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TADAitsnick
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Joined: 03 Jan 2025
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Location: Indiana, USA
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 Posted: Fri Jan 03, 2025 6:11 am Post subject: [SOLVED] dev-lang/julia freezing on emerge |
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Hello everyone. New to gentoo and loving it so far. This is my first post.
I am studying computational physics and I'm familiar with C++ and Fortran but I've just recently learned about Julia. I thought that it would be a good idea to give it a try and see just how useful it can be in my career later on or in grad school.
Unfortunately, I'm having issues emerging dev-lang/julia-1.8.5-r1. The dependencies were emerged successfully and the build seemed to be going fine, although it took a very long time. Since it took so long to build, I let it run while I was sleeping and I'm not sure what happened, but it was frozen on this message when I woke up:
| Code: | | Generating REPL precompile statements... 25/40 |
I thought that my cat had just stepped on my laptop while I was sleeping, so I tried again several times. It always stops at 25/40 and stays there for hours. Last time I tried, I let it run for 18 hours uninterrupted.
I saw this bug. The solution for that different version of julia was to kill busybox and I have no such process running, nor do I even think I have it installed. Also, that issue was supposed to be resolved.
To emphasize, I have never installed julia before. I prefer to install things through portage as I really like it so far but I do have a directory of other apps that I have cloned from git such as 'st'. I believe I have plenty of RAM/SWAP to handle this task to get ahead of that question as you can see in 'emerge --info' below. I have also compressed build.log to upload it, but there isn't a way to upload files to forums? Only for bugs? I would be happy to provide that, as well, if anyone can point me towards the right way to include it here. I did not make a post in bugs.gentoo.org because I am not sure that this is a bug and not user error of some kind.
Any help would be greatly appreciated!
| Code: | | emerge --info dev-lang/julia |
| Code: | ortage 3.0.66.1 (python 3.12.8-final-0, default/linux/amd64/23.0/hardened, gcc-14, glibc-2.40-r7, 6.12.3-gentoo x86_64)
=================================================================
System Settings
=================================================================
System uname: Linux-6.12.3-gentoo-x86_64-Intel-R-_Core-TM-_i7-6600U_CPU_@_2.60GHz-with-glibc2.40
KiB Mem: 16253936 total, 6371496 free
KiB Swap: 22020092 total, 22020092 free
Timestamp of repository gentoo: Mon, 30 Dec 2024 07:00:00 +0000
Head commit of repository gentoo: 174d902ba36ac55e0860bdd2620a5be24462380e
Timestamp of repository guru: Sun, 29 Dec 2024 18:03:14 +0000
Head commit of repository guru: 76952bd4abea2a7f305b9012f9a8599fcb6deee1
Timestamp of repository x11: Tue, 17 Dec 2024 22:21:06 +0000
Head commit of repository x11: 65e5ca74f923881451af9f311333b77691446b4b
sh bash 5.2_p37
ld GNU ld (Gentoo 2.43 p3) 2.43.1
app-misc/pax-utils: 1.3.8::gentoo
app-shells/bash: 5.2_p37::gentoo
dev-build/autoconf: 2.72-r1::gentoo
dev-build/automake: 1.17-r1::gentoo
dev-build/cmake: 3.31.3::gentoo
dev-build/libtool: 2.5.4::gentoo
dev-build/make: 4.4.1-r100::gentoo
dev-build/meson: 1.6.1::gentoo
dev-java/java-config: 2.3.4::gentoo
dev-lang/perl: 5.40.0-r1::gentoo
dev-lang/python: 3.10.16_p1::gentoo, 3.12.8::gentoo, 3.13.1::gentoo
dev-lang/rust-bin: 1.83.0::gentoo
llvm-core/clang: 18.1.8-r6::gentoo, 19.1.6::gentoo
llvm-core/llvm: 18.1.8-r6::gentoo, 19.1.6::gentoo
sys-apps/baselayout: 2.17::gentoo
sys-apps/openrc: 0.55.1::gentoo
sys-apps/sandbox: 2.42::gentoo
sys-devel/binutils: 2.43-r2::gentoo
sys-devel/binutils-config: 5.5.2::gentoo
sys-devel/gcc: 14.2.1_p20241221::gentoo
sys-devel/gcc-config: 2.12.1::gentoo
sys-kernel/linux-headers: 6.12::gentoo (virtual/os-headers)
sys-libs/glibc: 2.40-r7::gentoo
Repositories:
gentoo
location: /var/db/repos/gentoo
sync-type: rsync
sync-uri: rsync://rsync.gentoo.org/gentoo-portage
priority: -1000
volatile: False
sync-rsync-extra-opts:
sync-rsync-verify-metamanifest: yes
sync-rsync-verify-max-age: 3
sync-rsync-verify-jobs: 1
guru
location: /var/db/repos/guru
sync-type: git
sync-uri: https://github.com/gentoo-mirror/guru.git
masters: gentoo
volatile: False
x11
location: /var/db/repos/x11
sync-type: git
sync-uri: https://github.com/gentoo-mirror/x11.git
