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intel-mkl, science-kit and original science overlay


I hope this hasn't been asked before (my searches have returned nil though): Prior to kits deployment, I used Intel's math kernel library via the science overlay's ebuild (sci-libs/mkl- With the current master branch of science-kit, the latest version is substantially older:

# eix mkl -Ic
[?] sci-libs/mkl [1] ([?]@06/16/2017 -> (~)^ms): Intel(R) Math Kernel Library: linear algebra, fft, math functions
[1] "science-kit" /var/git/meta-repo/kits/science-kit

So mkl- is the most recent version available on the master branch. But this ebuild has a problem with its license file, which is apparently expired: 

# cat /var/tmp/portage/sci-libs/mkl-  | tail -n 20
Mon 09 10:35:49 shell.c:35	runShellCmd():Command to execute: 'uname -m 2>/dev/null'
Mon 09 10:35:49 shell.c:76	runShellCmd():Capturing STDOUT
Mon 09 10:35:49 shell.c:89	runShellCmd():GOT 7 bytes from STDOUT
Mon 09 10:35:49 shell.c:119	runShellCmd():waitpid() status for the executed command: 0
Mon 09 10:35:49 check_license.c:98	determineFLEXLM_platform():Trying to determine FLEXlm platform for machine name x86_64
Mon 09 10:35:49 check_license.c:448	check_license_file():Checking file /var/tmp/portage/sci-libs/mkl- for valid FLEXlm license
Mon 09 10:35:49 check_license.c:449	check_license_file():runpath /var/tmp/portage/sci-libs/mkl-
Mon 09 10:35:49 check_license.c:450	check_license_file():-a -q
Mon 09 10:35:49 check_license.c:451	check_license_file():chklic_f_opt -fMKernL -fMKern -fCLMKernL -fCLMKern 
Mon 09 10:35:49 check_license.c:452	check_license_file():chklic_c_opt -c"/var/tmp/portage/sci-libs/mkl-"
Mon 09 10:35:49 check_license.c:453	check_license_file():chklic_p_opt -pi86_r -pi86_re -pit64_lr -pit64_re
Mon 09 10:35:49 check_license.c:282	call_flexlm_chklic():Call a /var/tmp/portage/sci-libs/mkl- -a -fMKernL -fMKern -fCLMKernL -fCLMKern  -c"/var/tmp/portage/sci-libs/mkl-" -pi86_r -pi86_re -pit64_lr -pit64_re &>/dev/null command.
Mon 09 10:35:49 shell.c:29	runShellCmd():Interpreter: 'sh'
Mon 09 10:35:49 shell.c:35	runShellCmd():Command to execute: '/var/tmp/portage/sci-libs/mkl- -a -fMKernL -fMKern -fCLMKernL -fCLMKern  -c"/var/tmp/portage/sci-libs/mkl-" -pi86_r -pi86_re -pit64_lr -pit64_re &>/dev/null'
Mon 09 10:35:49 shell.c:119	runShellCmd():waitpid() status for the executed command: 512
Mon 09 10:35:49 check_license.c:288	call_flexlm_chklic():Chklic value 2
Mon 09 10:35:49 check_license.c:455	check_license_file():Chklic ret value is 2 
Mon 09 10:35:49 check_license.c:167	chklic_evaluate():Expired FLEXlm license was found in /var/tmp/portage/sci-libs/mkl-
Mon 09 10:35:49 check_license.c:457	check_license_file():Chklic auth value is 0 
Mon 09 10:35:49 install.c:80	fatal_exit():failed to install the product

The above license problem is also identified here: https://forums.gentoo.org/viewtopic-p-8027848.html

If I try to set up a local overlay using the ebuild from the original science overlay (mkl-, this produces a dependency to alternatives-2.eclass, which is apparently not supported:

* ERROR: sci-libs/mkl- failed (depend phase):
 *   alternatives-2.eclass could not be found by inherit()
 * Call stack:
 *               ebuild.sh, line 611:  Called source '/usr/local/portage/sci-libs/mkl/mkl-'
 *   mkl-, line  12:  Called inherit 'alternatives-2' 'intel-sdp-r1' 'numeric-int64-multibuild'
 *               ebuild.sh, line 284:  Called die
 * The specific snippet of code:
 *   		[[ -z ${location} ]] && die "${1}.eclass could not be found by inherit()"
 * If you need support, post the output of `emerge --info '=sci-libs/mkl-'`,
 * the complete build log and the output of `emerge -pqv '=sci-libs/mkl-'`.
 * Working directory: '/usr/lib64/python2.7/site-packages'
 * S: '/var/tmp/portage/sci-libs/mkl-'

Do anyone have a idea on how to solve this problem?

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alright, there seems edit performed to add new information. you should not use that gentoo file in /etc/portage/repos.conf. ports-2017 was alpha version of meta-repo, please follow:


and notice the overlay wiki page i posted above and pay attention to the symlink creation, so that you will be able to use meta-repo and sage overlay.

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Hi Oleg, thanks for your help, I am trying to do exactly this in terms of several overlays (science, sage-on-gentoo, etc.). To incorporate the overlays previously added via layman, I've simply followed the instructions you linked and added the overlays per the instructions on Funtoo's SageMath page:

# cd /var/git/overlay
# git clone https://github.com/cschwan/sage-on-gentoo.git

I added a sage.conf file in /var/git/meta-repo/repos.conf

priority = 50
location = /var/git/overlay/sage-on-gentoo
sync-type = git
sync-uri = https://github.com/cschwan/sage-on-gentoo.git
auto-sync = Yes

Other overlays (originally maintained by layman) were added in a similar fashion. Lastly, the ebuilds that originally resided in /usr/local/portage were moved to /var/git/overlay/mylocal. This also seems to work, i.e., eix-update and emerge --sync. However, I see errors when using equery and the like, complaining about

Unavailable repository 'gentoo' referenced by masters entry in '/var/git/overlay/science/metadata/layout.conf'
Unavailable repository 'gentoo' referenced by masters entry in '/var/git/overlay/dotnet/metadata/layout.conf'
Unavailable repository 'gentoo' referenced by masters entry in '/var/git/overlay/sage-on-gentoo/metadata/layout.conf'

Can you tell me how I would correct the above. Thanks again for all your hard work.


Edit* added:

OK, I see I forgot to add the to gentoo file in /etc/portage/repos.conf:

main-repo = gentoo

location = /usr/portage
sync-type = git
sync-uri = git://github.com/funtoo/ports-2017.git
auto-sync = yes

But I still seem to have screwed up something, as portage now warns:

!!! Repository name or alias 'gentoo', defined for repository 'core-kit', overrides existing alias or repository.
!!! Repository 'core-kit' is missing masters attribute in '/var/git/meta-repo/kits/core-kit/metadata/layout.conf'
!!! Set 'masters = gentoo' in this file for future compatibility

Can you tell me how I might correct this?

Edited by rsa4046

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