Problem With Fedora Nektar++ Installation and HDF5
******************* This email 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 https://spam.ic.ac.uk/SpamConsole/Senders.aspx 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
Hi Isaac, Have you also built Nektar++ with Hdf5 by activating the option NEKTAR_USE HDF5 ? Many thanks, Alexandra On Mon, 23 Sept 2024, 11:42 Isaac Rosin, <isaac.rosin1@ucalgary.ca> wrote:
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 <https://spam.ic.ac.uk/SpamConsole/Senders.aspx> 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 _______________________________________________ Nektar-users mailing list Nektar-users@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/nektar-users
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<https://spam.ic.ac.uk/SpamConsole/Senders.aspx> 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
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<https://spam.ic.ac.uk/SpamConsole/Senders.aspx> 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
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 Sent from Outlook for Android<https://aka.ms/AAb9ysg> ________________________________ 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<https://spam.ic.ac.uk/SpamConsole/Senders.aspx> 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
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 Sent from Outlook for Android<https://aka.ms/AAb9ysg> ________________________________ 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<https://spam.ic.ac.uk/SpamConsole/Senders.aspx> 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
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<https://aka.ms/AAb9ysg> ________________________________ 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 Sent from Outlook for Android<https://aka.ms/AAb9ysg> ________________________________ 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<https://spam.ic.ac.uk/SpamConsole/Senders.aspx> 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
Hi Alexandra, I found the directory with the executables, but not the configuration file. I'm not sure if there is a certain name I should be looking for. It seems like no module called nektar++-openmpi-hdf5-incnavierstokes-solver exists, however nektar++-openmpi-incnavierstokes-solver does. If we can't figure this out, then I could switch to the ccmake method of installing Nektar (the one you mentioned). Thanks, Isaac ________________________________ From: Liosi, Alexandra <a.liosi22@imperial.ac.uk> Sent: Monday, September 23, 2024 2:33 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 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<https://aka.ms/AAb9ysg> ________________________________ 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 Sent from Outlook for Android<https://aka.ms/AAb9ysg> ________________________________ 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<https://spam.ic.ac.uk/SpamConsole/Senders.aspx> 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
Hi Isaac, I am not sure if there are already precompiled binaries of Nektar++ that include hdf5 in Fedora. If hdf5 is a feature that you would like to use, then I would recommend to clone and build the code from source, instead of yum install the precompiled binaries. PS this is the reason why you could not find a build directory, as with yum install, you download a precompiled binary of Nektar++. Best wishes, Alexandra On Tue, 24 Sept 2024, 08:03 Isaac Rosin, <isaac.rosin1@ucalgary.ca> wrote:
Hi Alexandra,
I found the directory with the executables, but not the configuration file. I'm not sure if there is a certain name I should be looking for. It seems like no module called nektar++-openmpi-hdf5-incnavierstokes-solver exists, however nektar++-openmpi-incnavierstokes-solver does.
If we can't figure this out, then I could switch to the ccmake method of installing Nektar (the one you mentioned).