masters: gentoo
volatile: False
Binary Repositories:
gentoobinhost
priority: 1
sync-uri: https://distfiles.gentoo.org/releases/amd64/binpackages/23.0/x86-64_hardened
ACCEPT_KEYWORDS="amd64 ~amd64"
ACCEPT_LICENSE="* -@EULA"
CBUILD="x86_64-pc-linux-gnu"
CFLAGS="-march=skylake -O2 -pipe -fno-semantic-interposition"
CHOST="x86_64-pc-linux-gnu"
CONFIG_PROTECT="/etc /usr/share/gnupg/qualified.txt"
CONFIG_PROTECT_MASK="/etc/ca-certificates.conf /etc/dconf /etc/env.d /etc/fonts/fonts.conf /etc/gconf /etc/gentoo-release /etc/revdep-rebuild /etc/sandbox.d"
CXXFLAGS="-march=skylake -O2 -pipe -fno-semantic-interposition"
DISTDIR="/var/cache/distfiles"
ENV_UNSET="CARGO_HOME DBUS_SESSION_BUS_ADDRESS DISPLAY GDK_PIXBUF_MODULE_FILE GOBIN GOPATH PERL5LIB PERL5OPT PERLPREFIX PERL_CORE PERL_MB_OPT PERL_MM_OPT XAUTHORITY XDG_CACHE_HOME XDG_CONFIG_HOME XDG_DATA_HOME XDG_RUNTIME_DIR XDG_STATE_HOME"
FCFLAGS="-march=skylake -O2 -pipe -fno-semantic-interposition"
FEATURES="assume-digests binpkg-docompress binpkg-dostrip binpkg-logs binpkg-multi-instance buildpkg-live config-protect-if-modified distlocks ebuild-locks fixlafiles ipc-sandbox merge-sync merge-wait multilib-strict network-sandbox news parallel-fetch pid-sandbox pkgdir-index-trusted preserve-libs protect-owned qa-unresolved-soname-deps sandbox sfperms strict unknown-features-warn unmerge-logs unmerge-orphans userfetch userpriv usersandbox usersync xattr"
FFLAGS="-march=skylake -O2 -pipe -fno-semantic-interposition"
GENTOO_MIRRORS="http://www.gtlib.gatech.edu/pub/gentoo https://mirrors.mit.edu/gentoo-distfiles/ https://gentoo.osuosl.org/ https://mirrors.rit.edu/gentoo/ http://gentoo-mirror.flux.utah.edu/"
LANG="C.UTF8"
LDFLAGS="-Wl,-O1 -Wl,--as-needed -Wl,-z,pack-relative-relocs"
LEX="flex"
MAKEOPTS="-j4"
PKGDIR="/var/cache/binpkgs"
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 --exclude=/.git"
PORTAGE_TMPDIR="/var/tmp"
SHELL="/bin/bash"
USE="X acl alsa amd64 bzip2 cet crypt cxx debug elogind fortran gdbm hardened iconv ipv6 jpeg lapack libtirpc man multilib native-extensions ncurses nls opengl openmp pam pcre pdf pic pie pulseaudio python readline seccomp ssl ssp test-rust unicode vim wifi xattr xscreensaver xtpax zlib" ABI_X86="64 32" ADA_TARGET="gcc_13" APACHE2_MODULES="authn_core authz_core socache_shmcb unixd actions alias auth_basic authn_anon authn_dbm authn_file authz_dbm authz_groupfile authz_host authz_owner authz_user autoindex cache cgi cgid dav dav_fs dav_lock deflate dir env expires ext_filter file_cache filter headers include info log_config logio mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" CALLIGRA_FEATURES="karbon sheets words" COLLECTD_PLUGINS="df interface irq load memory rrdtool swap syslog" CPU_FLAGS_X86="mmx mmxext sse sse2 aes avx avx2 f16c fma3 pclmul popcnt rdrand sse3 sse4_1 sse4_2 ssse3" ELIBC="glibc" GPSD_PROTOCOLS="ashtech aivdm earthmate evermore fv18 garmin garmintxt gpsclock greis isync itrax navcom oceanserver oncore rtcm104v2 rtcm104v3 sirf skytraq superstar2 tsip tripmate tnt ublox" GRUB_PLATFORMS="efi-64" GUILE_SINGLE_TARGET="3-0" GUILE_TARGETS="3-0" INPUT_DEVICES="libinput synaptics" KERNEL="linux" LCD_DEVICES="bayrad cfontz glk hd44780 lb216 lcdm001 mtxorb text" LUA_SINGLE_TARGET="lua5-1" LUA_TARGETS="lua5-1" OFFICE_IMPLEMENTATION="libreoffice" PHP_TARGETS="php8-2" POSTGRES_TARGETS="postgres16" PYTHON_SINGLE_TARGET="python3_12" PYTHON_TARGETS="python3_12 python3_10" RUBY_TARGETS="ruby32" VIDEO_CARDS="intel" XTABLES_ADDONS="quota2 psd pknock lscan length2 ipv4options ipp2p iface geoip fuzzy condition tarpit sysrq proto logmark ipmark dhcpmac delude chaos account"
Unset: ADDR2LINE, AR, ARFLAGS, AS, ASFLAGS, CC, CCLD, CONFIG_SHELL, CPP, CPPFLAGS, CTARGET, CXX, CXXFILT, ELFEDIT, EMERGE_DEFAULT_OPTS, EXTRA_ECONF, F77FLAGS, FC, GCOV, GPROF, INSTALL_MASK, LC_ALL, LD, LFLAGS, LIBTOOL, LINGUAS, MAKE, MAKEFLAGS, NM, OBJCOPY, OBJDUMP, PORTAGE_BINHOST, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS, PYTHONPATH, RANLIB, READELF, RUSTFLAGS, SIZE, STRINGS, STRIP, YACC, YFLAGS
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Last edited by TADAitsnick on Sun Jan 05, 2025 4:45 am; edited 1 time in total |
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Banana
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TADAitsnick
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Joined: 03 Jan 2025
Posts: 7
Location: Indiana, USA
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| Posted: Fri Jan 03, 2025 11:20 am Post subject: |
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That's a useful package. Thanks.
