Update failed: hdf5-openmpi and hdf5 packages are in conflict

Hello, I'm trying to run a garuda update and I'm running into a package conflict:

garuda-update
:: Synchronizing package databases...
 garuda is up to date
 core is up to date
 extra is up to date
 community is up to date
 multilib is up to date
 chaotic-aur is up to date
 sneed-arch-repo                 739.0   B  1668   B/s 00:00 [--------------------------------] 100%

--> Refreshing mirrorlists using reflector, please be patient..
################################################################################
################# Arch Linux mirrorlist generated by Reflector #################
################################################################################

# With:       reflector --latest 5 --age 2 --fastest 5 --protocol https --sort rate --save /etc/pacman.d/mirrorlist
# When:       2022-08-12 17:29:21 UTC
# From:       https://archlinux.org/mirrors/status/json/
# Retrieved:  2022-08-12 17:29:05 UTC
# Last Check: 2022-08-12 17:22:49 UTC

:: Synchronizing package databases...
 garuda                           86.6 KiB   182 KiB/s 00:00 [--------------------------------] 100%
 core                            159.1 KiB   374 KiB/s 00:00 [--------------------------------] 100%
 extra                          1709.7 KiB  1877 KiB/s 00:01 [--------------------------------] 100%
 community                         6.7 MiB  4.55 MiB/s 00:01 [--------------------------------] 100%
 multilib                        176.1 KiB   424 KiB/s 00:00 [--------------------------------] 100%
 chaotic-aur                    2012.5 KiB  2.66 MiB/s 00:01 [--------------------------------] 100%
 sneed-arch-repo                 739.0   B   886   B/s 00:01 [--------------------------------] 100%
spawn pacman -Su
:: Starting full system upgrade...
:: Replace med with community/med-openmpi? [Y/n] y
resolving dependencies...
looking for conflicting packages...
:: hdf5-openmpi and hdf5 are in conflict. Remove hdf5? [y/N]

Selecting no cancels the install. Selecting yes brings up a bunch of python conflicts:

:: hdf5-openmpi and hdf5 are in conflict. Remove hdf5? [y/N] y
y
:: hdf5-openmpi and python-h5py are in conflict. Remove python-h5py? [y/N] y
y
error: failed to prepare transaction (could not satisfy dependencies)
:: removing python-h5py breaks dependency 'python-h5py' required by python-keras
:: removing python-h5py breaks dependency 'python-h5py' required by python-tensorflow-cuda

Arch Wiki on Pacman has zero information on resolving package conflicts. And there is no way I am uninstalling my Python packages.

Any ideas?


