MPI_SEEK_SET
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alexandr...@gmail.com
Aug 12, 2014, 4:11:55 PM8/12/14
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Hi everybody,
i'm trying to compile an application that uses deal.ii and during compilation i get the following error message:
/home/ubuntu/pdd_tools/deal.II/include/deal.II/base/mpi.h:29:6: error: #error "The buildsystem included an insufficient mpi.h header that does not export MPI_SEEK_SET"
# error "The buildsystem included an insufficient mpi.h header that does not export MPI_SEEK_SET"
^
compilation terminated due to -Wfatal-errors.Deal.II is configured with MPI support. Also i have the following installed on my system:
ubuntu@almatest2:~/pdd/src_mpi$ mpicc -vUsing built-in specs.COLLECT_GCC=/usr/bin/gccCOLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-linux-gnu/4.8/lto-wrapperTarget: x86_64-linux-gnuConfigured with: ../src/configure -v --with-pkgversion='Ubuntu 4.8.2-19ubuntu1' --with-bugurl=file:///usr/share/doc/gcc-4.8/README.Bugs --enable-languages=c,c++,java,go,d,fortran,objc,obj-c++ --prefix=/usr --program-suffix=-4.8 --enable-shared --enable-linker-build-id --libexecdir=/usr/lib --without-included-gettext --enable-threads=posix --with-gxx-include-dir=/usr/include/c++/4.8 --libdir=/usr/lib --enable-nls --with-sysroot=/ --enable-clocale=gnu --enable-libstdcxx-debug --enable-libstdcxx-time=yes --enable-gnu-unique-object --disable-libmudflap --enable-plugin --with-system-zlib --disable-browser-plugin --enable-java-awt=gtk --enable-gtk-cairo --with-java-home=/usr/lib/jvm/java-1.5.0-gcj-4.8-amd64/jre --enable-java-home --with-jvm-root-dir=/usr/lib/jvm/java-1.5.0-gcj-4.8-amd64 --with-jvm-jar-dir=/usr/lib/jvm-exports/java-1.5.0-gcj-4.8-amd64 --with-arch-directory=amd64 --with-ecj-jar=/usr/share/java/eclipse-ecj.jar --enable-objc-gc --enable-multiarch --disable-werror --with-arch-32=i686 --with-abi=m64 --with-multilib-list=m32,m64,mx32 --with-tune=generic --enable-checking=release --build=x86_64-linux-gnu --host=x86_64-linux-gnu --target=x86_64-linux-gnuThread model: posixgcc version 4.8.2 (Ubuntu 4.8.2-19ubuntu1) ubuntu@almatest2:~/pdd/src_mpi$ mpiexec --versionmpiexec (OpenRTE) 1.6.5
Report bugs to http://www.open-mpi.org/community/help/ubuntu@almatest2:~/pdd/src_mpi$ mpirun --versionmpirun (Open MPI) 1.6.5
Report bugs to http://www.open-mpi.org/community/help/ubuntu@almatest2:~/pdd/src_mpi$ ompi_info Package: Open MPI buildd@allspice Distribution Open MPI: 1.6.5 Open MPI SVN revision: r28673 Open MPI release date: Jun 26, 2013 Open RTE: 1.6.5 Open RTE SVN revision: r28673 Open RTE release date: Jun 26, 2013 OPAL: 1.6.5 OPAL SVN revision: r28673 OPAL release date: Jun 26, 2013 MPI API: 2.1 Ident string: 1.6.5 Prefix: /usr Configured architecture: x86_64-pc-linux-gnu Configure host: allspice Configured by: buildd Configured on: Sat Dec 28 23:38:31 UTC 2013 Configure host: allspice Built by: buildd Built on: Sat Dec 28 23:41:47 UTC 2013 Built host: allspice C bindings: yes C++ bindings: yes Fortran77 bindings: yes (all) Fortran90 bindings: yes Fortran90 bindings size: small C compiler: gcc C compiler absolute: /usr/bin/gcc C compiler family name: GNU C compiler version: 4.8.2 C++ compiler: g++ C++ compiler absolute: /usr/bin/g++ Fortran77 compiler: gfortran Fortran77 