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OOFEM forum → General Help → Windows parallel version?
Hello everyone,
there is a OOFEM parallel version for Windows? It is supported?
I cannot find any information in the site or in Google; I'd like to learn how to use domain decomposition. Anyone has some stuff to start with?
Thanks
There should be no problems, other than that PETSc might be tedious/difficult to install.
I know PETSc 3.2 moved to CMake, so maybe it has gotten easier to install. And then there is configuring and installing OOFEM itself, but that is no big difference from the sequential build.
After a logn time (one year!), I'm back...
Thank you for the answer, I successfully installed PETSc in Cygwin (my machine works with VS2008 + Ifort 11.1).
I cannot find detailed instruction for what to do to compile the parallel version. I've done the installation guide for windows:
until the phrase "TinyXML2 is required to read input files ..."; I can't really understand this part.
Please help,
thanks a lot
Giovanni
The TinyXML2 library is optional, only necessary for CemHyd support. If you don't need cemhyd then just ignore that section.
Just run the "cmake" command and then the "make" command.
Thanks a lot. And where do I specify the directive USE_PARALLEL="ON" ?
To use oofem in structural analysis may I have to use also ParMETIS? Or PETSc would be enough?
Giovanni
ps.
following the previous procedure to compile oofem, I get oofem.exe with a size of 54.4MB, while the binary on hte official site is only 2.6MB. Why? Have I done something wrong?
Hi. You have likely compiled the debug version, which contains all debug symbols (very useful for developing). If you haven't specified
If you compile for the "Release" target it should be much smaller (if nothing is specified, "Debug" is default) and much much faster.
This is the value for the "CMAKE_BUILD_TYPE" parameter in cmake, which you can set from the command line, or with the graphical interface for CMake
ParMETIS isn't required. SLEPc would be required if you want to run any eigenvalue analysis (in parallel at least)
If you have managed to compile OOFEM, run the tests to see if it works properly, either with CTest directly or "make tests" or equivalent.
thank you for the explanation, now it's clear.
last thing: I tried to compile in cygwin with PETSc (which has been previously compiled with default options). I get the following error on make:
casa2@casa2-PC ~/oofem.git/target
$ mingw32-make.exe
Scanning dependencies of target sm
[ 0%] Building CXX object src/sm/CMakeFiles/sm.dir/structuralelementevaluator.C
.obj
C:\cygwin\home\casa2\oofem.git\src\sm\structuralelementevaluator.C:1:0: warning:
-fPIC ignored for target (all code is position independent) [enabled by default
]
In file included from C:/cygwin/home/casa2/oofem.git/src/oofemlib/engngm.h:66:0,
from C:/cygwin/home/casa2/oofem.git/src/oofemlib/timestep.h:44,
from C:/cygwin/home/casa2/oofem.git/src/oofemlib/material.h:43,
from C:/cygwin/home/casa2/oofem.git/src/oofemlib/crosssection.h
:42,
from C:\cygwin\home\casa2\oofem.git\src\sm\structuralelementeva
luator.C:44:
C:/cygwin/home/casa2/oofem.git/src/oofemlib/petsccontext.h:41:24: fatal error: p
etscvec.h: No such file or directory
compilation terminated.
mingw32-make[2]: *** [src/sm/CMakeFiles/sm.dir/structuralelementevaluator.C.obj]
Error 1
mingw32-make[1]: *** [src/sm/CMakeFiles/sm.dir/all] Error 2
mingw32-make: *** [all] Error 2
Is the file "petscvec.h" missing?
Last thing: what file should be used for the cmake var PETSC_MPI_LIB?
Thanks again,
Giovanni
You have to specify the path to petsc, and the petsc arch and it should work.
