problems on a 64bit machine

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vp
Posts: 2
Joined: Tue Jun 27, 2006 2:45 pm

problems on a 64bit machine

Post by vp » Tue Jun 27, 2006 2:57 pm

I've installed Neuron from the latest RPM on AMD64 machine with Fedora Core 2. When I'm trying to run HOC files I'm always getting something like this:

>nrngui rundemo.hoc
NEURON -- Version 5.9 2006-5-20 18:55:15 Main (39)
by John W. Moore, Michael Hines, and Ted Carnevale
Duke and Yale University -- Copyright 1984-2005

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.
oc>/usr/local/nrn/i686/bin/nrniv: NEURONMainMenu : a template cannot be redefined
in /usr/local/nrn/share/nrn/lib/hoc/stdrun.hoc near line 5
begintemplate NEURONMainMenu // avoid some namespace pollution
^
xopen("$(NEURONHOME)/lib/hoc/stdrun.hoc")
xopen("demo_PY_RS.oc")
run_RS()

Is this a problem with installation? How to fix it?

vp
Posts: 2
Joined: Tue Jun 27, 2006 2:45 pm

compiling

Post by vp » Tue Jun 27, 2006 3:10 pm

Also, when I'm compiling I always get this error:

>nrnivmodl IM.mod
IM.mod
IM.mod
"/usr/local/nrn/i686/bin/nocmodl" IM
Translating IM.mod into IM.c
Warning: Default 36 of PARAMETER celsius will be ignored and set by NEURON.
"/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 IM
.lo IM.c
mkdir .libs
gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/local/nrn/include/nrn -I/usr/local/nrn/i68 6/lib -g -O2 -c IM.c -fPIC -DPIC -o .libs/IM.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 mo d_func.lo mod_func.c
gcc -DHAVE_CONFIG_H -I. -I.. -I/usr/local/nrn/include/nrn -I/usr/local/nrn/i68 6/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 libnrn mech.la -rpath "/usr/local/nrn/i686/lib" IM.lo mod_func.lo -L"/usr/local/nrn/ i686/lib" -lnrnoc -loc -lmemacs -lscopmath -lsparse13 -lreadline -lncurses -ldl -lm
gcc -shared .libs/IM.o .libs/mod_func.o -Wl,--rpath -Wl,/usr/local/nrn/i686/l ib -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 /us r/local/nrn/i686/lib/libmemacs.so /usr/local/nrn/i686/lib/libscopmath.so /usr/l ocal/nrn/i686/lib/libsparse13.so /usr/local/nrn/i686/lib/libreadline.so -lncurs es -ldl -lm -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0
/usr/local/nrn/i686/lib/libnrnoc.so: could not read symbols: File in wrong form at
collect2: ld returned 1 exit status
make: *** [libnrnmech.la] Error 1

ted
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Location: Yale University School of Medicine
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Re: problems on a 64bit machine

Post by ted » Wed Jun 28, 2006 12:36 am

vp wrote: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.
This is meaningless unless you are one of the handful of people who are
using Java with NEURON.
oc>/usr/local/nrn/i686/bin/nrniv: NEURONMainMenu : a template cannot be redefined
in /usr/local/nrn/share/nrn/lib/hoc/stdrun.hoc near line 5
begintemplate NEURONMainMenu // avoid some namespace pollution
^
xopen("$(NEURONHOME)/lib/hoc/stdrun.hoc")
xopen("demo_PY_RS.oc")
run_RS()
It is a symptom of idiosyncratic programming in demo_PY_RS.oc, which
is probably "legacy code" that uses strategies that worked fine at one
time but are now deprecated if not obsolete. The fix is to edit that file,
changing
xopen("$(NEURONHOME)/lib/hoc/stdrun.hoc")
to
load_file("stdrun.hoc")

ted
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Posts: 5601
Joined: Wed May 18, 2005 4:50 pm
Location: Yale University School of Medicine
Contact:

Re: compiling

Post by ted » Wed Jun 28, 2006 12:40 am

vp wrote:Also, when I'm compiling I always get this error:
Dunno about this one. Given what we know about the aforementioned hoc
file, my suspicion is that the mod file is at fault--but can't be sure without
seeing it. If you email it to me
ted dot carnevale at yale dot edu
then I can have an informed opinion.

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