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nrnivmodl fails--"libnrnoc.so: could not read symbols"
Posted: Mon Mar 09, 2009 5:18 pm
by costas
Dear All
I am trying to compile my NEURON-code in UNIX that I have been running on my Mac (therefore, I know the code runs). While all membrane mechanisms are read successfully by the compiler, at the end (of the nrnivmodl-procedure) I receive the following error message:
Code: Select all
.o .libs/kd.o .libs/kk.o .libs/km.o .libs/naf.o .libs/nax.o .libs/node.o .libs/mod_func.o -Wl,--rpath -Wl,/usr/local/lib -Wl,--rpath -Wl,/usr/local/lib -L/usr/local/lib /usr/local/lib/libnrnoc.so /usr/local/lib/liboc.so -L/usr/X11R6/lib /usr/local/lib/libmemacs.so /usr/local/lib/libnrnmpi.so /usr/local/lib/libscopmath.so /usr/local/lib/libsparse13.so -lreadline -lncurses /usr/local/lib/libnrniv.so /usr/local/lib/libivoc.so /usr/local/lib/libneuron_gnu.so /usr/local/lib/libmeschach.so /usr/local/lib/libsundials.so /usr/local/lib/libIVhines.so -lSM -lICE -lX11 -ldl -lm -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0
/usr/local/lib/libnrnoc.so: could not read symbols: File in wrong format
collect2: ld returned 1 exit status
make: *** [libnrnmech.la] Error 1
Does anybody know what I am supposed to do to overcome this obstacle?
Thanks a lot!
Costas
Re: nrnivmodl fails--"libnrnoc.so: could not read symbols"
Posted: Tue Mar 10, 2009 1:05 pm
by ted
My guess is that UNIX tried to use some .o files that had been generated under OS X (did you zip up a whole directory tree on your Mac--including files output by prevously running nrnivmodl--then transferred it to your UNIX box and expanded it there?)
Delete all .o and .c files.
Delete any .i686 directory and its contents.
Run nrnivmodl again.
Re: nrnivmodl fails--"libnrnoc.so: could not read symbols"
Posted: Fri Jul 09, 2010 7:45 pm
by eschombu
I don't think Costas ever got this working, and I'm now having the same problem. We have NEURON 7.1 on our (unix) server. The mod files DO compile on my mac (with NEURON 7.2). Here's where I think the nrnivmodl output starts to indicate problems (or thereabouts; I can send a full printout if it would be helpful):
Code: Select all
"/usr/local/share/nrn/libtool" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath "/usr/local/lib" h.lo kadist.lo kaprox.lo kdrca1.lo na3n.lo naxn.lo mod_func.lo -L"/usr/local/lib" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L"/usr/local/lib" "/usr/local/lib/libnrniv.la" -livoc -lneuron_gnu -lmeschach -lsundials -lm -ldl
libtool: link: warning: library `/usr/local/lib/liboc.la' was moved.
libtool: link: warning: library `/usr/local/lib/libmemacs.la' was moved.
libtool: link: warning: library `/usr/local/lib/libnrnmpi.la' was moved.
libtool: link: warning: library `/usr/local/lib/libscopmath.la' was moved.
libtool: link: warning: library `/usr/local/lib/libsparse13.la' was moved.
libtool: link: warning: library `/usr/local/lib/libnrniv.la' was moved.
libtool: link: warning: library `/usr/local/lib/libivoc.la' was moved.
libtool: link: warning: library `/usr/local/lib/libneuron_gnu.la' was moved.
libtool: link: warning: library `/usr/local/lib/libmeschach.la' was moved.
libtool: link: warning: library `/usr/local/lib/libsundials.la' was moved.
gcc -shared .libs/h.o .libs/kadist.o .libs/kaprox.o .libs/kdrca1.o .libs/na3n.o .libs/naxn.o .libs/mod_func.o -Wl,--rpath -Wl,/usr/local/lib -Wl,--rpath -Wl,/usr/local/lib -L/usr/local/lib /usr/local/lib/libnrnoc.so /usr/local/lib/liboc.so /usr/local/lib/libmemacs.so /usr/local/lib/libnrnmpi.so /usr/local/lib/libscopmath.so /usr/local/lib/libsparse13.so -lreadline -lncurses /usr/local/lib/libnrniv.so /usr/local/lib/libivoc.so /usr/local/lib/libneuron_gnu.so /usr/local/lib/libmeschach.so /usr/local/lib/libsundials.so -lm -ldl -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0
/usr/local/lib/libnrnoc.so: could not read symbols: File in wrong format
collect2: ld returned 1 exit status
make: *** [libnrnmech.la] Error 1
Any recommendations on what to try? I'm running this in a folder that I don't think has any files from a mac compilation (whether in hidden or non-hidden folders).
