[Dune] using metis & parmetis creates a build problem
Benedikt Oswald
benedikt.oswald at lspr.ch
Fri May 16 13:37:13 CEST 2014
Dear Dune, it seems that we are still plagued by this ‘old’ problem;
mpicxx -std=c++11 -DHAVE_CONFIG_H -I. -I../../.. -I/Users/oswald/gitwork/hades-pure-dune/dune-common -I/Users/oswald/gitwork/hades-pure-dune/dune-common -I/Users/oswald/gitwork/hades-pure-dune/dune-geometry -I/Users/oswald/gitwork/hades-pure-dune/dune-geometry -I/Users/oswald/gitwork/hades-pure-dune/dune-grid -I/Users/oswald/gitwork/hades-pure-dune/dune-grid -I/Users/oswald/gitwork/hades-pure-dune/dune-istl -I/Users/oswald/gitwork/hades-pure-dune/dune-istl -DMPICH_IGNORE_CXX_SEEK -O2 -g0 -DHAVE_SUPERLU_DIST -I/Users/oswald/extlib/superludist/3.3/openmpi/1.6.5/gcc/4.8.1/SRC -I/Users/oswald/extlib/boost/1.55.0/gcc/4.8.1/include -I/Users/oswald/extlib/petsc/3.4.2/openmpi/1.6.5/gcc/4.8.1/include -DHAVE_PETSC -I/Users/oswald/gitwork/hades-pure-dune/dune-common -I/Users/oswald/gitwork/hades-pure-dune/dune-common -I/Users/oswald/gitwork/hades-pure-dune/dune-geometry -I/Users/oswald/gitwork/hades-pure-dune/dune-geometry -I/Users/oswald/gitwork/hades-pure-dune/dune-grid -I/Users/oswald/gitwork/hades-pure-dune/dune-grid -I/Users/oswald/gitwork/hades-pure-dune/dune-istl -I/Users/oswald/gitwork/hades-pure-dune/dune-istl -I/Users/oswald/extlib/openmpi/1.6.5/gcc/4.8.1/include -DMPIPP_H -DENABLE_MPI=1 -DWITH_INDEX_SETS -DMPICH_IGNORE_CXX_SEEK -O2 -g0 --no-strict-aliasing -MT pamgtest1-pamgtest1.o -MD -MP -MF .deps/pamgtest1-pamgtest1.Tpo -c -o pamgtest1-pamgtest1.o `test -f 'pamgtest1.cc' || echo './'`pamgtest1.cc
In file included from /Users/oswald/gitwork/hades-pure-dune/dune-istl/dune/istl/matrixredistribute.hh:5:0,
from /Users/oswald/gitwork/hades-pure-dune/dune-istl/dune/istl/paamg/transfer.hh:7,
from /Users/oswald/gitwork/hades-pure-dune/dune-istl/dune/istl/paamg/amg.hh:10,
from pamgtest1.cc:23:
/Users/oswald/gitwork/hades-pure-dune/dune-istl/dune/istl/repartition.hh:791:67: error: ‘idxtype’ has not been declared
inline bool isValidGraph(std::size_t noVtx, std::size_t gnoVtx, idxtype noEdges, idxtype* xadj,
^
/Users/oswald/gitwork/hades-pure-dune/dune-istl/dune/istl/repartition.hh:791:84: error: ‘idxtype’ has not been declared
inline bool isValidGraph(std::size_t noVtx, std::size_t gnoVtx, idxtype noEdges, idxtype* xadj,
^
/Users/oswald/gitwork/hades-pure-dune/dune-istl/dune/istl/repartition.hh:792:28: error: ‘idxtype’ has not been declared
idxtype* adjncy, bool checkSymmetry)
^
/Users/oswald/gitwork/hades-pure-dune/dune-istl/dune/istl/repartition.hh: In function ‘bool Dune::isValidGraph(std::size_t, std::size_t, int, int*, int*, bool)’:
/Users/oswald/gitwork/hades-pure-dune/dune-istl/dune/istl/repartition.hh:796:9: error: ‘idxtype’ was not declared in this scope
