[ramcdougal]

I installed OpenFOAM on my 64-bit Ubuntu 11.10 system on campus today with no difficulty by following the instructions at

http://www.openfoam.org/download/ubuntu.php

When I tried the same thing tonight at home (also 64-bit Ubuntu 11.10), the following happens

$ source /opt/openfoam210/etc/bashrc
gcc: error: unrecognized option ‘--showme:compile’
gcc: error: unrecognized option ‘--showme:link’

I'm not the only one who has had this problem. One bug report links it to openmpi:
http://www.openfoam.com/mantisbt/view.php?id=369
but I'm not sure what they're doing with modules and their solution doesn't work verbatim in Ubuntu. I do have openmpi installed at home, but I'm not sure what the situation is on campus.

There was an earlier forum post presumed to involve Ubuntu, but no solution
http://www.cfd-online.com/Forums/ope...c-problem.html

I'm not sure where to start looking for a difference between the two machines. Any advice? Thanks!

[wyldckat]

Greetings Robert and welcome to the forum!

Mmm... indeed, this is odd, but at least you've provided a lot more information than the other forum user

OK, try running the following commands:

which mpirun
mpirun --version

The first one should show you where mpirun is located and the second one should show which version you've got installed.
If neither show any information, then it might not be working due to either one of several reasons:

• Open-MPI didn't install properly, due to some strange reason. It's known to have a glitch during installation, since normal people don't have Infiniband on their computers, but it still comes with support for it pre-packaged...
• Another reason for a bad installation is if the "alternatives" system failed to add an alternative for Open-MPI. I'm not sure what's the solution here, but I'd guess that reinstalling Open-MPI wouldn't hurt.
• Yet another is for said "alternatives" system not having updated until you reboot.

And don't forget to have your system fully up-to-date, just in case...

Best regards,
Bruno

[ramcdougal]

Thanks Bruno, but there is no obvious difference in mpi setup. They are both setup through Ubuntu's repositories; I don't do anything unusual with MPI. Any other ideas?

At home:

robert@desktop-2010:~$ which mpirun
/usr/bin/mpirun
robert@desktop-2010:~$ mpirun --version
mpirun (Open MPI) 1.4.3

Report bugs to http://www.open-mpi.org/community/help/

At the office:

ramcdougal@ramcdougal-VirtualBox:~$ which mpirun
/usr/bin/mpirun
ramcdougal@ramcdougal-VirtualBox:~$ mpirun --version
mpirun (Open MPI) 1.4.3

Report bugs to http://www.open-mpi.org/community/help/

You'll notice that at the office I run in a virtual machine, so I suppose that could make some subtle differences in active kernel drivers.

I have a much longer $PATH at home. Are there any known conflicts? For example, does Enthought provide a conflicting MPI?

As an aside: Why does it need to call gcc every time I open a terminal?

[wyldckat]

Hi Robert,

The code that is giving you that error message is this one (the two lines in the middle):

# Set compilation flags here instead of in wmake/rules/../mplibSYSTEMOPENMPI
    export PINC="`mpicc --showme:compile`"
    export PLIBS="`mpicc --showme:link`"
    libDir=`echo "$PLIBS" | sed -e 's/.*-L\([^ ]*\).*/\1/'`

Source: "etc/config/settings.sh"
Therefore, perhaps it is Enthought that is disturbing OpenFOAM's thought process

For further debugging:

• Try checking which mpicc is getting picked up, by testing the same way I wrote for mpirun, namely:

  which mpicc
  mpicc --version

• Try loading first OpenFOAM's environment and then Enthought's environment.
• Try having separate environments: Advanced tips for working with the OpenFOAM shell environment

Best regards,
Bruno

[ramcdougal]

Both machines report

robert@desktop-2010:~$ which mpicc
/usr/bin/mpicc
robert@desktop-2010:~$ mpicc --version
gcc (Ubuntu/Linaro 4.6.1-9ubuntu3) 4.6.1

Just to be safe, I reinstalled every package with mpi in it's name; that didn't fix things.

I commented out all of the non-standard lines at the end of my ~/.bashrc, added the OpenFOAM source line, and I still got the same problem as before. I think this means Enthought is innocent, but once again I'm out of ideas.