Thanks, Isaac ------------------------------ *From:* Liosi, Alexandra <a.liosi22@imperial.ac.uk> *Sent:* Monday, September 23, 2024 2:33 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 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 <https://aka.ms/AAb9ysg> ------------------------------ *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
Sent from Outlook for Android <https://aka.ms/AAb9ysg> ------------------------------ *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 <https://spam.ic.ac.uk/SpamConsole/Senders.aspx> 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 _______________________________________________ Nektar-users mailing list Nektar-users@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/nektar-users
Hi Alexandra, While HDF5 is mentioned in the .spec file for Fedora 35, it seems like you are correct about it not being included in the binaries. Also, I was able to build Nektar from source. In case future members are trying to build from source on Fedora, just know you are going to run into issues with cmake not detecting your openmpi installation. Jeremy Cohen provided a very simple solution to this problem on March 30, 2023: https://mailman.ic.ac.uk/mailman/htdig/nektar-users/2023-April/002060.html The only issue I am encountering now is that mpiexec works for the utilities and solvers I want, but not mpirun. I want to run FieldConvert -m interppoints in parallel. mpiexec runs this but it doesn't seem like it's actually executing the task in parallel. It produces the messages such as "Writing <filename>" the same number of times as processors I am using, and the computation time is the same as when I run on 1 processor. When I try mpirun, I get the error: ``` Fatal : Level 0 assertion violation No elements are set. Are the interpolated points within the domain given by the xml files? terminate called after throwing an instance of 'Nektar::ErrorUtil::NekError' what(): Level 0 assertion violation No elements are set. Are the interpolated points within the domain given by the xml files? ``` The same thing happens when I try mpirun with IncNavierStokesSolver. mpiexec seems to work fine for this though. Thanks, Isaac ________________________________ From: Alexandra Liosi <liosi.alex@gmail.com> Sent: Tuesday, September 24, 2024 4:23 AM To: Isaac Rosin <isaac.rosin1@ucalgary.ca> Cc: Liosi, Alexandra <a.liosi22@imperial.ac.uk>; Xing, Jacques <j.xing@imperial.ac.uk>; nektar-users <nektar-users@imperial.ac.uk> Subject: Re: [Nektar-users] Problem With Fedora Nektar++ Installation and HDF5 [△EXTERNAL] Hi Isaac, I am not sure if there are already precompiled binaries of Nektar++ that include hdf5 in Fedora. If hdf5 is a feature that you would like to use, then I would recommend to clone and build the code from source, instead of yum install the precompiled binaries. PS this is the reason why you could not find a build directory, as with yum install, you download a precompiled binary of Nektar++. Best wishes, Alexandra On Tue, 24 Sept 2024, 08:03 Isaac Rosin, <isaac.rosin1@ucalgary.ca<mailto:isaac.rosin1@ucalgary.ca>> wrote: Hi Alexandra, I found the directory with the executables, but not the configuration file. I'm not sure if there is a certain name I should be looking for. It seems like no module called nektar++-openmpi-hdf5-incnavierstokes-solver exists, however nektar++-openmpi-incnavierstokes-solver does. If we can't figure this out, then I could switch to the ccmake method of installing Nektar (the one you mentioned). Thanks, Isaac ________________________________ From: Liosi, Alexandra <a.liosi22@imperial.ac.uk<mailto:a.liosi22@imperial.ac.uk>> Sent: Monday, September 23, 2024 2:33 PM To: Isaac Rosin <isaac.rosin1@ucalgary.ca<mailto:isaac.rosin1@ucalgary.ca>>; Xing, Jacques <j.xing@imperial.ac.uk<mailto:j.xing@imperial.ac.uk>>; nektar-users <nektar-users@imperial.ac.uk<mailto:nektar-users@imperial.ac.uk>> Subject: Re: Problem With Fedora Nektar++ Installation and HDF5 [△EXTERNAL] 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<https://aka.ms/AAb9ysg> ________________________________ From: Isaac Rosin <isaac.rosin1@ucalgary.ca<mailto:isaac.rosin1@ucalgary.ca>> Sent: Monday, September 23, 2024 9:28:16 PM To: Liosi, Alexandra <a.liosi22@imperial.ac.uk<mailto:a.liosi22@imperial.ac.uk>>; Xing, Jacques <j.xing@imperial.ac.uk<mailto:j.xing@imperial.ac.uk>>; nektar-users <nektar-users@imperial.ac.uk<mailto: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<mailto:a.liosi22@imperial.ac.uk>> Sent: Monday, September 23, 2024 2:25 PM To: Isaac Rosin <isaac.rosin1@ucalgary.ca<mailto:isaac.rosin1@ucalgary.ca>>; Xing, Jacques <j.xing@imperial.ac.uk<mailto:j.xing@imperial.ac.uk>>; nektar-users <nektar-users@imperial.ac.uk<mailto: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 Sent from Outlook for Android<https://aka.ms/AAb9ysg> ________________________________ From: Isaac Rosin <isaac.rosin1@ucalgary.ca<mailto:isaac.rosin1@ucalgary.ca>> Sent: Monday, September 23, 2024 9:20:24 PM To: Liosi, Alexandra <a.liosi22@imperial.ac.uk<mailto:a.liosi22@imperial.ac.uk>>; Xing, Jacques <j.xing@imperial.ac.uk<mailto:j.xing@imperial.ac.uk>>; nektar-users <nektar-users@imperial.ac.uk<mailto: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<mailto:j.xing@imperial.ac.uk>> Sent: Monday, September 23, 2024 6:22 AM To: Isaac Rosin <isaac.rosin1@ucalgary.ca<mailto:isaac.rosin1@ucalgary.ca>>; nektar-users <nektar-users@imperial.ac.uk<mailto: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<mailto:nektar-users-bounces@imperial.ac.uk> <nektar-users-bounces@imperial.ac.uk<mailto:nektar-users-bounces@imperial.ac.uk>> on behalf of Isaac Rosin <isaac.rosin1@ucalgary.ca<mailto:isaac.rosin1@ucalgary.ca>> Sent: 21 September 2024 01:51 To: nektar-users <nektar-users@imperial.ac.uk<mailto:nektar-users@imperial.ac.uk>> Subject: [Nektar-users] Problem With Fedora Nektar++ Installation and HDF5 This email from isaac.rosin1@ucalgary.ca<mailto: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<https://spam.ic.ac.uk/SpamConsole/Senders.aspx> 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 _______________________________________________ Nektar-users mailing list Nektar-users@imperial.ac.uk<mailto:Nektar-users@imperial.ac.uk> https://mailman.ic.ac.uk/mailman/listinfo/nektar-users
Hi Isaac, What is the command that you are using when you receive these errors? Also, could you provide more details for the problem you are trying to run? Best wishes, Alexandra On Tue, 24 Sept 2024, 19:32 Isaac Rosin, <isaac.rosin1@ucalgary.ca> wrote:
Hi Alexandra,
While HDF5 is mentioned in the .spec file for Fedora 35, it seems like you are correct about it not being included in the binaries. Also, I was able to build Nektar from source. In case future members are trying to build from source on Fedora, just know you are going to run into issues with cmake not detecting your openmpi installation. Jeremy Cohen provided a very simple solution to this problem on March 30, 2023: https://mailman.ic.ac.uk/mailman/htdig/nektar-users/2023-April/002060.html
The only issue I am encountering now is that mpiexec works for the utilities and solvers I want, but not mpirun. I want to run FieldConvert -m interppoints in parallel. mpiexec runs this but it doesn't seem like it's actually executing the task in parallel. It produces the messages such as "Writing <filename>" the same number of times as processors I am using, and the computation time is the same as when I run on 1 processor. When I try mpirun, I get the error: ``` Fatal : Level 0 assertion violation No elements are set. Are the interpolated points within the domain given by the xml files? terminate called after throwing an instance of 'Nektar::ErrorUtil::NekError' what(): Level 0 assertion violation No elements are set. Are the interpolated points within the domain given by the xml files? ``` The same thing happens when I try mpirun with IncNavierStokesSolver. mpiexec seems to work fine for this though.
Thanks, Isaac ------------------------------ *From:* Alexandra Liosi <liosi.alex@gmail.com> *Sent:* Tuesday, September 24, 2024 4:23 AM *To:* Isaac Rosin <isaac.rosin1@ucalgary.ca> *Cc:* Liosi, Alexandra <a.liosi22@imperial.ac.uk>; Xing, Jacques < j.xing@imperial.ac.uk>; nektar-users <nektar-users@imperial.ac.uk> *Subject:* Re: [Nektar-users] Problem With Fedora Nektar++ Installation and HDF5
[△EXTERNAL]
Hi Isaac,
I am not sure if there are already precompiled binaries of Nektar++ that include hdf5 in Fedora.
If hdf5 is a feature that you would like to use, then I would recommend to clone and build the code from source, instead of yum install the precompiled binaries.
PS this is the reason why you could not find a build directory, as with yum install, you download a precompiled binary of Nektar++.
Best wishes, Alexandra
On Tue, 24 Sept 2024, 08:03 Isaac Rosin, <isaac.rosin1@ucalgary.ca> wrote:
Hi Alexandra,
I found the directory with the executables, but not the configuration file. I'm not sure if there is a certain name I should be looking for. It seems like no module called nektar++-openmpi-hdf5-incnavierstokes-solver exists, however nektar++-openmpi-incnavierstokes-solver does.