compiler abs: /usr/bin/gfortran Fortran90 compiler: gfortran Fortran90 compiler abs: /usr/bin/gfortran C profiling: yes C++ profiling: yes Fortran77 profiling: yes Fortran90 profiling: yes C++ exceptions: no Thread support: posix (MPI_THREAD_MULTIPLE: no, progress: no) Sparse Groups: no Internal debug support: no MPI interface warnings: no MPI parameter check: runtimeMemory profiling support: noMemory debugging support: no libltdl support: yes Heterogeneous support: yes mpirun default --prefix: no MPI I/O support: yes MPI_WTIME support: gettimeofday Symbol vis. support: yes Host topology support: yes MPI extensions: affinity example FT Checkpoint support: yes (checkpoint thread: yes) VampirTrace support: no MPI_MAX_PROCESSOR_NAME: 256 MPI_MAX_ERROR_STRING: 256 MPI_MAX_OBJECT_NAME: 64 MPI_MAX_INFO_KEY: 36 MPI_MAX_INFO_VAL: 256 MPI_MAX_PORT_NAME: 1024 MPI_MAX_DATAREP_STRING: 128 MCA backtrace: execinfo (MCA v2.0, API v2.0, Component v1.6.5) MCA memory: linux (MCA v2.0, API v2.0, Component v1.6.5) MCA paffinity: hwloc (MCA v2.0, API v2.0, Component v1.6.5) MCA carto: auto_detect (MCA v2.0, API v2.0, Component v1.6.5) MCA carto: file (MCA v2.0, API v2.0, Component v1.6.5) MCA shmem: mmap (MCA v2.0, API v2.0, Component v1.6.5) MCA shmem: posix (MCA v2.0, API v2.0, Component v1.6.5) MCA shmem: sysv (MCA v2.0, API v2.0, Component v1.6.5) MCA maffinity: first_use (MCA v2.0, API v2.0, Component v1.6.5) MCA maffinity: hwloc (MCA v2.0, API v2.0, Component v1.6.5) MCA timer: linux (MCA v2.0, API v2.0, Component v1.6.5) MCA installdirs: env (MCA v2.0, API v2.0, Component v1.6.5) MCA installdirs: config (MCA v2.0, API v2.0, Component v1.6.5) MCA sysinfo: linux (MCA v2.0, API v2.0, Component v1.6.5) MCA hwloc: external (MCA v2.0, API v2.0, Component v1.6.5) MCA crs: none (MCA v2.0, API v2.0, Component v1.6.5) MCA dpm: orte (MCA v2.0, API v2.0, Component v1.6.5) MCA pubsub: orte (MCA v2.0, API v2.0, Component v1.6.5) MCA allocator: basic (MCA v2.0, API v2.0, Component v1.6.5) MCA allocator: bucket (MCA v2.0, API v2.0, Component v1.6.5) MCA coll: basic (MCA v2.0, API v2.0, Component v1.6.5) MCA coll: hierarch (MCA v2.0, API v2.0, Component v1.6.5) MCA coll: inter (MCA v2.0, API v2.0, Component v1.6.5) MCA coll: self (MCA v2.0, API v2.0, Component v1.6.5) MCA coll: sm (MCA v2.0, API v2.0, Component v1.6.5) MCA coll: sync (MCA v2.0, API v2.0, Component v1.6.5) MCA coll: tuned (MCA v2.0, API v2.0, Component v1.6.5) MCA io: romio (MCA v2.0, API v2.0, Component v1.6.5) MCA mpool: fake (MCA v2.0, API v2.0, Component v1.6.5) MCA mpool: rdma (MCA v2.0, API v2.0, Component v1.6.5) MCA mpool: sm (MCA v2.0, API v2.0, Component v1.6.5) MCA pml: bfo (MCA v2.0, API v2.0, Component v1.6.5) MCA pml: crcpw (MCA v2.0, API v2.0, Component v1.6.5) MCA pml: csum (MCA v2.0, API v2.0, Component v1.6.5) MCA pml: ob1 (MCA v2.0, API v2.0, Component v1.6.5) MCA pml: v (MCA v2.0, API v2.0, Component v1.6.5) MCA bml: r2 (MCA v2.0, API v2.0, Component v1.6.5) MCA rcache: vma (MCA v2.0, API v2.0, Component v1.6.5) MCA btl: ofud (MCA v2.0, API v2.0, Component v1.6.5) MCA btl: openib (MCA v2.0, API v2.0, Component v1.6.5) MCA btl: self (MCA v2.0, API v2.0, Component v1.6.5) MCA btl: sm (MCA v2.0, API v2.0, Component v1.6.5) MCA btl: tcp (MCA v2.0, API v2.0, Component v1.6.5) MCA topo: unity (MCA