for(idxtype vtx=0; vtx<(idxtype)noVtx; ++vtx) {
^
/Users/oswald/gitwork/hades-pure-dune/dune-istl/dune/istl/repartition.hh:796:17: error: expected ‘;’ before ‘vtx’
for(idxtype vtx=0; vtx<(idxtype)noVtx; ++vtx) {
^
/Users/oswald/gitwork/hades-pure-dune/dune-istl/dune/istl/repartition.hh:796:24: error: ‘vtx’ was not declared in this scope
for(idxtype vtx=0; vtx<(idxtype)noVtx; ++vtx) {
^
/Users/oswald/gitwork/hades-pure-dune/dune-istl/dune/istl/repartition.hh:796:37: error: expected ‘;’ before ‘noVtx’
for(idxtype vtx=0; vtx<(idxtype)noVtx; ++vtx) {
^
/Users/oswald/gitwork/hades-pure-dune/dune-istl/dune/istl/repartition.hh:796:42: error: expected ‘)’ before ‘;’ token
for(idxtype vtx=0; vtx<(idxtype)noVtx; ++vtx) {
^
/Users/oswald/gitwork/hades-pure-dune/dune-istl/dune/istl/repartition.hh:796:46: error: ‘vtx’ was not declared in this scope
for(idxtype vtx=0; vtx<(idxtype)noVtx; ++vtx) {
^
/Users/oswald/gitwork/hades-pure-dune/dune-istl/dune/istl/repartition.hh:796:49: error: expected ‘;’ before ‘)’ token
for(idxtype vtx=0; vtx<(idxtype)noVtx; ++vtx) {
^
pamgtest1.cc:254:1: error: expected ‘}’ at end of input
}
^
pamgtest1.cc: At global scope:
pamgtest1.cc:254:1: error: expected ‘}’ at end of input
we use the following opts file:
CONFIGURE_FLAGS="DUNE_LDFLAGS='-L$HOME/extlib/superludist/3.3/openmpi/1.6.5/gcc/4.8.1/lib -lsuperludist -L$HOME/extlib/parmetis/4.0.3/openmpi/1.6.5/gcc/4.8.1/lib -lparmetis -L$HOME/extlib/metis/5.1.0/gcc/4.8.1/lib -lmetis -framework vecLib '
CXX='mpicxx' CC='mpicc' LD='mpicxx' F77='mpif77'
CXXFLAGS='-DMPICH_IGNORE_CXX_SEEK -O2 -g0 --no-strict-aliasing '
CPPFLAGS='-DMPICH_IGNORE_CXX_SEEK -O2 -g0 -DHAVE_SUPERLU_DIST -I$HOME/extlib/superludist/3.3/openmpi/1.6.5/gcc/4.8.1/SRC '
CFLAGS='-DMPICH_IGNORE_CXX_SEEK -O2 -g0 -fomit-frame-pointer --no-strict-aliasing '
--enable-hades3deltd
--enable-hades3dfetd
--enable-hades3ddges
--enable-hades3ddgfd
--enable-hades3dfeqs
--enable-hades3dfefd
--disable-documentation
--enable-petsc
--enable-parallel
--enable-debug-output
--enable-fieldvector-size-is-method
--enable-experimental-grid-extensions
--without-gmp
--with-boost='$HOME/extlib/boost/1.55.0/gcc/4.8.1'
--with-metis='$HOME/extlib/metis/5.1.0/gcc/4.8.1'
--with-parmetis='$HOME/extlib/parmetis/4.0.3/openmpi/1.6.5/gcc/4.8.1'
--with-alugrid='$HOME/extlib/alugrid/1.96/openmpi/1.6.5/gcc/4.8.1'
--with-petsc='$HOME/extlib/petsc/3.4.2/openmpi/1.6.5/gcc/4.8.1'
--prefix='$HOME/hades'
“
platform is:
Darwin vpn-a-183-088.epfl.ch 13.1.0 Darwin Kernel Version 13.1.0: Wed Apr 2 23:52:02 PDT 2014; root:xnu-2422.92.1~2/RELEASE_X86_64 x86_64
gcc 4.8.1
latest dune from trunk
Could you have a look ? Thanks a lot! Greetings, Benedikt
---
On 02 May 2014, at 12:34, Benedikt Oswald <benedikt.oswald at lspr.ch> wrote:
> Hello Markus, thanks!
