Gentoo Websites Logo
Go to: Gentoo Home Documentation Forums Lists Bugs Planet Store Wiki Get Gentoo!
Bug 669644 - [science-overlay] [Prefix] sci-libs/lapack-reference versions 3.7.0-r100 and 3.8.0-r100 do not respect system selected blas libs
Summary: [science-overlay] [Prefix] sci-libs/lapack-reference versions 3.7.0-r100 and ...
Status: RESOLVED FIXED
Alias: None
Product: Gentoo/Alt
Classification: Unclassified
Component: Prefix Support (show other bugs)
Hardware: All Linux
: Normal normal (vote)
Assignee: Gentoo Prefix
URL:
Whiteboard:
Keywords:
Depends on:
Blocks:
 
Reported: 2018-10-25 22:04 UTC by Steven Trogdon
Modified: 2019-07-03 12:34 UTC (History)
0 users

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


Attachments
build log (build.log.gz,32.63 KB, application/gzip)
2018-10-25 22:05 UTC, Steven Trogdon
Details
lapack-config.cmake (lapack-config.cmake,456 bytes, text/x-cmake)
2018-10-25 22:32 UTC, Steven Trogdon
Details
lapack-targets.cmake (lapack-targets.cmake,2.53 KB, text/x-cmake)
2018-10-25 22:33 UTC, Steven Trogdon
Details

Note You need to log in before you can comment on or make changes to this bug.
Description Steven Trogdon 2018-10-25 22:04:18 UTC
eselect blas list
Available providers for blas:
  [1]   openblas-openmp *
  [2]   reference

In fact blas-reference is not installed:

eix -I sci-libs/blas-reference
No matches found

From build.log

>>> Install lapack-reference-3.8.0-r100 into /storage/strogdon/gentoo-rap/var/tmp/portage/sci-libs/lapack-reference-3.8.0-r100/image/ category sci-libs
 ^[[32;01m*^[[0m abi_x86_64.amd64_int32: running numeric-int64-multibuild_multilib_wrapper cmake-utils_src_install
>>> Working in BUILD_DIR: "/storage/strogdon/gentoo-rap/var/tmp/portage/sci-libs/lapack-reference-3.8.0-r100/work/lapack-3.8.0-abi_x86_64.amd64_int32"
make -j13 install
[  7%] Built target blas
[100%] Built target reflapack
Install the project...
-- Install configuration: "Gentoo"
-- Installing: /storage/strogdon/gentoo-rap/var/tmp/portage/sci-libs/lapack-reference-3.8.0-r100/image/storage/strogdon/gentoo-rap/usr/lib64/cmake/lapack-3.8.0/lapack-targets.cmake
-- Installing: /storage/strogdon/gentoo-rap/var/tmp/portage/sci-libs/lapack-reference-3.8.0-r100/image/storage/strogdon/gentoo-rap/usr/lib64/cmake/lapack-3.8.0/lapack-targets-gentoo.cmake
-- Installing: /storage/strogdon/gentoo-rap/var/tmp/portage/sci-libs/lapack-reference-3.8.0-r100/image/storage/strogdon/gentoo-rap/usr/lib64/pkgconfig/reflapack.pc
