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koshmar
n00b
Joined: 02 Nov 2016
Posts: 26
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 Posted: Tue Nov 15, 2016 5:38 am Post subject: how to install Julia 0.5? |
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I am a new Gentoo user, I went for it to have more stable/better quality packages then in my Arch linux (I have installed both). But after installation, I tried to install Julia, and could not succeed which was unexpected. I know it is due to the fact that Julia is new and probably buggy. Anyway I seek for the help.
I have standard Gentoo installation for amd 64 architecture with more or less default options.
First obstacle is that I could not compile "sci-libs/spqr-1.2.3-r1" thus I emerged "sci-libs/spqr-1.3.1"
Finally I started emerging Julia but I have encountered an error. I could not emerge Julia neither Julia-9999.
Google advised me to reinstall llvm to 3.9, so I did and repeated everything - installing Julia/Julia-9999 with its dependencies.
But the error persist. I saw in the internet that others also have problems with Julia 0.5 instalation, but I could not find a success story which will help me understand what to do.
Thank you!
p.s. I do not want to install Julia without packet manager.
p.p.s. https://forums.gentoo.org/viewtopic-t-1052662-highlight-julia.html here people disscuss the problem with spqr-1.2.3-r1 which I avoided by using spqr-1.3.1
Here is the error and build logs (at the end)
| Code: |
initdefs.jl
Terminals.jl
LineEdit.jl
REPLCompletions.jl
REPL.jl
client.jl
util.jl
linalg/linalg.jl
signal (11): Segmentation fault
while loading linalg/blas.jl, in expression starting on line 79
unknown function (ip: 0x7fe4c092c96a)
unknown function (ip: 0x7fe4c092c979)
unknown function (ip: 0x7fe4c092cad6)
unknown function (ip: 0x7fe4c092d1a9)
unknown function (ip: 0x7fe4c0858fe7)
unknown function (ip: 0x7fe6cc548369)
unknown function (ip: 0x7fe6cc54847a)
unknown function (ip: 0x7fe6cc54c9df)
unknown function (ip: 0x7fe6cc548213)
unknown function (ip: 0x7fe6cc54c072)
unknown function (ip: 0x7fe6cbb21fd8)
unknown function (ip: 0x7fe6cc548213)
unknown function (ip: 0x7fe6cbb22588)
dlopen at /lib64/libdl.so.2 (unknown line)
unknown function (ip: 0x7fe6cbd76f38)
unknown function (ip: 0x7fe6cbd9831c)
unknown function (ip: 0x7fe6cbdbd7ea)
unknown function (ip: 0x7fe6cbdcdbb5)
unknown function (ip: 0x7fe6cbdc6ac0)
unknown function (ip: 0x7fe6cbdca68e)
unknown function (ip: 0x7fe6cbdcb67b)
unknown function (ip: 0x7fe6cbdd750d)
unknown function (ip: 0x7fe6cbdd9d9b)
unknown function (ip: 0x7fe6cbddc3bb)
unknown function (ip: 0x7fe6cbd61837)
jl_apply_generic at /var/tmp/portage/dev-lang/julia-0.5.0-r2/work/julia-0.5.0/usr/bin/../lib/libjulia.so.0.5 (unknown line)
unknown function (ip: 0x7fe6cbd7217d)
unknown function (ip: 0x7fe6cbd712e4)
unknown function (ip: 0x7fe6cbd72163)
unknown function (ip: 0x7fe6cbd712e4)
unknown function (ip: 0x7fe6cbd7292b)
unknown function (ip: 0x7fe6cbd72c43)
unknown function (ip: 0x7fe6cbd874f7)
unknown function (ip: 0x7fe6cbd878ff)
unknown function (ip: 0x7fe6cbd874a8)
unknown function (ip: 0x7fe6cbd691bd)
jl_load at /var/tmp/portage/dev-lang/julia-0.5.0-r2/work/julia-0.5.0/usr/bin/../lib/libjulia.so.0.5 (unknown line)
jl_load_ at /var/tmp/portage/dev-lang/julia-0.5.0-r2/work/julia-0.5.0/usr/bin/../lib/libjulia.so.0.5 (unknown line)
