Nek5000 help

[Noorul Hasheem]

Hello  I am new to CFD and nek5000.   I am little stuck on a issue with running one of the tutorial  from nek5000 every dependencies are good every files is created but When I am trying to compile “makenek hillp” i get makefile error I have tried this simulation couple of times . I also downloaded the files I need for the compilation from the website periodic hill tutorial .Below I attached picture of the error I get along with my size file since I thought it was my size file. I did make some changes on the size file for one of the simulations b making lx1 = 4 instead of 8 . I did not change lelg as for the mesh for this case lelg >= number of elements.I attached screenshot of the error I have.

Thank you

[Valerio Lupi]

Hi,

you get this error when the allocated vectors are too large, which means you have too many elements per process, given by the parameter lelt in the SIZE file. 

Best,

Valerio

Il gio 23 mar 2023, 16:30 Noorul Hasheem <noorul...@gmail.com> ha scritto:

Hello  I am new to CFD and nek5000.   I am little stuck on a issue with running one of the tutorial  from nek5000 every dependencies are good every files is created but When I am trying to compile “makenek hillp” i get makefile error I have tried this simulation couple of times . I also downloaded the files I need for the compilation from the website periodic hill tutorial .Below I attached picture of the error I get along with my size file since I thought it was my size file. I did make some changes on the size file for one of the simulations b making lx1 = 4 instead of 8 . I did not change lelg as for the mesh for this case lelg >= number of elements.I attached screenshot of the error I have.

Thank you

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[Josuel Kruppa Rogenski]

Hi there,

It seems to be a memory problem. Maybe you could increase the number of processing elements and see what happens. Fortran also has an option you can add during compilation: -mc_model=medium

Cherrs

[Noorul Hasheem]

Hello Joshua thanks for your response ,

How do I exactly add that during the compilation. Will it just be ‘ -mc_model=medium makenek hillp’

Thank you 

Sent from my iPhone

On Mar 23, 2023, at 12:13 PM, Josuel Kruppa Rogenski <jkrog...@alumni.usp.br> wrote:



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[Noorul Hasheem]

Sorry for the typo in the name Josuel.

I am trying incorporate that command while compiling . 

Thank you 

Sent from my iPhone

On Mar 23, 2023, at 12:25 PM, Noorul Hasheem <noorul...@gmail.com> wrote:

Hello Joshua thanks for your response ,

[Josuel Kruppa Rogenski]

No problem. Look at https://nek5000.github.io/NekDoc/faq.html

Why does the compiler issue relocation errors?

relocation truncated to fit: R_X86_64 against symbol 'foo_' defined in COMMON section in obj/bar.o

This happens when the resultant executable requires more than 2GB of static data. The best way to avoid this is to increase the minimum number of MPI ranks, lpmin in SIZE. Alternatively, you can add -mcmodel=medium to the FFLAGS/CFLAGS variable in makenek. See Compiler Flags for more information.

[Noorul Hasheem]

So if I am right I add that on to the makenek file itself ? It did not generate makenek file , I copied the makenek file from the bin to the case directory .

Thank you 

Sent from my iPhone

On Mar 23, 2023, at 12:42 PM, Josuel Kruppa Rogenski <jkrog...@alumni.usp.br> wrote:



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[Dillon Shaver]

Before you try changing the makenek file, can you post your SIZE file? If you've decreased lx1, it should require less memory, not more. This problem shouldn't be anywhere near the memory limit requiring -mcmodel=medium.