garuda-inxi
System:
  Kernel: 5.18.16-zen1-1-zen arch: x86_64 bits: 64 compiler: gcc v: 12.1.1
    parameters: BOOT_IMAGE=/@/boot/vmlinuz-linux-zen
    root=UUID=64fbe2ab-4d15-48e2-82ed-f8f1e3308956 rw [email protected]
    quiet splash rd.udev.log_priority=3 vt.global_cursor_default=0
    systemd.unified_cgroup_hierarchy=1 loglevel=3 ibt=off
  Desktop: KDE Plasma v: 5.25.4 tk: Qt v: 5.15.5 info: latte-dock
    wm: kwin_x11 vt: 1 dm: SDDM Distro: Garuda Linux base: Arch Linux
Machine:
  Type: Desktop System: Dell product: Precision Tower 7910 v: N/A
    serial: <superuser required> Chassis: type: 7 serial: <superuser required>
  Mobo: Dell model: 0NK5PH v: A00 serial: <superuser required> UEFI: Dell
    v: A15 date: 09/11/2016
Battery:
  Device-1: hidpp_battery_0 model: Logitech M720 Triathlon Multi-Device Mouse
    serial: <filter> charge: 55% (should be ignored) rechargeable: yes
    status: discharging
CPU:
  Info: model: Intel Xeon E5-2630 v4 bits: 64 type: MT MCP SMP
    arch: Broadwell built: 2015-18 process: Intel 14nm family: 6
    model-id: 0x4F (79) stepping: 1 microcode: 0xB000040
  Topology: cpus: 2x cores: 10 tpc: 2 threads: 20 smt: enabled cache: L1: 2x
    640 KiB (1.2 MiB) desc: d-10x32 KiB; i-10x32 KiB L2: 2x 2.5 MiB (5 MiB)
    desc: 10x256 KiB L3: 2x 25 MiB (50 MiB) desc: 1x25 MiB
  Speed (MHz): avg: 2366 high: 3099 min/max: 1200/3100 scaling:
    driver: intel_cpufreq governor: performance cores: 1: 2511 2: 1672 3: 2678
    4: 2352 5: 2334 6: 2434 7: 1829 8: 1876 9: 2372 10: 2541 11: 2672
    12: 2620 13: 2864 14: 2943 15: 2557 16: 2657 17: 2797 18: 1409 19: 2233
    20: 3099 21: 2399 22: 2262 23: 2599 24: 2013 25: 2412 26: 2569 27: 2355
    28: 2528 29: 1716 30: 2072 31: 2862 32: 1980 33: 2845 34: 1884 35: 2928
    36: 1461 37: 2853 38: 2518 39: 2654 40: 1304 bogomips: 175730
  Flags: avx avx2 ht lm nx pae sse sse2 sse3 sse4_1 sse4_2 ssse3 vmx
  Vulnerabilities:
  Type: itlb_multihit status: KVM: VMX disabled
  Type: l1tf mitigation: PTE Inversion; VMX: conditional cache flushes, SMT
    vulnerable
  Type: mds mitigation: Clear CPU buffers; SMT vulnerable
  Type: meltdown mitigation: PTI
  Type: mmio_stale_data mitigation: Clear CPU buffers; SMT vulnerable
  Type: retbleed status: Not affected
  Type: spec_store_bypass mitigation: Speculative Store Bypass disabled via
    prctl
  Type: spectre_v1 mitigation: usercopy/swapgs barriers and __user pointer
    sanitization
  Type: spectre_v2 mitigation: Retpolines, IBPB: conditional, IBRS_FW,
    STIBP: conditional, RSB filling
  Type: srbds status: Not affected
  Type: tsx_async_abort mitigation: Clear CPU buffers; SMT vulnerable
Graphics:
  Device-1: NVIDIA GM204GL [Quadro M4000] driver: nvidia v: 515.65.01
    alternate: nouveau,nvidia_drm non-free: 515.xx+ status: current (as of
    2022-07) arch: Maxwell code: GMxxx process: TSMC 28nm built: 2014-19
    pcie: gen: 3 speed: 8 GT/s lanes: 16 bus-ID: 03:00.0 chip-ID: 10de:13f1
    class-ID: 0300
  Display: x11 server: X.Org v: 21.1.4 with: Xwayland v: 22.1.3
    compositor: kwin_x11 driver: X: loaded: nvidia gpu: nvidia display-ID: :0
    screens: 1
  Screen-1: 0 s-res: 3840x1080 s-dpi: 94 s-size: 1038x292mm (40.87x11.50")
    s-diag: 1078mm (42.45")
  Monitor-1: DP-5 pos: primary,left res: 1920x1080 hz: 60 dpi: 94
    size: 521x293mm (20.51x11.54") diag: 598mm (23.53") modes: N/A
  Monitor-2: DP-6 pos: right res: 1920x1080 hz: 60 dpi: 82
    size: 598x336mm (23.54x13.23") diag: 686mm (27.01") modes: N/A
  OpenGL: renderer: Quadro M4000/PCIe/SSE2 v: 4.6.0 NVIDIA 515.65.01