And, for the record, this is a problem I'm having with

robert@desktop-2010:~$ uname -a
Linux desktop-2010 3.0.0-16-generic #28-Ubuntu SMP Fri Jan 27 17:44:39 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux

[wyldckat]

Hi Robert,

I forgot to mention that looks can be deceiving:

ls -l `which mpicc`

If this shows that it is linking to another file, then check what that file is and if itself is yet another link!

Best regards,
Bruno

[Linse]

Just for the case there are any doubts about the problem being due to mpi:
Did you check in the OpenFOAM-2.1.x/etc/config/settings.sh (or the one corresponding to your shell) if the correct C++-compiler is set there?

I just had serious build problems because I had not set the gcc46 manually...

[rnebot]

Hi,

I am a newbie and had the same problem. I have Ubuntu 12.04 and OpenFoam 2.1.1

The post from wyldckat about looking "mpicc -v" output gave me the clue. I had installed both "mpich2" and "openmpi" and the former was the one controlling "mpicc". Uninstalled "mpich2" and now it works.

Hope it helps

[iperetta]

Greetings,

I know it's an old post, but the problem is still there... I'm working with OpenFoam 2.1.1 and Ubuntu Precise Pangolin (12.04LTS) and have the same errors with "gcc --showme:compile" and "gcc --showme:link". I'm a fan of MPICH2, so I don't have Open-MPI installed.

Searching a little in the internet, I've found out that "--showme:compile" and "--showme:link" are Open-MPI options only. To change that to work with MPICH2, I've had to edit "/opt/openfoam211/etc/config/settings.sh" file and exchange "mpicc --showme:compile" and "mpicc --showme:link" for "mpicc -compile-info" and "mpicc -link-info".

Hope this information is useful for somebody else.

Best wishes!

[wyldckat]

Greetings Igor and welcome to the forum!

Many thanks for sharing this information about using the system's MPICH2! It would indeed be worth while sharing this at the bug tracker as well: http://www.openfoam.org/bugs/

But I still have got one question: did you use the Debian package installation of OpenFOAM for Ubuntu, or did you build from source?

Best regards,
Bruno

[iperetta]

Hi, wyldckat (Bruno)

By the way, I'm using 64-bit Ubuntu...

I get it from apt-get, I suppose it is from an official Ubuntu repository... See what you get with this:

sudo apt-get install openfoam211 paraviewopenfoam3120

I'm also working with swap4Foam (groovyBC library) and this one I got to build from code...

I've already tried to post in http://www.openfoam.org/bugs/, but the site doesn't let me post there (it seems that they're looking for bugs, not solutions ).

Well... Keep it going! Hugs!

[wyldckat]

Hi Igor,

Wait... you're using the system's MPICH2 with the pre-built installation of OpenFOAM that was built with Open-MPI?
How does it not crash when running in parallel?

Or did you at least re-build the Pstream library for using MPICH2?

Best regards,
Bruno

[iperetta]

Originally Posted by wyldckat

Wait... you're using the system's MPICH2 with the pre-built installation of OpenFOAM that was built with Open-MPI?
How does it not crash when running in parallel?

Sorry, Bruno... I didn't mean to confuse you... The error I mentioned showed up when I was running terminals... Please, identify to me a source (or example from tutorials) that I could run with MPI to ensure what's going on here. Actually, I'm a sort of newbie and I'm not running MPI applications right now...

As far as I though, "apt-get install" gets the source and build it for your machine. Correct me if I'm wrong, please. I don't know what comes with MPI build options...

[wyldckat]

In this case, apt-get will only install the packages, it doesn't build anything

As for a tutorial: go to the folder "multiphase/interFoam/laminar" in your own copy of the tutorials and run Allrun like this:

./Allrun

When it's finished, check in the folder "damBreakFine" and see what the file "log.interFoam" provides.

[mripepi]

Hello everybody,

I had the same problem about the gcc '--showme:compile' and '--showme:link' errors, when installing OpenFoam 2.0.0 on my 64-bit Ubuntu 12.04 LTS system.
I solved it by adding in the etc/ folder a pref.sh file containing the following line:

export WM_MPLIB=OPENMPI

The pref.sh file will be automatically sourced by the OpenFOAM etc/bashrc, and it will replace the WM_MPLIB=SYSTEMOPENMPI setting.
Alternatively you can try with one of the following setting, depending on the MPI implementation you have on your system:

WM_MPLIB = SYSTEMOPENMPI | OPENMPI | MPICH | MPICH-GM | HPMPI | GAMMA | MPI | QSMPI


Hope this could help somebody else.


