Hi Hamed,

Thanks for providing this information.

I assume that when you run “ccmake ../“, you get the cmake text based user interface where you can turn various options on and off?

Nektar++ has a wide range of different elements than can be optionally built. It also has a number of third-party dependencies that can be built as part of the Nektar++ build process if they’re not found on the local system.

Have you’ve turned on any additional options beyond the default settings? Are you seeing this error when you press “c” to run the configuration in the cmake user interface?

To provide further assistance I think we’ll need more details to be able to help debug this issue.

Can you provide us with a list of any CMake settings you’ve changed, and the value of the setting after you’ve changed it. 

I’m a little confused by the error but it looks like your system is picking up libstdc++ from a toolchain within an OpenFOAM installation. I presume you have OpenFOAM installed on your system and it looks like maybe either you, or the OpenFOAM installation scripts, have modified the system PATH to use gcc from within the OpenFOAM installation?

If you can give us the output of the commands “gcc --version” and “which gcc” that will help to see whether you’re using a version of GCC that is not the main system version. From the information below, it looks like you may be using gcc 6.3.0 whereas the standard version of gcc installed from packages on Ubuntu 20.04 is gcc 9.3.0.

What I think is probably happening here is that somewhere in the cmake configure process, some Python code is being run and when it tries to import the “apt_pkg” module, it tries to load the system library "/lib/x86_64-linux-gnu/libapt-pkg.so.6.0”. This should be linking against other standard system libraries but for some reason it’s picking up libstdc++.so.6 in the "/mnt/c/OpenFoam/OpenFOAM/ThirdParty-v2006/platforms/linux64/gcc-6.3.0/lib64/“ directory rather than in "/lib/x86_64-linux-gnu/“. I suspect this could be because you have a custom LD_LIBRARY_PATH set. To help verify this, could you also provide the output of the following commands: 

 - “echo $LD_LIBRARY_PATH”
 - “ldd /lib/x86_64-linux-gnu/libapt-pkg.so.6.0”

Thanks,
Jeremy



On 30 Nov 2020, at 18:46, Hamed Faghanpourganji <h.f.ganji@gmail.com> wrote:

Hello Jeremy,

Thanks for replying. I really appreciate it.

- What version of Ubuntu are you running? (run: "cat /etc/issue”)
  Ubuntu 20.04.1 LTS \n \l  
 - Are you trying to build Nektar++ from source code or you’ve installed/tried to install binary packages for Ubuntu?
I tried to build Nektar++  from source code.
 - Which version of Nektar++ are you trying to install? - If you downloaded a .zip or .tar.gz file from the website, can you let us know which one? Otherwise are you trying to build/install code cloned from git?
I downloaded the latest version on the website. To be specific, nektar++-5.0.0
 - Can you let us know exactly which command you ran that resulted in the error?
ccmake../
 - Also, please provide any further output that was displayed along with the error
Traceback (most recent call last):
  File "/usr/lib/command-not-found", line 28, in <module>
    from CommandNotFound import CommandNotFound
  File "/usr/lib/python3/dist-packages/CommandNotFound/CommandNotFound.py", line 19, in <module>
    from CommandNotFound.db.db import SqliteDatabase
  File "/usr/lib/python3/dist-packages/CommandNotFound/db/db.py", line 5, in <module>
    import apt_pkg
ImportError: /mnt/c/OpenFoam/OpenFOAM/ThirdParty-v2006/platforms/linux64/gcc-6.3.0/lib64/libstdc++.so.6: version `GLIBCXX_3.4.26' not found (required by /lib/x86_64-linux-gnu/libapt-pkg.so.6.0)
 - If you’re trying to build from source code, can you tell us the steps you’ve completed so far when you get the error (such as the commands you ran as part of the build process prior to the command that gives this error)
tar -zxvf nektar++-5.0.0.tar.gz   
mkdir -p build && cd build
 they worked but not ccmake ../

Sincerely,
Hamed

On Mon, Nov 30, 2020 at 9:57 AM Jeremy Cohen <jeremy.cohen@imperial.ac.uk> wrote:
Hi Hamed,

Can you provide us with a bit more information about your system and the error you’re getting so that we can try and help to identify the problem:

 - What version of Ubuntu are you running? (run: "cat /etc/issue”)

 - Are you trying to build Nektar++ from source code or you’ve installed/tried to install binary packages for Ubuntu?

 - Which version of Nektar++ are you trying to install? - If you downloaded a .zip or .tar.gz file from the website, can you let us know which one? Otherwise are you trying to build/install code cloned from git?

 - Can you let us know exactly which command you ran that resulted in the error?

 - Also, please provide any further output that was displayed along with the error

 - If you’re trying to build from source code, can you tell us the steps you’ve completed so far when you get the error (such as the commands you ran as part of the build process prior to the command that gives this error)

If you can provide us with this information, we will hopefully be able to see what is causing the issue.

Thanks,

Jeremy


On 29 Nov 2020, at 17:59, Hamed Faghanpourganji <h.f.ganji@gmail.com> wrote:

Hi Sherwin,

you were right regarding gcc installation, but it is not working yet and I got the similar error again.

Kind regards,
Hamed

On Sun, Nov 29, 2020 at 6:41 PM Sherwin, Spencer J <s.sherwin@imperial.ac.uk> wrote:
HI Hamed,

It seems as if you might not have installed gcc on your machine. If you type ‘gcc —version’ do you get a message from the c compiler. 

Regards
Spencer.

Spencer Sherwin FREng, FRAeS
Head of Aerodynamics Section,
Director of Research Computing Service,
Professor of Computational Fluid Mechanics,
Department of Aeronautics,
South Kensington Campus,
Imperial College London, SW7 2AZ,  UK
Phone: +44 (0)20 7594 5052

On 26 Nov 2020, at 16:51, Hamed Faghanpourganji <h.f.ganji@gmail.com> wrote:

This email from h.f.ganji@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 friends,

I have tried to install Nektar++ on Ubuntu, but I got the noted error in subject of this Emial. I already google it, but following links didn't help 

https://unix.stackexchange.com/questions/456918/how-do-i-install-glibcxx

https://github.com/ufo-project/ufochain/issues/3

https://askubuntu.com/questions/1166292/version-glibcxx-3-4-26-not-found-even-though-libstdc-so-6-recent-enough

Anyone can help me with the installation?

Thank you very much in advance.
Kind regards,
Hamed

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