-- Installing: /storage/strogdon/gentoo-rap/var/tmp/portage/sci-libs/lapack-reference-3.8.0-r100/image/storage/strogdon/gentoo-rap/usr/lib64/cmake/lapack-3.8.0/lapack-config.cmake
-- Installing: /storage/strogdon/gentoo-rap/var/tmp/portage/sci-libs/lapack-reference-3.8.0-r100/image/storage/strogdon/gentoo-rap/usr/lib64/cmake/lapack-3.8.0/lapack-config-version.cmake
-- Installing: /storage/strogdon/gentoo-rap/var/tmp/portage/sci-libs/lapack-reference-3.8.0-r100/image/storage/strogdon/gentoo-rap/usr/lib64/pkgconfig/blas.pc
-- Installing: /storage/strogdon/gentoo-rap/var/tmp/portage/sci-libs/lapack-reference-3.8.0-r100/image/storage/strogdon/gentoo-rap/usr/lib64/libblas.so.3.8.0
-- Installing: /storage/strogdon/gentoo-rap/var/tmp/portage/sci-libs/lapack-reference-3.8.0-r100/image/storage/strogdon/gentoo-rap/usr/lib64/libblas.so.3
-- Set runtime path of "/storage/strogdon/gentoo-rap/var/tmp/portage/sci-libs/lapack-reference-3.8.0-r100/image//storage/strogdon/gentoo-rap/usr/lib64/libblas.so.3.8.0" to "/storage/strogdon/gentoo-rap/usr/x86_64-pc-linux-gnu/lib/gcc:/storage/strogdon/gentoo-rap/usr/x86_64-pc-linux-gnu/lib:/storage/strogdon/gentoo-rap/usr/lib64:/storage/strogdon/gentoo-rap/lib64"
-- Installing: /storage/strogdon/gentoo-rap/var/tmp/portage/sci-libs/lapack-reference-3.8.0-r100/image/storage/strogdon/gentoo-rap/usr/lib64/libblas.so
-- Installing: /storage/strogdon/gentoo-rap/var/tmp/portage/sci-libs/lapack-reference-3.8.0-r100/image/storage/strogdon/gentoo-rap/usr/lib64/libreflapack.so.3.8.0
-- Installing: /storage/strogdon/gentoo-rap/var/tmp/portage/sci-libs/lapack-reference-3.8.0-r100/image/storage/strogdon/gentoo-rap/usr/lib64/libreflapack.so.3
-- Set runtime path of "/storage/strogdon/gentoo-rap/var/tmp/portage/sci-libs/lapack-reference-3.8.0-r100/image//storage/strogdon/gentoo-rap/usr/lib64/libreflapack.so.3.8.0" to "/storage/strogdon/gentoo-rap/usr/x86_64-pc-linux-gnu/lib/gcc:/storage/strogdon/gentoo-rap/usr/x86_64-pc-linux-gnu/lib:/storage/strogdon/gentoo-rap/usr/lib64:/storage/strogdon/gentoo-rap/lib64"
-- Installing: /storage/strogdon/gentoo-rap/var/tmp/portage/sci-libs/lapack-reference-3.8.0-r100/image/storage/strogdon/gentoo-rap/usr/lib64/libreflapack.so
 ^[[32;01m*^[[0m abi_x86_64.amd64_int32: running numeric-int64-multibuild_multilib_wrapper pc_file lapack reference
 ^[[32;01m*^[[0m int32: running numeric-int64-multibuild_multilib_wrapper pc_install lapack reference
>>> Completed installing lapack-reference-3.8.0-r100 into /storage/strogdon/gentoo-rap/var/tmp/portage/sci-libs/lapack-reference-3.8.0-r100/image/