If we can't figure this out, then I could switch to the ccmake method of installing Nektar (the one you mentioned).
Thanks, Isaac ------------------------------ *From:* Liosi, Alexandra <a.liosi22@imperial.ac.uk> *Sent:* Monday, September 23, 2024 2:33 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 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 <https://aka.ms/AAb9ysg> ------------------------------ *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
Sent from Outlook for Android <https://aka.ms/AAb9ysg> ------------------------------ *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 <https://spam.ic.ac.uk/SpamConsole/Senders.aspx> 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 _______________________________________________ Nektar-users mailing list Nektar-users@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/nektar-users
Hi Alexandra, Thanks again for your help. It turned out that the commands I was using were trying to access a part of the domain outside of the mesh. I didn't think this would be an issue because I was using periodic boundaries, but I was wrong. Everything is working now. All the best, Isaac ________________________________ From: Alexandra Liosi <liosi.alex@gmail.com> Sent: Thursday, September 26, 2024 5:52 AM To: Isaac Rosin <isaac.rosin1@ucalgary.ca> Cc: Liosi, Alexandra <a.liosi22@imperial.ac.uk>; Xing, Jacques <j.xing@imperial.ac.uk>; nektar-users <nektar-users@imperial.ac.uk> Subject: Re: [Nektar-users] Problem With Fedora Nektar++ Installation and HDF5 [△EXTERNAL] Hi Isaac, What is the command that you are using when you receive these errors? Also, could you provide more details for the problem you are trying to run? Best wishes, Alexandra On Tue, 24 Sept 2024, 19:32 Isaac Rosin, <isaac.rosin1@ucalgary.ca<mailto:isaac.rosin1@ucalgary.ca>> wrote: Hi Alexandra, While HDF5 is mentioned in the .spec file for Fedora 35, it seems like you are correct about it not being included in the binaries. Also, I was able to build Nektar from source. In case future members are trying to build from source on Fedora, just know you are going to run into issues with cmake not detecting your openmpi installation. Jeremy Cohen provided a very simple solution to this problem on March 30, 2023: https://mailman.ic.ac.uk/mailman/htdig/nektar-users/2023-April/002060.html The only issue I am encountering now is that mpiexec works for the utilities and solvers I want, but not mpirun. I want to run FieldConvert -m interppoints in parallel. mpiexec runs this but it doesn't seem like it's actually executing the task in parallel. It produces the messages such as "Writing <filename>" the same number of times as processors I am using, and the computation time is the same as when I run on 1 processor. When I try mpirun, I get the error: ``` Fatal : Level 0 assertion violation No elements are set. Are the interpolated points within the domain given by the xml files? terminate called after throwing an instance of 'Nektar::ErrorUtil::NekError' what(): Level 0 assertion violation No elements are set. Are the interpolated points within the domain given by the xml files? ``` The same thing happens when I try mpirun with IncNavierStokesSolver. mpiexec seems to work fine for this though. Thanks, Isaac ________________________________ From: Alexandra Liosi <liosi.alex@gmail.com<mailto:liosi.alex@gmail.com>> Sent: Tuesday, September 24, 2024 4:23 AM To: Isaac Rosin <isaac.rosin1@ucalgary.ca<mailto:isaac.rosin1@ucalgary.ca>> Cc: Liosi, Alexandra <a.liosi22@imperial.ac.uk<mailto:a.liosi22@imperial.ac.uk>>; Xing, Jacques <j.xing@imperial.ac.uk<mailto:j.xing@imperial.ac.uk>>; nektar-users <nektar-users@imperial.ac.uk<mailto:nektar-users@imperial.ac.uk>> Subject: Re: [Nektar-users] Problem With Fedora Nektar++ Installation and HDF5 [△EXTERNAL] Hi Isaac, I am not sure if there are already precompiled binaries of Nektar++ that include hdf5 in