Summary: | [science-overlay] [Prefix] sci-libs/lapack-reference versions 3.7.0-r100 and 3.8.0-r100 do not respect system selected blas libs | ||
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Product: | Gentoo/Alt | Reporter: | Steven Trogdon <strogdon> |
Component: | Prefix Support | Assignee: | Gentoo Prefix <prefix> |
Status: | RESOLVED FIXED | ||
Severity: | normal | ||
Priority: | Normal | ||
Version: | unspecified | ||
Hardware: | All | ||
OS: | Linux | ||
Whiteboard: | |||
Package list: | Runtime testing required: | --- | |
Attachments: |
build log
lapack-config.cmake lapack-targets.cmake |
Description
Steven Trogdon
2018-10-25 22:04:18 UTC
Created attachment 553052 [details]
build log
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. Created attachment 553054 [details]
lapack-config.cmake
Created attachment 553056 [details]
lapack-targets.cmake
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 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 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. 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(-) 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(-) |