Fail to import hoc file using mos2nrn on Ubuntu
Fail to import hoc file using mos2nrn on Ubuntu
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.
Re: Fail to import hoc file using mos2nrn on Ubuntu
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:
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.
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$ /usr/local/nrn/i686/bin/mos2nrn file.nrnzip
Re: Fail to import hoc file using mos2nrn on Ubuntu
I'm running the following command
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:
I haven't tried running this model on another machine yet, thats my next step.
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/usr/local/nrn/x86_64/bin/mos2nrn CoHCS2000.nrnzip
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
Re: Fail to import hoc file using mos2nrn on Ubuntu
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
or
will help?
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sudo apt-get install lib64ncurses5 lib64ncurses5-dev
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sudo apt-get install libncurses5 libncurses5-dev
Re: Fail to import hoc file using mos2nrn on Ubuntu
lib64ncurses5 doesnt exist in the universe package repository for Ubuntu, though libncurses5 (which includes amd64 packages) is installed.csh wrote:orCode: Select all
sudo apt-get install lib64ncurses5 lib64ncurses5-dev
will help?Code: Select all
sudo apt-get install libncurses5 libncurses5-dev
Re: Fail to import hoc file using mos2nrn on Ubuntu
At the risk of talking about something irrelevant, on my centos5 x86_64 machine I see
Isn't libncurses.so in your /usr/lib64 directory? If not, but
libncurses.so.5 is, then make a symbolic link.
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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
libncurses.so.5 is, then make a symbolic link.
Re: Fail to import hoc file using mos2nrn on Ubuntu
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.
Re: Fail to import hoc file using mos2nrn on Ubuntu
Installing libncurses5-dev seems to bypass this issue.
Re: Fail to import hoc file using mos2nrn on Ubuntu
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)
http://www.neuron.yale.edu/phpBB/viewto ... f=6&t=1015
It works for me (Ubuntu 9.04 64 bits, Neuron 7)