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Tasklist

FS#79359 - [openmpi] rebuild required

Attached to Project: Arch Linux
Opened by Kishore (Doctor_Zoidberg) - Saturday, 12 August 2023, 13:47 GMT
Last edited by Christian Heusel (gromit) - Saturday, 12 August 2023, 15:30 GMT
Task Type Bug Report
Category Packages: Extra
Status Closed
Assigned To Levente Polyak (anthraxx)
Architecture All
Severity High
Priority Normal
Reported Version
Due in Version Undecided
Due Date Undecided
Percent Complete 100%
Votes 0
Private No

Details

Description:
After updating my system today, I get the following output when running mpirun:
```
$ mpirun
double free or corruption (!prev)
fish: Job 1, 'mpirun' terminated by signal SIGABRT (Abort)
```

If I rebuild the openmpi package locally, it runs correctly:
```
mpirun
--------------------------------------------------------------------------
mpirun could not find anything to do.

It is possible that you forgot to specify how many processes to run
via the "-np" argument.
--------------------------------------------------------------------------
```

Installing the repo version by doing `sudo pacman -Suu` breaks it again.

Additional info:
openmpi version: 4.1.5-2

Here is a list of packages that I updated today. I tried downgrading a few likely culprits (openssh, openssl, gcc, gcc-libs, lib32-gcc-libs), but the issue still persisted (i.e. I have not been able to narrow down exactly which package is responsible).
```
[2023-08-12T16:22:47+0530] [ALPM] upgraded linux-api-headers (6.3-1 -> 6.4-1)
[2023-08-12T16:22:47+0530] [ALPM] upgraded glibc (2.37-3 -> 2.38-2)
[2023-08-12T16:22:50+0530] [ALPM] upgraded openssl (3.1.1-1 -> 3.1.2-1)
[2023-08-12T16:22:51+0530] [ALPM] upgraded gcc-libs (13.1.1-2 -> 13.2.1-3)
[2023-08-12T16:22:51+0530] [ALPM] upgraded libldap (2.6.4-2 -> 2.6.6-1)
[2023-08-12T16:22:51+0530] [ALPM] upgraded audit (3.1.1-1 -> 3.1.2-1)
[2023-08-12T16:22:51+0530] [ALPM] upgraded xz (5.4.3-1 -> 5.4.4-1)
[2023-08-12T16:22:51+0530] [ALPM] upgraded gmp (6.2.1-2 -> 6.3.0-1)
[2023-08-12T16:22:51+0530] [ALPM] upgraded systemd-libs (253.7-1 -> 254.1-1)
[2023-08-12T16:22:51+0530] [ALPM] upgraded libelf (0.189-1 -> 0.189-3)
[2023-08-12T16:22:52+0530] [ALPM] upgraded binutils (2.40-6 -> 2.41-3)
[2023-08-12T16:22:52+0530] [ALPM] upgraded libxml2 (2.11.4-1 -> 2.11.5-1)
[2023-08-12T16:22:52+0530] [ALPM] upgraded mesa (23.1.4-2 -> 1:23.1.5-1)
