
Posts: 34
Joined: Thu Feb 28, 2013 4:17 am

Re: Segmentation Violation 7.3

Post by Martenzi » Sun Jun 09, 2013 2:40 am

NEURON -- Release 7.3 (849:5be3d097b917) 2013-04-11
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2013
See http://www.neuron.yale.edu/neuron/credits

oc>loading membrane mechanisms from ./Branco_2010/mod.files/nrnmech.dll
dlopen failed -
Exec format error
I get this error message. Could it be the problem with undefined units on the dll?

Martenzi
Posts: 34
Joined: Thu Feb 28, 2013 4:17 am

Re: Segmentation Violation 7.3

Post by Martenzi » Sun Jun 09, 2013 3:08 am

Previously I asked for help on a segmentation violation due to 7.3 version. It was about compiling proper dll files from Brancos mod files. You saw that he had not clearly defined what units and the two last last codes is how you told me to correct it. I did and I got this error while compiling. Any idea?

Code: Select all

gcc -DDLL_EXPORT -DPIC  -I/cygdrive/C/nrn73/src/scopmath -I/cygdrive/C/     /nrnoc -I/cygdrive/C/nrn73/src/oc  -I/cygdrive/C/nrn73/lib -I/cygdrive/     ccinc -I/cygdrive/C/nrn73/gcc3inc -L/cygdrive/C/nrn73/gcclib -c mod_fun
nocmodl NMDA_Mg_T
Translating NMDA_Mg_T.mod into NMDA_Mg_T.c
Notice: Use of POINTER is not thread safe.
NEURON's CVode method ignores conservation
Notice: Assignment to the GLOBAL variable, "rmd2u", is not thread safe
Notice: Assignment to the GLOBAL variable, "rmd2b", is not thread safe
Notice: Assignment to the GLOBAL variable, "rmd1u", is not thread safe
Notice: Assignment to the GLOBAL variable, "rmd1b", is not thread safe
gcc -DDLL_EXPORT -DPIC  -I/cygdrive/C/nrn73/src/scopmath -I/cygdrive/C/     /nrnoc -I/cygdrive/C/nrn73/src/oc  -I/cygdrive/C/nrn73/lib -I/cygdrive/     ccinc -I/cygdrive/C/nrn73/gcc3inc -L/cygdrive/C/nrn73/gcclib -c NMDA_Mg
gcc -I/cygdrive/C/nrn73/lib -I/cygdrive/C/nrn73/gccinc -I/cygdrive/C/nr     nc -L/cygdrive/C/nrn73/gcclib -shared -o nrnmech.dll mod_func.o CaT.o H     _Mg_T.o ar.o ca.o caL3d.o cad.o h.o inwardrect.o kca.o kir.o km.o kv.o      ase_BMK.o \
  -L/cygdrive/C/nrn73/bin -lnrniv -lpthread
CaT.o: file not recognized: File format not recognized
collect2: ld returned 1 exit status
/cygdrive/C/nrn73/lib/mknrndll.mak:71: recipe for target `nrnmech.dll' 
make: *** [nrnmech.dll] Error 1

There was an error in the process of creating nrnmech.dll
Press Return key to exit
Fortunately, modlunit often provides useful clues. Also, the person who wrote this NMODL file was good about declaring the units used by parameters and variables. This error message
CODE: SELECT ALL
0.001 m2-kg/sec2-coul
The previous expression is not dimensionless at line 174 in file NMDA_Mg_T.mod

Code: Select all

   rmb    = Rmb    * mg * (1e3) * exp((v-40) * valence * memb_fraction /25<<ERROR>>)
flags the 25 in the denominator because it doesn't have the same units as the numerator (which is in mV). The fix is to replace this line with
CODE: SELECT ALL

Code: Select all

:   rmb    = Rmb    * mg * (1e3) * exp((v-40) * valence * memb_fraction /25)
   rmb    = Rmb    * mg * (1e3) * exp((v-40) * valence * memb_fraction / (25 (mV)) )
Check this file with modlunit again, and you'll see a similar error message about the line that starts
rmu = . . .

Martenzi
Posts: 34
Joined: Thu Feb 28, 2013 4:17 am

Re: Segmentation Violation 7.3

Post by Martenzi » Sun Jun 09, 2013 3:35 am

The changes you postulated prohibits the make dll from being succesfull with versions dating back to 7.1

Im not sure what to do becuase i need the NMDA file from Branco to work, otherwise my model is useless.

Martenzi
Posts: 34
Joined: Thu Feb 28, 2013 4:17 am

Re: Segmentation Violation 7.3

Post by Martenzi » Sun Jun 09, 2013 3:35 am

Does it matter that Branco used Python under linux?

ted
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Re: Segmentation Violation 7.3

Post by ted » Sun Jun 09, 2013 11:03 am

Has nothing to do with units or Python. This error message provides whatever clue there may be:

Code: Select all

CaT.o: file not recognized: File format not recognized
collect2: ld returned 1 exit status
/cygdrive/C/nrn73/lib/mknrndll.mak:71: recipe for target `nrnmech.dll'
make: *** [nrnmech.dll] Error 1

There was an error in the process of creating nrnmech.dll
On my PC with Win 7, the mod files compile without difficulty. I suspect there is a problem with the version of NEURON that you installed. What is the first line that NEURON prints to its interpreter window when you run nrngui? Does neurondemo run successfully? Have you been able to compile the mod files from any model at all? (the Mainen & Sejnowski model
https://senselab.med.yale.edu/modeldb/S ... model=2488
would be a good test)

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