v2.0, API v2.0, Component v1.6.5) MCA osc: pt2pt (MCA v2.0, API v2.0, Component v1.6.5) MCA osc: rdma (MCA v2.0, API v2.0, Component v1.6.5) MCA crcp: bkmrk (MCA v2.0, API v2.0, Component v1.6.5) MCA iof: hnp (MCA v2.0, API v2.0, Component v1.6.5) MCA iof: orted (MCA v2.0, API v2.0, Component v1.6.5) MCA iof: tool (MCA v2.0, API v2.0, Component v1.6.5) MCA oob: tcp (MCA v2.0, API v2.0, Component v1.6.5) MCA odls: default (MCA v2.0, API v2.0, Component v1.6.5) MCA ras: cm (MCA v2.0, API v2.0, Component v1.6.5) MCA ras: gridengine (MCA v2.0, API v2.0, Component v1.6.5) MCA ras: loadleveler (MCA v2.0, API v2.0, Component v1.6.5) MCA ras: slurm (MCA v2.0, API v2.0, Component v1.6.5) MCA ras: tm (MCA v2.0, API v2.0, Component v1.6.5) MCA rmaps: load_balance (MCA v2.0, API v2.0, Component v1.6.5) MCA rmaps: rank_file (MCA v2.0, API v2.0, Component v1.6.5) MCA rmaps: resilient (MCA v2.0, API v2.0, Component v1.6.5) MCA rmaps: round_robin (MCA v2.0, API v2.0, Component v1.6.5) MCA rmaps: seq (MCA v2.0, API v2.0, Component v1.6.5) MCA rmaps: topo (MCA v2.0, API v2.0, Component v1.6.5) MCA rml: ftrm (MCA v2.0, API v2.0, Component v1.6.5) MCA rml: oob (MCA v2.0, API v2.0, Component v1.6.5) MCA routed: binomial (MCA v2.0, API v2.0, Component v1.6.5) MCA routed: cm (MCA v2.0, API v2.0, Component v1.6.5) MCA routed: direct (MCA v2.0, API v2.0, Component v1.6.5) MCA routed: linear (MCA v2.0, API v2.0, Component v1.6.5) MCA routed: radix (MCA v2.0, API v2.0, Component v1.6.5) MCA routed: slave (MCA v2.0, API v2.0, Component v1.6.5) MCA plm: rsh (MCA v2.0, API v2.0, Component v1.6.5) MCA plm: slurm (MCA v2.0, API v2.0, Component v1.6.5) MCA plm: tm (MCA v2.0, API v2.0, Component v1.6.5) MCA snapc: full (MCA v2.0, API v2.0, Component v1.6.5) MCA filem: rsh (MCA v2.0, API v2.0, Component v1.6.5) MCA errmgr: default (MCA v2.0, API v2.0, Component v1.6.5) MCA ess: env (MCA v2.0, API v2.0, Component v1.6.5) MCA ess: hnp (MCA v2.0, API v2.0, Component v1.6.5) MCA ess: singleton (MCA v2.0, API v2.0, Component v1.6.5) MCA ess: slave (MCA v2.0, API v2.0, Component v1.6.5) MCA ess: slurm (MCA v2.0, API v2.0, Component v1.6.5) MCA ess: slurmd (MCA v2.0, API v2.0, Component v1.6.5) MCA ess: tm (MCA v2.0, API v2.0, Component v1.6.5) MCA ess: tool (MCA v2.0, API v2.0, Component v1.6.5) MCA grpcomm: bad (MCA v2.0, API v2.0, Component v1.6.5) MCA grpcomm: basic (MCA v2.0, API v2.0, Component v1.6.5) MCA grpcomm: hier (MCA v2.0, API v2.0, Component v1.6.5) MCA notifier: command (MCA v2.0, API v1.0, Component v1.6.5) MCA notifier: syslog (MCA v2.0, API v1.0, Component v1.6.5)
Any idea?
Thx.
Alex
Timo Heister
Aug 12, 2014, 4:59:54 PM8/12/14
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Hey Alex,
does your mpi.h include MPI_SEEK_SET and is the correct mpi.h picked
up (check detailed.log for the paths)?
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Timo Heister
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does your mpi.h include MPI_SEEK_SET and is the correct mpi.h picked
up (check detailed.log for the paths)?
> The deal.II project is located at http://www.dealii.org/
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alexandros spyrou
Aug 12, 2014, 5:13:49 PM8/12/14
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Hi Timo,
bellow is the detailed log..