Here is my build.log. |
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sam_
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| Posted: Fri Jan 03, 2025 11:21 am Post subject: |
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| Could you show us ps faux output when it's been stuck for a little bit? |
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TADAitsnick
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Joined: 03 Jan 2025
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Location: Indiana, USA
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| Posted: Fri Jan 03, 2025 1:51 pm Post subject: |
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| sam_ wrote: | | Could you show us ps faux output when it's been stuck for a little bit? |
Sure. Here you go. |
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sam_
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| Posted: Fri Jan 03, 2025 1:59 pm Post subject: |
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OK, nothing obvious.
Try: a) dropping -fno-semantic-interposition from *FLAGS, or b) dropping -march as well. Of course, that's just a workaround, but let's try it.
If that doesn't help (or even if it does), please attach gdb to 2486 (or the equivalent on another run) and get a backtrace. |
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TADAitsnick
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Joined: 03 Jan 2025
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Location: Indiana, USA
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| Posted: Fri Jan 03, 2025 2:02 pm Post subject: |
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| sam_ wrote: |
Try: a) dropping -fno-semantic-interposition from *FLAGS, or b) dropping -march as well. |
Either of these options would require a full rebuild of my system would they not? And they aren't guaranteed solutions. |
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sam_
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| Posted: Fri Jan 03, 2025 2:11 pm Post subject: |
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| TADAitsnick wrote: | | sam_ wrote: |
Try: a) dropping -fno-semantic-interposition from *FLAGS, or b) dropping -march as well. |
Either of these options would require a full rebuild of my system would they not? And they aren't guaranteed solutions. |
No, I was suggesting just dropping them for julia (either by temporarily modifying make.conf or using a package.env just for julia). |
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Banana
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TADAitsnick
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Joined: 03 Jan 2025
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Location: Indiana, USA
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| Posted: Fri Jan 03, 2025 9:40 pm Post subject: |
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| sam_ wrote: |
No, I was suggesting just dropping them for julia (either by temporarily modifying make.conf or using a package.env just for julia). |
Oh yes that was pretty silly of me. I temporarily changed make.conf to try both of those. I get the exact same behavior. I suppose it's looking more likely that it is a bug than something I did wrong? |
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sam_
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| Posted: Fri Jan 03, 2025 11:15 pm Post subject: |
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| Yeah, I think so. Can you grab a backtrace? |
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TADAitsnick
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Location: Indiana, USA
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TADAitsnick
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Joined: 03 Jan 2025
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Location: Indiana, USA
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| Posted: Sun Jan 05, 2025 4:45 am Post subject: |
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Okay, so here's an update. I'm marking this as solved. I have not fixed the issue with emerging the gentoo package for julia.
I worked on trying to get a backtrace for a while but I have not been able to. Instead, I went to the julia github page.
Note that it says this in the readme:
| Code: | | Note: Although some OS package managers provide Julia, such installations are neither maintained nor endorsed by the Julia project. They may be outdated, broken and/or unmaintained. We recommend you use the official Julia binaries instead. |
Indeed, it seems like the julia package in dev-lang is an older version: v1.8.5
The most recent stable version is v1.11.1 and that is what the developers recommend most people install.
Like I said in my original post, I prefer to use portage to maintain packages but I followed the advice of the julia devs and cloned the github and compiled v1.11.1
So, Julia is now installed and I have been using it for abstract algebra problems today. It works perfectly.
On the other hand, I still want to try and help improve the gentoo package by providing any diagnostics I can. Should I open a bug instead?
Thanks for the help folks!
~~~~~~~~~~~~~~~~~~~~~~
Nick |
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