[2023-08-12T16:22:52+0530] [ALPM] upgraded libjpeg-turbo (2.1.5.1-1 -> 3.0.0-1)
[2023-08-12T16:22:52+0530] [ALPM] upgraded libsysprof-capture (3.48.0-2 -> 3.48.0-4)
[2023-08-12T16:22:52+0530] [ALPM] upgraded libproxy (0.5.3-1 -> 0.5.3-2)
[2023-08-12T16:22:52+0530] [ALPM] upgraded harfbuzz (8.0.1-1 -> 8.1.1-1)
[2023-08-12T16:22:52+0530] [ALPM] upgraded device-mapper (2.03.21-1 -> 2.03.22-1)
[2023-08-12T16:22:53+0530] [ALPM] upgraded systemd (253.7-1 -> 254.1-1)
[2023-08-12T16:23:07+0530] [ALPM] upgraded qt5-base (5.15.10+kde+r139-1 -> 5.15.10+kde+r147-1)
[2023-08-12T16:23:07+0530] [ALPM] upgraded libtool (2.4.7+4+g1ec8fa28-4 -> 2.4.7+4+g1ec8fa28-6)
[2023-08-12T16:23:07+0530] [ALPM] upgraded polkit (122-1 -> 123-1)
[2023-08-12T16:23:07+0530] [ALPM] upgraded mpfr (4.2.0.p12-1 -> 4.2.0.p12-3)
[2023-08-12T16:23:07+0530] [ALPM] upgraded bluedevil (1:5.27.6-1 -> 1:5.27.7-1)
[2023-08-12T16:23:07+0530] [ALPM] upgraded kdecoration (5.27.6-1 -> 5.27.7-1)
[2023-08-12T16:23:07+0530] [ALPM] upgraded breeze (5.27.6-1 -> 5.27.7-1)
[2023-08-12T16:23:07+0530] [ALPM] upgraded breeze-gtk (5.27.6-1 -> 5.27.7-1)
[2023-08-12T16:23:07+0530] [ALPM] upgraded cpupower (6.3-2 -> 6.3-4)
[2023-08-12T16:23:07+0530] [ALPM] upgraded drkonqi (5.27.6-1 -> 5.27.7-1)
[2023-08-12T16:23:07+0530] [ALPM] upgraded enchant (2.3.4-2 -> 2.5.0-1)
[2023-08-12T16:23:08+0530] [ALPM] upgraded noto-fonts (1:23.7.1-1 -> 1:23.8.1-1)
[2023-08-12T16:23:08+0530] [ALPM] upgraded libmfx (23.2.2-1 -> 23.2.2-2)
[2023-08-12T16:23:08+0530] [ALPM] upgraded sdl2 (2.28.1-1 -> 2.28.2-1)
[2023-08-12T16:23:09+0530] [ALPM] upgraded openexr (3.1.9-1 -> 3.1.10-1)
[2023-08-12T16:23:09+0530] [ALPM] upgraded gtk-update-icon-cache (1:4.10.4-1 -> 1:4.10.5-1)
[2023-08-12T16:23:10+0530] [ALPM] upgraded firefox (115.0.3-1 -> 116.0.2-1)
[2023-08-12T16:23:10+0530] [ALPM] upgraded fuse-common (3.15.1-1 -> 3.16.1-1)
[2023-08-12T16:23:10+0530] [ALPM] upgraded fuse3 (3.15.1-1 -> 3.16.1-1)
[2023-08-12T16:23:52+0530] [ALPM] upgraded gcc (13.1.1-2 -> 13.2.1-3)
[2023-08-12T16:23:53+0530] [ALPM] upgraded gcc-fortran (13.1.1-2 -> 13.2.1-3)
[2023-08-12T16:23:53+0530] [ALPM] upgraded perl (5.36.1-2 -> 5.38.0-1)
[2023-08-12T16:23:53+0530] [ALPM] upgraded graphviz (8.1.0-1 -> 8.1.0-2)
[2023-08-12T16:23:55+0530] [ALPM] upgraded harfbuzz-icu (8.0.1-1 -> 8.1.1-1)
[2023-08-12T16:23:55+0530] [ALPM] upgraded openpmix (4.2.3-2 -> 4.2.5-1)