detailed.log
--------------
###
#
# deal.II configuration:
# CMAKE_BUILD_TYPE: DebugRelease
# BUILD_SHARED_LIBS: ON
# CMAKE_INSTALL_PREFIX: /home/ubuntu/pdd_tools/deal.II
# CMAKE_SOURCE_DIR: /home/ubuntu/pdd_tools_install/deal.II.latest (Version 8.2.pre)
# CMAKE_BINARY_DIR: /home/ubuntu/pdd_tools_install/deal.II.latest/build
# CMAKE_CXX_COMPILER: GNU 4.8.2 on platform Linux x86_64
# /usr/bin/c++
# CMAKE_C_COMPILER: /usr/bin/cc
# CMAKE_Fortran_COMPILER: /usr/bin/gfortran
# CMAKE_GENERATOR: Unix Makefiles
#
# Base configuration (prior to feature configuration):
# DEAL_II_CXX_FLAGS: -pedantic -fpic -Wall -Wpointer-arith -Wwrite-strings -Wsynth -Wsign-compare -Wswitch -Wno-unused-local-typedefs -Wno-long-long -Wno-deprecated -Wno-deprecated-declarations -std=c++11
# DEAL_II_CXX_FLAGS_RELEASE: -O2 -funroll-loops -funroll-all-loops -fstrict-aliasing -Wno-unused
# DEAL_II_CXX_FLAGS_DEBUG: -Og -ggdb -Wa,--compress-debug-sections
# DEAL_II_LINKER_FLAGS: -Wl,--as-needed -rdynamic
# DEAL_II_LINKER_FLAGS_RELEASE:
# DEAL_II_LINKER_FLAGS_DEBUG: -ggdb
# DEAL_II_DEFINITIONS:
# DEAL_II_DEFINITIONS_RELEASE:
# DEAL_II_DEFINITIONS_DEBUG: DEBUG
# DEAL_II_USER_DEFINITIONS:
# DEAL_II_USER_DEFINITIONS_REL:
# DEAL_II_USER_DEFINITIONS_DEB: DEBUG
# DEAL_II_INCLUDE_DIRS
# DEAL_II_USER_INCLUDE_DIRS:
# DEAL_II_BUNDLED_INCLUDE_DIRS:
# DEAL_II_LIBRARIES: m
# DEAL_II_LIBRARIES_RELEASE:
# DEAL_II_LIBRARIES_DEBUG:
#
# Configured Features (DEAL_II_ALLOW_BUNDLED = ON, DEAL_II_ALLOW_AUTODETECTION = ON):
# ( DEAL_II_WITH_64BIT_INDICES = OFF )
# ( DEAL_II_WITH_ARPACK = OFF )
# DEAL_II_WITH_BOOST set up with bundled packages
# BOOST_BUNDLED_INCLUDE_DIRS = /home/ubuntu/pdd_tools_install/deal.II.latest/bundled/boost-1.49.0/include
# ( DEAL_II_WITH_BZIP2 = OFF )
# DEAL_II_WITH_CXX11 = ON
# DEAL_II_WITH_HDF5 set up with external dependencies
# HDF5_INCLUDE_DIRS = /usr/include
# HDF5_USER_INCLUDE_DIRS = /usr/include
# HDF5_LIBRARIES = /usr/lib/x86_64-linux-gnu/libhdf5_hl.so;/usr/lib/x86_64-linux-gnu/libhdf5.so;/usr/lib/libmpi.so;dl;/usr/lib/x86_64-linux-gnu/libhwloc.so
# DEAL_II_WITH_LAPACK set up with external dependencies
# LAPACK_LINKER_FLAGS =
# LAPACK_LIBRARIES = /usr/lib/liblapack.so;/usr/lib/libf77blas.so;/usr/lib/libatlas.so;gfortran;quadmath;m;c
# ( DEAL_II_WITH_METIS = OFF )
# DEAL_II_WITH_MPI set up with external dependencies
# MPI_VERSION = 2.1
# OMPI_VERSION = 1.6.5
# MPI_C_COMPILER = /usr/bin/mpicc
# MPI_CXX_COMPILER = /usr/bin/mpicxx
# MPI_Fortran_COMPILER = /usr/bin/mpif90
# MPI_CXX_FLAGS =
# MPI_LINKER_FLAGS =
# MPI_INCLUDE_DIRS = /usr/lib/openmpi/include;/usr/lib/openmpi/include/openmpi
# MPI_USER_INCLUDE_DIRS = /usr/lib/openmpi/include;/usr/lib/openmpi/include/openmpi
# MPI_LIBRARIES = /usr/lib/libmpi_cxx.so;/usr/lib/libmpi_f90.so;/usr/lib/libmpi_f77.so;/usr/lib/libmpi.so;dl;/usr/lib/x86_64-linux-gnu/libhwloc.so
# ( DEAL_II_WITH_MUMPS = OFF )
# DEAL_II_WITH_MUPARSER set up with bundled packages
# MUPARSER_BUNDLED_INCLUDE_DIRS = /home/ubuntu/pdd_tools_install/deal.II.latest/bundled/muparser_v2_2_3//include
# ( DEAL_II_WITH_NETCDF = OFF )
# ( DEAL_II_WITH_P4EST = OFF )
# ( DEAL_II_WITH_PETSC = OFF )
# ( DEAL_II_WITH_SLEPC = OFF )
# DEAL_II_WITH_THREADS set up with bundled packages
# THREADS_CXX_FLAGS = -Wno-parentheses -Wno-long-long
# THREADS_LINKER_FLAGS = -pthread
# THREADS_DEFINITIONS_DEBUG = TBB_USE_DEBUG;TBB_DO_ASSERT=1
# THREADS_USER_DEFINITIONS_DEBUG = TBB_USE_DEBUG;TBB_DO_ASSERT=1
# THREADS_BUNDLED_INCLUDE_DIRS = /home/ubuntu/pdd_tools_install/deal.II.latest/bundled/tbb41_20130401oss/include
# THREADS_LIBRARIES = dl
# ( DEAL_II_WITH_TRILINOS = OFF )
# DEAL_II_WITH_UMFPACK set up with bundled packages
# UMFPACK_BUNDLED_INCLUDE_DIRS = /home/ubuntu/pdd_tools_install/deal.II.latest/bundled/umfpack/UMFPACK/Include;/home/ubuntu/pdd_tools_install/deal.II.latest/bundled/umfpack/AMD/Include
# DEAL_II_WITH_ZLIB set up with external dependencies
# ZLIB_VERSION = 1.2.8
# ZLIB_INCLUDE_DIRS = /usr/include
# ZLIB_LIBRARIES = /usr/lib/x86_64-linux-gnu/libz.so
#
# Component configuration:
# DEAL_II_COMPONENT_COMPAT_FILES
# ( DEAL_II_COMPONENT_DOCUMENTATION = OFF )
# DEAL_II_COMPONENT_EXAMPLES
# DEAL_II_COMPONENT_MESH_CONVERTER
# ( DEAL_II_COMPONENT_PARAMETER_GUI = OFF )
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Timo Heister
Aug 12, 2014, 5:21:55 PM8/12/14
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>> does your mpi.h include MPI_SEEK_SET and is the correct mpi.h picked
>> up (check detailed.log for the paths)?
>
>> up (check detailed.log for the paths)?
>
> bellow is the detailed log..
> [...]
> # MPI_INCLUDE_DIRS =
> /usr/lib/openmpi/include;/usr/lib/openmpi/include/openmpi
Well, is this the correct mpi.h? Does it contain MPI_SEEK_SET?
> /usr/lib/openmpi/include;/usr/lib/openmpi/include/openmpi
Could it be that you have another mpi.h somehwere in the search path?
(it looks like you have MPI I/O enabled which is good)
alexandros spyrou
Aug 12, 2014, 5:28:47 PM8/12/14
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It seems that is getting the wrong include dirs. i will install mpich3 and will do a reconfigure and see if it gets the correct headers....i will let you know as soon as possible,,,
alexandros spyrou
Aug 12, 2014, 6:04:45 PM8/12/14
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Hi again.
despite the fact that i removed completly mpich2 and installed fresh mpich3.
ubuntu@almatest2:~/pdd_tools_install/deal.II.latest/build$ mpichversion
MPICH Version: 3.0.4
MPICH Release date: Wed Apr 24 10:08:10 CDT 2013
MPICH Device: ch3:nemesis
MPICH configure: --build=x86_64-linux-gnu --prefix=/usr --includedir=${prefix}/include --mandir=${prefix}/share/man --infodir=${prefix}/share/info --sysconfdir=/etc --localstatedir=/var --libdir=${prefix}/lib/x86_64-linux-gnu --libexecdir=${prefix}/lib/x86_64-linux-gnu --disable-maintainer-mode --disable-dependency-tracking --enable-shared --prefix=/usr --enable-fc --disable-rpath --disable-wrapper-rpath --sysconfdir=/etc/mpich --libdir=/usr/lib/x86_64-linux-gnu --includedir=/usr/include/mpich --docdir=/usr/share/doc/mpich --with-hwloc-prefix=system --enable-checkpointing --with-hydra-ckpointlib=blcr
MPICH CC: cc -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -O2
MPICH CXX: c++ -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -O2
MPICH F77: gfortran -g -O2 -g -O2 -O
==========
detailed log
# DEAL_II_WITH_MPI set up with external dependencies
# MPI_VERSION = 2.1
# OMPI_VERSION = 1.6.5
# MPI_C_COMPILER = /usr/bin/mpicc
# MPI_CXX_COMPILER = /usr/bin/mpicxx
# MPI_Fortran_COMPILER = /usr/bin/mpif90
# MPI_CXX_FLAGS =
# MPI_LINKER_FLAGS =
# MPI_INCLUDE_DIRS = /usr/lib/openmpi/include;/usr/lib/openmpi/include/openmpi
# MPI_USER_INCLUDE_DIRS = /usr/lib/openmpi/include;/usr/lib/openmpi/include/openmpi
# MPI_LIBRARIES = /usr/lib/libmpi_cxx.so;/usr/lib/libmpi_f90.so;/usr/lib/libmpi_f77.so;/usr/lib/libmpi.so;dl;/usr/lib/x86_64-linux-gnu/libhwloc.so
how can i fix that?
if i remove openmpi
i get the wrong include dirs.
