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Date: Thu, 22 Aug 2013 16:11:44 +0800
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Subject: Re: [gentoo-science] sage on gentoo -- only use system atlas
From: P Purkayastha <ppurka@gmail.com>
To: gentoo-science <gentoo-science@lists.gentoo.org>
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On Thu, Aug 22, 2013 at 8:39 AM, Fran=E7ois Bissey <fbissey@slingshot.co.nz=
>wrote:
> On 2013-08-22 00:19, Burcin Erocal wrote:
>
>> Hi,
>>
>> On Wed, 21 Aug 2013 20:02:02 +0800
>> P Purkayastha <ppurka@gmail.com> wrote:
>>
>> I need to have a personal installation of Sage to do development
>>> work. However, I also want to reduce my upgrade times by installing a
>>> system atlas.
>>>
>>> To do so, I added the science overlay and emerged
>>> sci-libs/atlas[lapack,fortran,threads]. Thereafter, I added the
>>> environment variable
>>>
>>> SAGE_ATLAS_LIB=3D/usr/lib
>>>
>>> and proceeded to compile sage in my home directory. Atlas fails with
>>> the error that it can not find liblapack. The exact error message is
>>> given below:
>>>
>>> Cannot find liblapack.* in /usr/lib
>>> Unable to find one of liblapack, libcblas, libatlas or libf77blas
>>> in the directory None
>>> Set SAGE_ATLAS_LIB to the directory containing liblapack, libcblas,
>>> libatlas and libf77blas (either .a, .so, .dylib extensions) if
>>> you wish to use existing ATLAS libraries. For more details, see
>>> http://sagemath.org/doc/installation/source.html#environment-variables
>>> Unset SAGE_ATLAS_LIB to build ATLAS from source.
>>>
>>
>> if you make Sage believe that the atlas package was installed properly,
>> the installation proceeds without trouble. So as a quick workaround,
>> just do
>>
>> touch spkg/installed/atlas-<version_number>
>>
>> I always do this on my system. It would be good to find out the proper
>> solution of course. :)
>>
>
Thanks! This makes the compilation proceed further. FYI, in sage-git, the
corresponding directory is SAGE_ROOT/local/var/lib/sage/installed
One question though: can this trick be used with the other packages such as
R, givaro, etc. If this can be done, then it will be so much easier to
upgrade sage! I wouldn't have to rely on luck on whether the build finishes
in some finite time. :-)
>> The main problem here is that Gentoo support the installation of
> multiple BLAS/LAPACK at once.
> For that reason there is no libraries on the system installed with the
> names:
> libcblas.*
> libf77blas.*
> liblapack.*
>
> My recommendation for you is to create a folder in your home directory an=
d
> link all the libraries you need with the appropriate name in a lib
> subfolder
> and pass the parent directory to SAGE_ATLAS_LIB.
>
> Francois
Actually I do have those libraries. Only missing one is liblapack.*. It is
probably one of the similarly named libraries, except I don't know which. I
don't want to find out by hit and trial given how finicky atlas is.