I'm on linux so i have petsc compiled into a folder named "/home/micket/petsc-3.3-p5/arch-linux2-c-debug/"
in which case you need to specify exactly
MY_PETSC_DIR /home/micket/petsc-3.3-p5/
MY_PETSC_ARCH arch-linux2-c-debugtogether with "USE_PARALLEL" and "USE_PETSC" set on (you must use version 3.3 of PETSc)
I have never done anything with PETSC_MPI_LIB
I tried with petsc-3.3-p6 and setting MY_PETSC_DIR and MY_PETSC_ARCH as you said; PETSC_MPI_LIB is still required; I set temporarly to the same lib as in PETSC_LIB. Unfortunately the make command causes this error:
C:/cygwin/home/casa2/petsc-3.3-p6/arch-mswin-c-debug/include/petscfix.h:7:13: er
ror: conflicting declaration 'typedef int mode_t'
c:\mingw\bin\../lib/gcc/mingw32/4.6.2/../../../../include/sys/types.h:99:17: err
or: 'mode_t' has a previous declaration as 'typedef _mode_t mode_t'
mingw32-make[2]: *** [src/fm/CMakeFiles/fm.dir/cbs.C.obj] Error 1
mingw32-make[1]: *** [src/fm/CMakeFiles/fm.dir/all] Error 2
mingw32-make: *** [all] Error 2
I think that there is still something wrong compiling with ptesc in windows.
I've never compiled PETSc on Windows, but on linux, PETSc automatically finds my OpenMPI installation. I checked my cache and i have
//Path to a library.
PETSC_MPI_LIB:FILEPATH=/usr/lib/openmpi/lib/libmpi.soI thought PETSc downloaded MPI itself by default, but it seems you have to specify it manually.
Either download and install som MPI library, but the most likely easier version, tell PETSc to download it for you
./configure --download-openmp=yes --download-cholmod=yes(cholmod is an excellent direct solver for positive definite problems, so get that as well, others you can try is UMFPACK, PASTIX, SUPERLU, ...)
Hi Mikael, thank again for your support.
The command arguments:
--download-openmp=yes --download-cholmod=yes
don't work in Cygwin, but I was able to install the packages via Cygwin's setup.exe. I'm trying to recompile, using also libmpi.dll.
In the meanwhile, I'm trying to get a compiled version via VS2008. IML support is still missing, I'm trying to resolve. In the meanwhile, I kindly ask you how I can launch a parallel analysis and, if you have it, a test file for a parallel run. My final aim is to bring the parallel analysis with oofem in Windows.
Giovanni R.
I made a typo, it should have been
--download-openmpi=yesbut you should be able to specify the library manually as well.
I highly recommend using graphical, or ncurses interface for CMake, which will show you all the options, where you can enable IML support (IML is very slow in my experience).
OOFEM has plenty of tests available, including parallel tests located in test/partest/
Specify to OOFEM to run in parallel by using the "-p" flag
mpirun -np 4 ./oofem -p -f path/to/oofem/tests/partests/planestress/planestress.oofem.inAs you can see from the cmake GUI there is also support for OpenMP (not to be confused with OpenMPI), and the PastiX solver in PETSc also runs in shared memory, so for a single machine you don't need to subdivide the domain as with MPI.
Thanks again. PETSc is fine now, but the oofem make cannot ho ahead. Now the error is the following:
C:/cygwin/home/Giovanni/petsc-3.3-p6/arch-mswin-c-debug/include/petscfix.h: At global scope:
C:/cygwin/home/Giovanni/petsc-3.3-p6/arch-mswin-c-debug/include/petscfix.h:7:13: error: conflicting declaration 'typedef int mode_t'
c:\mingw\bin\../lib/gcc/mingw32/4.6.2/../../../../include/sys/types.h:99:17: error: 'mode_t' has a previous declaration as 'typedef _mode_t mode_t'
mingw32-make[2]: *** [src/sm/CMakeFiles/sm.dir/lspace.C.obj] Error 1
mingw32-make[1]: *** [src/sm/CMakeFiles/sm.dir/all] Error 2
mingw32-make: *** [all] Error 2
I attach the cmakecache:
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This actually doesn't have anything to do with OOFEM.
It is a petsc header which conflicts with a mingw header.
This seems like something petsc is supposed to look for when configuring. My only guess is that you configured/compiled PETSc with different compiler suite/version, for which the fixes was missing.
I used the guide at this url:
http://www.mcs.anl.gov/petsc/documentat … ml#windows
In particular, I used the command:
"./configure --with-cc='win32fe cl' --with-fc='win32fe ifort' --with-cxx='win32fe cl' --download-f-blas-lapack"
So that's a PETSc problem (PETSc website suggests to compile it on windows using Intel Fortran and VS2005); I suppose that the "parallel" oofem hasn't tried on windows yet.