Regards,
Matteo

[Annier]

Originally Posted by wyldckat

Greetings Robert and welcome to the forum!

Mmm... indeed, this is odd, but at least you've provided a lot more information than the other forum user

OK, try running the following commands:

which mpirun
mpirun --version

The first one should show you where mpirun is located and the second one should show which version you've got installed.
If neither show any information, then it might not be working due to either one of several reasons:

• Open-MPI didn't install properly, due to some strange reason. It's known to have a glitch during installation, since normal people don't have Infiniband on their computers, but it still comes with support for it pre-packaged...
• Another reason for a bad installation is if the "alternatives" system failed to add an alternative for Open-MPI. I'm not sure what's the solution here, but I'd guess that reinstalling Open-MPI wouldn't hurt.
• Yet another is for said "alternatives" system not having updated until you reboot.

And don't forget to have your system fully up-to-date, just in case...

Best regards,
Bruno

Hi Bruno,
when i typed which mpirun, it showed me

 $ which mpirun
/opt/moose/mpich/mpich-3.2/gcc-opt/bin/mpirun

I run MOOSE framework software in Ubuntu 16.04 and this depends upon MPICH interface and so i plan to work with both MOOSE and OpenFOAM in the same computer.

1. Compilation error with OpenFoam that is based upon OpenMPI

...
gcc: error: unrecognized command line option ‘--showme:compile’; did you mean ‘--assume-compiled’?
g++ -std=c++0x -m64 -Dlinux64 -DWM_ARCH_OPTION=64 -DWM_DP -DWM_LABEL_SIZE=32 -Wall -Wextra -Wold-style-cast -Wnon-virtual-dtor -Wno-unused-parameter -Wno-invalid-offsetof -O3  -DNoRepository -ftemplate-depth-100 -I/opt/openfoam4/src/transportModels/twoPhaseMixture/lnInclude -I/opt/openfoam4/src/transportModels -I/opt/openfoam4/src/transportModels/incompressible/lnInclude -I/opt/openfoam4/src/transportModels/interfaceProperties/lnInclude -I/opt/openfoam4/src/TurbulenceModels/turbulenceModels/lnInclude -I/opt/openfoam4/src/TurbulenceModels/incompressible/lnInclude -I/opt/openfoam4/src/transportModels/immiscibleIncompressibleTwoPhaseMixture/lnInclude -I/opt/openfoam4/src/finiteVolume/lnInclude -I/opt/openfoam4/src/meshTools/lnInclude -I/opt/openfoam4/src/sampling/lnInclude -I../commSplit/lnInclude -I../coupleElmer/lnInclude -DOMPI_SKIP_MPICXX  -IlnInclude -I. -I/opt/openfoam4/src/OpenFOAM/lnInclude -I/opt/openfoam4/src/OSspecific/POSIX/lnInclude   -fPIC -Xlinker --add-needed -Xlinker --no-as-needed Make/linux64GccDPInt32Opt/mhdInterFoam.o -L/opt/openfoam4/platforms/linux64GccDPInt32Opt/lib \
    -limmiscibleIncompressibleTwoPhaseMixture -lturbulenceModels -lincompressibleTurbulenceModels -lfiniteVolume -lfvOptions -lmeshTools -lsampling -L/home/username/OpenFOAM/username-4.1/platforms/linux64GccDPInt32Opt/lib -lPstream -lElmer -lOpenFOAM -ldl  \
     -lm -o /home/username/OpenFOAM/username-4.1/platforms/linux64GccDPInt32Opt/bin/mhdInterFoam
Make/linux64GccDPInt32Opt/mhdInterFoam.o: In function `main':
mhdInterFoam.C:(.text.startup+0xa751): undefined reference to `MPI_Wtime'
mhdInterFoam.C:(.text.startup+0xa7d3): undefined reference to `MPI_Wtime'
mhdInterFoam.C:(.text.startup+0xa83a): undefined reference to `MPI_Wtime'
mhdInterFoam.C:(.text.startup+0xa886): undefined reference to `MPI_Wtime'
/home/username/OpenFOAM/username-4.1/platforms/linux64GccDPInt32Opt/lib/libPstream.so: undefined reference to `MPI_Comm_rank'
