| Summary: | sci-libs/scipy-0.12.1 with sci-libs/mkl - libraries mkl_gf_lp64kl_sequentialkl_core,mkl_gf_lp64kl_sequentialkl_core not found in ['/opt/intel/mkl/10.0.5.025/lib/em64t', '/usr/lib64'] | ||
|---|---|---|---|
| Product: | Gentoo Linux | Reporter: | HMolina <hmolina.cuentas> |
| Component: | [OLD] Library | Assignee: | Gentoo Science Related Packages <sci> |
| Status: | RESOLVED TEST-REQUEST | ||
| Severity: | normal | ||
| Priority: | Normal | ||
| Version: | unspecified | ||
| Hardware: | AMD64 | ||
| OS: | Linux | ||
| Whiteboard: | |||
| Package list: | Runtime testing required: | --- | |
| Attachments: |
emerge -vpq sci-libs/scipy
build.log |
||
Created attachment 371216 [details]
emerge -vpq sci-libs/scipy
Hi,
Just, changing the function form:
pc_libs() {
$(tc-getPKG_CONFIG) --libs-only-l $@ | \
sed -e 's/[ ]-l*\(pthread\|m\)[ ]*//g' \
-e 's/^-l//' -e 's/[ ]*-l/,/g' -e 's/[ ]*$//'
}
to
pc_libs() {
$(tc-getPKG_CONFIG) --libs-only-l $@ | \
sed -e 's/[ ]-l*\(pthread\|m \)[ ]*//g' \
-e 's/^-l//' -e 's/[ ]*-l/,/g' -e 's/[ ]*$//'
}
The sed filter works correctly.
H.
Other comment: The same problem in all scipy versions 0.12.1 till 0.13.3 And in numpy 1.8.0-r1 :-| T.I.A. H. Comment on attachment 371216 [details]
emerge -vpq sci-libs/scipy
That's not the build log.
Please attach the entire build log to this bug report. Created attachment 371392 [details]
build.log
The build log for the command:
emerge -aD scipy
Version 0.12.1
Looks the line 44, where looks for the blas libraries.
the correct set is:
mkl_gf_lp64,mkl_sequential,mkl_core
and generates
mkl_gf_lp64kl_sequentialkl_core
T.I.A.
Please see whether this is still valid for scipy 0.14/0.15. |
When tries to compile the scipy-0.12.1 using Intel MKL libraries, the compilation is broken. The problem is in the pc_libs function in the scipy-0.12.1.ebuild file. Reproducible: Always Steps to Reproduce: emerge -aD scipy Actual Results: Do not compile The set of MKL libraries begins with m letter, so, the list of libraries for blas looks like: -lmkl_gf_lp64 -lmkl_sequential -lmkl_core -lpthread The function pc_libs is: pc_libs() { $(tc-getPKG_CONFIG) --libs-only-l $@ | \ sed -e 's/[ ]-l*\(pthread\|m\)[ ]*//g' \ -e 's/^-l//' -e 's/[ ]*-l/,/g' -e 's/[ ]*$//' } when execute this function: pkg-config --libs-only-l blas, the results are: -lmkl_gf_lp64 -lmkl_sequential -lmkl_core -lpthread But with the sed filter: pkg-config --libs-only-l blas | sed -e 's/[ ]-l*\(pthread\|m\)[ ]*//g' the library list are: -lmkl_gf_lp64kl_sequentialkl_core Which are ill formed and the compilation fails. The emerge info is: Portage 2.2.7 (default/linux/amd64/13.0/desktop, gcc-4.7.3, glibc-2.17, 3.10.25-gentoo x86_64) ================================================================= System Settings ================================================================= System uname: Linux-3.10.25-gentoo-x86_64-Intel-R-_Xeon-R-_CPU_E5-2670_0_@_2.60GHz-with-gentoo-2.2 KiB Mem: 66089512 total, 49125812 free KiB Swap: 67108860 total, 67108860 free Timestamp of tree: Sat, 22 Feb 2014 21:00:01 +0000 ld GNU ld (GNU Binutils) 2.23.2 distcc 3.1 x86_64-pc-linux-gnu [disabled] app-shells/bash: 4.2_p45 dev-java/java-config: 2.1.12-r1 dev-lang/python: 2.7.5-r3, 3.2.5-r3, 3.3.3 dev-util/cmake: 2.8.11.2 dev-util/pkgconfig: 0.28 sys-apps/baselayout: 2.2 sys-apps/openrc: 0.12.4 sys-apps/sandbox: 2.6-r1 sys-devel/autoconf: 2.13::<unknown repository>, 2.69 sys-devel/automake: 1.4_p6-r1, 1.5-r1, 1.6.3-r1, 1.7.9-r2, 1.8.5-r4, 1.9.6-r3, 1.10.3, 1.11.6, 1.12.6, 1.13.4 sys-devel/binutils: 2.23.2 sys-devel/gcc: 4.7.3-r1 sys-devel/gcc-config: 1.7.3 sys-devel/libtool: 2.4.2 sys-devel/make: 3.82-r4 sys-kernel/linux-headers: 3.9 (virtual/os-headers) sys-libs/glibc: 2.17 Repositories: gentoo ACCEPT_KEYWORDS="amd64" ACCEPT_LICENSE="*" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-O3 -march=core2 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt /var/lib/hsqldb" CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d /etc/terminfo /etc/texmf/language.dat.d /etc/texmf/language.def.d /etc/texmf/updmap.d /etc/texmf/web2c" CXXFLAGS="-O3 -march=core2 -pipe" DISTDIR="/usr/portage/distfiles" FCFLAGS="-O2 -pipe" FEATURES="assume-digests binpkg-logs config-protect-if-modified distlocks ebuild-locks fixlafiles merge-sync news parallel-fetch preserve-libs protect-owned sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync" FFLAGS="-O2 -pipe" GENTOO_MIRRORS="http://distfiles.gentoo.org" LDFLAGS="-Wl,-O1 -Wl,--as-needed" MAKEOPTS="-j16" PKGDIR="/usr/portage/packages" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --omit-dir-times --compress --force --whole-file --delete --stats --human-readable --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/export/cressida/portage/portage_xeon64" PORTDIR_OVERLAY="" The logs will attached after. H.