www.neuron.yale.edu

Dear All,

I wrote a code connecting 4 neurons(as given on the neuron webpage),
It worked fine.
Now I tried adding a calcium mechanish, essentially taking code from
neuron website naming the file "CaT.mod"
I put both my hoc file "test6.hoc" and "CaT.mod" in a common directory
and ran nrnivmodl in the same directory .
Though it gives the following error initially

CaT.mod
CaT.mod
"/usr/local/nrn/i686/bin/nocmodl" CaT
Translating CaT.mod into CaT.c
INITIAL not allowed in this kind of block at line 45 in file CaT.mod
}
make: *** [CaT.lo] Error 1[/color]

I run it again it works fine and creates a directory i686 in the current
directory giving the following message.....

/home/rishabh/acads/scratch/neuron_codes/Calcium
CaT.mod
CaT.mod
"/usr/local/nrn/share/nrn/libtool" --mode=compile gcc -DHAVE_CONFIG_H
-I. -I.. -I"/usr/local/nrn/include/nrn" -I"/usr/local/nrn/i686/lib" -g
-O2 -c -o CaT.lo `test -f 'CaT.c' || echo '/'`CaT.c
mkdir .libs
gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/local/nrn/include/nrn
-I/usr/local/nrn/i686/lib -g -O2 -c CaT.c -fPIC -DPIC -o .libs/CaT.o
"/usr/local/nrn/share/nrn/libtool" --mode=compile gcc -DHAVE_CONFIG_H
-I. -I.. -I"/usr/local/nrn/include/nrn" -I"/usr/local/nrn/i686/lib" -g
-O2 -c -o mod_func.lo mod_func.c
gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/local/nrn/include/nrn
-I/usr/local/nrn/i686/lib -g -O2 -c mod_func.c -fPIC -DPIC -o
.libs/mod_func.o
"/usr/local/nrn/share/nrn/libtool" --mode=link gcc -module -g -O2 -o
libnrnmech.la -rpath "/usr/local/nrn/i686/lib" CaT.lo mod_func.lo
-L"/usr/local/nrn/i686/lib" -lnrnoc -loc -lmemacs -lscopmath -lsparse13
-lreadline -lncurses -ldl -lm
gcc -shared .libs/CaT.o .libs/mod_func.o -Wl,--rpath
-Wl,/usr/local/nrn/i686/lib -Wl,--rpath -Wl,/usr/local/nrn/i686/lib
-L/usr/local/nrn/i686/lib /usr/local/nrn/i686/lib/libnrnoc.so
/usr/local/nrn/i686/lib/liboc.so -L/usr/X11R6/lib
/usr/local/nrn/i686/lib/libmemacs.so
/usr/local/nrn/i686/lib/libscopmath.so
/usr/local/nrn/i686/lib/libsparse13.so
/usr/local/nrn/i686/lib/libreadline.so -lncurses -ldl -lm -Wl,-soname
-Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0
(cd .libs && rm -f libnrnmech.so.0 && ln -s libnrnmech.so.0.0.0
libnrnmech.so.0)
(cd .libs && rm -f libnrnmech.so && ln -s libnrnmech.so.0.0.0
libnrnmech.so)
creating libnrnmech.la

creating libnrnmech.la
(cd .libs && rm -f libnrnmech.la && ln -s ../libnrnmech.la
libnrnmech.la)
Successfully created i686/special


However the problem is the following ..........., when I run the .hoc
file (which has been modified by adding "insert CaT statements" etc. it
gives the following error(I think it does not compile after insert CaT
statement.......


loading membrane mechanisms from
/home/rishabh/acads/scratch/neuron_codes/Calcium/i686/.libs/libnrnmech.so
dlopen failed -
/home/rishabh/acads/scratch/neuron_codes/Calcium/i686/.libs/libnrnmech.so:
undefined symbol: _CaT_reg
dlopen("libjvm.so") failed: libjvm.so: cannot open shared object file:
No such file or directory
JNI_CreateJavaVM returned -1
Info: optional feature Java VM is not present.
1
/usr/local/nrn/i686/bin/nrniv: syntax error
in test6.hoc near line 28
insert CaT


I cant figure what to do, plz tell

I'm not sure I understand. First, I have no idea what CaT.mod file you are referring to.
Second, if nrnivmodl reported this error message then CaT.mod has a serious error. When you say

I run it again it works fine

does that mean that you edited the mod file and corrected the error? If the answer is no,
then nothing that follows is valid.

thanx
i checked the .mod file, there was some minor error.
Its working now

when I run the .hoc file

Exactly how do you "run the .hoc file"? i.e. what is the command line?
What message do you see if you just type
nrngui
at the system prompt?

I run the file as

nrngui file_name

Message recieved when typing just nrngui.......

dlopen("libjvm.so") failed: libjvm.so: cannot open shared object file: No such file or directory
JNI_CreateJavaVM returned -1
Info: optional feature Java VM is not present.

whatever that message implies , the main toolbar comes up and the graph, shape plots etc work fine .......

Sounds like compilation was not successful. To diagnose the problem, it is necessary for
me to be able to reproduce it. If you zip up all the mod files that are in the directory where
you invoked nrnivmodl and send the zip file to me
ted dot carnevale at yale dot edu
I will try to figure out what is the cause and how to fix it.