dependencies (Gentoo)

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jyamad

dependencies (Gentoo)

Post by jyamad » Wed Sep 09, 2009 1:45 pm

I am trying to put together an ebuild of NEURON for the portage package management system that comes with Gentoo Linux. To do this, one of the major steps in defining all of the dependencies.

Is there a good place for me to look to ferret out all the dependencies? I've checked the debian and rpm builds but I think there may be missing packages on that list.

A complicating factor is the flexible way Gentoo does dependencies. For those unfamiliar, the portage system actually compiles the program according to USE flags that can turn on/off different dependencies. For instance, a "python" use flag would issue the "--with-nrnpython" option to ./configure and would require python. This means I need to associate dependencies with configure options and include build-time dependencies.

Thanks for the help. And, of course, I'll happily share the ebuild once I get it working.

hines
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Joined: Wed May 18, 2005 3:32 pm

Re: dependencies (Gentoo)

Post by hines » Wed Sep 09, 2009 4:04 pm

I might be misunderstanding your question, but the only way I know of determining dependencies is to infer them from which libraries
are needed. For example, the list below for the nrnmpi configuration I built seems to require
libreadline.so.5
libncurses.so.5
libpython2.5.so.1.0
libmpichcxx.so.1.1
libmpich.so.1.1
and a bunch of system libraries.
For binary distributions for linux and max os x
I normally build with a configure option of --with-nrnpython=dynamic which works with any or no version
of python. But to build it you have to have all the versions of python installed with the Include path specified in
nrn/src/nrnpython/nrnpydynam.sh

Code: Select all

[hines@hines490 neuron]$ ldd nrnmpi/x86_64/bin/nrniv
        libnrnoc.so.0 => /home/hines/neuron/nrnmpi/x86_64/lib/libnrnoc.so.0 (0x00002b0aefdab000)
        liboc.so.0 => /home/hines/neuron/nrnmpi/x86_64/lib/liboc.so.0 (0x00002b0aeffff000)
        libX11.so.6 => /usr/lib64/libX11.so.6 (0x00000036acc00000)
        libnrniv.so.0 => /home/hines/neuron/nrnmpi/x86_64/lib/libnrniv.so.0 (0x00002b0af0247000)
        libivoc.so.0 => /home/hines/neuron/nrnmpi/x86_64/lib/libivoc.so.0 (0x00002b0af0553000)
        libnrnmpi.so.0 => /home/hines/neuron/nrnmpi/x86_64/lib/libnrnmpi.so.0 (0x00002b0af0872000)
        libneuron_gnu.so.0 => /home/hines/neuron/nrnmpi/x86_64/lib/libneuron_gnu.so.0 (0x00002b0af0a78000)
        libscopmath.so.0 => /home/hines/neuron/nrnmpi/x86_64/lib/libscopmath.so.0 (0x00002b0af0c85000)
        libsparse13.so.0 => /home/hines/neuron/nrnmpi/x86_64/lib/libsparse13.so.0 (0x00002b0af0ea9000)
        libsundials.so.0 => /home/hines/neuron/nrnmpi/x86_64/lib/libsundials.so.0 (0x00002b0af10bd000)
        libmemacs.so.0 => /home/hines/neuron/nrnmpi/x86_64/lib/libmemacs.so.0 (0x00002b0af12f0000)
        libmeschach.so.0 => /home/hines/neuron/nrnmpi/x86_64/lib/libmeschach.so.0 (0x00002b0af1506000)
        libIVhines.so.3 => /home/hines/neuron/iv/x86_64/lib/libIVhines.so.3 (0x00002b0af1753000)
        libreadline.so.5 => /usr/lib64/libreadline.so.5 (0x00000036aa000000)
        libncurses.so.5 => /usr/lib64/libncurses.so.5 (0x00000036bbe00000)
        libnrnpython.so.0 => /home/hines/neuron/nrnmpi/x86_64/lib/libnrnpython.so.0 (0x00002b0af1b81000)
        libpython2.5.so.1.0 => /usr/lib/libpython2.5.so.1.0 (0x0000003cd6c00000)
        libpthread.so.0 => /lib64/libpthread.so.0 (0x00000036ab000000)
        libutil.so.1 => /lib64/libutil.so.1 (0x00000036b7a00000)
        libdl.so.2 => /lib64/libdl.so.2 (0x00000036aac00000)
        libmpichcxx.so.1.1 => /home/hines/mpich2/lib/libmpichcxx.so.1.1 (0x00002b0af1d94000)
        libmpich.so.1.1 => /home/hines/mpich2/lib/libmpich.so.1.1 (0x00002b0af1fb9000)
        librt.so.1 => /lib64/librt.so.1 (0x00000036ab400000)
        libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00000036bc200000)
        libm.so.6 => /lib64/libm.so.6 (0x00000036aa800000)
        libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00000036bae00000)
        libc.so.6 => /lib64/libc.so.6 (0x00000036aa400000)
        libXau.so.6 => /usr/lib64/libXau.so.6 (0x00000036ac800000)
        libXdmcp.so.6 => /usr/lib64/libXdmcp.so.6 (0x00000036ac400000)
        /lib64/ld-linux-x86-64.so.2 (0x00000036a9400000)
[hines@hines490 neuron]$ 

Keivan
Posts: 127
Joined: Sat Apr 22, 2006 4:28 am

Re: dependencies (Gentoo)

Post by Keivan » Mon Nov 22, 2010 12:48 pm

I've compiled neuron in gentoo linux + KDE, but there is an error I do'nt know how to fix?

Code: Select all

nrniv: unable to open font "*helvetica-medium-r-normal*--14*", using "fixed"

hines
Site Admin
Posts: 1577
Joined: Wed May 18, 2005 3:32 pm

Re: dependencies (Gentoo)

Post by hines » Mon Nov 22, 2010 1:17 pm

The font is specified in <prefix>/share/nrn/lib/nrn.defaults .
It appears that you do not have that font installed. Try commenting out the font lines in the
nrn.defaults file or else replace the font with one that is perhaps more generic.
I admit to being not very familiar with font name standards.

hines
Site Admin
Posts: 1577
Joined: Wed May 18, 2005 3:32 pm

unable to open font (ubuntu)

Post by hines » Wed Oct 26, 2011 9:20 am

For ubuntu 11.04 I was able to fix
nrniv: unable to open font "*helvetica-medium-r-normal*--14*", using "fixed"
with
sudo apt-get install xfonts-100dpi
and then logging out and logging back in.

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