cannot find libnrnmech.so
cannot find libnrnmech.so
it said:
Successfully created x86_64/special
but I cannot run
x86_64/special
here is an error:
loading membrane mechanisms from /u/home3/liujk/neuron/nrn/share/nrn/demo/release/x86_64/.libs/libnrnmech.so
dlopen failed -
/u/home3/liujk/neuron/nrn/share/nrn/demo/release/x86_64/.libs/libnrnmech.so: cannot open shared object file: No such file or directory
I get into /x86_64/.libs/, no libnrnmech.so at all. Anything wrong? Thanks.
Successfully created x86_64/special
but I cannot run
x86_64/special
here is an error:
loading membrane mechanisms from /u/home3/liujk/neuron/nrn/share/nrn/demo/release/x86_64/.libs/libnrnmech.so
dlopen failed -
/u/home3/liujk/neuron/nrn/share/nrn/demo/release/x86_64/.libs/libnrnmech.so: cannot open shared object file: No such file or directory
I get into /x86_64/.libs/, no libnrnmech.so at all. Anything wrong? Thanks.
Sorry for confusion.
I try to install NEURON under my user account in the cluster. So I am just a regular user. I follow the steps as in the post:
how to run NEURON in supercomputer
I follow the steps in
NRNIV only (no GUI)
tar xzf nrn-nn.tar.gz
# renaming the new directory to nrn makes life simpler later on
mv nrn-n.n nrn
cd nrn
./configure --prefix=`pwd` --without-iv
make
make install
all above steps are OK. Then I test
3. Test NEURON by running its "demonstration" program.
./config.guess #your hostcpu is printed in the form hostcpu-vendor-osversion
cd share/nrn/demo/release
# for this concrete example, we assume hostcpu is i686
$HOME/neuron/nrn/i686/bin/nrnivmodl
~~~~~~~~~~~~~~~~~~ it's OK, it said:
Successfully created x86_64/special.
there are some warnings, I assume they are OK. Then I run:
x86_64/special
I got the error:
loading membrane mechanisms from /u/home3/liujk/neuron/nrn/share/nrn/demo/release/x86_64/.libs/libnrnmech.so
dlopen failed -
/u/home3/liujk/neuron/nrn/share/nrn/demo/release/x86_64/.libs/libnrnmech.so: cannot open shared object file: No such file or directory
I get into x86_64/.libs/, not the root directory, no libnrnmech.so at all.
here are some results, I am not the superuser.
uname -a
Linux login1 2.6.18-8.el5 #1 SMP Thu Mar 15 19:46:53 EDT 2007 x86_64 x86_64 x86_64 GNU/Linux
g++ -v
Using built-in specs.
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-libgcj-multifile --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --enable-plugin --with-java-home=/usr/lib/jvm/java-1.4.2-gcj-1.4.2.0/jre --with-cpu=generic --host=x86_64-redhat-linux
Thread model: posix
gcc version 4.1.2 20070626 (Red Hat 4.1.2-14)
any suggestions?
I try to install NEURON under my user account in the cluster. So I am just a regular user. I follow the steps as in the post:
how to run NEURON in supercomputer
I follow the steps in
NRNIV only (no GUI)
tar xzf nrn-nn.tar.gz
# renaming the new directory to nrn makes life simpler later on
mv nrn-n.n nrn
cd nrn
./configure --prefix=`pwd` --without-iv
make
make install
all above steps are OK. Then I test
3. Test NEURON by running its "demonstration" program.
./config.guess #your hostcpu is printed in the form hostcpu-vendor-osversion
cd share/nrn/demo/release
# for this concrete example, we assume hostcpu is i686
$HOME/neuron/nrn/i686/bin/nrnivmodl
~~~~~~~~~~~~~~~~~~ it's OK, it said:
Successfully created x86_64/special.
there are some warnings, I assume they are OK. Then I run:
x86_64/special
I got the error:
loading membrane mechanisms from /u/home3/liujk/neuron/nrn/share/nrn/demo/release/x86_64/.libs/libnrnmech.so
dlopen failed -
/u/home3/liujk/neuron/nrn/share/nrn/demo/release/x86_64/.libs/libnrnmech.so: cannot open shared object file: No such file or directory
I get into x86_64/.libs/, not the root directory, no libnrnmech.so at all.
here are some results, I am not the superuser.
uname -a
Linux login1 2.6.18-8.el5 #1 SMP Thu Mar 15 19:46:53 EDT 2007 x86_64 x86_64 x86_64 GNU/Linux
g++ -v
Using built-in specs.
