[GenABEL-dev] omicabelnomm Instalation

[L.C. Karssen]

Dear Jürgen,

On 27-10-14 13:59, "Riegel, Jürgen" wrote:
> Dear list,
> 
>  
> 
> Alvaro asked me to install the latest omicabelnomm on our local compute
> server, but it seems you have changed the way of installation. 

Actually, we didn't :-). It is just that for the current development
version (as of this weekend) does an extended check for MPI compilers.
This check was added because Alvaro will allow users to compile
OmicABELnoMM without MPI support as well, if the user so desires.

The new Autoconf check (an autoconf macro called AX_PROG_CXX_MPI) is not
part of the standard autoconf install, but part of the Autoconf Archives
[1]. Most distributions have the Archives packaged as well [2].

So, the question is how you compiled/installed OmicABELnoMM before. If
you did an SVN checkout and ran autoreconf -i, ./configure, make and
make install than nothing will have changed if you install the
autoconf-archives package. If you can't or don't want to install that
package, you can download the macro from [1], save it in the directory
where you checked out OmicABELnoMM and run
 autoconf -i -I.
instead, followed by the other commands.


> Is there
> any package / binary / RPM / repository where I can get the latest
> stable version for installation, or what is the preferred / suggested
> way of installation now?

We don't provide RPMs (yet), for several reasons: 1) we don't have the
man power currently to create spec files (contributions are more than
welcome!), 2) the current developers work on Debian derivatives, and 3)
because the code is best compiled on the machines that will run
OmicABELnoMM themselves in order to make most out of the hardware of
each individual server, since Alvaro's algorithms are programmed very
'close' to the hardware/CPU.

Once OmicABELnoMM is declared 'ready for release' we will set up a page
for it on www.genabel.org, where you will be able to download official
releases of the source code.



Hope this helps,

Lennart.


[1]
http://www.gnu.org/software/autoconf-archive/ax_prog_cxx_mpi.html#ax_prog_cxx_mpi
[2] http://pkgs.org/download/autoconf-archive

> 
>  
> 
> Thanks in advance,
> 
> Jürgen
> 
>  
> 
>  
> 
>  
> 
>  
> 
> Best regards,
> 
> Jürgen Riegel
> 
>  
> 
> ---
> 
> Jürgen Riegel, Dipl.-Inf. (FH)
> 
> IT Admin for IGE + AME
> 
>  
> 
> institute for genetic epidemiology (IGE)
> 
> division for molecular epidemiology (AME)
> 
>  
> 
>  
> 
>  
> 
>  
> 
> *Von:*Frank Ramirez, Alvaro Jesus
> *Gesendet:* Montag, 27. Oktober 2014 13:29
> *An:* Riegel, Jürgen
> *Betreff:* omicabelnomm Instalation
> 
>  
> 
> Hi Jürgen,
> 
>  
> 
> The GenABEL people (Yurii’s group) inform me that omicabelnomm will be
> installed in a different way (compared to how I have been doing it
> untilnow).
> 
> The latest build broke my installation procedure. Could you contact
> genabel-devel at lists.r-forge.r-project.org
> <mailto:genabel-devel at lists.r-forge.r-project.org>  to obtain a proper
> installation rocedure foromicabelnomm?
> 
> It should be a very simple Linux package for distributions.
> 
> Email:
> 
> genabel-devel at lists.r-forge.r-project.org
> <mailto:genabel-devel at lists.r-forge.r-project.org> 
> 
>  
> 
>  
> 
> Best,
> 
> Alvaro
> 
> 
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-- 
*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
L.C. Karssen
Utrecht
The Netherlands

lennart at karssen.org
http://blog.karssen.org
GPG key ID: A88F554A
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