Compiling error.

[Gilberto Montiel]

Hello!

I'm just starting with nek5000 and I followed the instructions in the Quickstart: "Running your very first simulation".

First issue I had was with the command:

cd ~/Nek5000/tools; ./maketools genmap

Then I installed gfortran (I'm on Ubuntu 16.04) with the shell command:

sudo apt-get install gfortran

After that, I can continue, but then when I pass the command

makenek eddy_uv

I get the answer:

using source path: /home/hp/Nek5000
generating makefile ... done
building 3rd-party dependencies ...
An ERROR occured, see build.log for details

When I open build.log, the reported error is:

In file included from src/sarray_transfer.c:9:0:
src/comm.h:67:10: fatal error: mpi.h: No such file or directory
 #include <mpi.h>

          ^~~~~~~

Do you have any suggestion? I appreciate a lot your time and attention.

Gilberto Montiel.

[Fischer, Paul]

Dear Gilberto,

Have you installed mpi (either openmpi or mpich) ?

Paul Fischer

---

From: nek...@googlegroups.com <nek...@googlegroups.com> on behalf of Gilberto Montiel <jose.gil...@gmail.com>
Sent: Tuesday, March 2, 2021 9:24 PM
To: Nek5000 <nek...@googlegroups.com>
Subject: [nek5000] Compiling error.

 

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[Gilberto Montiel]

Hi, Paul! Sorry about the delay.

I tried to install open mpi manually but I've been struggling during the week, so I ended installing it with:

sudo apt-get install openmpi-bin openmpi-common openssh-client openssh-server libopenmpi1.10 libopenmpi-dbg libopenmpi-dev

Unfortunately,  I keep getting an error and an instruction to look at build.log, and again it shows:

In file included from src/sarray_transfer.c:9:0:
src/comm.h:67:10: fatal error: mpi.h: No such file or directory
 #include <mpi.h>
          ^~~~~~~

Do you recommend keep trying manual installation or remove open mpi and install mpich?

Any other idea?

Thanks a lot. Hope you are fine, best wishes.

Gilberto Montiel.

[Gilberto Montiel]

Hi Byron.

Thanks a los for your response; I’m still getting the same error although I installed open mpi. Do you suggest mpich? 

Best wishes,

Gilberto

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[Arsen Iskhakov]

I also encountered this error today compiling Nek5000 on NCSU Henry 2 machine. My solution was to try to use different compilers... If I remember correctly “pure” Openmpi and intel mpi did not work at all. Some sort of old versions of mixed openmpi/gcc compiler worked (I do not remember exactly the version and the name of the compiler). If you are interested - I will check it tomorrow when I get my laptop...

Anyway, mpich should work (use stable version). If you have opportunity to install it, it should solve your problems.

Good luck!

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--

Sincerely,

Arsen Iskhakov, PhD                     isk...@ncsu.edu

PhD-student                             (984) 255-3069

Department of Nuclear Engineering       Campus Box 7909

North Carolina State University         Raleigh, NC 27695

[Guillaume Chauvat]

Hi Gilberto,

Sorry if I missed it, but did you use the MPI compiler in the makenek? Something like
FC="mpif77"
CC="mpicc"


Guillaume

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[Stefan K.]

This list is not intended to discuss general MPI questions/issues.

> To view this discussion on the web visit https://groups.google.com/d/msgid/nek5000/36f67ba7-4815-d944-6638-10c56249fc0c%40mech.kth.se.

[Gilberto Montiel]

Hi, Guillaume. Thanks a lot for your response.

I didn't indicate those at the beggining, but now that I've done it, I get another error:

gcc: error: unrecognized command line option ‘-fno-plt’

I'm trying to solve this, meanwhile, do you have any thoughts?

Best,

Gilberto

[Gilberto Montiel]

Hi, Arsen.

Thanks a lot for your response; I’ll try that.

Best wishes!

Gilberto.

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