[2023-08-12T16:23:56+0530] [ALPM] upgraded openssh (9.3p2-1 -> 9.4p1-2)
[2023-08-12T16:23:56+0530] [ALPM] upgraded imagemagick (7.1.1.15-1 -> 7.1.1.15-2)
[2023-08-12T16:23:56+0530] [ALPM] upgraded intel-ucode (20230613-1 -> 20230808-1)
[2023-08-12T16:23:56+0530] [ALPM] upgraded python-jsonschema-specifications (2023.06.1-1 -> 2023.7.1-1)
[2023-08-12T16:23:56+0530] [ALPM] upgraded python-jsonschema (4.18.3-1 -> 4.19.0-1)
[2023-08-12T16:23:56+0530] [ALPM] upgraded jupyter-nbformat (5.9.1-1 -> 5.9.2-1)
[2023-08-12T16:23:57+0530] [ALPM] upgraded python-pygments (2.15.1-1 -> 2.16.1-1)
[2023-08-12T16:23:57+0530] [ALPM] upgraded python-rich (13.5.1-1 -> 13.5.2-1)
[2023-08-12T16:23:57+0530] [ALPM] upgraded python-jupyter-events (0.6.3-4 -> 0.7.0-1)
[2023-08-12T16:23:57+0530] [ALPM] upgraded python-overrides (7.3.1-2 -> 7.4.0-1)
[2023-08-12T16:23:57+0530] [ALPM] upgraded python-comm (0.1.3-2 -> 0.1.4-1)
[2023-08-12T16:23:57+0530] [ALPM] upgraded python-nest-asyncio (1.5.6-2 -> 1.5.7-1)
[2023-08-12T16:23:57+0530] [ALPM] upgraded python-ipykernel (6.25.0-1 -> 6.25.1-1)
[2023-08-12T16:23:57+0530] [ALPM] upgraded python-mistune (2.0.5-2 -> 3.0.1-1)
[2023-08-12T16:23:57+0530] [ALPM] upgraded python-chardet (5.1.0-3 -> 5.2.0-1)
[2023-08-12T16:23:57+0530] [ALPM] upgraded jupyterlab (4.0.3-2 -> 4.0.4-1)
[2023-08-12T16:23:57+0530] [ALPM] upgraded kactivitymanagerd (5.27.6-1 -> 5.27.7-1)
[2023-08-12T16:23:57+0530] [ALPM] upgraded kde-cli-tools (5.27.6-1 -> 5.27.7-1)
[2023-08-12T16:23:57+0530] [ALPM] upgraded kde-gtk-config (5.27.6-1 -> 5.27.7-1)
[2023-08-12T16:23:57+0530] [ALPM] upgraded libksysguard (5.27.6-1 -> 5.27.7-1)
[2023-08-12T16:23:57+0530] [ALPM] upgraded ksystemstats (5.27.6-1 -> 5.27.7-1)
[2023-08-12T16:23:57+0530] [ALPM] upgraded milou (5.27.6-1 -> 5.27.7-1)
[2023-08-12T16:23:57+0530] [ALPM] upgraded layer-shell-qt (5.27.6-1 -> 5.27.7-1)
[2023-08-12T16:23:57+0530] [ALPM] upgraded libkscreen (5.27.6-1 -> 5.27.7-1)
[2023-08-12T16:23:57+0530] [ALPM] upgraded kscreenlocker (5.27.6-1 -> 5.27.7-1)
[2023-08-12T16:23:57+0530] [ALPM] upgraded libpipewire (1:0.3.76-2 -> 1:0.3.77-1)
[2023-08-12T16:23:57+0530] [ALPM] upgraded pipewire (1:0.3.76-2 -> 1:0.3.77-1)
[2023-08-12T16:23:58+0530] [ALPM] upgraded kwin (5.27.6-1 -> 5.27.7-1)
[2023-08-12T16:23:58+0530] [ALPM] upgraded plasma-integration (5.27.6-1 -> 5.27.7-1)
