Arch Linux

radmac

Member

Registered: 2019-03-12

Posts: 18

[SOLVED] Upgrade issue with hdf5, hdf5-openmpi, and python-h5py

Here is the mentioned dependency issue:
(The electron and python-llvmlite has probably nothing to do with it.)

:: Synchronizing package databases...
 core is up to date
 extra is up to date
 community is up to date
 multilib is up to date
:: Starting full system upgrade...
:: Replace med with community/med-openmpi? [Y/n] 
resolving dependencies...
looking for conflicting packages...
:: hdf5-openmpi and hdf5 are in conflict. Remove hdf5? [y/N] y
:: hdf5-openmpi and python-h5py are in conflict. Remove python-h5py? [y/N] y
error: failed to prepare transaction (could not satisfy dependencies)
:: installing electron (20.0.0-1) breaks dependency 'electron19' required by element-desktop
:: removing python-h5py breaks dependency 'python-h5py' required by python-keras
:: installing python-llvmlite (0.39.0-1) breaks dependency 'python-llvmlite<0.39' required by python-numba
:: removing python-h5py breaks dependency 'python-h5py' required by python-tensorflow

Last edited by radmac (2022-08-10 13:25:50)

Lone_Wolf

Administrator

From: Netherlands, Europe

Registered: 2005-10-04

Posts: 12,930

Re: [SOLVED] Upgrade issue with hdf5, hdf5-openmpi, and python-h5py

for the electron issue see https://bbs.archlinux.org/viewtopic.php?id=278618

:: Replace med with community/med-openmpi? [Y/n]

It appears there are now 2 versions of med in the repos : med & med-openmpi .
Not sure why med-openmpi replaces med, but for now answer NO to that question to allow the upgrade to continue .

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radmac

Member

Registered: 2019-03-12

Posts: 18

Re: [SOLVED] Upgrade issue with hdf5, hdf5-openmpi, and python-h5py

for the electron issue see https://bbs.archlinux.org/viewtopic.php?id=278618

:: Replace med with community/med-openmpi? [Y/n]

It appears there are now 2 versions of med in the repos : med & med-openmpi .
Not sure why med-openmpi replaces med, but for now answer NO to that question to allow the upgrade to continue .

Thank you for the electron part, however regarding med-openmpi I tried all combinations of YESes and NOes and none seems to allow for the upgrade to continue.
See for instance:

# pacman -Syu
:: Synchronizing package databases...
 core is up to date
 extra is up to date
 community is up to date
 multilib is up to date
:: Starting full system upgrade...
:: Replace med with community/med-openmpi? [Y/n] n
resolving dependencies...
looking for conflicting packages...
warning: removing 'med' from target list because it conflicts with 'med-openmpi'
:: med-openmpi and med are in conflict. Remove med? [y/N] n
error: unresolvable package conflicts detected
error: failed to prepare transaction (conflicting dependencies)
:: med-openmpi and med are in conflict

# pacman -Syu
:: Synchronizing package databases...
 core is up to date
 extra is up to date
 community is up to date
 multilib is up to date
:: Starting full system upgrade...
:: Replace med with community/med-openmpi? [Y/n] n
resolving dependencies...
looking for conflicting packages...
warning: removing 'med' from target list because it conflicts with 'med-openmpi'
:: med-openmpi and med are in conflict. Remove med? [y/N] y
:: hdf5-openmpi and hdf5 are in conflict. Remove hdf5? [y/N] n
error: unresolvable package conflicts detected
error: failed to prepare transaction (conflicting dependencies)
:: hdf5-openmpi and hdf5 are in conflict

# pacman -Syu
:: Synchronizing package databases...
 core is up to date
 extra is up to date
 community is up to date
 multilib is up to date
:: Starting full system upgrade...
:: Replace med with community/med-openmpi? [Y/n] n
resolving dependencies...
looking for conflicting packages...
warning: removing 'med' from target list because it conflicts with 'med-openmpi'
:: med-openmpi and med are in conflict. Remove med? [y/N] y
:: hdf5-openmpi and hdf5 are in conflict. Remove hdf5? [y/N] y
:: hdf5-openmpi and python-h5py are in conflict. Remove python-h5py? [y/N] n
error: unresolvable package conflicts detected
error: failed to prepare transaction (conflicting dependencies)
:: hdf5-openmpi and python-h5py are in conflict