However, many thanks for your help,
Giovanni
The problem is that mingw32 and intels cl are incompatible. You probably could modify "petscfix.h" (which is automatically generated when you run ./configure) to remove this conflicts.
Though I bet you could use mingw32 to compile PETSc as well.
Since you have the Intel compilers (which are usually great), you should be able to use them to compile OOFEM as well.
To tell CMake to do use a different compiler, add the following flag
cmake -DCMAKE_CXX_COMPILER='cl' /path/to/oofem/1. Whenever you try to change compilers, you need to remove the cache first, so delete CMakeCache.txt
2. I'm not sure what the commands are for intels compiler suite. You might need some other command than "cl"
3. I'm not sure what that win32fe thing does either.
And you're correct, I don't think anyone has compiled a parallel version of OOFEM under windows yet, exactly because PETSc is such a big inconvenience on that platform. Any external libraries are a pain to work with under windows.
Worth pointing out is that you can actually use OpenMP (experimental support) without any external libraries, but it will only assemble the system in parallel. The actual solvers included in OOFEM (which are slower than what you can get with PETSc) run sequentially.
I tried both (compiling all with intel compiler, compiling all with mingw), there are too many errors in both cases. I report the error that I get when I try compiòling with intel. Using cmake, the following definitions are missing:
PETSC_DL_LIB (ADVANCED)
linked by target "liboofem_static" in directory C:/cygwin/home/s133674/oofem-2.2
PETSC_ESMTP_LIB (ADVANCED)
linked by target "liboofem_static" in directory C:/cygwin/home/s133674/oofem-2.2
PETSC_GCC_EH_LIB (ADVANCED)
linked by target "liboofem_static" in directory C:/cygwin/home/s133674/oofem-2.2
PETSC_GCC_S_LIB (ADVANCED)
linked by target "liboofem_static" in directory C:/cygwin/home/s133674/oofem-2.2
PETSC_GFORTRAN_LIB (ADVANCED)
linked by target "liboofem_static" in directory C:/cygwin/home/s133674/oofem-2.2
PETSC_MPI_F90_LIB (ADVANCED)
linked by target "liboofem_static" in directory C:/cygwin/home/s133674/oofem-2.2
PETSC_M_LIB (ADVANCED)
linked by target "liboofem_static" in directory C:/cygwin/home/s133674/oofem-2.2
PETSC_PTHREAD_LIB (ADVANCED)
linked by target "liboofem_static" in directory C:/cygwin/home/s133674/oofem-2.2
PETSC_X11_LIB (ADVANCED)
linked by target "liboofem_static" in directory C:/cygwin/home/s133674/oofem-2.2
Just a question: compiling petsc with mingw I get the libraries with the extension ".a" and not ".lib" as I get with intel compilers. To add petsc to oofem in windows, these libraries have to be the extension ".lib" for sure?
Thanks,
Giovanni
ps
can you provide the project files for visual studio to compile oofem? I think it will be better for me to get the petsc libraries and add them in VS. In this old topic:
http://www.oofem.org/forum/viewtopic.php?id=374
I got a compiled version using VS only, but in the version 2.2 of oofem many things have changed.
Hi,
under windows, when you have cmake installed, cmake can create Visual Studio solution for you.
under windows, when you have cmake installed, cmake can create Visual Studio solution for you.
Hi, I've already tried in 2pcs, in the former it simply doesn't work (I have visual studio 2008 pro installed and I cannot install the SDK, cmake tells me that cl.exe cannot compile); in the second pc I got the SLN file but I cannot understand (because I'm not a C++ developer) how to add the PARALLEL flags (and for PETSC and MPI too).
Giovanni
* What is this SDK you mention?
* What test did the compiler fail to compile?
* A SLN file if a visual studio project, so I guess it did work on the second PC then?
* When configuring OOFEM with the CMake GUI, it'll show you all the configuration settings for OOFEM, including "USE_PARALLEL", "USE_PETSC", "MY_PETSC_DIR", "MY_PETSC_ARCH", and many more. I don't even think it is possible to miss these. Configure once, make your choices, configure again then generate your project files.
I haven't tried VS2008, but it definitely works for VS2010 and VS2012.