[2023-08-12T16:23:58+0530] [ALPM] upgraded kpipewire (5.27.6-1 -> 5.27.7-1)
[2023-08-12T16:23:58+0530] [ALPM] upgraded oxygen-sounds (5.27.6-1 -> 5.27.7-1)
[2023-08-12T16:23:58+0530] [ALPM] upgraded libinih (56-1 -> 57-1)
[2023-08-12T16:23:58+0530] [ALPM] upgraded plasma-workspace (5.27.6-2 -> 5.27.7-2)
[2023-08-12T16:23:59+0530] [ALPM] upgraded kdeplasma-addons (5.27.6-2 -> 5.27.7-1)
[2023-08-12T16:23:59+0530] [ALPM] upgraded systemsettings (5.27.6-1 -> 5.27.7-1)
[2023-08-12T16:23:59+0530] [ALPM] upgraded kgamma5 (5.27.6-1 -> 5.27.7-1)
[2023-08-12T16:23:59+0530] [ALPM] upgraded khotkeys (5.27.6-1 -> 5.27.7-1)
[2023-08-12T16:24:00+0530] [ALPM] upgraded libmm-glib (1.20.6-1 -> 1.20.6-2)
[2023-08-12T16:24:01+0530] [ALPM] upgraded kinfocenter (5.27.6-1 -> 5.27.7-1)
[2023-08-12T16:24:01+0530] [ALPM] upgraded kmenuedit (5.27.6-1 -> 5.27.7-1)
[2023-08-12T16:24:01+0530] [ALPM] upgraded kscreen (5.27.6-1 -> 5.27.7-1)
[2023-08-12T16:24:01+0530] [ALPM] upgraded ksshaskpass (5.27.6-1 -> 5.27.7-1)
[2023-08-12T16:24:01+0530] [ALPM] upgraded kwallet-pam (5.27.6-1 -> 5.27.7-1)
[2023-08-12T16:24:01+0530] [ALPM] upgraded kwayland-integration (5.27.6-1 -> 5.27.7-1)
[2023-08-12T16:24:01+0530] [ALPM] upgraded kwrited (5.27.6-1 -> 5.27.7-1)
[2023-08-12T16:24:01+0530] [ALPM] upgraded lib32-glibc (2.37-3 -> 2.38-2)
[2023-08-12T16:24:02+0530] [ALPM] upgraded lib32-gcc-libs (13.1.1-2 -> 13.2.1-3)
[2023-08-12T16:24:02+0530] [ALPM] upgraded lib32-harfbuzz (8.0.1-1 -> 8.1.1-1)
[2023-08-12T16:24:03+0530] [ALPM] upgraded lib32-openssl (1:3.1.1-1 -> 1:3.1.2-1)
[2023-08-12T16:24:03+0530] [ALPM] upgraded lib32-libldap (2.6.4-1 -> 2.6.6-1)
[2023-08-12T16:24:03+0530] [ALPM] upgraded lib32-xz (5.4.3-1 -> 5.4.4-1)
[2023-08-12T16:24:03+0530] [ALPM] upgraded lib32-libxml2 (2.11.4-1 -> 2.11.5-1)
[2023-08-12T16:24:04+0530] [ALPM] upgraded lib32-llvm-libs (15.0.7-1 -> 15.0.7-3)
[2023-08-12T16:24:06+0530] [ALPM] upgraded lib32-mesa (23.1.4-2 -> 1:23.1.5-1)
[2023-08-12T16:24:06+0530] [ALPM] upgraded libimagequant (4.1.1-1 -> 4.2.0-1)
[2023-08-12T16:24:13+0530] [ALPM] upgraded linux (6.4.7.arch1-1 -> 6.4.10.arch1-1)
[2023-08-12T16:24:13+0530] [ALPM] upgraded linux-firmware-whence (20230625.ee91452d-5 -> 20230804.7be2766d-2)
[2023-08-12T16:24:16+0530] [ALPM] upgraded linux-firmware (20230625.ee91452d-5 -> 20230804.7be2766d-2)
[2023-08-12T16:24:23+0530] [ALPM] upgraded linux-headers (6.4.7.arch1-1 -> 6.4.10.arch1-1)
