Hi Isaac,

I would recommend 2 things. 

1. Try and use: which IncNavierStokesSolver to find the path of your executables and the configuration file for the nektar build
2. You might be able to modify your Nektar build:
yum install nektar++-openmpi-hdf5-incnavierstokes-solver

I have never used yum to build Nektar++, so it might crash and burn.

Best wishes,
Alexandra 

Sent from Outlook for Android
From: Isaac Rosin <isaac.rosin1@ucalgary.ca>
Sent: Monday, September 23, 2024 9:28:16 PM
To: Liosi, Alexandra <a.liosi22@imperial.ac.uk>; Xing, Jacques <j.xing@imperial.ac.uk>; nektar-users <nektar-users@imperial.ac.uk>
Subject: Re: Problem With Fedora Nektar++ Installation and HDF5
 
Hi Alexandra,

I am following the steps on this page specifically for Fedora https://www.nektar.info/getting-started/installation/

Everything seems to install fine and I can use the Nektar++ commands, but there's just that issue with HDF5.

Best,
Isaac
From: Liosi, Alexandra <a.liosi22@imperial.ac.uk>
Sent: Monday, September 23, 2024 2:25 PM
To: Isaac Rosin <isaac.rosin1@ucalgary.ca>; Xing, Jacques <j.xing@imperial.ac.uk>; nektar-users <nektar-users@imperial.ac.uk>
Subject: Re: Problem With Fedora Nektar++ Installation and HDF5
 
[△EXTERNAL]


Hi Isaac,

I am not I understood how you build your code. In any Linux environment such as Fedora, Ubuntu, or Windows, I normally:
1. git clone PathToSourceCode
2. cd Nektar++ (which is produced by the previous command)
3. mkdir build && cd build
4. ccmake ../ (to configure my installation)
5. make -j 3 install 

Which steps are you following to build Nektar?

Best wishes,
Alexandra 

From: Isaac Rosin <isaac.rosin1@ucalgary.ca>
Sent: Monday, September 23, 2024 9:20:24 PM
To: Liosi, Alexandra <a.liosi22@imperial.ac.uk>; Xing, Jacques <j.xing@imperial.ac.uk>; nektar-users <nektar-users@imperial.ac.uk>
Subject: Re: Problem With Fedora Nektar++ Installation and HDF5
 
Hi Alexandra and Jacques,

Thank you for your responses.

The commands for compiling with certain modules activated are not mentioned in the Fedora installation guide. It also doesn't seem to create a nektar++ directory in the home folder like the git cloning installation method does, so there is nowhere to go to create a build directory and do ccmake .. Is there a point when the different Linux installations start following the same steps? This isn't mentioned in the user guide or on the website.

I would be grateful for your assistance.

Best,
Isaac
From: Xing, Jacques <j.xing@imperial.ac.uk>
Sent: Monday, September 23, 2024 6:22 AM
To: Isaac Rosin <isaac.rosin1@ucalgary.ca>; nektar-users <nektar-users@imperial.ac.uk>
Subject: Re: Problem With Fedora Nektar++ Installation and HDF5
 
[△EXTERNAL]


Hi Isaac,

You need to turn-on the HDF5 compilation flag (NEKTAR_USE_HDF5), either using the ccmake gui, or by using cmake .. -DNEKTAR_USE_HDF5=ON command line

Cheers,
Jacques
From: nektar-users-bounces@imperial.ac.uk <nektar-users-bounces@imperial.ac.uk> on behalf of Isaac Rosin <isaac.rosin1@ucalgary.ca>
Sent: 21 September 2024 01:51
To: nektar-users <nektar-users@imperial.ac.uk>
Subject: [Nektar-users] Problem With Fedora Nektar++ Installation and HDF5
 

This email from isaac.rosin1@ucalgary.ca originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe senders list to disable email stamping for this address.

 

Hello Nektar++ users,

I just installed Fedora 36 on my computer. I chose this distribution specifically because Nektar++ supports it.

I made sure to install all of the required packages for each utility and solver I needed before installing libnektar++, libnektar++-openmpi and libnektar++-mpich. Then I installed the libnektar++ packages, nekmesh, fieldconvert serial and mpi versions and the incnavierstokes-solver and tried to run the command `NekMesh geometry.msh geometry.nekg` and got the following message:
```
Fatal   : Level 0 assertion violation
No such module: HDF5

Available classes: 
  Xml:
    IO with Xml geometry
  XmlCompressed:
    IO with Xml geometry

terminate called after throwing an instance of 'Nektar::ErrorUtil::NekError'
  what():  Level 0 assertion violation
No such module: HDF5

Available classes: 
  Xml:
    IO with Xml geometry
  XmlCompressed:
    IO with Xml geometry

Aborted (core dumped)
```

I know that my files are not the issue because I have been able to execute this command with my past installations of Nektar++. I got the same error when I tried FieldConvert too using a version of the .nekg mesh I had already created on a previous installation. It seems like NekMesh does not see my HDF5 installations. How may I resolve this?

Best regards,
Isaac