Re: Packaging AxPcoords for Debian
Hi David,
AxPcoords.c:171: warning: incompatible implicit declaration of built-in
function ‘strcpy’
AxPcoords.c:181: warning: incompatible implicit declaration of built-in
function ‘strcat’
AxPcoords.c:199: warning: incompatible implicit declaration of built-in
function ‘strcpy’
But I've added a patch, this is a minor issue.
Thanks.
The real issue is this:
gcc -O3 -fomit-frame-pointer -funroll-loops -D_USE_LAPACK -D_USE_ACML
-I../acml3.6.0/gnu32/include/ -c AxPcoords.c -o AxPcoordsACML.o
AxPcoords.c:47:18: error: acml.h: No such file or directory
make: *** [AxPcoordsACML.o] Error 1
Evidently, there is a problem with the include path that needs to be updated "-I../acml3.6.0/gnu32/include/"
or adapted to your local installation.
However, I would just use the GSL instead of ACML for AxPcoords.
The main reason for this is that in a typical analysis using the AxPcoords
and AxParafit programs, the execution times for AxPcoords are significantly smaller than
those of AxParafit, thus it does not matter that much if AxPcoords does not use a highly optimized
LAPACK library.
I guess that this will make your life much easier.
Cheers,
Alexis
I've already contacted AMD (yes, I did, really) to ask if they could relicense
their ACML under a free license (GPL/BSD/Artistic/...). Here's their reply:
From: tech.support@AMD.COM
To: d.paleino@GMAIL.COM
Subject: Re: ACML-Support
Date: Mon, 4 Feb 2008 04:52:03 -0800 (GMTUK)
Reply-to: tech.support@AMD.COM
X-Mailer: SAP Web Application Server 6.20
Dear David,
thanks for contacting the AMD/ATI Tech Support.
Basically ACML is a free library. You only need to provide us your details for
using this library in commercial projects.
You should be able to use ACML for Debian as well:
http://developer.amd.com/tools/acml/downloads/Pages/default.aspx
Just use a GFortran of PGI compiler. For instance Gfortran is available for
debian here:
http://packages.debian.org/gfortran
If you have further questions, feel free to contact us.
Best regards
Robert
AMD EURO TSC London
What I'm asking is: can this library go in non-free? Or is that some of those
packages because it's "impossible to distribute" without permission from AMD?
Thanks,
David
P.S.: I'm finishing the packaging and injecting a patched version which doesn't
compile the ACML version.
--
Dr. Alexandros Stamatakis, Junior Research Group Leader
The Exelixis Lab
Teaching and Research Unit Bioinformatics
Department of Computer Science
Ludwig-Maximilians-University Munich
Tel: +49 162 8541515 (Mobile)
Skype: stamatak
Email: stamatakis@bio.ifi.lmu.de
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