On 21/04/16 09:46, Andreas Tille wrote:
Hi Ghislain,
On Wed, Apr 20, 2016 at 09:35:32PM +0100, Ghislain Vaillant wrote:
You should be able to use the packaged lapacke instead of clapack.
Both should respect the same LAPACK API.
I somehow brute forced a patch
--- a/include/external_libs.h
+++ b/include/external_libs.h
@@ -39,8 +39,8 @@
#else
#ifndef SKIP_LAPACK
-#include <f2c.h>
-#include <clapack.h>
+/* #include <f2c.h> */
+#include <lapacke.h>
#define LAPACK_INT integer
#define LAPACK_DOUBLE doublereal
#endif /*ifndef SKIP_LAPACK */
integer and doublereal are defined in f2c/clapack, which your patch
actually replace with lapacke hence the unknown type.
I believe lapacke defines lapack_int and lapack_double, which should be
used in the macros. In the end, they are all typedefs to standard int
and double.
into the preliminary packaging which is now available in Git[1] but its
probably not that simple since
./munge-help.sh consEntropy.help_src > consEntropy.help
gcc -O3 -Wall -I/build/phast-1.4/src/util/../../include -DPHAST_VERSION=\"v1.3\"
-DPHAST_HOME=\"/build/phast-1.4/src/util/../..\"
-I/build/phast-1.4/src/util/../../src/lib/pcre -fno-strict-al
In file included from /build/phast-1.4/src/util/../../include/vector.h:19:0,
from /build/phast-1.4/src/util/../../include/matrix.h:18,
from /build/phast-1.4/src/util/../../include/misc.h:21,
from indelHistory.c:15:
/build/phast-1.4/src/util/../../include/external_libs.h:45:23: error: unknown
type name 'doublereal'
#define LAPACK_DOUBLE doublereal
^
/build/phast-1.4/src/util/../../include/matrix.h:348:31: note: in expansion of
macro 'LAPACK_DOUBLE'
void mat_to_lapack(Matrix *m, LAPACK_DOUBLE *arr);
^
/build/phast-1.4/src/util/../../include/external_libs.h:45:23: error: unknown
type name 'doublereal'
#define LAPACK_DOUBLE doublereal
^
/build/phast-1.4/src/util/../../include/matrix.h:355:33: note: in expansion of
macro 'LAPACK_DOUBLE'
void mat_from_lapack(Matrix *m, LAPACK_DOUBLE *arr);
^
Makefile:17: recipe for target 'indelHistory.o' failed
Consequence of my comment above.
So I wonder whether it is harder to adapt the code or rather package
clapack. Upstream is in CC - may be someone might try to explain the
advantage of lapacke over clapack.
See this blog post for a good reasoning:
http://nicolas.limare.net/pro/notes/2014/10/31_cblas_clapack_lapacke/
Kind regards
Andreas.
On 20/04/16 20:50, Andreas Tille wrote:
Hi folks,
I wonder whether somebody has dealt with CLAPACK. A search via
apt-file search clapack
uncovers some clapack.h but it seems I need to package this first.
Any hint would be welcome before I start with this.
Kind regards
Andreas.
----- Forwarded message from "Ramani, Ritika" <[email protected]> -----
Date: Wed, 20 Apr 2016 18:50:09 +0000
From: "Ramani, Ritika" <[email protected]>
To: Andreas Tille <[email protected]>
CC: PhastHelp <[email protected]>, Debian Med Project List
<[email protected]>
Subject: RE: Please provide release tags for Phast on Github and may be you
could uncover Debian packaging code
Hey Andreas,
CLAPACK is different from the Lapack package you mention. Clapack provides
LAPACK for non Fortran compilers using f2c. - http://www.netlib.org/clapack/
Thanks!
Ritika
________________________________________
From: Andreas Tille [[email protected]]
Sent: Wednesday, April 20, 2016 2:11 PM
To: Ramani, Ritika
Cc: PhastHelp; Debian Med Project List
Subject: Re: Please provide release tags for Phast on Github and may be you
could uncover Debian packaging code
Hi Ritika,
On Wed, Apr 20, 2016 at 05:40:45PM +0000, Ramani, Ritika wrote:
Hello Andreas,
Thank you so much for your message.
Thanks a lot for your quick response.
I have tagged the releases on Github. Our last released version was v1.3 in
March 2013. But we are planning on releasing a new version soon. I have tagged
this version as pre-release v1.4 on Github so you can use that for the Debian
mirror.
Thanks for the tagging and the information about the new version.
We do have the source tarball for v1.3 available on the phast website if you
select the source option. Here is the link to download the source for v1.3 -
http://compgen.cshl.edu/phast/downloads/phast.v1_3.tgz
Fine. May be it was just me. The tagging on Github is perfectly
sufficient anyway.
I had used the same v1.3 source code to package into debian with CLAPACK.
How do you plan to add phast to the mirror considering it has the CLAPACK
dependency?
Debian has the liblapacke-dev[1]. Is this any difference to CLAPACK? If
yes we need to package CLAPACK first. I have not yet investigated into
this question.
Let me know if you need any more information.
Thanks, I'll do.
Kind regards
Andreas.
[1] http://www.netlib.org/lapack/
--
http://fam-tille.de
----- End forwarded message -----