Bruno Turcksin
Aug 12, 2014, 6:32:34 PM8/12/14
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I think your problem is that your application is using mpich but deal.II is compiled using openmpi. You can either delete mpich and use openmpi with your application or use mpich for both deal.ii and your application. If this is what you want to do look at https://groups.google.com/forum/#!searchin/dealii/mpi/dealii/y1xS0Fe-k6w/h2iI-iH81ooJ
Best,
Bruno
Best,
Bruno
Timo Heister
Aug 12, 2014, 8:39:53 PM8/12/14
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did you delete the deal.II build directory and start fresh? What is
your cmake command line? Can you compile a simple MPI hello world program?
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your cmake command line? Can you compile a simple MPI hello world program?
> "deal.II User Group" group.
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alexandros spyrou
Aug 13, 2014, 8:45:56 AM8/13/14
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Hi TImo,
yes i can compile and execute mpi programs.
THe command that i give for the deal.II installation is this one.
cmake -DCMAKE_C_COMPILER="/usr/bin/mpicc" -DCMAKE_CXX_COMPILER="/usr/bin/mpicxx" -DDEAL_II_WITH_MPI=ON -DCMAKE_INSTALL_PREFIX=/home/ubuntu/pdd_tools/deal.II.latest ../
i have deleted the build directory and created a new one. from that directory i issue the above cmake command.
I issue also mpichversion and i get 3.0.4 . THough what i get into the detailed log of the deal.ii is 2.0 with mpiunclude dirs the ones from openmpi....
BRs,
Alex.
Matthias Maier
Aug 13, 2014, 9:02:01 AM8/13/14
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Am 13. Aug 2014, 14:45 schrieb alexandros spyrou <alexandr...@gmail.com>:
> cmake -DCMAKE_C_COMPILER="/usr/bin/mpicc" -DCMAKE_CXX_COMPILER="/usr/bin/mpicxx"
are these the mpi wrapper of your mpich-installation?
Best,
Matthias
alexandros spyrou
Aug 13, 2014, 10:09:48 AM8/13/14
to dea...@googlegroups.com
now i got this fixed regarding the mpi version.
detailed log
# DEAL_II_WITH_MPI set up with external dependencies
# MPI_VERSION = 3.0
# MPI_C_COMPILER = /usr/bin/mpicc.mpich
# MPI_CXX_COMPILER = /usr/bin/mpicxx.mpich
# MPI_Fortran_COMPILER = /usr/bin/gfortran
# MPI_CXX_FLAGS = -fstack-protector
# MPI_LINKER_FLAGS = -Wl,-Bsymbolic-functions -Wl,-z,relro
# MPI_INCLUDE_DIRS = /usr/include/mpich
# MPI_USER_INCLUDE_DIRS = /usr/include/mpich
# MPI_LIBRARIES = /usr/lib/x86_64-linux-gnu/libmpichcxx.so;/usr/lib/x86_64-linux-gnu/libmpich.so;/usr/lib/x86_64-linux-gnu/libopa.so;/usr/lib/x86_64-linux-gnu/libmpl.so;rt;/usr/lib/libcr.so;pthread
but when i compile my application i get again this
/home/ubuntu/pdd_tools/deal.II.latest/include/deal.II/base/mpi.h:29:6: error: #error "The buildsystem included an insufficient mpi.h header that does not export MPI_SEEK_SET"
# error "The buildsystem included an insufficient mpi.h header that does not export MPI_SEEK_SET"
Matthias Maier
Aug 13, 2014, 10:14:14 AM8/13/14
to dea...@googlegroups.com
Am 13. Aug 2014, 16:09 schrieb alexandros spyrou <alexandr...@gmail.com>:
> now i got this fixed regarding the mpi version.