# sudo pacman -Syu
:: Synchronizing package databases...
 core is up to date
 extra is up to date
 community is up to date
 multilib is up to date
:: Starting full system upgrade...
:: Replace med with community/med-openmpi? [Y/n] n
resolving dependencies...
looking for conflicting packages...
warning: removing 'med' from target list because it conflicts with 'med-openmpi'
:: med-openmpi and med are in conflict. Remove med? [y/N] y
:: hdf5-openmpi and hdf5 are in conflict. Remove hdf5? [y/N] y
:: hdf5-openmpi and python-h5py are in conflict. Remove python-h5py? [y/N] y
error: failed to prepare transaction (could not satisfy dependencies)
:: removing python-h5py breaks dependency 'python-h5py' required by python-keras
:: installing python-llvmlite (0.39.0-1) breaks dependency 'python-llvmlite<0.39' required by python-numba
:: removing python-h5py breaks dependency 'python-h5py' required by python-tensorflow

Last edited by radmac (2022-08-10 12:19:23)

Lone_Wolf

Administrator

From: Netherlands, Europe

Registered: 2005-10-04

Posts: 12,930

Re: [SOLVED] Upgrade issue with hdf5, hdf5-openmpi, and python-h5py

apparently something on your system wants to pull in med-openmpi, and there's only 1 package in repos that requires it : freecad

Do you have freecad installed ?

---

Disliking systemd intensely, but not satisfied with alternatives so focusing on taming systemd.

clean chroot building not flexible enough ?
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radmac

Member

Registered: 2019-03-12

Posts: 18

Re: [SOLVED] Upgrade issue with hdf5, hdf5-openmpi, and python-h5py

Yes, I do.
Even though Iwould like to keep it, if removing it helps I can sacrifice it.

Lone_Wolf

Administrator

From: Netherlands, Europe

Registered: 2005-10-04

Posts: 12,930

Re: [SOLVED] Upgrade issue with hdf5, hdf5-openmpi, and python-h5py

freecad indeed switched from med to med-openmpi , https://github.com/archlinux/svntogit-c … 9f64c2269e

python-numba is an aur package and will probably need a rebuild against the  new python-llvmlite package.
for now remove python-numba .

Also remove freecad and med .
run the update, if succesfull try re-installing freecad.

Last edited by Lone_Wolf (2022-08-10 12:57:02)

---

Disliking systemd intensely, but not satisfied with alternatives so focusing on taming systemd.

clean chroot building not flexible enough ?
Try clean chroot manager by graysky

radmac

Member

Registered: 2019-03-12

Posts: 18

Re: [SOLVED] Upgrade issue with hdf5, hdf5-openmpi, and python-h5py

Thank you!
The system is up to date.
(BTW, how do I mark it [SOLVED]?)

... if succesfull try re-installing freecad

:: hdf5-openmpi and hdf5 are in conflict

Freecad depends on med-openmpi which depends on hdf5-openmpi, which conflicts with hdf5.
However, I need hdf5 package for python-h5py (which also conflicts with hdf5-openmpi) which I need for python-tensorflow...

2ManyDogs

Forum Fellow

Registered: 2012-01-15

Posts: 4,645

Re: [SOLVED] Upgrade issue with hdf5, hdf5-openmpi, and python-h5py

(BTW, how do I mark it [SOLVED]?)

Edit your first post and add [SOLVED] to the title.

radmac

Member

Registered: 2019-03-12

Posts: 18

Re: [SOLVED] Upgrade issue with hdf5, hdf5-openmpi, and python-h5py

(BTW, how do I mark it [SOLVED]?)

Edit your first post and add [SOLVED] to the title.

Unfortunatelly I can not. It looks there is a limit to tile length...

Lone_Wolf

Administrator

From: Netherlands, Europe

Registered: 2005-10-04

Posts: 12,930

Re: [SOLVED] Upgrade issue with hdf5, hdf5-openmpi, and python-h5py

Yes, there is.
Just remove some words from the tittle.

A quick peek at hdf5 suggests hdf5-openmpi can substitute for it, but that's best dealt with in a separate thread.

Last edited by Lone_Wolf (2022-08-10 13:22:59)

---

Disliking systemd intensely, but not satisfied with alternatives so focusing on taming systemd.

clean chroot building not flexible enough ?
Try clean chroot manager by graysky