    direct render: Yes
Audio:
  Device-1: Intel C610/X99 series HD Audio vendor: Dell driver: snd_hda_intel
    v: kernel bus-ID: 00:1b.0 chip-ID: 8086:8d20 class-ID: 0403
  Device-2: NVIDIA GM204 High Definition Audio driver: snd_hda_intel
    v: kernel pcie: gen: 3 speed: 8 GT/s lanes: 16 bus-ID: 03:00.1
    chip-ID: 10de:0fbb class-ID: 0403
  Sound Server-1: ALSA v: k5.18.16-zen1-1-zen running: yes
  Sound Server-2: PulseAudio v: 16.1 running: no
  Sound Server-3: PipeWire v: 0.3.56 running: yes
Network:
  Device-1: Intel Ethernet I217-LM vendor: Dell driver: e1000e v: kernel
    port: 9020 bus-ID: 00:19.0 chip-ID: 8086:153a class-ID: 0200
  IF: enp0s25 state: up speed: 100 Mbps duplex: full mac: <filter>
  Device-2: Intel I210 Gigabit Network vendor: Dell driver: igb v: kernel
    pcie: gen: 1 speed: 2.5 GT/s lanes: 1 port: 6000 bus-ID: 09:00.0
    chip-ID: 8086:1533 class-ID: 0200
  IF: enp9s0 state: down mac: <filter>
Drives:
  Local Storage: total: 4.09 TiB used: 215.44 GiB (5.1%)
  SMART Message: Unable to run smartctl. Root privileges required.
  ID-1: /dev/nvme0n1 maj-min: 259:0 vendor: Samsung model: SSD 970 EVO Plus
    500GB size: 465.76 GiB block-size: physical: 512 B logical: 512 B
    speed: 31.6 Gb/s lanes: 4 type: SSD serial: <filter> rev: 2B2QEXM7
    temp: 45.9 C scheme: GPT
  ID-2: /dev/sda maj-min: 8:0 type: USB vendor: Seagate
    model: ST1000LM049-2GH172 size: 931.51 GiB block-size: physical: 4096 B
    logical: 512 B type: HDD rpm: 7200 serial: <filter> scheme: GPT
  ID-3: /dev/sdb maj-min: 8:16 type: USB vendor: Western Digital
    model: WD10EZEX-75ZF5A0 size: 931.51 GiB block-size: physical: 4096 B
    logical: 512 B type: N/A serial: <filter> scheme: GPT
  ID-4: /dev/sdc maj-min: 8:32 type: USB vendor: Western Digital model: WD
    My Passport 259D size: 1.82 TiB block-size: physical: 512 B
    logical: 512 B type: N/A serial: <filter> rev: 1005 scheme: GPT
Partition:
  ID-1: / raw-size: 236.51 GiB size: 236.51 GiB (100.00%) used: 215.39 GiB
    (91.1%) fs: btrfs dev: /dev/nvme0n1p4 maj-min: 259:4
  ID-2: /boot/efi raw-size: 512 MiB size: 598.8 MiB (116.96%) used: 58.8
    MiB (9.8%) fs: vfat dev: /dev/nvme0n1p1 maj-min: 259:1
  ID-3: /home raw-size: 236.51 GiB size: 236.51 GiB (100.00%) used: 215.39
    GiB (91.1%) fs: btrfs dev: /dev/nvme0n1p4 maj-min: 259:4
  ID-4: /var/log raw-size: 236.51 GiB size: 236.51 GiB (100.00%) used: 215.39
    GiB (91.1%) fs: btrfs dev: /dev/nvme0n1p4 maj-min: 259:4
  ID-5: /var/tmp raw-size: 236.51 GiB size: 236.51 GiB (100.00%) used: 215.39
    GiB (91.1%) fs: btrfs dev: /dev/nvme0n1p4 maj-min: 259:4
Swap:
  Kernel: swappiness: 133 (default 60) cache-pressure: 100 (default)
  ID-1: swap-1 type: zram size: 62.81 GiB used: 1.5 MiB (0.0%)
    priority: 100 dev: /dev/zram0
Sensors:
  System Temperatures: cpu: 61.0 C mobo: N/A sodimm: SODIMM C gpu: nvidia
    temp: 82 C
  Fan Speeds (RPM): cpu: 989 gpu: nvidia fan: 73%
Info:
  Processes: 598 Uptime: 17h 38m wakeups: 55 Memory: 62.81 GiB used: 10.92
  GiB (17.4%) Init: systemd v: 251 default: graphical tool: systemctl
  Compilers: gcc: 12.1.1 alt: 11 clang: 14.0.6 Packages: pacman: 2256
  lib: 522 Shell: fish v: 3.5.1 running-in: alacritty inxi: 3.3.20
Garuda (2.6.5-1):
  System install date:     2021-11-23
  Last full system update: 2022-08-04
  Is partially upgraded:   Yes
  Relevant software:       NetworkManager
  Windows dual boot:       No/Undetected
  Snapshots:               Snapper
  Failed units:            bluetooth-autoconnect.service systemd-networkd-wait-online.service