The problems you pointed out before
PETSC_DL_LIB (ADVANCED)
linked by target "liboofem_static" in directory C:/cygwin/home/s133674/oofem-2.2doesn't actually say that anything is wrong. The only thing that comes to mind if you have cmake problems is that you might have forgotten to clear the cache what you have done something like changing compilers.
As for static libraries; the mingw linker seems to prefer lib*.a extensions instead of *.lib. If you are working with mingw, you need to use the mingw linker as well.
* The SDK is that for Windows 7 and Server 2008
* I cannot know what test fails to compile, the make test simply hangs once started
* the SLN (which is solution file, not a single project file) works on the second machine
* my difficulty is that, configuring "USE_PARALLEL", "USE_PETSC", "MY_PETSC_DIR", "MY_PETSC_ARCH", when opening the SLN file, VS tell me that "there are dependencies that cannot be loaded".
Have you tried in VS2010 to compile the parallel version?
I'll give another try and reports to you a more detailed error log...
You can find this error logs in the target directory under CMakeFiles/CmakeError.log and possibly CMakeFiles/CMakeOutput.log
And , no, I haven't tried VS2010 with parallel support, because PETSc requires cygwin.
I was under the impression that you had managed to connect PETSc with Visual Studio since you said it was easier to work with.
Technically, there is nothing from OOFEM's point of view that requires cygwin. All we do is rely on the cmake configuration file that PETSc produces.
The file is located in petsc-version/your-configured-arch/conf/PETScConfig.cmake
This is a file produces by PETSc that sets all the external libraries and such, and OOFEM will happily use those (as well as the PETSc headers of course).
CMake tends to use full paths, so I don't think it's a problem with not actually finding them, so perhaps it doesn't like the format of the libraries? I'm really just guessing at this point since I dont have a windows machine to try it out on.
Just, to confirm a few things;
1. Without parallel + petsc on, can you get OOFEM to work?
2. When entering USE_PARALLEL + etc., does configure + generate from CMake work fine (without warnings/errors) ?
To both questions:
1. yes
2. not completely, I have to trick some values to get out from "Cmake" with no errors or warnings.
When I'll have more time, I'll post a complete error report.
After a long time, I'm trying again. Now, after entering USE_PARALLEL + PETSC, CMake works fine. I get 2 different situations:
1 - when I compile in VS 2008 9.0 from the major release source (ZIP file in OOFEM site), I get a lot errors because the file "petsccontext.h" is missing. I cannot understand where to specify in the project the inclusion folder;
2 - when trying from the source downloaded via GIT (maybe not updated to the actual version), I get a lot of errors again because there are sintax errors in "petscvec.h" and "petscsysvec.h".
In both cases, I tried PETSC version 3.3-p6 and 3.4.3 (the most recent).
Any suggestion or clue?
thanks
ps.
during one of my several test with oofem source 2.3 (from ZIP file), on my laptop CMake hanged on the error "PKG_CONFIG_EXECUTABLE not found". Does it depend on the installed GNU compilers?
Hi
First, I'd like to mention that the latest version from GIT doesn't actually require PETSc to run in parallel. However(!) most problems will require a parallel solver, and there PETSc is the only option (or maybe the FETI solver could be used? I don't know anything about that one).
Building parallel without PETSc might be useful in some cases though, like for explicit dynamic simulations.
Also, shared memory computers can use OpenMP for parallel computations
PETSc support under windows has been never been tested, and I wouldn't expect it to work.
1. I don't know why that happens. petsccontext.h is included in src/oofemlib/
2. "petscvec.h" and "petscsysvec.h" are header files from PETSc. I don't know what to say about error messages there.
I use PKG_CONFIG for configuring the compilation and linking information from PETSc.
Basically two things;
1. Find the include directories ${PS_PETSC_INCLUDE_DIRS}
2. Find all the external libraries petsc was compiled with ${PS_PETSC_LIBRARIES} and ${PC_PETSC_LIBRARY_DIRS}.
You should be able to hardcode those options directly into the CMakeLists.txt file though, or you might be able to get pkg_config running under windows (i don't know how that works).
Doesn't MinGW include a pkg_config executable? Anyway, pkg_config doesn't do anything difficult.
I tried asking the PETSc developers to make generate proper cmake files that could be used, but they just started berating me for making such a "stupid suggestion", so using PKG_CONFIG was the only option.
OOFEM forum → General Help → Windows parallel version?
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