******************* 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. ******************* Dear All, Recently, i tried to compile nektar++ with mpi. And i'm facing some issues with the compilation. The problem seems to be that "MPI_SEND" is not found as shown in the figure. Therefore, when i try to launch my applications on multiple nodes on an HPC cluster i have problems. If someone can help me i will be glad. Thank you in advance, Nicola
Hi Nico, Thank you for reaching out! What is the compilation error aside from the CMake output? Or you aren't able to configure the project completely? Best wishes, Alexandra On Wed, 7 Feb 2024, 21:55 Nico Clinco, <nicoclinco@gmail.com> wrote:
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Dear All,
Recently, i tried to compile nektar++ with mpi. And i'm facing some issues with the compilation. The problem seems to be that "MPI_SEND" is not found as shown in the figure. Therefore, when i try to launch my applications on multiple nodes on an HPC cluster i have problems.
If someone can help me i will be glad. Thank you in advance, Nicola
_______________________________________________ Nektar-users mailing list Nektar-users@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/nektar-users
Hi Nicola, We have several instructions on how to build nektar++ on different machines, see the following links [intel compiler] https://www.nektar.info/nektar-ic-hpc/ [gnu compiler] https://www.nektar.info/nektar-on-archer2/ [intel compiler] https://faculty.ustc.edu.cn/gaoankang/zh_CN/article/620934/content/3473.htm#... In your case, it seems the c and c++ compilers are not properly recoganized. You can try to define CC=mpicc CXX=mpicxx before running cmake. Hope it helps. Cheers Ankang -----Original Messages----- From:"Nico Clinco" <nicoclinco@gmail.com> Sent Time:2024-02-08 04:55:25 (Thursday) To: nektar-users@imperial.ac.uk Cc: Subject: [Nektar-users] Issues with compilation | This email from nicoclinco@gmail.com 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. | Dear All, Recently, i tried to compile nektar++ with mpi. And i'm facing some issues with the compilation. The problem seems to be that "MPI_SEND" is not found as shown in the figure. Therefore, when i try to launch my applications on multiple nodes on an HPC cluster i have problems. If someone can help me i will be glad. Thank you in advance, Nicola
******************* 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, i have tried also defining CC=mpiCC and CCX=mpiCXX but nothing, the same problem. I want to add that i am using the following modules: gnu9/9.4.0 cmake/3.24.2 openmpi4 Thanks in advance, Nicola
Hi Nicola, If possible, could you provide us with the exact CMake command you are running and the full output from CMake - it will make it much easier for us to help you diagnose the problem. Are you running a CMake command with a series of options on the command line or you’re using the CCMake text-based GUI to set the options? Nektar++ has a lot of optional dependencies and does a number of checks at configuration time for different system properties and the existence of a number of different libraries. Without more detailed information it’s very difficult to know exactly what is causing the problem. I think you originally highlighted that the CMake output was showing MPI_Send as being not found - this shouldn’t actually be an issue, I believe it’s a common message. Because there are many different implementations of MPI that need to be checked for in different ways, you will sometimes see things saying that something is not found. In some cases, CMake will then make other checks for different implementations of required libraries and it may still find an installed library that it can use. Anyway, if you can provide some further information, we can try to help identify and resolve the issue. Many thanks, Jeremy
On 8 Feb 2024, at 14:37, Nico Clinco <nicoclinco@gmail.com> wrote:
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Hello, i have tried also defining CC=mpiCC and CCX=mpiCXX but nothing, the same problem.
I want to add that i am using the following modules: gnu9/9.4.0 cmake/3.24.2 openmpi4 Thanks in advance, Nicola _______________________________________________ Nektar-users mailing list Nektar-users@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/nektar-users
Thank you. I'm currently using only the cmake-gui based option "ccmake" and i'm compiling only the compressible-flow solver, the libraries and with the option nektar_use_mpi. Thank you. Il giorno gio 8 feb 2024 alle ore 15:48 Jeremy Cohen < jeremy.cohen@imperial.ac.uk> ha scritto:
Hi Nicola,
If possible, could you provide us with the exact CMake command you are running and the full output from CMake - it will make it much easier for us to help you diagnose the problem.
