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: Quote:
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,
Quote:
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: Code:
gcc g++ flex So, if you run this command: Code:
ls -l $MPI_ARCH_PATH Code:
drwxr-xr-x 7 user user 4096 2010-10-09 01:50 ./ 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: Code:
configure: error: no vtf3.h found; check path for VTF3 package first... 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:
Best regards, Bruno |
Hi Bruno,
me again 1.5 years later. I've got new pc with new Debian Code:
(Linux version 2.6.32-5-amd64 (Debian 2.6.32-45) (dannf@debian.org) (gcc version 4.3.5 (Debian 4.3.5-4) )) Quote:
Quote:
Quote:
Best regards, Ilya |
Hi Ilya,
I'll need more info about which Debian version you're using. Try this command: Code:
cat /etc/lsb-release Best regards, Bruno |
1 Attachment(s)
Hi Bruno,
there is no lsb-release in /etc But: Code:
$ lsb_release -a 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:
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): Code:
sudo apt-get install libscotch-dev libopenmpi-dev ____ 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 Quote:
Quote:
Quote:
2) Quote:
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 : And like I wrote before, the trick for your system should be: Quote:
Best regards, Bruno |
Hi Bruno,
Quote:
Quote:
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: Quote:
Best regards, Ilya |
Hi Ilya,
This should be enough, without having to rebuild the whole OpenFOAM source: Code:
src Bruno |
1 Attachment(s)
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 |
OK, then there must be a conflict of MPI versions... what do these commands output:
Code:
mpirun --version |
Hi,
sorry, I didn't notice your answer because of the new page. Quote:
Quote:
Quote:
Quote:
Quote:
Ilya |
Hi Ilya,
OK, then the "LD_LIBRARY_PATH" variable must be contaminated - what does this output :confused:: Code:
echo $LD_LIBRARY_PATH Best regards, Bruno |
Hi,
here it comes: Quote:
Best regards, Iyla |
Hi Ilya,
Took me a while to get back to you... OK, edit OpenFOAM's "etc/bashrc" file once again and search for these lines: Code:
#- Clean LD_LIBRARY_PATH Code:
cleaned=`$foamClean "$LD_LIBRARY_PATH" "/usr/local/mpich/lib/"` && LD_LIBRARY_PATH="$cleaned" Code:
cleaned=`$foamClean "$LD_LIBRARY_PATH" "/usr/local/mpich/lib/:/opt/intel/Compiler/11.1/069/lib/intel64:/opt/intel/Compiler/11.1/069/lib/intel64/"` && LD_LIBRARY_PATH="$cleaned" Again, better start a new terminal. Rebuilding only "Pstream" is also a good idea, after you check if the variable mentioned before is cleaned. If you still have problems, the environment variable "PATH" is also a suspect ;) Best regards, Bruno |
Hi Bruno,
thanks a lot, step by step we are getting closer. After cleaning the LD_LIBRARY_PATH the error reduced to Quote:
Quote:
Best regards, Ilya |
Do any of these appear:
Code:
which mpirun If not, then try building again OpenFOAM's own Open-MPI 1.5.3 ;) Don't forget to switch back from SYSTEMOPENMPI to OPENMPI in "etc/bashrc". |
mpirun -> negative; but mpicc (2,4,6) is still there.
Quote:
|
Try these again, still with the SYSTEMOPENMPI:
Quote:
Code:
sudo update-alternatives --config mpirun |
Ok, here it is:
Quote:
|
You can also check:
Code:
update-alternatives --config mpirun Code:
ls -l /usr/bin/mpirun.* |
it doesn't look good:
Quote:
Quote:
|
Then switch back to the normal OPENMPI option in OpenFOAM's etc/bashrc file and start a new terminal.
Then: Code:
foam3rdParty |
1 Attachment(s)
Unfortunately not. There are still the same errors.
|
I think it is mpicc's fault here... but I don't know how to disable it without removing it :(
By the way, does this output anything: Code:
echo $GREP_OPTIONS |
Quote:
|
Hi Ilya,
It's taking me a while in trying to reproduce the same error. And the "debian-security" server seems to be offline for a couple of minutes to help... I did find something interesting: seems that you might have installed on your machine the package "mpi-default-dev" but not the "mpi-default-bin". Without the second one, it's not possible to use the system Open-MPI properly. To check if they are installed: Code:
dpkg-query -s mpi-default-bin Code:
Status: install ok installed This command can help figure out if there are other surrounding packages: Code:
dpkg-query -W "*mpi*" Code:
synaptic Best regards, Bruno |
Hi Ilya,
And I'm out of ideas. I haven't been able to reproduce the problem you're having. My guess would be that the other application to blame could be the Icc compiler that is installed in your machine. Nonetheless, my suggestion is to:
Bruno |
Hi Bruno,
first thanks a lot for the time you spent trying to figure out, what's goin on here. None of the mpi-default-... packages is installed. Unfortunately though, I don't even have the sudo privileges, so I'll have to beg our admins at Monday to install them. I wish you a nice weekend! Ilya |
Hi Ilya,
Maybe instead of begging for installing those packages, then perhaps it would be best to request more information about what's installed in the machine and also ask which packages could be affecting OpenFOAM's proper installation! Over this long attempt to get things running, we've found that:
Nonetheless, in the end, you might have to switch to building with Icc instead of Gcc, which OpenFOAM supports, as long as the Icc version isn't too old... edit: and have a nice weekend as well :) Best regards, Bruno |
All times are GMT -4. The time now is 01:07. |