Try this:

sudo pacman -Syu python-hdf5-openmpi med-openmpi

sudo pacman -Syu python-hdf5-openmpi med-openmpi
:: Synchronizing package databases...
 garuda is up to date
 core is up to date
 extra is up to date
 community is up to date
 multilib is up to date
 chaotic-aur is up to date
 sneed-arch-repo                 739.0   B  1914   B/s 00:00 [--------------------------------] 100%
error: target not found: python-hdf5-openmpi

Sorry, that was a typo on my part.

sudo pacman -Syu python-h5py-openmpi med-openmpi

4 Likes

Same issue :frowning_face:

sudo pacman -Syu python-h5py-openmpi med-openmpi
:: Synchronizing package databases...
 garuda is up to date
 core is up to date
 extra is up to date
 community                         6.7 MiB  4.76 MiB/s 00:01 [--------------------------------] 100%
 multilib is up to date
 chaotic-aur                    2012.3 KiB  2.06 MiB/s 00:01 [--------------------------------] 100%
 sneed-arch-repo                 739.0   B  1498   B/s 00:00 [--------------------------------] 100%
:: Starting full system upgrade...
:: Replace med with community/med-openmpi? [Y/n]
resolving dependencies...
looking for conflicting packages...
warning: removing 'med' from target list because it conflicts with 'med-openmpi'
:: python-h5py-openmpi and python-h5py are in conflict. Remove python-h5py? [y/N]

Why not say yes? Until you say yes to the prompts and show the error you're getting, we're not going to get any closer to an answer.

whoah...Ill give it a shot. thanks!


sudo pacman -Syu python-h5py-openmpi med-openmpi
:: Synchronizing package databases...
 garuda is up to date
 core is up to date
 extra is up to date
 community is up to date
 multilib is up to date
 chaotic-aur is up to date
 sneed-arch-repo                 739.0   B  2.25 KiB/s 00:00 [--------------------------------] 100%
:: Starting full system upgrade...
:: Replace med with community/med-openmpi? [Y/n]
resolving dependencies...
looking for conflicting packages...
warning: removing 'med' from target list because it conflicts with 'med-openmpi'
:: python-h5py-openmpi and python-h5py are in conflict. Remove python-h5py? [y/N] y
:: hdf5-openmpi and hdf5 are in conflict. Remove hdf5? [y/N] y
warning: dependency cycle detected:
warning: nvidia-utils will be installed before its libglvnd dependency
warning: dependency cycle detected:
warning: nvidia-utils will be installed before its libglvnd dependency
warning: dependency cycle detected:
warning: nvidia-utils will be installed before its libglvnd dependency
warning: dependency cycle detected:
warning: libglvnd will be installed before its mesa dependency
warning: dependency cycle detected:
warning: lib32-libglvnd will be installed before its lib32-mesa dependency
warning: dependency cycle detected:
warning: ruby-bundler will be installed before its ruby dependency
warning: dependency cycle detected:
warning: ruby-bundler will be installed before its ruby dependency
warning: dependency cycle detected:
warning: ruby-date will be installed before its ruby dependency
warning: dependency cycle detected:
warning: ruby-net-http will be installed before its ruby dependency
warning: dependency cycle detected:
warning: ruby-uri will be installed before its ruby dependency
warning: dependency cycle detected:
warning: ruby-open-uri will be installed before its ruby dependency
warning: dependency cycle detected:
warning: ruby-time will be installed before its ruby dependency
warning: dependency cycle detected:
warning: ruby-open-uri will be installed before its ruby dependency
warning: dependency cycle detected:
warning: ruby-stdlib will be installed before its ruby dependency
warning: dependency cycle detected:
warning: ruby-stdlib will be installed before its ruby dependency
warning: dependency cycle detected:
warning: ruby-stdlib will be installed before its ruby dependency
warning: dependency cycle detected:
warning: ruby-stdlib will be installed before its ruby dependency
warning: dependency cycle detected:
warning: ruby-stdlib will be installed before its ruby dependency
warning: dependency cycle detected:
warning: ruby-minitest will be installed before its ruby dependency
warning: dependency cycle detected:
warning: ruby-bundledgems will be installed before its ruby dependency
warning: dependency cycle detected:
warning: ruby-bundledgems will be installed before its ruby dependency
warning: dependency cycle detected:
warning: ruby-bundledgems will be installed before its ruby dependency
warning: dependency cycle detected:
warning: ruby-bundledgems will be installed before its ruby dependency

