Using native MPI libraries
 

I was trying to build for Altix 4000, i found a patch for compiling with intel icc10 , i dont want to build the WM.../lib/openmpi/libPstrem.so nor link with the WM../src/openmpi/lib/*,

Instead we have our own mpi implementation (sgi mpi libraries) , any idea which files/lines I have to change or create (in rules or bashrc and .bashrc ) ...

Any help will be greatly appreciated http://www.cfd-online.com/OpenFOAM_D...part/happy.gif

In the bashrc you'll have to s
 

In the bashrc you'll have to see another default mpi implementation.

In the .bashrc you'll have to set the path/libs accordingly and set variables such as SGIMPI_ARCH_PATH=...

In the wmake/rule/linuxXXXX/
you'll need to add a rule for mplibSGIMPI

In src/Pstream/Allwmake you'll need to ajust the if [ ... ] to include your implementation.


Good luck with rebuilding.

thanks I never will guess the
 

thanks I never will guess the src/Pstream/Allwmake part i will try during the weekend i hope it works !

Hi foamers i am follow your s
 

Hi foamers i am follow your steps , lets see

I think i am close, to test I link with the mpi implented by altix and the gcc 4.2.0


the Pstream is built using our libmpi from sgi altix
ldd libPstream.so returns
...
libmpi.so => /lrz/sys/mpi_altix/lib/libmpi.so (0x2000000800080000)
...

It compiles the whole buch of libraries in lib/linuxIA64Gcc with no error -- all of them --
and these are linked in turn with the new libPstream.so. However, when it tries to compile the applications (cd solver; ./wmake all ...)it dies with the 1st one (i tried to compile some others at ramdon )

i get the following from the linker
/lrz/sys/mpi_altix/lib/libPstream.so: undefined reference to `MPI::Is_initialized()'
/lrz/sys/mpi_altix/lib/libPstream.so: undefined reference to `op_intercept(void*, void*, int*, unsigned int*)'
/lrz/sys/mpi_altix/lib/libPstream.so: undefined reference to `PMPI::Comm::mpi_comm_map'
/lrz/sys/mpi_altix/lib/libPstream.so: undefined reference to `MPI:http://www.cfd-online.com/OpenFOAM_D...part/proud.gifp::Init(void (*)(void const*, void*, int, MPI::Datatype const&), bool)'
/lrz/sys/mpi_altix/lib/libPstream.so: undefined reference to `MPI:http://www.cfd-online.com/OpenFOAM_D...part/proud.gifp::Free()'
/lrz/sys/mpi_altix/lib/libPstream.so: undefined reference to `PMPI::Comm::ignored_status'
/lrz/sys/mpi_altix/lib/libPstream.so: undefined reference to `PMPI::Intracomm::current_op'
/lrz/sys/mpi_altix/lib/libPstream.so: undefined reference to `PMPI::Request::ignored_status'
collect2: ld returned 1 exit status

It is clear that libPstream is missing some functions, any idea how come this happened and if there is a solution

Hi foamers i am following you
 

Hi foamers i am following your steps , lets see

I think i am close, to test I link with the mpi implented by altix and the gcc 4.2.0


the Pstream is built using our libmpi from sgi altix
ldd libPstream.so returns
...
libmpi.so => /lrz/sys/mpi_altix/lib/libmpi.so (0x2000000800080000)
...

It compiles the whole buch of libraries in lib/linuxIA64Gcc with no error -- all of them --
and these are linked in turn with the new libPstream.so. However, when it tries to compile the applications (cd solver; ./wmake all ...)it dies with the 1st one (i tried to compile some others at ramdon )

i get the following from the linker
/lrz/sys/mpi_altix/lib/libPstream.so: undefined reference to `MPI::Is_initialized()'
/lrz/sys/mpi_altix/lib/libPstream.so: undefined reference to `op_intercept(void*, void*, int*, unsigned int*)'
/lrz/sys/mpi_altix/lib/libPstream.so: undefined reference to `PMPI::Comm::mpi_comm_map'
/lrz/sys/mpi_altix/lib/libPstream.so: undefined reference to `MPI:http://www.cfd-online.com/OpenFOAM_D...part/proud.gifp::Init(void (*)(void const*, void*, int, MPI::Datatype const&), bool)'
/lrz/sys/mpi_altix/lib/libPstream.so: undefined reference to `MPI:http://www.cfd-online.com/OpenFOAM_D...part/proud.gifp::Free()'
/lrz/sys/mpi_altix/lib/libPstream.so: undefined reference to `PMPI::Comm::ignored_status'
/lrz/sys/mpi_altix/lib/libPstream.so: undefined reference to `PMPI::Intracomm::current_op'
/lrz/sys/mpi_altix/lib/libPstream.so: undefined reference to `PMPI::Request::ignored_status'
collect2: ld returned 1 exit status

It is clear that libPstream is missing some functions, any idea how come this happened and if there is a solution

This (linking the libraries, n
 

This (linking the libraries, not linking the applications) happens because when linking a library the linker says "can't find this symbol, propably someone else will take care of it", but when linking an application it must find a definition for _every_ symbol.

