Fail to import hoc file using mos2nrn on Ubuntu

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Zerocool
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Location: Trinity College

Fail to import hoc file using mos2nrn on Ubuntu

Post by Zerocool »

I installed Neuron 6.2 on x86 Ubuntu 8.04 using alien to convert the rpm. The installation was successful and nrngui can be run. However downloading a nrnzip file from the modelDB and using mos2nrn to unpack it fails. Is there a recommendation for working around this? Would the best option be to grab the source and compile it myself? I would appreciate any help you could offer.
csh
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Re: Fail to import hoc file using mos2nrn on Ubuntu

Post by csh »

Could you give some more details, e.g. which nrnzip file exactly did you use, and what was the error message? On my system, mos2nrn works when installed from an "alienated" rpm. From the command line, I can do:

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$ /usr/local/nrn/i686/bin/mos2nrn file.nrnzip
which will pop up a new shell, compile the mod files and launch mosinit.hoc. Note that the binaries are installed in /usr/local/nrn/i686/bin/ by default, which might not be in your path.
Zerocool
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Location: Trinity College

Re: Fail to import hoc file using mos2nrn on Ubuntu

Post by Zerocool »

I'm running the following command

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/usr/local/nrn/x86_64/bin/mos2nrn CoHCS2000.nrnzip
In this case the neuron path is as above and is not in my path.
I'm running a model file by Graham et al. http://senselab.med.yale.edu/ModelDB/Sh ... odel=19747

Mos2nrn initiates a new terminal and asks for execution. It fails after a few seconds with the following:

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/usr/bin/ld: cannot find -lncurses
/usr/local/nrn/x86_64/mos2nrn2.sh: 143: ./x86_64/special: not found
I haven't tried running this model on another machine yet, thats my next step.
csh
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Re: Fail to import hoc file using mos2nrn on Ubuntu

Post by csh »

I don't have any experience with 64 bit systems. However, my guess would be that the 64-bit version of the ncurses library is missing on your system. Maybe

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sudo apt-get install lib64ncurses5 lib64ncurses5-dev
or

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sudo apt-get install libncurses5 libncurses5-dev
will help?
Zerocool
Posts: 6
Joined: Thu Oct 23, 2008 12:20 am
Location: Trinity College

Re: Fail to import hoc file using mos2nrn on Ubuntu

Post by Zerocool »

csh wrote:

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sudo apt-get install lib64ncurses5 lib64ncurses5-dev
or

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sudo apt-get install libncurses5 libncurses5-dev
will help?
lib64ncurses5 doesnt exist in the universe package repository for Ubuntu, though libncurses5 (which includes amd64 packages) is installed.
hines
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Re: Fail to import hoc file using mos2nrn on Ubuntu

Post by hines »

At the risk of talking about something irrelevant, on my centos5 x86_64 machine I see

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$ /sbin/ldconfig -p | grep ncur
        libncursesw.so.5 (libc6,x86-64) => /usr/lib64/libncursesw.so.5
        libncursesw.so.5 (libc6) => /usr/lib/libncursesw.so.5
        libncursesw.so (libc6,x86-64) => /usr/lib64/libncursesw.so
        libncursesw.so (libc6) => /usr/lib/libncursesw.so
        libncurses.so.5 (libc6,x86-64) => /usr/lib64/libncurses.so.5
        libncurses.so.5 (libc6) => /usr/lib/libncurses.so.5
        libncurses.so (libc6,x86-64) => /usr/lib64/libncurses.so
        libncurses.so (libc6) => /usr/lib/libncurses.so
Isn't libncurses.so in your /usr/lib64 directory? If not, but
libncurses.so.5 is, then make a symbolic link.
Zerocool
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Joined: Thu Oct 23, 2008 12:20 am
Location: Trinity College

Re: Fail to import hoc file using mos2nrn on Ubuntu

Post by Zerocool »

On Ubuntu systems /lib64 is a symbolic link to /lib. I have however discovered that there is no lib64ncurses installed on my system or listed on any of the repositories. It is listed on the Ubuntu repository website http://packages.ubuntu.com/hardy/lib64ncurses5. I've posted in the Ubuntu forums to find out why, and why libncurses is listed as having 32 and 64-bit source included. I'll let you know what I find.
Zerocool
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Location: Trinity College

Re: Fail to import hoc file using mos2nrn on Ubuntu

Post by Zerocool »

Installing libncurses5-dev seems to bypass this issue.
jtejada
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Joined: Mon Aug 24, 2009 4:46 pm

Re: Fail to import hoc file using mos2nrn on Ubuntu

Post by jtejada »

Just see the this post

http://www.neuron.yale.edu/phpBB/viewto ... f=6&t=1015

It works for me (Ubuntu 9.04 64 bits, Neuron 7)
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