Are you running a CMake command with a series of options on the command line or you’re using the CCMake text-based GUI to set the options?
Nektar++ has a lot of optional dependencies and does a number of checks at configuration time for different system properties and the existence of a number of different libraries. Without more detailed information it’s very difficult to know exactly what is causing the problem.
I think you originally highlighted that the CMake output was showing MPI_Send as being not found - this shouldn’t actually be an issue, I believe it’s a common message. Because there are many different implementations of MPI that need to be checked for in different ways, you will sometimes see things saying that something is not found. In some cases, CMake will then make other checks for different implementations of required libraries and it may still find an installed library that it can use.
Anyway, if you can provide some further information, we can try to help identify and resolve the issue.
Many thanks, Jeremy
On 8 Feb 2024, at 14:37, Nico Clinco <nicoclinco@gmail.com> wrote:
This email from nicoclinco@gmail.com 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, i have tried also defining CC=mpiCC and CCX=mpiCXX but nothing, the same problem.
I want to add that i am using the following modules: gnu9/9.4.0 cmake/3.24.2 openmpi4 Thanks in advance, Nicola _______________________________________________ Nektar-users mailing list Nektar-users@imperial.ac.uk https://mailman.ic.ac.uk/mailman/listinfo/nektar-users
Ah, ok, do you have the log output that is produced when you press the Generate button? I presume this is a Linux system? The log output should be written to a file if you’re not able to see it in the terminal in order to copy and paste it to an email. Thanks, Jeremy
On 8 Feb 2024, at 14:50, Nico Clinco <nicoclinco@gmail.com> wrote:
Thank you. I'm currently using only the cmake-gui based option "ccmake" and i'm compiling only the compressible-flow solver, the libraries and with the option nektar_use_mpi. Thank you.
Il giorno gio 8 feb 2024 alle ore 15:48 Jeremy Cohen <jeremy.cohen@imperial.ac.uk <mailto:jeremy.cohen@imperial.ac.uk>> ha scritto: Hi Nicola,
If possible, could you provide us with the exact CMake command you are running and the full output from CMake - it will make it much easier for us to help you diagnose the problem.
Are you running a CMake command with a series of options on the command line or you’re using the CCMake text-based GUI to set the options?
Nektar++ has a lot of optional dependencies and does a number of checks at configuration time for different system properties and the existence of a number of different libraries. Without more detailed information it’s very difficult to know exactly what is causing the problem.
I think you originally highlighted that the CMake output was showing MPI_Send as being not found - this shouldn’t actually be an issue, I believe it’s a common message. Because there are many different implementations of MPI that need to be checked for in different ways, you will sometimes see things saying that something is not found. In some cases, CMake will then make other checks for different implementations of required libraries and it may still find an installed library that it can use.
Anyway, if you can provide some further information, we can try to help identify and resolve the issue.
Many thanks, Jeremy
On 8 Feb 2024, at 14:37, Nico Clinco <nicoclinco@gmail.com <mailto:nicoclinco@gmail.com>> wrote:
This email from nicoclinco@gmail.com <mailto:nicoclinco@gmail.com> 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, i have tried also defining CC=mpiCC and CCX=mpiCXX but nothing, the same problem.