Maybe there are some additionaly libs that have to be linked to PStream (mip_cxx.so or such stuff). Check the examples that come with your MPI-implementation

Another brute force-way to find the offenders is
grep PMPI::Comm::ignored_status /usr/lib
(or wherever you expect them to be found)

thanks i found which librari
 

[SOlVED] thanks i found which libraries were missing for c++ http://www.cfd-online.com/OpenFOAM_D...part/happy.gif

How did you solve that?

Similar error here whilie trying the compile applications with intel mpi:

Any suggestions?

Thanks.

How Solved
 

Hi, how did you solve it. Please share.

Quick answer: That was almost a lifetime ago, in an Internet temporal reference...

It's easier if you provide more details about your problem. Specifically which MPI version and OpenFOAM versions that you're using, along with any changes you might have already done in trying to fix this, so that it's easier to diagnose the problem.

Linking libraries
 

Thanks wyldckat for a quick response.
I would provide the max possible details for your convenience.

My Foam version of 2.3.0.

Major settings in /OpenFOAM/etc/cshrc (file attached) are:
I believe the MPI libraries are taken from /opt/sgi/mpt/mpt-2.01 as I can see following line in compilation screen output:
The files included from /opt/sgi/mpt/mpt-2.01 are shown in attached screenshot.

Other files settings related file such as /OpenFOAM/etc/config/settings.csh, ~/.cshrc etc.

System is having intel compiler by default. So, I execute following command before compiling to avoid error of type 'This intel math.h is for intel compilers only'.
Compilation log is attached at https://www.dropbox.com/s/b4np7p7ctp...g_new.txt?dl=0
Compilation screen output log is attached at https://www.dropbox.com/s/6754u4qxm4...utLog.txt?dl=0

Other system configuration:
uname -m
echo $WM_ARCH
icc --version
icc --version

Greetings Rahul,

The first note I want to make is that you can redirect all of the output (standard+error outputs) into a single file in csh by using ">&", for example:
I say this because the file "make_log_new.txt" that you provided via Dropbox does not have any warning messages nor error messages, which seems to imply that something went wrong and wasn't logged. The other detail in that file is that it's using Open-MPI and not SGI's MPI; the reason seems to be related to the detail I refer to later below.


From the "screenOutputLog.txt", the following error is still occurring:
Which seems to imply that you didn't unload Intel's compiler before this build.


As for the other files, in the file "system-cshrc.txt" that you provided, has the following line:
You should either change "WM_MPLIB=OPENMPI" to "WM_MPLIB=SGIMPI", or simply remove it from that line.

Another detail in that file "system-cshrc.txt", is that these lines will not work from here:

• and there is a typo in the last line "linux64GccDPO", which probably should be "linux64GccDPOpt".

The reason why it will not work from here is because these will be replaced/removed when you source OpenFOAM's "cshrc" file. Which means that if you want to do these changes, you need to place them at the end of "OpenFOAM-2.3.0/etc/cshrc".


Another detail that is intriguing me is that the files you've provided have a log of backslashes '\'. Is that because of how you copied the information from the remote connection or perhaps due to the text editor that you are using remotely?
Because the original lines above are shown as follows from the files you've provided:

After you've solved these details, hopefully the build will work as intended.

Best regards,
Bruno

Results after suggested changes
 

Thanks Bruno for a quick response. Yes, you are right I am trying to compile on a remote system.


Following things I have done:
1. unloaded the intel compiler, In fact marked it to not to load later as well.

2. Changed
3. Commented following lines
4. After that I executed following two commands for precaution
5. used mpi-selector-menu command which to setup following:
6. Created the logfile by following command:
The file is attached at https://www.dropbox.com/s/24degn98hhvib7d/make.log?dl=0

Still logfile is showing several errors especially related to openmpi, undefined references and declarations. Also, it still shows inclusion of openmpi-1.6.5.