>
> detailed log
>
> # DEAL_II_WITH_MPI set up with external dependencies
> # MPI_VERSION = 3.0
> # MPI_C_COMPILER = /usr/bin/mpicc.mpich
> # MPI_CXX_COMPILER = /usr/bin/mpicxx.mpich
> # MPI_Fortran_COMPILER = /usr/bin/gfortran
> # MPI_CXX_FLAGS = -fstack-protector
> # MPI_LINKER_FLAGS = -Wl,-Bsymbolic-functions
> -Wl,-z,relro
> # MPI_INCLUDE_DIRS = /usr/include/mpich
> # MPI_USER_INCLUDE_DIRS = /usr/include/mpich
> # MPI_LIBRARIES = /usr/lib/x86_64-linux-gnu/
> libmpichcxx.so;/usr/lib/x86_64-linux-gnu/libmpich.so;/usr/lib/
> x86_64-linux-gnu/libopa.so;/usr/lib/x86_64-linux-gnu/libmpl.so;rt;/
> usr/lib/libcr.so;pthread
So, deal.II compiles and links? Do the quick tests, i.e. $ make test in
the build directory run fine?
>
> but when i compile my application i get again this
>
How do you compile your application? I.e. what build system do you use,
and how does the full compile command look like?
Best,
Matthias
alexandros spyrou
Aug 13, 2014, 11:42:27 AM8/13/14
to dea...@googlegroups.com
ok Let me take it from the begining.
lsb_release -a
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 14.04.1 LTS
Release: 14.04
Codename: trusty
i have installed the following with the following order:
mpich (mpich3) ok
openmpi1.6-bin ok
openmpi1.6-common ok
g++ ok
gfortran ok
libopenblas-dev ok
liblapack-dev ok
zlib1g-dev ok
gnuplot ok
cmake ok
mpich3 ok
i compiled a hello world mpi program as follows
mpicc -o hello hello.c
and executed it ./hello and mpiexec.mpich ./hello
after that i downloaded deal.II from http://www.ces.clemson.edu/dealii/deal.II-8.1.0.tar.gz and i did
tar -xvf
cd
mkdir build
cd build
cmake -DCMAKE_C_COMPILER="/usr/bin/mpicc.mpich" -DCMAKE_CXX_COMPILER="/usr/bin/mpicxx.mpich" -DDEAL_II_WITH_MPI=ON -DCMAKE_INSTALL_PREFIX=/home/ubuntu/pdd_tools/deal.II
tar -xvf
cd
mkdir build
cd build
cmake -DCMAKE_C_COMPILER="/usr/bin/mpicc.mpich" -DCMAKE_CXX_COMPILER="/usr/bin/mpicxx.mpich" -DDEAL_II_WITH_MPI=ON -DCMAKE_INSTALL_PREFIX=/home/ubuntu/pdd_tools/deal.II
from the detailed log i can see the following:
###
#
# deal.II configuration:
# CMAKE_BUILD_TYPE: DebugRelease
# BUILD_SHARED_LIBS: ON
# CMAKE_INSTALL_PREFIX: /home/ubuntu/pdd_tools/deal.II
# CMAKE_SOURCE_DIR: /home/ubuntu/pdd_tools_install/deal.II (Version 8.1.0)
# CMAKE_BINARY_DIR: /home/ubuntu/pdd_tools_install/deal.II/build
# CMAKE_CXX_COMPILER: GNU 4.8.2 on platform Linux x86_64
# /usr/bin/mpicxx.mpich
# CMAKE_C_COMPILER: /usr/bin/mpicc.mpich
# CMAKE_Fortran_COMPILER: /usr/bin/gfortran
# CMAKE_GENERATOR: Unix Makefiles
#
# Compiler flags used for this build:
# CMAKE_CXX_FLAGS: -pedantic -fpic -Wall -Wpointer-arith -Wwrite-strings -Wsynth -Wsign-compare -Wswitch -Wno-unused-local-typedefs -Wno-long-long -Wno-deprecated -Wno-deprecated-declarations -fstack-protector -Wno-parentheses -Wno-long-long
# DEAL_II_CXX_FLAGS_RELEASE: -O2 -funroll-loops -funroll-all-loops -fstrict-aliasing -Wno-unused
# DEAL_II_CXX_FLAGS_DEBUG: -Og -ggdb -Wa,--compress-debug-sections
# DEAL_II_LINKER_FLAGS: -Wl,--as-needed -rdynamic -Wl,-Bsymbolic-functions -Wl,-z,relro
# DEAL_II_LINKER_FLAGS_RELEASE:
# DEAL_II_LINKER_FLAGS_DEBUG: -ggdb
#
# Configured Features (DEAL_II_ALLOW_BUNDLED = ON, DEAL_II_ALLOW_AUTODETECTION = ON):
# ( DEAL_II_WITH_64BIT_INDICES = OFF )
# ( DEAL_II_WITH_ARPACK = OFF )
# DEAL_II_WITH_BOOST set