makenek error

[Sai Pranay]

Hello

I am new to NEK5000 and I am trying to get a 2D mesh smoother implemented as shown in the file below.

If my understanding is correct, running NEK5000 would give a 2D smoothed mesh. I wish to preserve the resolution near the wall. 

Mesh is designed in gmsh and converted to re2 format and then to rea format and generating the corresponding map file.

When I am trying to execute makenek I am getting an error at the end as shown in the build.log. Let me know the source of the error.

Thank you

Pranay

[YuHsiang Lan]

Hi,

You need to add "#include "experimental/meshsmoother.f" at the beginning of the usr file.

See also the example https://github.com/Nek5000/NekExamples/blob/master/smoother/lpt.usr

Hope this helps,

Yu-Hsiang

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[Sai Pranay]

Thank you for the message. I manged to exeute makenek using the .usr file and when I set the lelt around 5K. But the actual mesh demands lelt around 7K. When I tried to increase lelt by reducing mpi or increasing lelg makenek fails with the error below. Tried updating the FFLAGS/CFLAGS to large and still no use.

Error:
Warning: Type mismatch between actual argument at (1) and actual argument at (2) (INTEGER(8)/INTEGER(4)).
building libnek5000.a ... ar: `u' modifier ignored since `D' is the default (see `U')
done
mpif77  -O2 -cpp -fdefault-real-8 -fdefault-double-8 -std=legacy  -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/sai/Desktop/NEK5000/Nek5000/run/final -I/home/sai/Desktop/NEK5000/Nek5000/core -I./ -I /home/sai/Desktop/NEK5000/Nek5000/core/experimental -o nek5000 /home/sai/Desktop/NEK5000/Nek5000/core/drive.f /home/sai/Desktop/NEK5000/Nek5000/run/final/final.o libnek5000.a -L/home/sai/Desktop/NEK5000/Nek5000/3rd_party/blasLapack -lblasLapack -L/home/sai/Desktop/NEK5000/Nek5000/3rd_party/gslib/lib -lgs -Wl,--allow-multiple-definition
/home/sai/Desktop/NEK5000/Nek5000/run/final/final.o: in function `fixcurs_':
final.f:(.text+0x31e0): relocation truncated to fit: R_X86_64_PC32 against symbol `ctmp0_' defined in COMMON section in libnek5000.a(navier5.o)
final.f:(.text+0x31fb): relocation truncated to fit: R_X86_64_PC32 against symbol `ctmp0_' defined in COMMON section in libnek5000.a(navier5.o)
final.f:(.text+0x3216): relocation truncated to fit: R_X86_64_PC32 against symbol `ctmp0_' defined in COMMON section in libnek5000.a(navier5.o)
final.f:(.text+0x325c): relocation truncated to fit: R_X86_64_PC32 against symbol `ctmp0_' defined in COMMON section in libnek5000.a(navier5.o)
final.f:(.text+0x3287): relocation truncated to fit: R_X86_64_PC32 against symbol `ctmp0_' defined in COMMON section in libnek5000.a(navier5.o)
libnek5000.a(drive2.o): in function `plan3_vol_':
drive2.f:(.text+0x5ce): relocation truncated to fit: R_X86_64_PC32 against symbol `scrvh_' defined in COMMON section in libnek5000.a(convect.o)
libnek5000.a(drive2.o): in function `plan4_vol_':
drive2.f:(.text+0x877): relocation truncated to fit: R_X86_64_PC32 against symbol `scrvh_' defined in COMMON section in libnek5000.a(convect.o)
drive2.f:(.text+0x916): relocation truncated to fit: R_X86_64_PC32 against symbol `scrvh_' defined in COMMON section in libnek5000.a(convect.o)
libnek5000.a(drive2.o): in function `plan2_vol_':
drive2.f:(.text+0x5f88): relocation truncated to fit: R_X86_64_PC32 against symbol `scrvh_' defined in COMMON section in libnek5000.a(convect.o)
libnek5000.a(plan5.o): in function `midstep_':
plan5.f:(.text+0x5a): relocation truncated to fit: R_X86_64_PC32 against symbol `scrvh_' defined in COMMON section in libnek5000.a(convect.o)
plan5.f:(.text+0x9d): additional relocation overflows omitted from the output
collect2: error: ld returned 1 exit status
make: *** [makefile:133: nek5000] Error 1

Is it beacuse of my system limitations, this is not happening?

Thank you

Pranay

[YuHsiang Lan]

HI,

> mpif77  -O2 -cpp -fdefault-real-8 -fdefault-double-8 -std=legacy  -DMPI -DUNDERSCORE -DGLOBAL_LONG_LONG -DTIMER -I/home/sai/Desktop/NEK5000/Nek5000/run/final -I/home/sai/Desktop/NEK5000/Nek5000/core -I./ -I /home/sai/Desktop/NEK5000/Nek5000/core/experimental -o nek5000 /home/sai/Desktop/NEK5000/Nek5000/core/drive.f /home/sai/Desktop/NEK5000/Nek5000/run/final/final.o libnek5000.a -L/home/sai/Desktop/NEK5000/Nek5000/3rd_party/blasLapack -lblasLapack -L/home/sai/Desktop/NEK5000/Nek5000/3rd_party/gslib/lib -lgs -Wl,--allow-multiple-definition
/home/sai/Desktop/NEK5000/Nek5000/run/final/final.o

I don't find -mcmodel=large in your compile command.

Can you post your makenek? and SIZE?

> Is it beacuse of my system limitations, this is not happening?

What's the size of your RAM?

Thanks,

Yu-Hsiang

--

[Sai Pranay]

Here you go :

Architecture:            x86_64
  CPU op-mode(s):        32-bit, 64-bit
  Address sizes:         39 bits physical, 48 bits virtual
  Byte Order:            Little Endian
CPU(s):                  12
  On-line CPU(s) list:   0-11
Vendor ID:               GenuineIntel
  Model name:            Intel(R) Xeon(R) W-1250P CPU @ 4.10GHz
    CPU family:          6
    Model:               165
    Thread(s) per core:  2
    Core(s) per socket:  6
    Socket(s):           1
    Stepping:            5
    CPU max MHz:         4800.0000
    CPU min MHz:         800.0000
    BogoMIPS:            8199.79

Thanks

Pranay

[Sai Pranay]

RAM availability: 64 GB
        64008 M total memory
         6974 M used memory
         9781 M active memory
        29160 M inactive memory
        21557 M free memory

Thanks

Pranay

[Fischer, Paul]

Lelt is the upper bound on the number of elements per rank.  The local (per rank) memory scales as O(lelt), to leading order.

I suggest to cut lelt by a factor of two and then use twice as many MPI ranks.

Or, a factor of 4 and use 4X the number of ranks, etc.

hth,

Paul

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From: nek...@googlegroups.com <nek...@googlegroups.com> on behalf of Sai Pranay <padakan...@gmail.com>
Sent: Friday, July 19, 2024 11:02 AM
To: Nek5000 <nek...@googlegroups.com>
Subject: [nek5000] Re: makenek error

 

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[YuHsiang Lan]

Hi,

It looks like you didn't uncomment these lines in your makenek
You will need to recompile with a full clean (makenek clean)

  FFLAGS="-mcmodel=large"
  CFLAGS="-mcmodel=large"

Hope this helps,

Yu-Hsiang

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[Sai Pranay]

Thank you this worked.