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Bug 638384 - sci-libs/arpack-3.5.0 : configure: error: cannot find BLAS libraries
Summary: sci-libs/arpack-3.5.0 : configure: error: cannot find BLAS libraries
Status: CONFIRMED
Alias: None
Product: Gentoo Linux
Classification: Unclassified
Component: Current packages (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Gentoo Science Related Packages
URL:
Whiteboard:
Keywords:
: 649892 (view as bug list)
Depends on: 700196 696256 698756
Blocks:
  Show dependency tree
 
Reported: 2017-11-21 19:21 UTC by Toralf Förster
Modified: 2020-05-31 05:11 UTC (History)
7 users (show)

See Also:
Package list:
Runtime testing required: ---


Attachments
emerge-info.txt (emerge-info.txt,15.52 KB, text/plain)
2017-11-21 19:21 UTC, Toralf Förster
Details
emerge-history.txt (emerge-history.txt,128.08 KB, text/plain)
2017-11-21 19:21 UTC, Toralf Förster
Details
environment (environment,93.78 KB, text/plain)
2017-11-21 19:21 UTC, Toralf Förster
Details
etc.portage.tbz2 (etc.portage.tbz2,16.73 KB, application/x-bzip)
2017-11-21 19:21 UTC, Toralf Förster
Details
logs.tbz2 (logs.tbz2,7.39 KB, application/x-bzip)
2017-11-21 19:21 UTC, Toralf Förster
Details
sci-libs:arpack-3.5.0:20171121-191437.log (sci-libs:arpack-3.5.0:20171121-191437.log,5.76 KB, text/plain)
2017-11-21 19:21 UTC, Toralf Förster
Details
temp.tbz2 (temp.tbz2,26.15 KB, application/x-bzip)
2017-11-21 19:21 UTC, Toralf Förster
Details

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Description Toralf Förster gentoo-dev 2017-11-21 19:21:27 UTC
checking for sgemm_ in -lblas... (cached) no
checking for sgemm_ in -lblas... (cached) no
configure: error: cannot find BLAS libraries

!!! Please attach the following file when seeking support:
!!! /var/tmp/portage/sci-libs/arpack-3.5.0/work/arpack-ng-3.5.0/config.log

  -------------------------------------------------------------------

  This is an unstable amd64 chroot image at a tinderbox (==build bot)
  name: 13.0-no-multilib_libressl_20171119-113915

  -------------------------------------------------------------------

gcc-config -l:
 [1] x86_64-pc-linux-gnu-7.2.0 *

Available Python interpreters, in order of preference:
  [1]   python3.4
  [2]   python2.7 (fallback)
Available Ruby profiles:
  [1]   ruby22 (with Rubygems) *



emerge -qpv sci-libs/arpack
[ebuild  N    ] sci-libs/arpack-3.5.0  USE="-doc -examples -mpi -static-libs"
Comment 1 Toralf Förster gentoo-dev 2017-11-21 19:21:30 UTC
Created attachment 505522 [details]
emerge-info.txt
Comment 2 Toralf Förster gentoo-dev 2017-11-21 19:21:34 UTC
Created attachment 505524 [details]
emerge-history.txt
Comment 3 Toralf Förster gentoo-dev 2017-11-21 19:21:39 UTC
Created attachment 505526 [details]
environment
Comment 4 Toralf Förster gentoo-dev 2017-11-21 19:21:42 UTC
Created attachment 505528 [details]
etc.portage.tbz2
Comment 5 Toralf Förster gentoo-dev 2017-11-21 19:21:47 UTC
Created attachment 505530 [details]
logs.tbz2
Comment 6 Toralf Förster gentoo-dev 2017-11-21 19:21:50 UTC
Created attachment 505532 [details]
sci-libs:arpack-3.5.0:20171121-191437.log
Comment 7 Toralf Förster gentoo-dev 2017-11-21 19:21:54 UTC
Created attachment 505534 [details]
temp.tbz2
Comment 8 François Bissey 2017-11-21 19:57:28 UTC
Could you provide config.log? I am fairly sure what kind of problem that is but config.log from arpack would be a nice addition for the diagnostics.
Comment 9 Toralf Förster gentoo-dev 2017-11-21 20:33:38 UTC
(In reply to François Bissey from comment #8)
pls look at the attached  logs.tbz2
Comment 10 François Bissey 2017-11-21 20:44:31 UTC
Thanks, I hadn't worked that out. And the problem seems to be of a kind I didn't expect:
configure:5227: x86_64-pc-linux-gnu-gcc -o conftest -O2 -pipe -march=native -Wall  -Wl,-O1 -Wl,--as-needed conftest.c -lblas   -L/usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0 -L/usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -L/usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/../../../../x86_64-pc-linux-gnu/lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/../../.. -lgfortran -lm -lquadmath >&5
/usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/../../../../x86_64-pc-linux-gnu/bin/ld: warning: libgfortran.so.3, needed by /usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/../../../../lib64/libblas.so, not found (try using -rpath or -rpath-link)
/usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/../../../../lib64/libblas.so: undefined reference to `_gfortran_stop_string@GFORTRAN_1.0'
/usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/../../../../lib64/libblas.so: undefined reference to `_gfortran_string_len_trim@GFORTRAN_1.0'
/usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/../../../../lib64/libblas.so: undefined reference to `_gfortran_st_write@GFORTRAN_1.0'
/usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/../../../../lib64/libblas.so: undefined reference to `_gfortran_st_write_done@GFORTRAN_1.0'
/usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/../../../../lib64/libblas.so: undefined reference to `_gfortran_transfer_character_write@GFORTRAN_1.4'
/usr/lib/gcc/x86_64-pc-linux-gnu/7.2.0/../../../../lib64/libblas.so: undefined reference to `_gfortran_transfer_integer_write@GFORTRAN_1.4'
collect2: error: ld returned 1 exit status