[2023-08-12T16:24:24+0530] [ALPM] upgraded thin-provisioning-tools (1.0.5-1 -> 1.0.6-1)
[2023-08-12T16:24:27+0530] [ALPM] upgraded lvm2 (2.03.21-1 -> 2.03.22-1)
[2023-08-12T16:24:28+0530] [ALPM] upgraded modemmanager (1.20.6-1 -> 1.20.6-2)
[2023-08-12T16:24:29+0530] [ALPM] upgraded nodejs (20.4.0-1 -> 20.5.0-1)
[2023-08-12T16:24:30+0530] [ALPM] upgraded openssl-1.1 (1.1.1.u-1 -> 1.1.1.v-1)
[2023-08-12T16:24:31+0530] [ALPM] upgraded oxygen (5.27.6-1 -> 5.27.7-1)
[2023-08-12T16:24:33+0530] [ALPM] upgraded perl-error (0.17029-4 -> 0.17029-5)
[2023-08-12T16:24:33+0530] [ALPM] upgraded perl-timedate (2.33-4 -> 2.33-5)
[2023-08-12T16:24:34+0530] [ALPM] upgraded perl-mailtools (2.21-6 -> 2.21-7)
[2023-08-12T16:24:35+0530] [ALPM] upgraded perl-switch (2.17-8 -> 2.17-9)
[2023-08-12T16:24:36+0530] [ALPM] upgraded plasma-browser-integration (5.27.6-1 -> 5.27.7-1)
[2023-08-12T16:24:36+0530] [ALPM] upgraded polkit-kde-agent (5.27.6-1 -> 5.27.7-1)
[2023-08-12T16:24:37+0530] [ALPM] upgraded powerdevil (5.27.6-3 -> 5.27.7-1)
[2023-08-12T16:24:39+0530] [ALPM] upgraded plasma-desktop (5.27.6-1 -> 5.27.7.1-1)
[2023-08-12T16:24:40+0530] [ALPM] upgraded smartmontools (7.3-1 -> 7.4-1)
[2023-08-12T16:24:40+0530] [ALPM] upgraded plasma-disks (5.27.6-1 -> 5.27.7-1)
[2023-08-12T16:24:40+0530] [ALPM] upgraded plasma-firewall (5.27.6-1 -> 5.27.7-1)
[2023-08-12T16:24:41+0530] [ALPM] upgraded plasma-nm (5.27.6-1 -> 5.27.7-1)
[2023-08-12T16:24:41+0530] [ALPM] upgraded plasma-pa (5.27.6-1 -> 5.27.7-1)
[2023-08-12T16:24:41+0530] [ALPM] upgraded plasma-sdk (5.27.6-1 -> 5.27.7.1-1)
[2023-08-12T16:24:41+0530] [ALPM] upgraded plasma-systemmonitor (5.27.6-1 -> 5.27.7-1)
[2023-08-12T16:24:41+0530] [ALPM] upgraded plasma-thunderbolt (5.27.6-1 -> 5.27.7-1)
[2023-08-12T16:24:42+0530] [ALPM] upgraded plasma-vault (5.27.6-1 -> 5.27.7-1)
[2023-08-12T16:24:42+0530] [ALPM] upgraded plasma-wayland-session (5.27.6-2 -> 5.27.7-2)
[2023-08-12T16:24:43+0530] [ALPM] upgraded plasma-workspace-wallpapers (5.27.6-1 -> 5.27.7-1)
[2023-08-12T16:24:44+0530] [ALPM] upgraded python-dill (0.3.6-2 -> 0.3.7-1)
[2023-08-12T16:24:44+0530] [ALPM] upgraded python-more-itertools (9.1.1-4 -> 10.1.0-1)
[2023-08-12T16:24:44+0530] [ALPM] upgraded python-pluggy (1.0.0-4 -> 1.2.0-1)
[2023-08-12T16:24:44+0530] [ALPM] upgraded python-sphinxcontrib-applehelp (1.0.4-3 -> 1.0.6-1)
[2023-08-12T16:24:44+0530] [ALPM] upgraded python-sphinxcontrib-devhelp (1.0.2-11 -> 1.0.4-1)
