www.neuron.yale.edu

Posted: **Mon Apr 20, 2009 7:18 pm**

Hi there,

I downloaded, compiled and installed the Linux version of Neuron 7.0 on my Windows Vista machine using Cygwin. My colleague did the same on his Windows XP machine using Cygwin. During the compilation and install process, we saw a few errors:
1. Sigpoll and I_getsig were not installed correctly
2. There was some type of warning involving libtools, about symbolic tools

When we tried to run the neurondemo after installation, I (Vista) received several messages that "special.exe" had stopped working. My colleague (XP) didn't even receive an error message; the command just ended. We both have installed a lot of extra packages; I thought we had all the necessary ones installed. Any ideas of what caused the special.exe error, including whether the above errors 1 or 2 are relevant?

Thanks

Posted: **Mon Apr 20, 2009 8:56 pm**

I downloaded, compiled and installed the Linux version of Neuron 7.0

A minor comment about terminology: the source code is the source code. It's not the "Linux version source code." It's the source code for UNIX, Linux, MSWin, and OS X.

So you installed NEURON by downloading and compiling the source code. And since you did it under MSWin, this discussion thread belongs in
NEURON installation and configuration : UNIX/Linux

During the compilation and install process, we saw a few errors

Exactly what error messages did _you_ see, and at what point in compiling and installing?

We both have installed a lot of extra packages; I thought we had all the necessary ones installed.

Lack of a required package is certainly one possibility; Cygwin keeps evolving, and the list of required packages has changed somewhat over time. But in order to decide the real origin of the problem, it is necessary to see the actual error messages.

Posted: **Wed Apr 22, 2009 8:03 am**

do SIGPOLL and I_GETSIG work: no But see config.log to see why it failed.

This is not an error, just a test to see if HAVE_SIGPOLL should be
defined or not. As long as configure creates a bunch of Makefile then
things are probably ok.

Next, I entered make; make install

For NEURON under mswin it is
make
make mswin
or you can avoid the "make mswin" by doing step 3 in
http://www.neuron.yale.edu/neuron/insta ... mswin.html
"make mswin" completes the build and copies all the files needed to create a setup.exe into
c:\marshalnrn\nrn
and then executes the nsis installer builder (which will fail if not installed but does not matter
since you can treat the c:\marshalnrn\nrn as the installed software.
By the way. Configureing with --with-nrnpython should work without further effort.
Configureing with --with-paranrn requires an cygwin installation of mpich2. See the last section of the.
nrn/mswinmpiconf file for how to build with mpi on a multicore workstation.

The nrnsetup....exe installers are built with the fragment in nrn/mkalpha.sh that is substantively:

Code: Select all

$NSRC/configure --prefix=`pwd` --with-nrnpython --srcdir=$NSRC --with-paranrn
make
make mswin

Posted: **Wed Apr 22, 2009 9:15 am**

So all those
configure: failed program was:
with nothing following are benign, and so is
configure: program exited with status 1
?

Posted: **Wed Apr 22, 2009 1:40 pm**

ted wrote: Is it correct to assume that you installed the most recent cygwin?
Were you able to install Interviews?

I installed the most recent version of cygwin three weeks ago; I think it's still the most recent one.
Interviews installed correctly.

hines wrote: By the way. Configureing with --with-nrnpython should work without further effort.
Configureing with --with-paranrn requires an cygwin installation of mpich2. See the last section of the.
nrn/mswinmpiconf file for how to build with mpi on a multicore workstation.

There was no file resembling mswinmpiconf in either my nrn or iv directories. I downloaded nrn-7.0.tar.gz and iv-17.tar.gz on April 10th. Was that file added later? I tried running with the "--with-paranrn" option anyway but of course it didn't work. Then I took that off but kept the "--with-nrnpython --srcdir=$NSRC" (and the prefix option), but I got the same errors in config.log as last time.

/********************/

Posted: **Wed Apr 22, 2009 1:57 pm**

neuromau wrote:
hines wrote: By the way. Configureing with --with-nrnpython should work without further effort.
Configureing with --with-paranrn requires an cygwin installation of mpich2. See the last section of the.
nrn/mswinmpiconf file for how to build with mpi on a multicore workstation.
There was no file resembling mswinmpiconf in either my nrn or iv directories. I downloaded nrn-7.0.tar.gz and iv-17.tar.gz on April 10th. Was that file added later? I tried running with the "--with-paranrn" option anyway but of course it didn't work. Then I took that off but kept the "--with-nrnpython --srcdir=$NSRC" (and the prefix option), but I got the same errors in config.log as last time.

It isn't packaged with the current gzipped tar files. It's part of the mercurial repository. To save you the trouble of installing mercurial, cloning the repository, etc. etc., here's mswinmpiconf in toto. The part Michael referred to starts with
#notes about building with mpich2 under cygwin.

Code: Select all

#!/bin/sh
# installed mpich2 from mpich2-1.0.3-1-win32-ia32.msi from
# http://www-unix.mcs.anl.gov/mpi/mpich2/index.htm#download
# Note: "This setup requires the .NET Framwork version 1.1.4322..." 
# and they really mean 1.1, not 2.0 and not 1.0.
# Installed in c:/mpich2 to avoid spaces in paths.
# First get to the point where you can run cpi.exe example. May need to
# give yourself a login password.

export CFLAGS="-mwindows -I/cygdrive/c/mpich2/include"
export CXXFLAGS="-mwindows -I/cygdrive/c/mpich2/include"
export LIBS="-L/cygdrive/c/mpich2/lib -lmpi"
export LDFLAGS="-e _mainCRTStartup"

#build InterViews with above environment also

./configure --prefix=`pwd` --with-paranrn --with-iv=$HOME/neuron/ivmpi

# make
# make mswin
# in the src/parallel directory one can launch any of the tests with, e.g.
# c:/mpich2/bin/mpiexec -np 1 c:\\marshalnrn\\nrn\\bin\\nrniv.exe -mpi test0.hoc


if false
#notes about building with mpich2 under cygwin.
#I have used it with multicore desktops.
#In my $HOME
curl -O http://www.mcs.anl.gov/research/projects/mpich2/downloads/tarballs/1.0.7
/mpich2-1.0.7.tar.gz
tar xzf mpich*gz
cd mpich*7
./configure --prefix=$HOME/mpich2 --with-device=ch3:nemesis \
  'pac_cv_f77_sizeof_integer=4' 'pac_cv_f77_sizeof_double_precision=8' \
  'CFLAGS=-DDLL_EXPORT -DPIC' 'CXXFLAGS=-DDLL_EXPORT -DPIC'
make >& build.stdout
#did not do a "make install"
# note that the build.stdout is needed by src/mswin/nrncygso.sh
# and also /home/hines/mpich2-1.0.7
# is hardwired in there as well in two places as well as in
# src/mswin/batch/instal.sh

fi

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neurondemo: Special.exe not working (Cygwin, Vista or XP)

neurondemo: Special.exe not working (Cygwin, Vista or XP)

Re: neurondemo: Special.exe not working (Cygwin, Vista or XP)

Re: neurondemo: Special.exe not working (Cygwin, Vista or XP)

Re: neurondemo: Special.exe not working (Cygwin, Vista or XP)

Re: neurondemo: Special.exe not working (Cygwin, Vista or XP)

Re: neurondemo: Special.exe not working (Cygwin, Vista or XP)