/home/username/OpenFOAM/username-4.1/platforms/linux64GccDPInt32Opt/lib/libPstream.so: undefined reference to `MPI_Abort'
/home/username/OpenFOAM/username-4.1/platforms/linux64GccDPInt32Opt/lib/libPstream.so: undefined reference to `MPI_Init'
/home/username/OpenFOAM/username-4.1/platforms/linux64GccDPInt32Opt/lib/libPstream.so: undefined reference to `MPI_Comm_group'
/home/username/OpenFOAM/username-4.1/platforms/linux64GccDPInt32Opt/lib/libPstream.so: undefined reference to `MPI_Comm_split'
/home/username/OpenFOAM/username-4.1/platforms/linux64GccDPInt32Opt/lib/libPstream.so: undefined reference to `MPI_Allreduce'
/home/username/OpenFOAM/username-4.1/platforms/linux64GccDPInt32Opt/lib/libPstream.so: undefined reference to `MPI_Bsend'
/home/username/OpenFOAM/username-4.1/platforms/linux64GccDPInt32Opt/lib/libPstream.so: undefined reference to `MPI_Buffer_detach'
/home/username/OpenFOAM/username-4.1/platforms/linux64GccDPInt32Opt/lib/libPstream.so: undefined reference to `MPI_Recv'
/home/username/OpenFOAM/username-4.1/platforms/linux64GccDPInt32Opt/lib/libPstream.so: undefined reference to `MPI_Wait'
/home/username/OpenFOAM/username-4.1/platforms/linux64GccDPInt32Opt/lib/libPstream.so: undefined reference to `MPI_Test'
/home/username/OpenFOAM/username-4.1/platforms/linux64GccDPInt32Opt/lib/libPstream.so: undefined reference to `MPI_Alltoall'
/home/username/OpenFOAM/username-4.1/platforms/linux64GccDPInt32Opt/lib/libPstream.so: undefined reference to `MPI_Comm_size'
/home/username/OpenFOAM/username-4.1/platforms/linux64GccDPInt32Opt/lib/libPstream.so: undefined reference to `MPI_Waitall'
/home/username/OpenFOAM/username-4.1/platforms/linux64GccDPInt32Opt/lib/libPstream.so: undefined reference to `MPI_Get_count'
/home/username/OpenFOAM/username-4.1/platforms/linux64GccDPInt32Opt/lib/libPstream.so: undefined reference to `MPI_Comm_create'
/home/username/OpenFOAM/username-4.1/platforms/linux64GccDPInt32Opt/lib/libPstream.so: undefined reference to `MPI_Group_incl'
/home/username/OpenFOAM/username-4.1/platforms/linux64GccDPInt32Opt/lib/libPstream.so: undefined reference to `MPI_Probe'
/home/username/OpenFOAM/username-4.1/platforms/linux64GccDPInt32Opt/lib/libPstream.so: undefined reference to `MPI_Send'
/home/username/OpenFOAM/username-4.1/platforms/linux64GccDPInt32Opt/lib/libPstream.so: undefined reference to `MPI_Irecv'
/home/username/OpenFOAM/username-4.1/platforms/linux64GccDPInt32Opt/lib/libPstream.so: undefined reference to `MPI_Comm_free'
/home/username/OpenFOAM/username-4.1/platforms/linux64GccDPInt32Opt/lib/libPstream.so: undefined reference to `MPI_Isend'
/home/username/OpenFOAM/username-4.1/platforms/linux64GccDPInt32Opt/lib/libPstream.so: undefined reference to `MPI_Finalize'
/home/username/OpenFOAM/username-4.1/platforms/linux64GccDPInt32Opt/lib/libPstream.so: undefined reference to `MPI_Buffer_attach'
/home/username/OpenFOAM/username-4.1/platforms/linux64GccDPInt32Opt/lib/libPstream.so: undefined reference to `MPI_Group_free'
/home/username/OpenFOAM/username-4.1/platforms/linux64GccDPInt32Opt/lib/libElmer.so: undefined reference to `MPI_Barrier'
collect2: error: ld returned 1 exit status
/opt/openfoam4/wmake/makefiles/general:132: recipe for target '/home/username/OpenFOAM/username-4.1/platforms/linux64GccDPInt32Opt/bin/mhdInterFoam' failed
make: *** [/home/username/OpenFOAM/username-4.1/platforms/linux64GccDPInt32Opt/bin/mhdInterFoam] Error 1