#523 at ./sysimg.jl:208
jl_apply_generic at /var/tmp/portage/dev-lang/julia-0.5.0-r2/work/julia-0.5.0/usr/bin/../lib/libjulia.so.0.5 (unknown line)
unknown function (ip: 0x7fe6cbd7217d)
unknown function (ip: 0x7fe6cbd712e4)
unknown function (ip: 0x7fe6cbd871c4)
unknown function (ip: 0x7fe6cbd878ff)
unknown function (ip: 0x7fe6cbd874a8)
unknown function (ip: 0x7fe6cbd691bd)
jl_load at /var/tmp/portage/dev-lang/julia-0.5.0-r2/work/julia-0.5.0/usr/bin/../lib/libjulia.so.0.5 (unknown line)
jl_load_ at /var/tmp/portage/dev-lang/julia-0.5.0-r2/work/julia-0.5.0/usr/bin/../lib/libjulia.so.0.5 (unknown line)
#523 at ./sysimg.jl:208
jl_apply_generic at /var/tmp/portage/dev-lang/julia-0.5.0-r2/work/julia-0.5.0/usr/bin/../lib/libjulia.so.0.5 (unknown line)
unknown function (ip: 0x7fe6cbd7217d)
unknown function (ip: 0x7fe6cbd712e4)
unknown function (ip: 0x7fe6cbd871c4)
unknown function (ip: 0x7fe6cbd878ff)
unknown function (ip: 0x7fe6cbd874a8)
unknown function (ip: 0x7fe6cbd691bd)
jl_load at /var/tmp/portage/dev-lang/julia-0.5.0-r2/work/julia-0.5.0/usr/bin/../lib/libjulia.so.0.5 (unknown line)
unknown function (ip: 0x40163b)
unknown function (ip: 0x401a30)
unknown function (ip: 0x401326)
__libc_start_main at /lib64/libc.so.6 (unknown line)
unknown function (ip: 0x401378)
unknown function (ip: 0xffffffffffffffff)
Allocations: 14628515 (Pool: 14627873; Big: 642); GC: 29
/bin/sh: line 1: 26800 Segmentation fault /var/tmp/portage/dev-lang/julia-0.5.0-r2/work/julia-0.5.0/usr/bin/julia -O3 -C native --output-o /var/tmp/portage/dev-lang/julia-0.5.0-r2/work/julia-0.5.0/usr/lib/julia/sys.o --startup-file=no --sysimage /var/tmp/portage/dev-lang/julia-0.5.0-r2/work/julia-0.5.0/usr/lib/julia/inference.ji sysimg.jl
*** This error is usually fixed by running `make clean`. If the error persists, try `make cleanall`. ***
Makefile:229: recipe for target '/var/tmp/portage/dev-lang/julia-0.5.0-r2/work/julia-0.5.0/usr/lib/julia/sys.o' failed
make[1]: *** [/var/tmp/portage/dev-lang/julia-0.5.0-r2/work/julia-0.5.0/usr/lib/julia/sys.o] Error 1
make[1]: Leaving directory '/var/tmp/portage/dev-lang/julia-0.5.0-r2/work/julia-0.5.0'
Makefile:99: recipe for target 'julia-sysimg-release' failed
make: *** [julia-sysimg-release] Error 2
* ERROR: dev-lang/julia-0.5.0-r2::gentoo failed (compile phase):
* emake failed
*
* If you need support, post the output of `emerge --info '=dev-lang/julia-0.5.0-r2::gentoo'`,
* the complete build log and the output of `emerge -pqv '=dev-lang/julia-0.5.0-r2::gentoo'`.
* The complete build log is located at '/var/tmp/portage/dev-lang/julia-0.5.0-r2/temp/build.log'.
* The ebuild environment file is located at '/var/tmp/portage/dev-lang/julia-0.5.0-r2/temp/environment'.
* Working directory: '/var/tmp/portage/dev-lang/julia-0.5.0-r2/work/julia-0.5.0'
* S: '/var/tmp/portage/dev-lang/julia-0.5.0-r2/work/julia-0.5.0'
>>> Failed to emerge dev-lang/julia-0.5.0-r2, Log file:
>>> '/var/tmp/portage/dev-lang/julia-0.5.0-r2/temp/build.log'
* Messages for package dev-lang/julia-0.5.0-r2:
* ERROR: dev-lang/julia-0.5.0-r2::gentoo failed (compile phase):
* emake failed
*
* If you need support, post the output of `emerge --info '=dev-lang/julia-0.5.0-r2::gentoo'`,
* the complete build log and the output of `emerge -pqv '=dev-lang/julia-0.5.0-r2::gentoo'`.
