[Nek5000-users] Compilation of nek5000 in ubuntu

Wed Jan 14 07:17:06 CST 2015

Hi Kamal,

Unfortunately, your suggestions does not change much of the compiling. The mpif77 compiler is still non-functional. When I do "sudo make" or "sudo make check install", no errors or warning appears except repeated similar words "Nothing to be done for 'xxxx (eg. all)' ". And when I do "sudo apt-get install build essential", it actually did not find out essential.

I will re-do the steps tomorrow to double check. Thanks again for your assistance.

Regards,

Simon

________________________________
From: nek5000-users-bounces at lists.mcs.anl.gov <nek5000-users-bounces at lists.mcs.anl.gov> on behalf of nek5000-users at lists.mcs.anl.gov <nek5000-users at lists.mcs.anl.gov>
Sent: Wednesday, 14 January, 2015 7:49 PM
To: nek5000-users at lists.mcs.anl.gov
Subject: Re: [Nek5000-users] Compilation of nek5000 in ubuntu

   Hi Simon,

   Could you try this ' export LD_LIBRARY_PATH=/usr/local/opempi/lib '  and then launching "./makenek eddy_uv".

   If that does not help, There are a couple of things to do :

  1) sudo apt-get update
  2) sudo apt-get upgrade
  3) Sudo apt-get install build essential

  do the above commands to install some Linux libraries and try recompiling openmpi with ' ./configure --prefix=/usr/local/openmpi FC=/usr/local/gfortran (path of your gfortran).

   just take look at the output when you do ' sudo make ' and see If everything is going perfectly.

   Best,
   Kamal

   PS: Check If your gfortran works properly

On 14/01/2015 12:31, nek5000-users at lists.mcs.anl.gov<mailto:nek5000-users at lists.mcs.anl.gov> wrote:

Hi Kamal,

I am really thankful that you give so detailed information on compilation of Open-mpi. Everything went well when following your first 4 steps except for Step 5 in which creation of dir /sur/local/openmpi/share was denied. So I re-do Step 5 with command "sudo make check install", and then it compiled well without errors.

Then I followed Step 6 but it was found that no mpif77 nor mpicc files were under dir /use/local/openmpi/. After checking files under dir /use/local/openmpi/bin, there exist mpiff77 and mpicc files. So finally I changed makenek to "F77 = /usr/local/openmpi/bin/mpif77" and " CC = /usr/local/openmpi/bin/mpicc" and then type "./makenek eddy_uv".

Unluckily, the error came again as following:

--------------------------------------------------------------------------
Unfortunately, this installation of Open MPI was not compiled with
Fortran 77 support.  As such, the mpif77 compiler is non-functional.
--------------------------------------------------------------------------
FATAL ERROR: Basic compiler test for /usr/local/openmpi/bin/mpif77 failed!

It seems fortran 77 not ready yet. Do you have any comments about it?

Thanks,

Simon

________________________________
From: nek5000-users-bounces at lists.mcs.anl.gov<mailto:nek5000-users-bounces at lists.mcs.anl.gov> <nek5000-users-bounces at lists.mcs.anl.gov><mailto:nek5000-users-bounces at lists.mcs.anl.gov> on behalf of nek5000-users at lists.mcs.anl.gov<mailto:nek5000-users at lists.mcs.anl.gov> <nek5000-users at lists.mcs.anl.gov><mailto:nek5000-users at lists.mcs.anl.gov>
Sent: Wednesday, 14 January, 2015 5:58 PM
To: nek5000-users at lists.mcs.anl.gov<mailto:nek5000-users at lists.mcs.anl.gov>
Subject: Re: [Nek5000-users] Compilation of nek5000 in ubuntu

  Hi Simon,

   1) Download the Open-Mpi file from here : www.open-mpi.org/software/ompi/v1.8/downloads/openmpi-1.8.4.tar.gz<http://www.open-mpi.org/software/ompi/v1.8/downloads/openmpi-1.8.4.tar.gz>, unpack it
   2) Create a folder ' sudo mkdir  /usr/local/openmpi '
   3) Go to the unpacked openmpi-1.8.4 folder and do ./configure --prefix = /usr/local/openmpi
   4) Then just type ' make '
   5) Then ' make check install '

   This will install open-mpi in the folder /usr/local/openmpi, now your mpi files will be in this folder.

   6) Open makenek and change ' F77 = /use/local/openmpi/mpif77 ' and ' CC = /usr/local/openmpi/mpicc '  or you can the path to ./bashrc file if you don't want to do this step.

   I hope this should work for you.

 Best Regards,
  Kamal

On 14/01/2015 10:24, nek5000-users at lists.mcs.anl.gov<mailto:nek5000-users at lists.mcs.anl.gov> wrote:
Hi Kamal,

Thank you very much for the suggestion. As I am a Linux user at very basic level, could you please tell a little bit more details on reinstalling open-mpi? Are u suggesting me reinstall the same version as installed in ubundu, or any other version? If it should be a certain version, I will download and install in.

To tell the truth, I installed a package f2c that can translate fortran77 to c language, but it does not help here. Do you think do u have to install fortran77 in Ubuntu? It is said installing f77 will cause more errors in the latest version of Ubuntu.

Thanks for your reply again.

Sincerely,
Simon

On 14 Jan, 2015, at 5:08 pm, "nek5000-users at lists.mcs.anl.gov<mailto:nek5000-users at lists.mcs.anl.gov>" <nek5000-users at lists.mcs.anl.gov<mailto:nek5000-users at lists.mcs.anl.gov>> wrote:

  Hi Simon,

  I would suggest you to reinstall OPEN-MPI in ubuntu and use mpif77 compiler.

  Best,
  Kamal

 PS: Install Open Mpi in a separate folder and the add the path in ./bashsrc or to the makenek directly

On 14/01/2015 09:30, nek5000-users at lists.mcs.anl.gov<mailto:nek5000-users at lists.mcs.anl.gov> wrote:
Hi there,

I am compiling the eddy example in my ubuntu OS, but the system returns error with "Error: Can't open included file 'mpif.h'". The fortran compiler in makenek file was changed to gfortran since mpif77 gives error:
--------------------------------------------------------------------------
Unfortunately, this installation of Open MPI was not compiled with
Fortran 77 support.  As such, the mpif77 compiler is non-functional.
--------------------------------------------------------------------------
FATAL ERROR: Basic compiler test for mpif77 failed!

Is there anyone experience the same problem when compiling in ubuntu? You assistance will be greatly appreciated.

Sincerely,
Simon

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