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
neurondemo: Special.exe not working (Cygwin, Vista or XP)
-
- Site Admin
- Posts: 6300
- Joined: Wed May 18, 2005 4:50 pm
- Location: Yale University School of Medicine
- Contact:
Re: neurondemo: Special.exe not working (Cygwin, Vista or XP)
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.I downloaded, compiled and installed the Linux version of Neuron 7.0
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
Exactly what error messages did _you_ see, and at what point in compiling and installing?During the compilation and install process, we saw a few errors
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.We both have installed a lot of extra packages; I thought we had all the necessary ones installed.
Re: neurondemo: Special.exe not working (Cygwin, Vista or XP)
This is not an error, just a test to see if HAVE_SIGPOLL should bedo SIGPOLL and I_GETSIG work: no But see config.log to see why it failed.
defined or not. As long as configure creates a bunch of Makefile then
things are probably ok.
For NEURON under mswin it isNext, I entered make; make install
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
-
- Site Admin
- Posts: 6300
- Joined: Wed May 18, 2005 4:50 pm
- Location: Yale University School of Medicine
- Contact:
Re: neurondemo: Special.exe not working (Cygwin, Vista or XP)
So all those
configure: failed program was:
with nothing following are benign, and so is
configure: program exited with status 1
?
configure: failed program was:
with nothing following are benign, and so is
configure: program exited with status 1
?
Re: neurondemo: Special.exe not working (Cygwin, Vista or XP)
I installed the most recent version of cygwin three weeks ago; I think it's still the most recent one.ted wrote: Is it correct to assume that you installed the most recent cygwin?
Were you able to install Interviews?
Interviews installed correctly.
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=$NSRC" (and the prefix option), but I got the same errors in config.log as last time.hines wrote: By the way. Configureing with --with-nrnpython should work without further effort.
Configureing with --with-paranrn requires an cygwin installation of mpich2. See the last section of the.
nrn/mswinmpiconf file for how to build with mpi on a multicore workstation.
/********************/
-
- Site Admin
- Posts: 6300
- Joined: Wed May 18, 2005 4:50 pm
- Location: Yale University School of Medicine
- Contact:
Re: neurondemo: Special.exe not working (Cygwin, Vista or XP)
It isn't packaged with the current gzipped tar files. It's part of the mercurial repository. To save you the trouble of installing mercurial, cloning the repository, etc. etc., here's mswinmpiconf in toto. The part Michael referred to starts withneuromau wrote:There was no file resembling mswinmpiconf in either my nrn or iv directories. I downloaded nrn-7.0.tar.gz and iv-17.tar.gz on April 10th. Was that file added later? I tried running with the "--with-paranrn" option anyway but of course it didn't work. Then I took that off but kept the "--with-nrnpython --srcdir=$NSRC" (and the prefix option), but I got the same errors in config.log as last time.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.
#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