Packages (140) appstream-glib-0.8.1-1  beautyline-1:20220806-1  binutils-2.39-2  bluez-5.65-2
               bluez-cups-5.65-2  bluez-hid2hci-5.65-2  bluez-libs-5.65-2  bluez-plugins-5.65-2
               bluez-utils-5.65-2  candy-icons-git-r925.b8a2ca7-1  crypto++-8.7.0-1  cuda-11.7.1-1
               cudnn-8.4.1.50-2  cups-filters-1.28.15-2  dkms-3.0.6-1
               dolphin-emu-1:5.0.r16793.3cd82b6193-1  double-conversion-3.2.1-1  draco-1.5.3-1
               duckstation-git-r5600.4652c5fa-1  edk2-ovmf-202205-2  faudio-22.08-1
               find-the-command-git-2.0.r2.gfecba1a-1  firedragon-103.0.1-1  firefox-103.0.2-1
               freecad-0.20.1-1  fzf-0.32.1-1  garuda-settings-manager-git-1.0.1.r2.ga885a4b-1
               garuda-settings-manager-kcm-git-1.0.1.r2.ga885a4b-1  garuda-setup-assistant-2.0.2-1
               gcab-1.5-1  gcr-3.41.1-2  gdk-pixbuf2-2.42.9-1  geocode-glib-3.26.4-1
               glib-networking-1:2.72.2-1  gnutls-3.7.7-1  graphviz-5.0.0-2  gsm-1.0.22-1
               hdf5-1.12.2-1 [removal]  hdf5-openmpi-1.12.2-3  hivex-1.3.21-7  hwinfo-22.0-1
               intel-ucode-20220809-1  latte-dock-git-0.10.6.r274.ga9d86870-1  lib2geom-1.2-2
               lib32-faudio-22.08-1  lib32-gdk-pixbuf2-2.42.9-1  lib32-libglvnd-1.4.0-3
               lib32-libvpx1.3-1.3.0-3  lib32-libwebp-1.2.4-1  lib32-mesa-22.1.6-1
               lib32-nspr-4.34.1-1  lib32-pango-1:1.50.9-1  lib32-smpeg-0.4.5-4
               lib32-systemd-251.4-1  lib32-util-linux-2.38.1-1  libadwaita-1:1.1.4-1
               libbluray-1.3.2-1  libevdev-1.13.0-1  libevent-2.1.12-2  libglvnd-1.4.0-3
               libguestfs-1.48.4-2  libimagequant-4.0.1-1  libnfs-5.0.2-1  libnm-1.38.4-1
               libshumate-git-1.0.0.alpha.1.r84.gf25fba9-1  libvirt-1:8.6.0-2  libwacom-2.4.0-1
               libwebp-1.2.4-1  libxcvt-0.1.2-1  lua-5.4.4-2  luajit-2.1.0.beta3.r439.g633f265f-1
               mailspring-1.10.5-1  med-4.1.0-8 [removal]  memavaild-0.6-2  mesa-22.1.6-1
               micro-2.0.11-4  musescore-3.6.2-7  nano-6.4-1  nettle-3.8.1-1
               networkmanager-1.38.4-1  networkmanager-l2tp-1.20.4-4  networkmanager-support-1-5
               nm-cloud-setup-1.38.4-1  npm-8.17.0-1  nspr-4.34.1-1  nvidia-dkms-515.65.01-2
               nvidia-utils-515.65.01-2  openblas-0.3.21-1  opencl-nvidia-515.65.01-2
               openimageio-2.3.18.0-1  pango-1:1.50.9-1  pcsx2-1.7.3187-3  php-8.1.9-1