* The complete build log is located at '/var/tmp/portage/dev-lang/julia-0.5.0-r2/temp/build.log'.
* The ebuild environment file is located at '/var/tmp/portage/dev-lang/julia-0.5.0-r2/temp/environment'.
* Working directory: '/var/tmp/portage/dev-lang/julia-0.5.0-r2/work/julia-0.5.0'
* S: '/var/tmp/portage/dev-lang/julia-0.5.0-r2/work/julia-0.5.0'
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# emerge --info '=dev-lang/julia-0.5.0-r2::gentoo'
https://owncloud.usask.ca/index.php/s/zOz4sRFQDOQLZCv
# emerge -pqv '=dev-lang/julia-0.5.0-r2::gentoo'
https://owncloud.usask.ca/index.php/s/dcT8oQWaKSMgR1j
build.log
https://owncloud.usask.ca/index.php/s/awyRyyvTnN6sAYv
environment
https://owncloud.usask.ca/index.php/s/08XVAOOmMBHLRqw |
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fedeliallalinea
Administrator
Joined: 08 Mar 2003
Posts: 31094
Location: here
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| Posted: Tue Nov 15, 2016 7:03 am Post subject: |
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You can reopen this bug
_________________
Questions are guaranteed in life; Answers aren't. |
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koshmar
n00b
Joined: 02 Nov 2016
Posts: 26
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| Posted: Thu Nov 17, 2016 4:46 am Post subject: how to reopen the bug? |
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Sorry, I could not figure out how to reopen it. How do I do it?
( I left additional comment for now) |
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fedeliallalinea
Administrator
Joined: 08 Mar 2003
Posts: 31094
Location: here
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| Posted: Thu Nov 17, 2016 6:53 am Post subject: Re: how to reopen the bug? |
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| koshmar wrote: | Sorry, I could not figure out how to reopen it. How do I do it?
( I left additional comment for now) |
It's correct, normal user can only add additional comment, are just developers who can reopen.
However I have seen that has been reopened and confirmed.
_________________
Questions are guaranteed in life; Answers aren't. |
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koshmar
n00b
Joined: 02 Nov 2016
Posts: 26
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| Posted: Thu Nov 17, 2016 2:44 pm Post subject: |
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| Thanks |
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koshmar
n00b
Joined: 02 Nov 2016
Posts: 26
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| Posted: Thu Nov 24, 2016 5:39 am Post subject: |
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| Well, bug is opened, and it will be resolved at some point. But I need to install Julia to use Gentoo in every day life) is there a work around? |
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vlaxose
n00b
Joined: 30 Nov 2016
Posts: 1
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| Posted: Wed Nov 30, 2016 8:30 am Post subject: |
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I had exact the same problem. Finally, i emerged julia-0.5.0-r2 after the following steps:
- add the science overlay
- emerge openblas-0.2.15
- eselect blas set 1 (openblas-openmp)
- emerge julia-0.5.0-r2 |
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koshmar
n00b
Joined: 02 Nov 2016
Posts: 26
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| Posted: Thu Dec 22, 2016 4:42 am Post subject: |
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Thanks! but now I have a stupid question now. new openblas causes a block with other julia dependencies (app-eselect/eselect-lapack). How have you resolved this? you just disregard app-eselect/eselect-lapack? I know it seems like a trivial thing, but I am still very new to gentoo 
| Code: |
kosh-pc kosh # emerge --ask julia
* IMPORTANT: 1 news items need reading for repository 'gentoo'.
* Use eselect news read to view new items.
These are the packages that would be merged, in order:
Calculating dependencies... done!