[2023-08-12T16:24:44+0530] [ALPM] upgraded python-sphinxcontrib-htmlhelp (2.0.1-3 -> 2.0.3-1)
[2023-08-12T16:24:44+0530] [ALPM] upgraded python-sphinxcontrib-qthelp (1.0.3-11 -> 1.0.5-1)
[2023-08-12T16:24:44+0530] [ALPM] upgraded python-sphinxcontrib-serializinghtml (1.1.5-6 -> 1.1.7-1)
[2023-08-12T16:24:45+0530] [ALPM] upgraded python-sphinx (7.1.1-1 -> 7.1.2-1)
[2023-08-12T16:24:45+0530] [ALPM] upgraded python-trove-classifiers (2023.7.6-1 -> 2023.8.7-1)
[2023-08-12T16:24:45+0530] [ALPM] upgraded sddm (0.20.0-1 -> 0.20.0-2)
[2023-08-12T16:24:45+0530] [ALPM] upgraded sddm-kcm (5.27.6-1 -> 5.27.7-1)
[2023-08-12T16:24:45+0530] [ALPM] upgraded systemd-sysvcompat (253.7-1 -> 254.1-1)
[2023-08-12T16:24:45+0530] [ALPM] upgraded turbostat (6.3-2 -> 6.3-4)
[2023-08-12T16:24:45+0530] [ALPM] upgraded vim-runtime (9.0.1676-1 -> 9.0.1678-1)
[2023-08-12T16:24:45+0530] [ALPM] upgraded vim (9.0.1676-1 -> 9.0.1678-1)
[2023-08-12T16:24:45+0530] [ALPM] upgraded xdg-dbus-proxy (0.1.4-1 -> 0.1.5-1)
[2023-08-12T16:24:46+0530] [ALPM] upgraded webkit2gtk (2.40.4-1 -> 2.40.5-1)
[2023-08-12T16:24:46+0530] [ALPM] upgraded xdg-desktop-portal-kde (5.27.6-1 -> 5.27.7-1)
[2023-08-12T16:26:18+0530] [ALPM] upgraded aosp-devel (0.9-1 -> 0.10-1)
[2023-08-12T16:26:18+0530] [ALPM] upgraded pikaur (1.18.1-1 -> 1.18.2-1)
[2023-08-12T18:45:21+0530] [ALPM] upgraded openssl (3.1.1-1 -> 3.1.2-1)
[2023-08-12T18:45:21+0530] [ALPM] upgraded openssh (9.3p2-1 -> 9.4p1-2)
[2023-08-12T18:47:15+0530] [ALPM] upgraded gcc-libs (13.1.1-2 -> 13.2.1-3)
[2023-08-12T18:47:15+0530] [ALPM] upgraded gcc (13.1.1-2 -> 13.2.1-3)
[2023-08-12T18:47:15+0530] [ALPM] upgraded gcc-fortran (13.1.1-2 -> 13.2.1-3)
```

Steps to reproduce:
1. Update system to latest (12-Aug-2023, 1:34 PM) version of all packages.
2. In your shell, run `mpirun`.
This task depends upon

Closed by  Christian Heusel (gromit)
Saturday, 12 August 2023, 15:30 GMT
Reason for closing:  Fixed
Additional comments about closing:  Fixed with version 4.1.5-3
Comment by Christian Heusel (gromit) - Saturday, 12 August 2023, 14:41 GMT
The problem also exists for me and a rebuild in a clean chroot also fixes it!
Comment by Christian Heusel (gromit) - Saturday, 12 August 2023, 15:30 GMT
So apparently this is broken by the new openpmix release, I rebuilt it :)

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