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
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
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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