Target: x86_64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-libgcj-multifile --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --enable-plugin --with-java-home=/usr/lib/jvm/java-1.4.2-gcj-1.4.2.0/jre --with-cpu=generic --host=x86_64-redhat-linux
Thread model: posix
gcc version 4.1.2 20070626 (Red Hat 4.1.2-14)
any suggestions?
hines wrote:What said? neurondemo?it said:
Or nrnivmodl?
How did you install? From tar.gz sources or from an rpm?
If the latter, which rpm did you use?
What is the result on your machine of:
uname -a
g++ -vYou have x86_64 in your root directory?I get into /x86_64/.libs/
Since it is a cluster, I presume you will want to run parallel programs.I try to install NEURON under my user account in the cluster
...
./configure --prefix=`pwd` --without-iv
In that case you would need to be explicit about using mpi.
Code: Select all
./configure --prefix=`pwd` --without-iv --with-paranrn
http://www.neuron.yale.edu/ftp/ted/neur ... _press.pdf
But that is for later and has nothing to do with your present problem.
I doubt there is anything wrong with your installation of NEURON but$HOME/neuron/nrn/i686/bin/nrnivmodl
~~~~~~~~~~~~~~~~~~ it's OK, it said:
Successfully created x86_64/special.
the test instructions need to be worked on.
I need to know the exact nrnivmodl command you typed and the working
directory you typed it in. Also send all the output resulting from the
command. It is best to do this by email to michael.hines@yale.edu.
(The thing that is wrong with the test instructions is that they could
interfere with a subsequent "neurondemo" command)
yes, I did. like this:
when I run the parallel test code, I found
any wrong? thanks. I send you a detail list.
Code: Select all
./configure --prefix=`pwd` --without-iv --disable-shared --with-paranrn
make
make install
cd share/nrn/demo/release
/u/home3/liujk/neuron/nrn/x86_64/bin/nrnivmodl
login1:~/neuron/nrn/share/nrn/demo/release {512}$
/u/home3/liujk/neuron/nrn/x86_64/bin/nrnivmodl
Code: Select all
login1:~/neuron/nrn/src/parallel {501}$ mpiexec -np 4 $HOME/neuron/nrn/x86_64/bin/nrniv -mpi test0.hoc
--------------------------------------------------------------------------
[0,1,0]: OpenIB on host login1 was unable to find any HCAs.
Another transport will be used instead, although this may result in
lower performance.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
[0,1,1]: OpenIB on host login1 was unable to find any HCAs.
Another transport will be used instead, although this may result in
lower performance.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
[0,1,3]: OpenIB on host login1 was unable to find any HCAs.
Another transport will be used instead, although this may result in
lower performance.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
[0,1,2]: OpenIB on host login1 was unable to find any HCAs.
Another transport will be used instead, although this may result in
lower performance.
--------------------------------------------------------------------------
numprocs=4
NEURON -- Release 6.1.2 (1927) 2007-12-30
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2007
See http://www.neuron.yale.edu/credits.html
There are 4 processes. My rank is 1 and I am on login1
There are 4 processes. My rank is 0 and I am on login1
There are 4 processes. My rank is 2 and I am on login1
There are 4 processes. My rank is 3 and I am on login1
any wrong? thanks. I send you a detail list.
hines wrote: Since it is a cluster, I presume you will want to run parallel programs.
In that case you would need to be explicit about using mpi.and you should consultCode: Select all
./configure --prefix=`pwd` --without-iv --with-paranrn
http://www.neuron.yale.edu/ftp/ted/neur ... _press.pdf
But that is for later and has nothing to do with your present problem.
I doubt there is anything wrong with your installation of NEURON but
the test instructions need to be worked on.
