missing vtf3.h BPatch.h papi.h
 

Hello OF-community,

trying to compile ThirdParty 1.7.1 I am expecting errors during the compilation of the openmpi-1.4.1. At the step "Configuring contributed software packages" it says:

Using aptitude search on debian linux 2.6.32-5-amd64 I don't find theese packages. Does anybody know, where to get the mentioned files and where to place them?

Regards,

Greetings Illya,

I know I've had this problem before, but I'm not 100% certain how I fixed it...

But how exactly are you building OpenMPI? Manually or using the Allwmake script in the ThirdParty folder?

Additionally, if you are using Debian, then this list of packages should work for you too: Building OpenFOAM1.7.0 from source post #4 and onward

Best regards,
Bruno

Hi Bruno,

thanks for the reply. Because of being newbie in OpenFOAM as well as in linux I use the Allwmake script.

There are quite a lot of packages listed in the thread. I hope that installing them will cure the problems.

EDIT: since I have no administrator rights, I can not install the packages by myself. And the admin refuses to install the whole bunch of packages until I exactly know which of them I do really need. So the question remains open.

Hi Illya,
Well, I can't remember by heart which one was it :( And I can't find those headers in my Ubuntu system either, so I can only assume that OpenMPI's configure script can deduce that there are better options than those specific headers/packages, once those options are available.
But this weekend I'll try to get some time to figure out which one might it be.

But you could also request your system administrator to simply install the OpenMPI version available for your system. And if not OpenMPI, any other MPI should work too, just a matter of configuring the script "$WM_PROJECT_DIR/etc/settings.sh" to the desired MPI library.

Those packages listed on that link, also include the necessary packages for building ParaView, albeit some of them might be available for your system, since it's a bit old.

Best regards,
Bruno

Hi Illya,

OK, I've tested in a virtual machine with Ubuntu 10.04 (which is based in Debian). The only packages that I needed for building OpenMPI were:By what I can figure out, what happens is this: even if a package is missing, OpenMPI will continue if possible. So, even if you got those three errors about VTF3, PAPI and BPatch, they aren't crucial since they are simply added value if available.
So, if you run this command:You should see something like this:This should mean, in a clean build (i.e., started from scratch), that OpenMPI was in fact built successfully :)

Now, if the Allwmake came to an end with an error in the end, then something else went wrong. Other than that, you should be good to continue building!

Best regards,
Bruno

Hi Bruno,

with ls -l $MPI_ARCH_PATH I can see the folder you listed and everything seems to be ok insofar. Thank you!

everything is fine or not?
 

Hello Bruno,
I am trying to install OpenFOAM 2.0.1 on a Gnome Debian 2.22.3. I am also getting the following:
however, the installation continues without further complains. In addition, the ls -l $MPI_ARCH_PATH command gives exactly what you said above.
In conclusion, I should not worry about those errors, should I?

mad

Hi Maddalena,

I vaguely remember seeing those errors and even with them everything else built properly, so I suppose so.
If:

• It had stopped at the end of the "configure" step;
• Or stopped during the build process, with an error related to one of the errors given during configure;

then yes, it would be a valid reason for concern! :)

Best regards,
Bruno

Hi Bruno,

me again 1.5 years later. I've got new pc with new Debian
Trying to compile the OF 2.1.x I'm getting almost the same erros as last time:
and additionally this one:
and at the end a couple of similar looking errors like:
This time ls -l $MPI_ARCH_PATH isn't successful, what means that MPI wasn't compiled. Do you have any idea what the reason could be? Obviously I am missing some packages.

Best regards,
Ilya

Hi Ilya,

I'll need more info about which Debian version you're using. Try this command: I'll look into this tomorrow night. Any special details about the Debian installation? And/or if you're using a shell other than Bash or Dash?

Best regards,
Bruno

Hi Bruno,

there is no lsb-release in /etc But:

Here is the complete ThirdParty make log, if it helps.

Thanks a lot!
Ilya

What I have to add, there is openmpi already installed in /usr/local/mpich independently from OF. So of the ThirdParty-openmpi installations fails, it may be possible to link the "external" openmpi to OF. What do you think about it?

Hi Ilya,

I'll try to replicate the installation on a virtual machine later today, with an up-to-date Debian 6 x86_64 (== amd64) installation.

As for MPICH:

1. Is it MPICH or MPICH2?
2. When you run:
   Code:

   ---

   which mpicc

   ---

   Is it the one from MPICH that appears or none appears?
3. How was MPICH installed? From Debian or manually installed?

Why not configure your OpenFOAM installation to use that MPI toolbox instead of Open-MPI? You'll need to configure these files:

1. "OpenFOAM-2.1.x/etc/bashrc" - change OPENMPI to MPICH
2. "OpenFOAM-2.1.x/etc/config/settings.sh" - find the MPICH entry and reconfigure the parameters located in that block of code!

____
edit:
Well, I've just tested now on a VM with Debian 6 and it built things just fine.
I've got feeling that you have a machine setup that is influencing the results you and I are getting. The installed MPICH version you got may be only the tip of the iceberg :(

But like I've wrote above: maybe it's best that you use the MPICH library you already have. By the way, which version do you have? Because I tried getting the source code for the old MPICH1 for trying to replicate the installation and didn't find it after a 5min search :(

Ah, last but not least, try installing the Open-MPI version that Debian has (scotch as well): Then in OpenFOAM's "etc/bashrc", change "OPENMPI" to "SYSTEMOPENMPI".

____

Best regards,
Bruno

Hi Bruno,

a general question, what's the difference between opnmpi & mpich? Does it matter, which one to use?

1) I have no idea. How can I find it out? A little bit strange is the following: the mpich dir contains dirs and there is a lot of ompi called stuff in bin & etc dirs:
So may be it isn't mpich at all, but openmpi installed into the mpich dir.

2)3) I suppose it was installed manually

P.S. libscotch-dev libopenmpi-dev are already there, so I don't need to install them

Hi Ilya,

I'm guessing that installing Open-MPI in those machines at your workplace can be a pain, which is why the administrator installs it manually.
The "mpich" folder must be a legacy thing, to keep things compatible with the workflow existent there.

I believe that version one of MPICH was created in a time when no other MPI was open-source. Open-MPI came to life as a need for a more generic and open MPI toolbox. But I guess that Wikipedia should know more than me :D :

• http://en.wikipedia.org/wiki/MPICH
• http://en.wikipedia.org/wiki/Open_MPI

And like I wrote before, the trick for your system should be:
Then run wmSET (or start a new terminal) and you can then go back to building OpenFOAM!

Best regards,
Bruno

Hi Bruno,

I made the change in the OF bashrc, but when I try to source it, I get the following error:
Best regards,
Ilya

Mmm... you better start a new terminal, because the environment is already contaminated with the old option.

Hi Bruno,

I've started a new terminal and executed ./Allwmake script from the OpenFOAM-2.1.x dir. There were no errors this time. But if I try to start a parallel simulation a get a bunch of errors looking like this:
should I recompile the complete OF build (wclean all bevor Allwmake)?

Best regards,
Ilya

Hi Ilya,

This should be enough, without having to rebuild the whole OpenFOAM source:
Best regards,
Bruno

Hi Bruno,

there are apparently no problems during the buid any more, but mpi still doesn't work properly. Here is an error log example.

Best,
Ilya