Thanks,
Erik
Re: nrnivmodl fails--"libnrnoc.so: could not read symbols"
Posted: Sat Jul 10, 2010 9:04 am
by hines
/usr/local/lib/libnrnoc.so: could not read symbols: File in wrong format
What is your machine type?
uname -a
What file did you use to install NEURON?
Re: nrnivmodl fails--"libnrnoc.so: could not read symbols"
Posted: Mon Jul 12, 2010 4:40 pm
by eschombu
The reply from our computer administrator:
What is your machine type?
Linux socrates.klab.caltech.edu 2.6.18-194.8.1.el5 #1 SMP Wed Jun 23 10:58:38 EDT 2010 i686 i686 i386 GNU/Linux
What file did you use to install NEURON?
I'm not sure what that question refers to. Maybe "nrn-7.1.tar.gz" is
what they meant?
He said he ran into other build issues you may be interested in. Could we start an email thread so I can include him? Since he did the install, it's hard for me to answer the questions related to it. I'm at the same username as on the forum, but at caltech.edu.
Thanks again,
Erik
Re: nrnivmodl fails--"libnrnoc.so: could not read symbols"
Posted: Mon Jul 12, 2010 5:31 pm
by hines
Yes. We can take this to email. michael dot hines at yale dot edu
I think you should try to install in a subdirectory of your $HOME so you do not have to become a root user
for installation. Try
mkdir $HOME/neuron
cd $HOME/neuron
curl -O
http://www.neuron.yale.edu/ftp/neuron/v ... -17.tar.gz
curl -O
http://www.neuron.yale.edu/ftp/neuron/v ... 445.tar.gz
tar xzf iv-17.tar.gz
tar xzf nrn-7.2.alpha-445.tar.gz
mv iv-17 iv
mv nrn-7.2 nrn
cd iv
./configure --prefix=`pwd`
make
make install
cd ../nrn
./configure --prefix=`pwd`
make
make install
export PATH=$HOME/nrn/i686/bin:$PATH
now try your code again.
Re: nrnivmodl fails--"libnrnoc.so: could not read symbols"
Posted: Mon Jul 12, 2010 5:32 pm
by hines
Sorry. I should have typed
export PATH=$HOME/neuron/nrn/i686/bin:$PATH
Re: nrnivmodl fails--"libnrnoc.so: could not read symbols"
Posted: Thu Sep 16, 2010 3:37 am
by athan
costas wrote:Dear All
I am trying to compile my NEURON-code in UNIX that I have been running on my Mac (therefore, I know the code runs). While all membrane mechanisms are read successfully by the compiler, at the end (of the nrnivmodl-procedure) I receive the following error message:
Code: Select all
.o .libs/kd.o .libs/kk.o .libs/km.o .libs/naf.o .libs/nax.o .libs/node.o .libs/mod_func.o -Wl,--rpath -Wl,/usr/local/lib -Wl,--rpath -Wl,/usr/local/lib -L/usr/local/lib /usr/local/lib/libnrnoc.so /usr/local/lib/liboc.so -L/usr/X11R6/lib /usr/local/lib/libmemacs.so /usr/local/lib/libnrnmpi.so /usr/local/lib/libscopmath.so /usr/local/lib/libsparse13.so -lreadline -lncurses /usr/local/lib/libnrniv.so /usr/local/lib/libivoc.so /usr/local/lib/libneuron_gnu.so /usr/local/lib/libmeschach.so /usr/local/lib/libsundials.so /usr/local/lib/libIVhines.so -lSM -lICE -lX11 -ldl -lm -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0
/usr/local/lib/libnrnoc.so: could not read symbols: File in wrong format
collect2: ld returned 1 exit status
make: *** [libnrnmech.la] Error 1
Does anybody know what I am supposed to do to overcome this obstacle?
Thanks a lot!
Costas
I was encountering the same problem. I eventually got NEURON to compile by following the full installation steps outlined by Michael.
After installing everything with the source code, I realized that the original problem was due to the fact that I had originally installed the wrong rpm. I had installed the i686 version but I was using a 64-bit machine. No problems/errors occurred until I tried running nrnivmodl at which time I got the same error message as Costas. I should have installed the x86_64 rpm version (which is basically what was installed from the complete installation from the source code -- with many more steps).