Trying to emerge (well, paludis --install) sci-mathematics/scilab-4.1.2-r1, with mkl-gfortran-threads (sci-libs/mkl-10.0.5.025) eselected as BLAS, fails with: --snip--...i686-pc-linux-gnu/bin/ld: cannot find libmkl_intel.so Reproducible: Always Steps to Reproduce: 1. paludis --install sci-mathematics/scilab (Assuming 4.1.2-r1) 2. Wait. 3. Groan. Actual Results: Build aborts with: make[1]: Leaving directory `/home/paludis/sci-mathematics-scilab-4.1.2-r1/work/scilab-4.1.2/pvm3' linking /usr/lib/gcc/i686-pc-linux-gnu/4.2.4/../../../../i686-pc-linux-gnu/bin/ld: cannot find libmkl_intel.so collect2: ld returned 1 exit status make: *** [bin/scilex] Error 1 Expected Results: scilab installed, much happiness in the world. I recognize paludis is non-standard, and would appreciate any suggestions on submitting bugs with paludis information. I mean, of course, aside from 'Ditch paludis, and come back to emerge.' If this advice were to be offered, with all due respect, it probably would not be appreciated. Not in a bad way, you understand. Just, well, not. I'd love to be able to give information in the most compatible way possible. I'll toss up the build log and messages from paludis as attachments. If they would be better posted in this field, please say so. Oh, and thank you! paludis 0.36.0 Paludis build information: Compiler: CXX: i686-pc-linux-gnu-g++ 4.2.4 (Gentoo 4.2.4-r1 p1.1) CXXFLAGS: -O2 -march=pentium4 -pipe LDFLAGS: -Wl,-O1 DATE: 2009-03-12T04:56:58-0500 Libraries: C++ Library: GNU libstdc++ 20080519 Reduced Privs: reduced_uid: 117 reduced_uid->name: paludisbuild reduced_uid->dir: /dev/null reduced_gid: 452 reduced_gid->name: paludisbuild Paths: DATADIR: /usr/share LIBDIR: /usr/lib LIBEXECDIR: /usr/libexec SYSCONFDIR: /etc PYTHONINSTALLDIR: RUBYINSTALLDIR: /usr/lib/ruby/site_ruby/1.8/i686-linux Environment: Format: paludis Config dir: /etc/paludis World file: /var/lib/portage/world Repository installed-virtuals: format: installed_virtuals root: / Repository virtuals: format: virtuals Repository gentoo: format: ebuild location: /home/portage append_repository_name_to_write_cache: true binary_destination: false binary_keywords: binary_uri_prefix: builddir: /home/paludis cache: /usr/portage/metadata/cache distdir: /home/portage/distfiles eapi_when_unknown: 0 eapi_when_unspecified: 0 eclassdirs: /usr/portage/eclass ignore_deprecated_profiles: false layout: traditional names_cache: /home/portage/.cache/names newsdir: /home/portage/metadata/news profile_eapi_when_unspecified: 0 profiles: /home/portage/profiles/default/linux/x86/2008.0 securitydir: /home/portage/metadata/glsa setsdir: /usr/portage/sets sync: rsync://rsync.us.gentoo.org/gentoo-portage sync_options: use_manifest: use write_cache: /var/cache/paludis/metadata Repository installed: format: vdb location: /var/db/pkg builddir: /var/tmp/paludis names_cache: /var/db/pkg/.cache/names provides_cache: /var/db/pkg/.cache/provides root: / Repository gentoo-gis: format: ebuild location: /home/portage/local/layman/gentoo-gis append_repository_name_to_write_cache: true binary_destination: false binary_keywords: binary_uri_prefix: builddir: /home/paludis cache: /var/empty distdir: /home/portage/distfiles eapi_when_unknown: 0 eapi_when_unspecified: 0 eclassdirs: /usr/portage/eclass /usr/portage/local/layman/gentoo-gis/eclass ignore_deprecated_profiles: false layout: traditional master_repository: gentoo names_cache: /home/portage/local/layman/gentoo-gis/.cache/names newsdir: /usr/portage/local/layman/gentoo-gis/metadata/news profile_eapi_when_unspecified: 0 profiles: /home/portage/profiles/default/linux/x86/2008.0 securitydir: /usr/portage/local/layman/gentoo-gis/metadata/glsa setsdir: /usr/portage/local/layman/gentoo-gis/sets sync: svn+https://gentoo-gis.svn.sourceforge.net/svnroot/gentoo-gis/stable sync_options: use_manifest: use write_cache: /var/cache/paludis/metadata Repository layman: format: ebuild location: /home/portage/local/layman append_repository_name_to_write_cache: true binary_destination: false binary_keywords: binary_uri_prefix: builddir: /home/paludis cache: /var/empty distdir: /home/portage/distfiles eapi_when_unknown: 0 eapi_when_unspecified: 0 eclassdirs: /usr/portage/eclass /usr/portage/local/layman/eclass ignore_deprecated_profiles: false layout: traditional master_repository: gentoo names_cache: /home/portage/local/layman/.cache/names newsdir: /usr/portage/local/layman/metadata/news profile_eapi_when_unspecified: 0 profiles: /home/portage/profiles/default/linux/x86/2008.0 securitydir: /usr/portage/local/layman/metadata/glsa setsdir: /usr/portage/local/layman/sets sync: sync_options: use_manifest: use write_cache: /var/cache/paludis/metadata Repository local-portage-overlay: format: ebuild location: /home/local/portage append_repository_name_to_write_cache: true binary_destination: false binary_keywords: binary_uri_prefix: builddir: /home/paludis cache: /var/empty distdir: /home/portage/distfiles eapi_when_unknown: 0 eapi_when_unspecified: 0 eclassdirs: /usr/portage/eclass /usr/local/portage/eclass ignore_deprecated_profiles: false layout: traditional master_repository: gentoo names_cache: /home/local/portage/.cache/names newsdir: /usr/local/portage/metadata/news profile_eapi_when_unspecified: 0 profiles: /home/portage/profiles/default/linux/x86/2008.0 securitydir: /usr/local/portage/metadata/glsa setsdir: /usr/local/portage/sets sync: sync_options: use_manifest: use write_cache: /var/cache/paludis/metadata Repository webapp-experimental: format: ebuild location: /var/paludis/repositories/webapps-experimental append_repository_name_to_write_cache: true binary_destination: false binary_keywords: binary_uri_prefix: builddir: /home/paludis cache: /var/empty distdir: /home/portage/distfiles eapi_when_unknown: 0 eapi_when_unspecified: 0 eclassdirs: /usr/portage/eclass /var/paludis/repositories/webapps-experimental/eclass ignore_deprecated_profiles: false layout: traditional master_repository: gentoo names_cache: /var/paludis/repositories/webapps-experimental/.cache/names newsdir: /var/paludis/repositories/webapps-experimental/metadata/news profile_eapi_when_unspecified: 0 profiles: /home/portage/profiles/default/linux/x86/2008.0 securitydir: /var/paludis/repositories/webapps-experimental/metadata/glsa setsdir: /var/paludis/repositories/webapps-experimental/sets sync: svn+http://overlays.gentoo.org/svn/proj/webapps/experimental sync_options: use_manifest: use write_cache: /var/cache/paludis/metadata Package sci-mathematics/scilab-4.1.2-r1:0::gentoo: >>> Running ebuild phase killold as paludisbuild:paludisbuild... >>> Starting builtin_killold >>> Done builtin_killold >>> Completed ebuild phase killold >>> Running ebuild phases initmisc infovars as paludisbuild:paludisbuild... >>> Starting builtin_initmisc >>> Done builtin_initmisc >>> Starting builtin_infovars ACCEPT_KEYWORDS=x86 CBUILD=i686-pc-linux-gnu CFLAGS=-O2 -march=pentium4 -pipe CHOST=i686-pc-linux-gnu CONFIG_PROTECT= CONFIG_PROTECT_MASK= CPPFLAGS= CTARGET= CXXFLAGS=-O2 -march=pentium4 -pipe DISTDIR=/home/portage/distfiles FEATURES=strict sfperms FFLAGS=-O2 -march=pentium4 -pipe GENTOO_MIRRORS= INSTALL_MASK= LANG= LC_ALL=C LDFLAGS=-Wl,-O1 LINGUAS= MAKEOPTS=-j1 PORTAGE_COMPRESS= PORTAGE_COMPRESS_FLAGS= PORTAGE_CONFIGROOT= PORTAGE_RSYNC_EXTRA_OPTS= PORTAGE_RSYNC_OPTS= PORTAGE_TMPDIR=/home/paludis PORTDIR=/home/portage PORTDIR_OVERLAY= SYNC= USE=Xaw3d gtk x86 alsa_cards_hda-intel alsa_pcm_plugins_adpcm alsa_pcm_plugins_alaw alsa_pcm_plugins_asym alsa_pcm_plugins_copy alsa_pcm_plugins_dmix alsa_pcm_plugins_dshare alsa_pcm_plugins_dsnoop alsa_pcm_plugins_empty alsa_pcm_plugins_extplug alsa_pcm_plugins_file alsa_pcm_plugins_hooks alsa_pcm_plugins_iec958 alsa_pcm_plugins_ioplug alsa_pcm_plugins_ladspa alsa_pcm_plugins_lfloat alsa_pcm_plugins_linear alsa_pcm_plugins_meter alsa_pcm_plugins_mmap_emul alsa_pcm_plugins_mulaw alsa_pcm_plugins_multi alsa_pcm_plugins_null alsa_pcm_plugins_plug alsa_pcm_plugins_rate alsa_pcm_plugins_route alsa_pcm_plugins_share alsa_pcm_plugins_shm alsa_pcm_plugins_softvol apache2_modules_actions apache2_modules_alias apache2_modules_auth_basic apache2_modules_authn_alias