[ebuild N ] sci-libs/suitesparseconfig-4.2.1 USE="-static-libs"
[ebuild N ] sys-libs/libunwind-1.1-r1 USE="-debug -debug-frame -libatomic -lzma -static-libs"
[ebuild N ] net-libs/http-parser-2.6.2 USE="-static-libs" ABI_X86="(64) -32 (-x32)"
[ebuild N ~] virtual/blas-3.6-r100 USE="-doc -int64" ABI_X86="(64) -32"
[ebuild N ] dev-util/patchelf-0.8
[ebuild N ] dev-util/scons-2.4.1 USE="-doc" PYTHON_TARGETS="python2_7 (-pypy)"
[ebuild N ] app-text/texi2html-5.0-r1 USE="unicode"
[ebuild N ] app-eselect/eselect-lapack-0.1
[ebuild N ] sci-libs/amd-2.3.1 USE="fortran -doc -static-libs"
[ebuild N ] sci-libs/fftw-3.3.4 USE="fortran openmp threads (-altivec) -doc -mpi (-neon) -quad -static-libs {-test} (-zbus)" ABI_X86="(64) -32 (-x32)" CPU_FLAGS_X86="sse sse2 -avx -fma3 -fma4"
[ebuild N ] dev-libs/libgit2-0.24.2 USE="threads -examples -gssapi (-libressl) -ssh {-test} -trace"
[ebuild N ] dev-lang/R-3.2.2 USE="X cairo icu jpeg nls openmp png readline tiff -doc -java -lapack -minimal -perl (-prefix) -profile -static-libs -tk"
[ebuild N ] app-emacs/ess-15.09.2
[ebuild N ] sci-mathematics/glpk-4.45 USE="-doc -examples -gmp -mysql -odbc -static-libs"
[ebuild N ] sci-libs/camd-2.3.1 USE="-doc -static-libs"
[ebuild N ~] dev-libs/double-conversion-2.0.1 USE="-static-libs"
[ebuild N ~] sci-libs/openlibm-0.3 USE="-static-libs"
[ebuild N ~] dev-libs/openspecfun-0.4-r1
[ebuild N ] sci-libs/colamd-2.8.0 USE="-static-libs"
[ebuild N ] sci-libs/lapack-reference-3.2.1-r4 USE="-doc"
[ebuild N ] sci-libs/cholmod-2.1.2 USE="-cuda -doc -lapack -metis -minimal -static-libs"
[ebuild N ] virtual/lapack-3.1
[ebuild N ] sci-libs/spqr-1.2.3-r1 USE="-doc -metis -static-libs -tbb"
[ebuild N ] sci-libs/arpack-3.1.3-r1 USE="-doc -examples -mpi -static-libs"
[ebuild N ] sci-libs/umfpack-5.6.2 USE="cholmod -doc -static-libs"
[ebuild N ~] dev-lang/julia-0.5.0-r2 USE="emacs"
[blocks B ] app-eselect/eselect-lapack ("app-eselect/eselect-lapack" is blocking sci-libs/openblas-0.2.15, app-admin/eselect-1.4.8-r100)
* Error: The above package list contains packages which cannot be
* installed at the same time on the same system.
(sci-libs/openblas-0.2.15:0/0::science, installed) pulled in by
>=sci-libs/openblas-0.2.11[int64?,abi_x86_32(-)?,abi_x86_64(-)?] (>=sci-libs/openblas-0.2.11[abi_x86_64(-)]) required by (virtual/blas-3.6-r100:0/0::science, ebuild scheduled for merge)
(app-eselect/eselect-lapack-0.1:0/0::gentoo, ebuild scheduled for merge) pulled in by
app-eselect/eselect-lapack required by (sci-libs/lapack-reference-3.2.1-r4:0/0::gentoo, ebuild scheduled for merge)
For more information about Blocked Packages, please refer to the following
section of the Gentoo Linux x86 Handbook (architecture is irrelevant):
https://wiki.gentoo.org/wiki/Handbook:X86/Working/Portage#Blocked_packages
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koshmar
n00b
Joined: 02 Nov 2016
Posts: 26
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| Posted: Sat Dec 24, 2016 10:29 pm Post subject: |
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I have overcome block with
| Code: |
emerge openblas lapack::science
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but the julia still does not emerge...
however my openblas in eselect is "openblas-threads" not "openblas-openmp". (adding openmp useflag did not help) |
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koshmar
n00b
Joined: 02 Nov 2016
Posts: 26
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| Posted: Sun Dec 25, 2016 5:59 pm Post subject: |
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| vlaxose wrote: | I had exact the same problem. Finally, i emerged julia-0.5.0-r2 after the following steps:
- add the science overlay
- emerge openblas-0.2.15
- eselect blas set 1 (openblas-openmp)
- emerge julia-0.5.0-r2 |
Could you please show me your julia dependenses and package.keywords for julia. I want to compare package by package, version by version=) because it seems that "openblas" helped a little bit - now I have different error |
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