~=BB ll /usr/lib/{libcblas.so,libf77blas.so,libatlas.so}
lrwxrwxrwx 1 root root 13 Aug 20 19:39 /usr/lib/libatlas.so -> libatlas.so.=
3
lrwxrwxrwx 1 root root 14 Sep 15 2012 /usr/lib/libcblas.so -> libgslcblas.s=
o
lrwxrwxrwx 1 root root 15 Aug 20 19:39 /usr/lib/libf77blas.so ->
libf77blas.so.3
--047d7b2e3efc3c44e004e484d7c7
Content-Type: text/html; charset=ISO-8859-1
Content-Transfer-Encoding: quoted-printable
<div dir=3D"ltr"><br><div class=3D"gmail_extra"><br><br><div class=3D"gmail=
_quote">On Thu, Aug 22, 2013 at 8:39 AM, Fran=E7ois Bissey <span dir=3D"ltr=
"><<a href=3D"mailto:fbissey@slingshot.co.nz" target=3D"_blank">fbissey@=
slingshot.co.nz</a>></span> wrote:<br>
<blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1p=
x #ccc solid;padding-left:1ex"><div class=3D""><div class=3D"h5">On 2013-08=
-22 00:19, Burcin Erocal wrote:<br>
<blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1p=
x #ccc solid;padding-left:1ex">
Hi,<br>
<br>
On Wed, 21 Aug 2013 20:02:02 +0800<br>
P Purkayastha <<a href=3D"mailto:ppurka@gmail.com" target=3D"_blank">ppu=
rka@gmail.com</a>> wrote:<br>
<br>
<blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 .8ex;border-left:1p=
x #ccc solid;padding-left:1ex">
=A0 I need to have a personal installation of Sage to do development<br>
work. However, I also want to reduce my upgrade times by installing a<br>
system atlas.<br>
<br>
=A0 To do so, I added the science overlay and emerged<br>
sci-libs/atlas[lapack,fortran,threads]. Thereafter, I added the<br>
environment variable<br>
<br>
SAGE_ATLAS_LIB=3D/usr/lib<br>
<br>
and proceeded to compile sage in my home directory. Atlas fails with<br>
the error that it can not find liblapack. The exact error message is<br>
given below:<br>
<br>
Cannot find liblapack.* in /usr/lib<br>
Unable to find one of liblapack, libcblas, libatlas or libf77blas<br>
in the directory None<br>
Set SAGE_ATLAS_LIB to the directory containing liblapack, libcblas,<br>
libatlas and libf77blas (either .a, .so, .dylib extensions) if<br>
you wish to use existing ATLAS libraries. For more details, see<br>
<a href=3D"http://sagemath.org/doc/installation/source.html#environment-var=
iables" target=3D"_blank">http://sagemath.org/doc/installation/source.html#=
environment-variables</a><br>
Unset SAGE_ATLAS_LIB to build ATLAS from source.<br>
</blockquote>
<br>
if you make Sage believe that the atlas package was installed properly,<br>
the installation proceeds without trouble. So as a quick workaround,<br>
just do<br>
<br>
touch spkg/installed/atlas-<version_number><br>
<br>
I always do this on my system. It would be good to find out the proper<br>
solution of course. :)<br></blockquote></div></div></blockquote><div><br></=
div><div>Thanks! This makes the compilation proceed further. FYI, in sage-g=
it, the corresponding directory is SAGE_ROOT/local/var/lib/sage/installed</=
div>
<div><br></div><div><br></div><div>One question though: can this trick be u=
sed with the other packages such as R, givaro, etc. If this can be done, th=
en it will be so much easier to upgrade sage! I wouldn't have to rely o=
n luck on whether the build finishes in some finite time. :-)</div>
<div>=A0</div><div><br></div><blockquote class=3D"gmail_quote" style=3D"mar=
gin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div class=3D""=
><div class=3D"h5"><blockquote class=3D"gmail_quote" style=3D"margin:0 0 0 =
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
</blockquote></div></div>
The main problem here is that Gentoo support the installation of multiple B=
LAS/LAPACK at once.<br>
For that reason there is no libraries on the system installed with the name=
s:<br>
libcblas.*<br>
libf77blas.*<br>
liblapack.*<br>
<br>
My recommendation for you is to create a folder in your home directory and<=
br>
link all the libraries you need with the appropriate name in a lib subfolde=
r<br>
and pass the parent directory to SAGE_ATLAS_LIB.<br>
<br>=A0Francois</blockquote><div><br></div><div>Actually I do have those li=
braries. Only missing one is liblapack.*. It is probably one of the similar=
ly named libraries, except I don't know which. I don't want to find=
out by hit and trial given how finicky atlas is.=A0</div>
</div></div><div class=3D"gmail_extra"><br></div><div class=3D"gmail_extra"=
>~=BB ll /usr/lib/{libcblas.so,libf77blas.so,libatlas.so}<br>lrwxrwxrwx 1 r=
oot root 13 Aug 20 19:39 /usr/lib/libatlas.so -> libatlas.so.3<br>lrwxrw=
xrwx 1 root root 14 Sep 15 2012 /usr/lib/libcblas.so -> libgslcblas.so<=
br>
lrwxrwxrwx 1 root root 15 Aug 20 19:39 /usr/lib/libf77blas.so -> libf77b=
las.so.3<br></div><div class=3D"gmail_extra"><br></div></div>
--047d7b2e3efc3c44e004e484d7c7--