apache2_modules_authn_anon apache2_modules_authn_dbm apache2_modules_authn_default apache2_modules_authn_file apache2_modules_authz_dbm apache2_modules_authz_default apache2_modules_authz_groupfile apache2_modules_authz_host apache2_modules_authz_owner apache2_modules_authz_user apache2_modules_autoindex apache2_modules_cache apache2_modules_dav apache2_modules_dav_fs apache2_modules_dav_lock apache2_modules_deflate apache2_modules_dir apache2_modules_disk_cache apache2_modules_env apache2_modules_expires apache2_modules_ext_filter apache2_modules_file_cache apache2_modules_filter apache2_modules_headers apache2_modules_include apache2_modules_info apache2_modules_log_config apache2_modules_logio apache2_modules_mem_cache apache2_modules_mime apache2_modules_mime_magic apache2_modules_negotiation apache2_modules_rewrite apache2_modules_setenvif apache2_modules_speling apache2_modules_status apache2_modules_unique_id apache2_modules_userdir apache2_modules_usertrack apache2_modules_vhost_alias cameras_canon cameras_directory elibc_glibc input_devices_keyboard input_devices_mouse kernel_linux lcd_devices_bayrad lcd_devices_cfontz lcd_devices_cfontz633 lcd_devices_glk lcd_devices_hd44780 lcd_devices_lb216 lcd_devices_lcdm001 lcd_devices_mtxorb lcd_devices_ncurses lcd_devices_text lirc_devices_audio_alsa lirc_devices_devinput lirc_devices_hauppauge userland_GNU video_cards_dummy video_cards_fbdev video_cards_fglrx video_cards_intel video_cards_radeon video_cards_vesa video_cards_vga x86 >>> Done builtin_infovars >>> Completed ebuild phases initmisc infovars >>> Running ebuild phase tidyup as paludisbuild:paludisbuild... >>> Starting builtin_tidyup >>> Done builtin_tidyup >>> Completed ebuild phase tidyup
Created attachment 186301 [details] Build messages from Paludis.
Created attachment 186303 [details] Build log from Paludis.
(In reply to comment #2) > Created an attachment (id=186303) [edit] > Build log from Paludis. > Any word on this bug?
Unfortunately, I don't have any machines with mkl installed at the moment so I can look at this very easily. This is probably an issue with scilab's build system but without a live system to test this on it is hard to tell. Best, Markus
Created attachment 201742 [details] scilab-4.1.2-r2.ebuild including patch for compiling with mkl-gfortran-threads. Be sure to confirm that the following files are linked: /usr/include/cblas.h -> /opt/intel/mkl/10.0.5.025/include/cblas.h /usr/include/mkl_types.h -> /opt/intel/mkl/10.0.5.025/include/mkl_types.h If either or both of these are absent, execute the following commands for each missing link: ln -s /opt/intel/mkl/10.0.5.025/include/cblas.h /usr/include/cblas.h ln -s /opt/intel/mkl/10.0.5.025/include/mkl_types.h /usr/include/mkl_types.h This ebuild will work with mkl-10.1.1.019 as well, using the ebuild from bug 260810. Just replace each occurrence of '10.0.5.025' with '10.1.1.019' in the ebuild and the following patch, and confirm that the above-mentioned files are linked to the correct version.
Created attachment 201743 [details, diff] Patch for compiling scilab-4.1.2-r2 with mkl-10.0.5.025 mkl-gfortran-threads, using ebuild attached to this bug. See ebuild attachment comments.
I've attached the ebuild and patch in the previous two comments to allow compilation with mkl-10.0.5.025 using mkl-gfortran-threads. The patch is a bit inelegant, but works well for me. See the comments with the ebuild above for more information. In a nutshell, the patch simply adds the mkl directory, libiomp5, and libpthread to LD_FLAGS in Makefile.incl.in and configure.in, in the top level directory of the scilab source. Hope this helps anyone encountering this problem (Not being able to compile scilab-4.1.2 using mkl-10.0.5.025 with the mkl-gfortran-threads implementation). (In reply to comment #6) > Created an attachment (id=201743) [edit] > Patch for compiling scilab-4.1.2-r2 with mkl-10.0.5.025 mkl-gfortran-threads, > using ebuild attached to this bug. > > See ebuild attachment comments. >
dropped from the tree, use sci overlay versions instead