It looks like blas-reference has been compiled with a different version of gfortran. gfortran from gcc-7.2 produce libgfortran.so.4 but libblas has been compiled with .so.3.
Rebuilding blas-reference (and lapack-reference afterwards) should solve the issue. Your emerge history confirms that gcc-7.2 was emerged after blas-reference. There is actually quite a number of things that would be affected.
Comment 11 Silvio 2017-12-06 07:54:59 UTC
emerge -1 blas-reference
emerge -1 arpack
solves this problema but than another problem appears:

checking for cheev_ in -llapack -lblas... no
checking for cheev_... no
checking for cheev_ in -llapack... no
checking for cheev_ in -llapack_rs6k... no
configure: error: cannot find LAPACK libraries

I re-emerging lapack-reference. I'll update you if it is the last problem.

I have to point out that I'm doing:

emerge -e world

and the problem appears. I think the sequence of the emerge should be more accurate: before the needed packages and than the 

arpack

shouoldn't it?
Comment 12 François Bissey 2017-12-06 07:58:04 UTC
It should have been
emerge -1v blas-reference
emerge -1v lapack-reference
emerge -1v arpack

I am not surprised at the result.
Comment 13 Silvio 2017-12-06 08:05:15 UTC
> I re-emerging lapack-reference. I'll update you if it is the last problem.

it worked

> 
> I have to point out that I'm doing:
> 
> emerge -e world
> 
> and the problem appears. I think the sequence of the emerge should be more
> accurate: before the needed packages and than the 
> 
> arpack
> 
> shouoldn't it?

about this?
Comment 14 Michael Hofmann 2018-02-18 00:35:10 UTC
I had the same problem with arpack-3.1.5 (stable).

I switched from GCC 6.4.0 to GCC 7.3.0 and started 
'emerge -e world'.

Emerge couldn't compile arpack and stopped with the
error message shown in the first comment.

After I executed the statements shown in comment 12,
arpack was installed and I could continue with
emerge --resume --skipfirst.

Thanks to everyone who posted in this thread. The 
fix shown in comment 12 saved me a couple of hours :-)
Comment 15 Bernd 2019-06-09 07:23:08 UTC
Seems to be a duplicate of bug #649892
Comment 16 Jeroen Roovers gentoo-dev 2019-07-11 06:33:07 UTC
*** Bug 649892 has been marked as a duplicate of this bug. ***
Comment 17 Benda Xu gentoo-dev 2019-08-08 01:35:10 UTC
Need stabilization of the new BLAS/LAPACK framework soon.
Comment 18 Andreas Sturmlechner gentoo-dev 2020-05-18 18:57:10 UTC
So?
Comment 19 Marek Bartosiewicz 2020-05-31 05:11:49 UTC
There is gcc10 patch here https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=957007