               plymouth-git-22.02.122.r63.g0b0e93c2-1  prelockd-0.9-2  ptex-2.4.2-1
               python-bottle-0.12.22-1  python-debugpy-1.6.2-2  python-h5py-3.7.0-1 [removal]
               python-mpi4py-3.1.3-2  python-tomlkit-0.11.3-1  python-trove-classifiers-2022.8.7-1
               python-urllib3-1.26.11-1  rpcs3-git-0.0.23.14045.7ff450985-1  rsync-3.2.5pre2-1
               ruby-3.0.4-5  ruby-bundledgems-3.0.4-5  ruby-bundler-2.3.19-1  ruby-date-3.2.2-1
               ruby-minitest-5.16.2-1  ruby-net-http-0.2.2-1  ruby-open-uri-0.2.0-2
               ruby-stdlib-3.0.4-5  ruby-time-0.2.0-2  ruby-uri-0.11.0-2  samba-4.16.4-3
               seabios-1.16.0-2  signal-desktop-5.54.0-1  smbclient-4.16.4-3  sqlite-3.39.2-1
               sweet-theme-full-git-r278.cc55578-1  systemd-251.4-1  systemd-libs-251.4-1
               systemd-sysvcompat-251.4-1  tracker3-3.3.3-1  unzip-6.0-19  usbredir-0.13.0-1
               util-linux-2.38.1-1  util-linux-libs-2.38.1-1  virt-install-4.1.0-1
               virt-manager-4.1.0-1  webkit2gtk-2.36.6-1  webkit2gtk-4.1-2.36.6-1
               wireplumber-0.4.11-3  wpa_supplicant-2:2.10-5  wpebackend-fdo-1.12.1-1
               xdg-user-dirs-0.18-1  xkeyboard-config-2.36-3  med-openmpi-4.1.1-2
               python-h5py-openmpi-3.7.0-1

Total Download Size:   3155.44 MiB
Total Installed Size:  9594.97 MiB
Net Upgrade Size:        65.95 MiB

:: Proceed with installation? [Y/n]

ARCHLINUX MOMENT oh my god

4 Likes

:rofl:

Worked like a charm! Thanks!

By the way, what causes stuff like this? Developers swapping out upstream dependencies and changes just not filtering through the packages in Pacman? Something else?

Also, is there a "resolving Pacman dependencies for dummies" page so I can learn this power?

Thanks again!

Seems like med was replaced with med-openmpi, which in exchange pulled in hdf5-openmpi, which replaces the normal hdf5. hdf5-openmpi is incompatible with python-h5py tho, but it doesn't pull in python-h5py-openmpi, probably because it doesn't need it, so the other packages which DID need python-h5py now wouldn't have the package they need anymore, causing pacman to detect the unresolved dependency. We helped pacman out by telling it to install python-h5py-openmpi, resolving the dependency.

Uhh, I guess it's a sort of intuition that comes over time >.>

You're welcome!

4 Likes

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