 ^[[32;01m*^[[0m Final size of build directory: 107132 KiB (104.6 MiB)
 ^[[32;01m*^[[0m Final size of installed tree:    7720 KiB (  7.5 MiB)

making executable: /usr/lib64/libblas.so.3.8.0
making executable: /usr/lib64/libreflapack.so.3.8.0
 ^[[33;01m*^[[0m One or more CMake variables were not used by the project:
 ^[[33;01m*^[[0m   BLAS_REQUIRES
 ^[[33;01m*^[[0m   BUILD_STATIC_LIBS
 ^[[33;01m*^[[0m   LAPACK_PKGCONFIG_FFLAGS
Comment 1 Steven Trogdon 2018-10-25 22:05:31 UTC
Created attachment 553052 [details]
build log
Comment 2 Steven Trogdon 2018-10-25 22:15:46 UTC
On the live system

ldd -r ~/usr/lib/libreflapack.so
	linux-vdso.so.1 (0x00007ffcd86b2000)
	libxblas.so.1.0 => /storage/strogdon/gentoo-rap/usr/lib64/libxblas.so.1.0 (0x00007ffae3b42000)
	libblas.so.3 => /storage/strogdon/gentoo-rap/usr/lib64/libblas.so.3 (0x00007ffae38ee000)
	libgfortran.so.5 => /storage/strogdon/gentoo-rap/usr/x86_64-pc-linux-gnu/lib/gcc/libgfortran.so.5 (0x00007ffae3476000)
	libm.so.6 => /storage/strogdon/gentoo-rap/lib64/libm.so.6 (0x00007ffae30de000)
	libgomp.so.1 => /storage/strogdon/gentoo-rap/usr/x86_64-pc-linux-gnu/lib/gcc/libgomp.so.1 (0x00007ffae2eb0000)
	libgcc_s.so.1 => /storage/strogdon/gentoo-rap/usr/x86_64-pc-linux-gnu/lib/gcc/libgcc_s.so.1 (0x00007ffae2c98000)
	libc.so.6 => /storage/strogdon/gentoo-rap/lib64/libc.so.6 (0x00007ffae28d0000)
	libpthread.so.0 => /storage/strogdon/gentoo-rap/lib64/libpthread.so.0 (0x00007ffae26b0000)
	libquadmath.so.0 => /storage/strogdon/gentoo-rap/usr/lib/gcc/x86_64-pc-linux-gnu/8.2.0/libquadmath.so.0 (0x00007ffae2470000)
	libz.so.1 => /storage/strogdon/gentoo-rap/usr/lib/../lib64/libz.so.1 (0x00007ffae2252000)
	/storage/strogdon/gentoo-rap/lib64/ld-linux-x86-64.so.2 (0x00007ffae50d0000)
	libdl.so.2 => /storage/strogdon/gentoo-rap/lib64/libdl.so.2 (0x00007ffae204e000)

and linking is to the wrong blas libs. From eselect linking should be to openblas libs.
Comment 3 Steven Trogdon 2018-10-25 22:32:40 UTC
Created attachment 553054 [details]
lapack-config.cmake
Comment 4 Steven Trogdon 2018-10-25 22:33:30 UTC
Created attachment 553056 [details]
lapack-targets.cmake
Comment 5 Steven Trogdon 2018-10-25 22:37:50 UTC
The installed lapack-reference

eix -I lapack-reference
[I] sci-libs/lapack-reference
     Available versions:  [m]3.2.1-r4 [m]3.6.0 [m]3.7.0 3.7.0-r100(0/3.7.0)[1] 3.8.0-r100(0/3.8.0)[1] **9999(0/9999)[1] {+deprecated doc int64 static-libs test xblas ABI_MIPS="n32 n64 o32" ABI_PPC="32 64" ABI_S390="32 64" ABI_X86="32 64 x32"}
     Installed versions:  3.8.0-r100(0/3.8.0)[1](04:09:22 PM 10/25/2018)(deprecated xblas -int64 -static-libs -test ABI_MIPS="-n32 -n64 -o32" ABI_PPC="-32 -64" ABI_S390="-32 -64" ABI_X86="64 -32 -x32")
     Homepage:            http://www.netlib.org/lapack/
     Description:         Reference implementation of LAPACK

[1] "science" /storage/strogdon/gentoo-rap/var/lib/layman/science
Comment 6 Steven Trogdon 2018-10-25 22:50:44 UTC
And on the live system blas.pc is not a symlink. My original symlink to openblas has been overwritten.

eselect blas list
Available providers for blas:
  [1]   openblas-openmp *
  [2]   reference

eselect blas set 1
!!! Error: Refusing to overwrite /storage/strogdon/gentoo-rap/usr/lib64/pkgconfig/blas.pc: is not a symlink (use --force to override)
!!! Error: Could not set provider openblas-openmp for alternative blas: see previous errors
Call stack:
    * alternatives_do_set (alternatives-common.bash:247)
    * do_set (alternatives.bash:124)
    * check_do (core.bash:24)
    * do_action (core.bash:105)
    * main (eselect:311)
exiting

pkg-config --libs blas
-lblas
Comment 7 Steven Trogdon 2018-10-26 00:03:57 UTC
This appears to be a cmake issue in Prefix and perhaps on Gentoo. The build listed here was done with dev-util/cmake-3.12.3. Downgrading to cmake-3.9.6 which is stable on Gentoo produces correct results.
Comment 8 Larry the Git Cow gentoo-dev 2019-06-26 06:07:15 UTC
The bug has been closed via the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=5f8a985b71b033d7a7c4d252c00dd83669ee5913

commit 5f8a985b71b033d7a7c4d252c00dd83669ee5913
Author:     Mo Zhou <cdluminate@gmail.com>
AuthorDate: 2019-06-26 02:27:40 +0000
Commit:     Benda Xu <heroxbd@gentoo.org>
CommitDate: 2019-06-26 06:06:09 +0000

    virtual/{blas,cblas,lapack,lapacke}: add/update virtual packages.
    
