Problem with the repos

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Mila
Posts: 9
Joined: 2021/05/04 14:36:39

Re: Problem with the repos

Post by Mila » 2021/05/05 07:36:43

Sorry MartinR.

I did not read well your message. Here is the content of the file subscription-manager.conf.

Thank you.

Mila


Code: Select all

[main]
enabled=1

# When following option is set to 1, then all repositories defined outside redhat.repo will be disabled
# every time subscription-manager plugin is triggered by dnf or yum
disable_system_repos=0


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jlehtone
Posts: 4523
Joined: 2007/12/11 08:17:33
Location: Finland

Re: Problem with the repos

Post by jlehtone » 2021/05/05 08:15:42

Mila wrote:
2021/05/05 07:23:57
I run the command and the code is showed below.
The output proves that the broken repo was the problem.

Now you can install mpich. If you will compile your own programs, then you probably do need the mpich-devel package too.

Mila
Posts: 9
Joined: 2021/05/04 14:36:39

Re: Problem with the repos

Post by Mila » 2021/05/05 08:29:44

Dear jlehtone.

It seems that I could install both mpich and mpich-devel.
Thank you very much for all your help.

Best.


Mila









Code: Select all

[msanchez@lab-bioit5 ~]$ sudo dnf list mpich*
Updating Subscription Management repositories.
Unable to read consumer identity

This system is not registered to Red Hat Subscription Management. You can use subscription-manager to register.

Last metadata expiration check: 0:08:57 ago on Wed 05 May 2021 10:14:51 CEST.
Installed Packages
mpich.x86_64                                     3.2.1-9.el8                               @appstream
mpich-devel.x86_64                               3.2.1-9.el8                               @appstream
Available Packages
mpich.i686                                       3.2.1-9.el8                               appstream 
mpich-devel.i686                                 3.2.1-9.el8                               appstream 

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jlehtone
Posts: 4523
Joined: 2007/12/11 08:17:33
Location: Finland

Re: Problem with the repos

Post by jlehtone » 2021/05/05 09:32:08

Good. What is the output of:

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module avail
Normal programs/libraries are directly on search path. There are more than one MPI-implementation. They provide files with same names. Those can't be all on search path; only one could be found.

The MPI packages use environment modules system to resolve that. You probably have to explicitly enable the mpich in your shell session before you can use it.

Mila
Posts: 9
Joined: 2021/05/04 14:36:39

Re: Problem with the repos

Post by Mila » 2021/05/05 10:31:15

Dear jlehtone.

The output is below. Yes, I need to explicitly enable the mpich in my shell session. How can I do that?

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[msanchez@lab-bioit5 ~]$ module avail

------------------------------- /etc/modulefiles -------------------------------
   mpi/mpich-x86_64    mpi/openmpi-x86_64 (D)

---------------------------- /usr/share/modulefiles ----------------------------
   pmi/pmix-x86_64

-------------------- /usr/share/lmod/lmod/modulefiles/Core ---------------------
   lmod    settarg

  Where:
   D:  Default Module

Use "module spider" to find all possible modules and extensions.
Use "module keyword key1 key2 ..." to search for all possible modules matching
any of the "keys".


Mila

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jlehtone
Posts: 4523
Joined: 2007/12/11 08:17:33
Location: Finland

Re: Problem with the repos

Post by jlehtone » 2021/05/05 10:53:52

You have two MPI versions installed:

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mpi/mpich-x86_64    mpi/openmpi-x86_64 (D)
The openmpi-x86_64 seems to be set explicitly as default.

Default means that if one does

Code: Select all

module add mpi
Then current shell's environment is modified to find the openmpi-x86_64.

If you do

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module add mpi/mpich-x86_64
then you get access to mpich.


It used to be common to
source config
use program

but then you have the config in environment and doing something else requires a new shell session.

The module add is essentially source config, but with most modules you can
module rm mpi/mpich-x86_64 or module purge to "undo the source", revert environment.

Environment modules has been in use in HPC clusters quite a while now.

Software Collections' (SCL, more prevalent in CentOS 7) scl does start a subshell with modified environment, rather than modifying env of current shell. SCL is similar to environment modules, but has different origin.

Mila
Posts: 9
Joined: 2021/05/04 14:36:39

Re: Problem with the repos

Post by Mila » 2021/05/05 12:01:38

Dear jlehtone.

It is done! And I will keep in mind about how to revert environment in case I need to use the other one.

Thank you very much for every thing.

Best.


Mila


Code: Select all

[msanchez@lab-bioit5 ~]$ module add mpi
[msanchez@lab-bioit5 ~]$ module add mpi/mpich-x86_64

The following have been reloaded with a version change:
  1) mpi/openmpi-x86_64 => mpi/mpich-x86_64

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