Fedora. If hdf5 is a feature that you would like to use, then I would recommend to clone and build the code from source, instead of yum install the precompiled binaries. PS this is the reason why you could not find a build directory, as with yum install, you download a precompiled binary of Nektar++. Best wishes, Alexandra On Tue, 24 Sept 2024, 08:03 Isaac Rosin, <isaac.rosin1@ucalgary.ca<mailto:isaac.rosin1@ucalgary.ca>> wrote: Hi Alexandra, I found the directory with the executables, but not the configuration file. I'm not sure if there is a certain name I should be looking for. It seems like no module called nektar++-openmpi-hdf5-incnavierstokes-solver exists, however nektar++-openmpi-incnavierstokes-solver does. If we can't figure this out, then I could switch to the ccmake method of installing Nektar (the one you mentioned). Thanks, Isaac ________________________________ From: Liosi, Alexandra <a.liosi22@imperial.ac.uk<mailto:a.liosi22@imperial.ac.uk>> Sent: Monday, September 23, 2024 2:33 PM To: Isaac Rosin <isaac.rosin1@ucalgary.ca<mailto:isaac.rosin1@ucalgary.ca>>; Xing, Jacques <j.xing@imperial.ac.uk<mailto:j.xing@imperial.ac.uk>>; nektar-users <nektar-users@imperial.ac.uk<mailto:nektar-users@imperial.ac.uk>> Subject: Re: Problem With Fedora Nektar++ Installation and HDF5 [△EXTERNAL] 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<https://aka.ms/AAb9ysg> ________________________________ From: Isaac Rosin <isaac.rosin1@ucalgary.ca<mailto:isaac.rosin1@ucalgary.ca>> Sent: Monday, September 23, 2024 9:28:16 PM To: Liosi, Alexandra <a.liosi22@imperial.ac.uk<mailto:a.liosi22@imperial.ac.uk>>; Xing, Jacques <j.xing@imperial.ac.uk<mailto:j.xing@imperial.ac.uk>>; nektar-users <nektar-users@imperial.ac.uk<mailto: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<mailto:a.liosi22@imperial.ac.uk>> Sent: Monday, September 23, 2024 2:25 PM To: Isaac Rosin <isaac.rosin1@ucalgary.ca<mailto:isaac.rosin1@ucalgary.ca>>; Xing, Jacques <j.xing@imperial.ac.uk<mailto:j.xing@imperial.ac.uk>>; nektar-users <nektar-users@imperial.ac.uk<mailto: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 Sent from Outlook for Android<https://aka.ms/AAb9ysg> ________________________________ From: Isaac Rosin <isaac.rosin1@ucalgary.ca<mailto:isaac.rosin1@ucalgary.ca>> Sent: Monday, September 23, 2024 9:20:24 PM To: Liosi, Alexandra <a.liosi22@imperial.ac.uk<mailto:a.liosi22@imperial.ac.uk>>; Xing, Jacques <j.xing@imperial.ac.uk<mailto:j.xing@imperial.ac.uk>>; nektar-users <nektar-users@imperial.ac.uk<mailto: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<mailto:j.xing@imperial.ac.uk>> Sent: Monday, September 23, 2024 6:22 AM To: Isaac Rosin <isaac.rosin1@ucalgary.ca<mailto:isaac.rosin1@ucalgary.ca>>; nektar-users <nektar-users@imperial.ac.uk<mailto: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<mailto:nektar-users-bounces@imperial.ac.uk> <nektar-users-bounces@imperial.ac.uk<mailto:nektar-users-bounces@imperial.ac.uk>> on behalf of Isaac Rosin <isaac.rosin1@ucalgary.ca<mailto:isaac.rosin1@ucalgary.ca>> Sent: 21 September 2024 01:51 To: nektar-users <nektar-users@imperial.ac.uk<mailto:nektar-users@imperial.ac.uk>> Subject: [Nektar-users] Problem With Fedora Nektar++ Installation and HDF5 This email from isaac.rosin1@ucalgary.ca<mailto: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<https://spam.ic.ac.uk/SpamConsole/Senders.aspx> 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 _______________________________________________ Nektar-users mailing list Nektar-users@imperial.ac.uk<mailto:Nektar-users@imperial.ac.uk> https://mailman.ic.ac.uk/mailman/listinfo/nektar-users
participants (4)
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Alexandra Liosi
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Isaac Rosin
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Liosi, Alexandra
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Xing, Jacques