      These virtual packages are used by the BLAS/LAPACK runtime switching
      mechanism.
    
      Drop old EAPI=5 ebuilds.
    
    Closes: https://github.com/gentoo/gentoo/pull/12323
    Closes: https://bugs.gentoo.org/373613
    Closes: https://bugs.gentoo.org/669644
    Closes: https://bugs.gentoo.org/564546
    Closes: https://bugs.gentoo.org/565776
    Closes: https://bugs.gentoo.org/646316
    Closes: https://bugs.gentoo.org/563674
    Closes: https://bugs.gentoo.org/659014
    Closes: https://bugs.gentoo.org/659264
    Closes: https://bugs.gentoo.org/657984
    Closes: https://bugs.gentoo.org/381801
    Closes: https://bugs.gentoo.org/646316
    Closes: https://bugs.gentoo.org/565776
    Closes: https://bugs.gentoo.org/498490
    
    Signed-off-by: Mo Zhou <cdluminate@gmail.com>
    Signed-off-by: Benda Xu <heroxbd@gentoo.org>

 virtual/blas/blas-1.0.ebuild       | 14 --------------
 virtual/blas/blas-3.8.ebuild       | 14 ++++++++++++++
 virtual/blas/metadata.xml          | 10 +++++++---
 virtual/cblas/cblas-1.0.ebuild     | 14 --------------
 virtual/cblas/cblas-3.8.ebuild     | 14 ++++++++++++++
 virtual/cblas/metadata.xml         | 10 +++++++---
 virtual/lapack/lapack-3.0.ebuild   | 13 -------------
 virtual/lapack/lapack-3.1.ebuild   | 13 -------------
 virtual/lapack/lapack-3.8.ebuild   | 14 ++++++++++++++
 virtual/lapack/metadata.xml        | 10 +++++++---
 virtual/lapacke/lapacke-3.8.ebuild | 14 ++++++++++++++
 virtual/lapacke/metadata.xml       | 16 ++++++++++++++++
 12 files changed, 93 insertions(+), 63 deletions(-)
Comment 9 Larry the Git Cow gentoo-dev 2019-07-03 12:34:09 UTC
The bug has been closed via the following commit(s):

https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=0721aba4db4bc8ce37d11eab06ff528f31e4ce9f

commit 0721aba4db4bc8ce37d11eab06ff528f31e4ce9f
Author:     Benda Xu <heroxbd@gentoo.org>
AuthorDate: 2019-06-27 05:41:31 +0000
Commit:     Benda Xu <heroxbd@gentoo.org>
CommitDate: 2019-07-03 12:30:39 +0000

    virtual/{blas,cblas,lapack,lapacke}: add virtual packages.
    
      These virtual packages are used by the BLAS/LAPACK runtime switching
      mechanism.
    
    Closes: https://github.com/gentoo/gentoo/pull/12323
    Closes: https://bugs.gentoo.org/373613
    Closes: https://bugs.gentoo.org/381801
    Closes: https://bugs.gentoo.org/498490
    Closes: https://bugs.gentoo.org/563674
    Closes: https://bugs.gentoo.org/564546
    Closes: https://bugs.gentoo.org/565776
    Closes: https://bugs.gentoo.org/646316
    Closes: https://bugs.gentoo.org/657984
    Closes: https://bugs.gentoo.org/659014
    Closes: https://bugs.gentoo.org/659264
    Closes: https://bugs.gentoo.org/669644
    
    Signed-off-by: Mo Zhou <cdluminate@gmail.com>
    Signed-off-by: Benda Xu <heroxbd@gentoo.org>

 virtual/blas/blas-3.8.ebuild       | 14 ++++++++++++++
 virtual/blas/metadata.xml          | 10 +++++++---
 virtual/cblas/cblas-3.8.ebuild     | 14 ++++++++++++++
 virtual/cblas/metadata.xml         | 10 +++++++---
 virtual/lapack/lapack-3.8.ebuild   | 14 ++++++++++++++
 virtual/lapack/metadata.xml        | 10 +++++++---
 virtual/lapacke/lapacke-3.8.ebuild | 14 ++++++++++++++
 virtual/lapacke/metadata.xml       | 16 ++++++++++++++++
 8 files changed, 93 insertions(+), 9 deletions(-)