I want to add that i am using the following modules: gnu9/9.4.0 cmake/3.24.2 openmpi4 Thanks in advance, Nicola _______________________________________________ Nektar-users mailing list Nektar-users@imperial.ac.uk <mailto:Nektar-users@imperial.ac.uk> https://mailman.ic.ac.uk/mailman/listinfo/nektar-users <https://mailman.ic.ac.uk/mailman/listinfo/nektar-users>
Hello Nico, The problem is probably not related to "MPI_SEND not found". The CMake file is trying first to find if there is a build-in mpi in the compiler. Since, it did not find one, it is looking for a MPI library, which it found at the path indicated in the screenshot that you sent us. Cheers, Jacques ________________________________ From: nektar-users-bounces@imperial.ac.uk <nektar-users-bounces@imperial.ac.uk> on behalf of Nico Clinco <nicoclinco@gmail.com> Sent: Thursday, February 8, 2024 2:37 PM To: ankanggao@ustc.edu.cn <ankanggao@ustc.edu.cn> Cc: nektar-users@imperial.ac.uk <nektar-users@imperial.ac.uk> Subject: Re: [Nektar-users] Issues with compilation You don't often get email from nicoclinco@gmail.com. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> This email from nicoclinco@gmail.com 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, i have tried also defining CC=mpiCC and CCX=mpiCXX but nothing, the same problem. I want to add that i am using the following modules: gnu9/9.4.0 cmake/3.24.2 openmpi4 Thanks in advance, Nicola
Hello, i have attached below the pics of the output of cmake. Thank you. Il giorno gio 8 feb 2024 alle ore 16:04 Jacques Xing <jacques.xing@kcl.ac.uk> ha scritto:
Hello Nico,
The problem is probably not related to "MPI_SEND not found". The CMake file is trying first to find if there is a build-in mpi in the compiler. Since, it did not find one, it is looking for a MPI library, which it found at the path indicated in the screenshot that you sent us.
Cheers, Jacques ------------------------------ *From:* nektar-users-bounces@imperial.ac.uk < nektar-users-bounces@imperial.ac.uk> on behalf of Nico Clinco < nicoclinco@gmail.com> *Sent:* Thursday, February 8, 2024 2:37 PM *To:* ankanggao@ustc.edu.cn <ankanggao@ustc.edu.cn> *Cc:* nektar-users@imperial.ac.uk <nektar-users@imperial.ac.uk> *Subject:* Re: [Nektar-users] Issues with compilation
You don't often get email from nicoclinco@gmail.com. Learn why this is important <https://aka.ms/LearnAboutSenderIdentification>
This email from nicoclinco@gmail.com 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, i have tried also defining CC=mpiCC and CCX=mpiCXX but nothing, the same problem.
I want to add that i am using the following modules: gnu9/9.4.0 cmake/3.24.2 openmpi4 Thanks in advance, Nicola
And these are the file in the CMakeFiles directory. There is a file in which some errors are reported. Hope that i have attached all the necessary files. Il giorno gio 8 feb 2024 alle ore 16:09 Nico Clinco <nicoclinco@gmail.com> ha scritto:
Hello, i have attached below the pics of the output of cmake. Thank you.
Il giorno gio 8 feb 2024 alle ore 16:04 Jacques Xing < jacques.xing@kcl.ac.uk> ha scritto:
Hello Nico,
The problem is probably not related to "MPI_SEND not found". The CMake file is trying first to find if there is a build-in mpi in the compiler. Since, it did not find one, it is looking for a MPI library, which it found at the path indicated in the screenshot that you sent us.
Cheers, Jacques ------------------------------ *From:* nektar-users-bounces@imperial.ac.uk < nektar-users-bounces@imperial.ac.uk> on behalf of Nico Clinco < nicoclinco@gmail.com> *Sent:* Thursday, February 8, 2024 2:37 PM *To:* ankanggao@ustc.edu.cn <ankanggao@ustc.edu.cn> *Cc:* nektar-users@imperial.ac.uk <nektar-users@imperial.ac.uk> *Subject:* Re: [Nektar-users] Issues with compilation
You don't often get email from nicoclinco@gmail.com. Learn why this is important <https://aka.ms/LearnAboutSenderIdentification>
This email from nicoclinco@gmail.com 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, i have tried also defining CC=mpiCC and CCX=mpiCXX but nothing, the same problem.
I want to add that i am using the following modules: gnu9/9.4.0 cmake/3.24.2 openmpi4 Thanks in advance, Nicola
participants (5)
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Alexandra Liosi
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ankanggao＠ustc.edu.cn
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Jacques Xing
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Jeremy Cohen
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Nico Clinco