>
> parmetis version 4.0.3/openmpi/1.6.5/gcc/4.8.1
>
> Greetings, Benedikt
>
>
>
>
>
>
> --------------------------------------------------------------------------------------------------------------------------------------------------------------
> Dr. sc. techn. Benedikt Oswald - first engineer - LSPR AG - phone - +41 43 366 90 74
> Technoparkstrasse 1, CH-8005 Zürich, benedikt.oswald at lspr.ch - labor vincit omnia improbus
> --------------------------------------------------------------------------------------------------------------------------------------------------------------
>
> On 02 May 2014, at 12:33, Dr. Markus Blatt <markus at dr-blatt.de> wrote:
>
>> On 1. Mai 2014 09:16:30 MESZ, Benedikt Oswald <benedikt.oswald at lspr.ch> wrote:
>>> Hello Markus, thanks for the fix. In fact, the metis.h not found error
>>> goes away,
>>> but there is another problem with istl:
>>>
>>> ===========
>>> In file included from
>>> /Users/oswald/gitwork/hades-pure-dune/dune-istl/dune/istl/matrixredistribute.hh:5:0,
>>> from
>>> /Users/oswald/gitwork/hades-pure-dune/dune-istl/dune/istl/paamg/transfer.hh:7,
>>> from
>>> /Users/oswald/gitwork/hades-pure-dune/dune-istl/dune/istl/paamg/amg.hh:10,
>>> from pamgtest1.cc:23:
>>> /Users/oswald/gitwork/hades-pure-dune/dune-istl/dune/istl/repartition.hh:
>>> At global scope:
>>> /Users/oswald/gitwork/hades-pure-dune/dune-istl/dune/istl/repartition.hh:791:67:
>>> error: ‘idxtype’ has not been declared
>>> inline bool isValidGraph(std::size_t noVtx, std::size_t gnoVtx, idxtype
>>> noEdges, idxtype* xadj,
>>> ^
>>> /Users/oswald/gitwork/hades-pure-dune/dune-istl/dune/istl/repartition.hh:791:84:
>>> error: ‘idxtype’ has not been declared
>>> inline bool isValidGraph(std::size_t noVtx, std::size_t gnoVtx, idxtype
>>> noEdges, idxtype* xadj,
>>> ^
>>> /Users/oswald/gitwork/hades-pure-dune/dune-istl/dune/istl/repartition.hh:792:28:
>>> error: ‘idxtype’ has not been declared
>>> idxtype* adjncy, bool checkSymmetry)
>>> ^
>>> /Users/oswald/gitwork/hades-pure-dune/dune-istl/dune/istl/repartition.hh:
>>> In function ‘bool Dune::isValidGraph(std::size_t, std::size_t, int,
>>> int*, int*, bool)’:
>>> /Users/oswald/gitwork/hades-pure-dune/dune-istl/dune/istl/repartition.hh:796:9:
>>> error: ‘idxtype’ was not declared in this scope
>>> for(idxtype vtx=0; vtx<(idxtype)noVtx; ++vtx) {
>>> ^
>>> /Users/oswald/gitwork/hades-pure-dune/dune-istl/dune/istl/repartition.hh:796:17:
>>> error: expected ‘;’ before ‘vtx’
>>> for(idxtype vtx=0; vtx<(idxtype)noVtx; ++vtx) {
>>> ^
>>> /Users/oswald/gitwork/hades-pure-dune/dune-istl/dune/istl/repartition.hh:796:24:
>>> error: ‘vtx’ was not declared in this scope
>>> for(idxtype vtx=0; vtx<(idxtype)noVtx; ++vtx) {
>>> ^
>>> /Users/oswald/gitwork/hades-pure-dune/dune-istl/dune/istl/repartition.hh:796:37:
>>> error: expected ‘;’ before ‘noVtx’
>>> for(idxtype vtx=0; vtx<(idxtype)noVtx; ++vtx) {
>>> ^
>>> /Users/oswald/gitwork/hades-pure-dune/dune-istl/dune/istl/repartition.hh:796:42:
>>> error: expected ‘)’ before ‘;’ token
>>> for(idxtype vtx=0; vtx<(idxtype)noVtx; ++vtx) {
>>> ^
>>> /Users/oswald/gitwork/hades-pure-dune/dune-istl/dune/istl/repartition.hh:796:46:
>>> error: ‘vtx’ was not declared in this scope
>>> for(idxtype vtx=0; vtx<(idxtype)noVtx; ++vtx) {
>>> =============
>>>
>>> In the opts file I use both metis and parmetis. I remember, a few
>>> months ago, there was something sounding similar ?
>>>
>>>
>>> platform is: mac os x, gcc 4.8.2, openmpi 1.8, latest Dune from trunk
>>>
>>>
>>>
>>> Greetings, Benedikt
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> On 29 Apr 2014, at 10:50, Markus Blatt <markus at dr-blatt.de> wrote:
>>>
>>>> Hi,
>>>>
>>>> thanks for the report. There were still some hickups in the fix and
>>>> the compile flags which are hopefully fixed by now. It might be worth
>>>> trying again.
>>>>
>>>> Markus
>>>> --
>>>> Do you need more support with DUNE or HPC in general?
>>>>
>>>> Dr. Markus Blatt - HPC-Simulation-Software & Services
>>> http://www.dr-blatt.de
>>>> Hans-Bunte-Str. 8-10, 69123 Heidelberg, Germany
>>>> Tel.: +49 (0) 160 97590858
>>
>> Hi,
>> Thanks for the feedback. Might have broken this one and will try to fix this. What version of parmetis are you using?
>>
>> Markus
>> --
>> Dr. Blatt HPC-Simulation-Software & Services
>> Hans-Bunte-Str. 8-10, 69123 Heidelberg, Germany
>
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