2. I have tried some options as suggested in earlier post of this thread and this reference of openfoam4 respectively:
(a)

export WM_MPLIB=OPENMPI

in /opt/openfoam4/etc/pref.sh file

(b) https://openfoam.org/download/4-1-ubuntu/

sudo update-alternatives --set mpi /usr/lib/openmpi/include

These options did the change the output of

$ which mpirun

3. How can I adjust for the system to work with both mpich and openmpi by using concepts such as alias?

4. This remains very important purpose as both MOOSE and OpenFoam uses /opt/ directory to implement the mpi interfaces. I am trying to use both softwares in a single computer.

Yours Sincerely,
Anil Kunwar

[Annier]

Hi guys,
I solved this issue by putting alias in the MOOSE environment to load and unload it within the terminal.
1. When moose environment is loaded, mpich is active or switched on over openmpi

username@username-Aspire-1602M:~$ aliasnameofmoose
username@username-Aspire-1602M:~$ which mpirun
/opt/moose/mpich/mpich-3.2/gcc-opt/bin/mpirun
username@username-Aspire-1602M:~$

2. When moose environment is not running, openmpi is working by default

username@username-Aspire-1602M:~$ which mpirun
/usr/bin/mpirun

Cheers,
Yours Sincerely,
Anil Kunwar

[ebringley]

Posting this as it is was a very simple solution for me. Installing OpenFOAM7 with Intel compilers and Intel MPI gave me this error when I forgot to update the etc/bashrc with:

# ~/OepnFOAM/OpenFOAM-7/etc/bashrc
export WM_COMPILER=Icc
export WM_MPLIB=INTELMPI

OpenFOAM is set up for gcc/openmpi by default, but your compiler and mpi library environments are set up for something else (e.g. intel/impi). Correctly telling OpenFOAM what you're using solves the problem. Other packages may be causing the problem as in previous answers.

[Madeinspace]

Originally Posted by ebringley

Posting this as it is was a very simple solution for me. Installing OpenFOAM7 with Intel compilers and Intel MPI gave me this error when I forgot to update the etc/bashrc with:

# ~/OepnFOAM/OpenFOAM-7/etc/bashrc
export WM_COMPILER=Icc
export WM_MPLIB=INTELMPI

OpenFOAM is set up for gcc/openmpi by default, but your compiler and mpi library environments are set up for something else (e.g. intel/impi). Correctly telling OpenFOAM what you're using solves the problem. Other packages may be causing the problem as in previous answers.

Hi Eric,

I am currently having this error when I load intel compiler intel/2018b that is availble in the cluster to install OpenFOAM 3.0.1. I have the following module loaded.

module list
1) GCCcore/7.3.0 4) icc/2018.3.222-GCC-7.3.0-2.30 7) imkl/2018.3.222
2) zlib/1.2.11 5) ifort/2018.3.222-GCC-7.3.0-2.30 8) intel/2018b
3) binutils/2.30 6) impi/2018.3.222

How do you update etc/bashrc? Do I write it at the end of my etc/bashrc file?

export WM_COMPILER=Icc
export WM_MPLIB=INTELMPI

Regards,

[ebringley]

Hi Madeinspace,



I cannot comment on your module set up, because this is cluster specific. You will need to work with your cluster admin to ensure you are using what you think you're using. Under the assumption that you are correctly setting up the shell environment...





The etc/bashrc file is the one included with OpenFOAM (not the /etc/ folder for clarity). You can see a copy of etc/bashrc for OpenFOAM 3 here:

https://github.com/OpenFOAM/OpenFOAM...ter/etc/bashrc
You will need to change the lines between 60 to 100 to the relevant options. These options are passed as variables to shell files in etc/config folder: https://github.com/OpenFOAM/OpenFOAM...ter/etc/config
This means its important that you use the options listed in etc/bashrc when changing the bashrc files.

If you add the options at the end of the etc/bashrc, the variables are set too late to be used in lines 101-256 of the etc/bashrc


Hope that helps!