Quick answer: Whenever you change the main ".cshrc" or ".bashrc" files, you should start a new terminal, to ensure you have a clean environment. Therefore, when you executed csh, it very likely inherited the shell environment from the parent csh shell from which you launched the new one.

OK, but a new error rose up, which is due to the old GCC version that you're trying to use (GCC 4.3):
If you check this page: http://openfoamwiki.net/index.php/In...ibility_Matrix - er, the wiki page is having a rendering problem at the moment... This specific error is explained here: http://www.cfd-online.com/Forums/ope...edhat-el5.html


Based on the GCC version and environment that you're using, I'm guessing that you're dealing with CentOS 5.x or RHEL 5.x. You can find detailed instructions on how to build a custom GCC version with OpenFOAM 2.3.0 here: http://openfoamwiki.net/index.php/In...EL#CentOS_5.10
From there you will need to:

• Use step #7.
• Use the option "foamCompiler=ThirdParty" from the step #8.
• Use steps #9 to #15, which will solve several of the problems that you are having right now.

SUSE Enterprise OS
 

Thanks wyldckat for a quick answer. I got some lead towards the further attempts. I will try with your suggestion for CentOS and will update in the post soon. Anyway my remote cluster is SUSE Enterprise, details are here:

cat /proc/version
icc --version
lsb_release -a
uname -m

Quick answer: Sorry, I didn't manage to get my hands on a trial version of SLES or SLED 11, I only managed SLED/SLES 12 (which have GCC 4.4), for which I wrote instructions here: http://openfoamwiki.net/index.php/In...nux_Enterprise

Incompatible file inclusion issue
 

Hi wyldckat and Bruno

Sorry to bother again.

As per the link http://openfoamwiki.net/index.php/In...EL#CentOS_5.10, I have successfully moved up to step 13. However, stucking at step 14 while doing makeCGAL with
I think its attempting to include libXext.so from /usr/lib/, but libXext.so.6 is also available in /usr/lib64/. Therefore, resulting in issue related to incompatible library files as files in /usr/lib/ are 32 bit. But system is trying to built in 64 bit. I can say this because it also included /usr/lib64/libX11.so and /usr/lib64/libQtOpenGL.so;/usr/lib64/libQtGui.so
How, to force it to use only 64 libraries.

The prominent snippets of log are:
I have made several attempts to resolve the issue by taking help from internet. But no luck.
The make and log file for your reference is attached. Please take a look.
Attachment 52399

Attachment 52400

Partially Solved
 

Some nice person's previous post in the forum helped me handling the error. Actually, I am installing OpenFOAM in remote cluster. And, there I need minimal installation. Pre/post processing I have to do locally. So, I believed most of the thirdparty packages that are troubling me are not actually required. And, troubling because of not having root/administrative privilege.

Here https://www.cfd-online.com/Forums/op...myhexmesh.html, I found that troublemaking CGAL package which eventually requires gmp and mpfr are required for foamHexMesh tutorial which I don't require at least for time being at least. So, tried some hacks to prevent make of foamyHexMesh. Certainly, commented following lines in OpenFOAM/OpenFOAM-2.3.0/applications/utilities/mesh/generation/Allwmake file:

Proceeding further with the steps suggested by wyldckat, I did:

Now, there is a new issue:

Help
 

Can anyone help me resolve the said issues.

Quick answer: Sorry, I didn't manage to get anything done this past weekend due to an annoying cold.

The error regarding "SRFIcoFoam.C" is very strange, because OpenFOAM 2.3.0 does not have that file anywhere in its source code. Which seems to suggest that this file refers to some custom code that was likely designed for some other version of OpenFOAM and not for 2.3.0.

Therefore, I strongly suggest that you first pull out the folder that contains that file, from the OpenFOAM standard folders. Because it would be preferable that you first manage to have OpenFOAM 2.3.0 fully built and only then move to the next issue regarding custom code.

Furthermore, it would be helpful to know a bit more about that custom code, in order to know how to diagnose it and change it to properly work with OpenFOAM 2.3.0.

[solved]
 

Sorry to bother everyone but it was not primarily an error. I found that the SRFIcoFoam codes were modified to suit installation. This was done by people from where I obtained the OpenFOAM source. I also found that SRFIcoFoam is not an important solver (at least for me) as it no more available with new versions of the OpenFOAM. So, I decided to drop it off. I simply deleted the SRFIcoFoam source directory and everything then worked fine.