I need to know the exact nrnivmodl command you typed and the working
directory you typed it in. Also send all the output resulting from the
command. It is best to do this by email to michael.hines@yale.edu.
(The thing that is wrong with the test instructions is that they could
interfere with a subsequent "neurondemo" command)
Code: Select all
./configure --prefix=`pwd` --without-iv --disable-shared --with-paranrn
library from nrnivmodl, that is why the dlopen fails. I recommend one more configure
option: linux_nrnmech=no
Note there is no '--' for that option.
Where did you find out about what configure line you should use. I need to read
that document and see if the instructions can be improved.
I found it here:
https://www.neuron.yale.edu/phpBB2/viewtopic.php?t=1171
I try to follow steps there, but something is wrong.
So I take minimum steps.
OK. it works by using
now I have
mod files are loaded. it's good. But when I run the sample code
'insert' doesn't work. I also try to run my code, same thing. Did I still miss something. Thanks
https://www.neuron.yale.edu/phpBB2/viewtopic.php?t=1171
I try to follow steps there, but something is wrong.
Code: Select all
../nrn/configure --prefix=`pwd` \
'--srcdir=../nrn' '--without-x' '--without-memacs' '--without-readline'\
'--disable-shared' '--with-paranrn' '--without-nmodl' \
CC=cc CXX=CC MPICC=cc MPICXX=CC linux_nrnmech=no \
java_dlopen=no \
am_cv_CC_dependencies_compiler_type=dashmstdout \
am_cv_CXX_dependencies_compiler_type=dashmstdout \
--host=x86_64-unknown-linux-gnu
===
configure: WARNING: If you wanted to set the --build type, don't use --host.
If a cross compiler is detected then cross compile mode will be used.
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for x86_64-unknown-linux-gnu-strip... no
checking for strip... strip
checking build system type... x86_64-redhat-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for style of include used by make... GNU
checking for x86_64-unknown-linux-gnu-g++... CC
checking for C++ compiler default output file name... configure: error: C++ compiler cannot create executables
See `config.log' for more details.
OK. it works by using
Code: Select all
./configure --prefix=`pwd` --without-iv --disable-shared --with-paranrn linux_nrnmech=no
Code: Select all
/u/home3/liujk/neuron/nrn/x86_64/bin/nrnivmodl
x86_64/special
NEURON -- Release 6.1.2 (1927) 2007-12-30
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2007
See http://www.neuron.yale.edu/credits.html
Additional mechanisms from files
cabpump.mod cachan1.mod camchan.mod capump.mod invlfire.mod khhchan.mod mcna.mod nacaex.mod nachan.mod release.mod
oc>
Code: Select all
login1:~/neuron/nrn/share/demo {593}$ /u/home3/liujk/neuron/nrn/x86_64/bin/nrniv release.hoc
NEURON -- Release 6.1.2 (1927) 2007-12-30
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2007
See http://www.neuron.yale.edu/credits.html
/u/home3/liujk/neuron/nrn/x86_64/bin/nrniv: syntax error
in release.hoc near line 13
{insert HHna insert HHk insert cachan insert cadifpmp }
^
hines wrote:--disable-shared is the problem. Since it also causes static linking of the nrnmechCode: Select all
./configure --prefix=`pwd` --without-iv --disable-shared --with-paranrn
library from nrnivmodl, that is why the dlopen fails. I recommend one more configure
option: linux_nrnmech=no
Note there is no '--' for that option.
Where did you find out about what configure line you should use. I need to read
that document and see if the instructions can be improved.
Code: Select all
/u/home3/liujk/neuron/nrn/x86_64/bin/nrniv release.hoc
Code: Select all
x86_64/special release.hoc
neuron librarires, main function, and all the linked mod files.
thanks, that works. I'm using something like
in my desktop. Never use the command like this. Good to know. Thanks a lot, now I can use our cluster to run NEURON.
Code: Select all
nrngui release.hoc
hines wrote:Because the special is statically linked, you need to run that directly.Code: Select all
/u/home3/liujk/neuron/nrn/x86_64/bin/nrniv release.hoc
The "special" is no longer a shell script but the full executable containing all theCode: Select all
x86_64/special release.hoc
neuron librarires, main function, and all the linked mod files.