up with bundled packages
# DEAL_II_WITH_FUNCTIONPARSER set up with bundled packages
# ( DEAL_II_WITH_HDF5 = OFF )
# DEAL_II_WITH_LAPACK set up with external dependencies
# LAPACK_LIBRARIES = /usr/lib/liblapack.so;/usr/lib/libblas.so;/usr/lib/gcc/x86_64-linux-gnu/4.8/libgfortran.so;/usr/lib/x86_64-linux-gnu/libm.so;/usr/lib/gcc/x86_64-linux-gnu/4.8/libquadmath.so;/usr/lib/x86_64-linux-gnu/libm.so;/usr/lib/x86_64-linux-gnu/libc.so
# ( DEAL_II_WITH_METIS = OFF )
# DEAL_II_WITH_MPI set up with external dependencies
# MPI_VERSION = 3.0
# MPI_CXX_COMPILER = /usr/bin/mpicxx.mpich
# MPI_CXX_COMPILE_FLAGS = -fstack-protector
# MPI_CXX_INCLUDE_PATH = /usr/include/mpich
# MPI_CXX_LIBRARIES = /usr/lib/x86_64-linux-gnu/libmpichcxx.so;/usr/lib/x86_64-linux-gnu/libmpich.so;/usr/lib/x86_64-linux-gnu/libopa.so;/usr/lib/x86_64-linux-gnu/libmpl.so;/usr/lib/x86_64-linux-gnu/librt.so;/usr/lib/libcr.so;/usr/lib/x86_64-linux-gnu/libpthread.so
# MPI_CXX_LINK_FLAGS = -Wl,-Bsymbolic-functions -Wl,-z,relro
# ( DEAL_II_WITH_MUMPS = OFF )
# ( DEAL_II_WITH_NETCDF = OFF )
# ( DEAL_II_WITH_P4EST = OFF )
# ( DEAL_II_WITH_PETSC = OFF )
# ( DEAL_II_WITH_SLEPC = OFF )
# DEAL_II_WITH_THREADS set up with bundled packages
# ( DEAL_II_WITH_TRILINOS = OFF )
# DEAL_II_WITH_UMFPACK set up with bundled packages
# DEAL_II_WITH_ZLIB set up with external dependencies
# ZLIB_VERSION = 1.2.8
# ZLIB_INCLUDE_DIRS = /usr/include
# ZLIB_LIBRARIES = /usr/lib/x86_64-linux-gnu/libz.so
#
# Component configuration:
# DEAL_II_COMPONENT_COMPAT_FILES
# ( DEAL_II_COMPONENT_DOCUMENTATION = OFF )
# DEAL_II_COMPONENT_EXAMPLES
# DEAL_II_COMPONENT_MESH_CONVERTER
# ( DEAL_II_COMPONENT_PARAMETER_GUI = OFF )
#
i did make -j8 all. and it was successful. Then i tried make test and it failed on mpi
mpi.debug: RUN failed. Output:
Hi from Hi from 0/1
ERROR: process does not see nproc=2!
0/1
ERROR: process does not see nproc=2!
--------------------------------------------------------------------------
mpirun noticed that the job aborted, but has no info as to the process
that caused that situation.
--------------------------------------------------------------------------
make[7]: *** [tests/quick_tests/CMakeFiles/mpi.debug.run] Error 1
make[6]: *** [tests/quick_tests/CMakeFiles/mpi.debug.run.dir/all] Error 2
make[5]: *** [tests/quick_tests/CMakeFiles/mpi.debug.run.dir/rule] Error 2
make[4]: *** [mpi.debug.run] Error 2
mpi.debug: ****** RUN failed *******
=============================== OUTPUT END ===============================
Expected stage PASSED - aborting
CMake Error at /home/ubuntu/pdd_tools_install/deal.II/cmake/scripts/run_test.cmake:124 (MESSAGE):
*** abort
now when i try to compile my code i give
mpic++ -Wfatal-errors -std=c++0x -o main.out main.cpp -I /home/ubuntu/pdd_tools/deal.II/include -I/home/ubuntu/pdd_tools/deal.II/include/deal.II -I/home/ubuntu/pdd_tools/deal.II/include/deal.II/base -I/home/ubuntu/pdd_tools/deal.II/include/lac/include -I/home/ubuntu/pdd_tools/deal.II/include/deal.II/bundled -I/home/ubuntu/pdd_tools/deal.II/include/deal.II/bundled/boost/include -I mba-1.1/include -I /home/ubuntu/pdd_tools/gsl/include Burkardt/spline/spline.o mba-1.1/lib/MBA.o mba-1.1/lib/MBAdata.o mba-1.1/lib/UCBsplineSurface.o mba-1.1/lib/UCBsplines.o mba-1.1/lib/UCButils.o /home/ubuntu/pdd_tools/deal.II/lib/libdeal_II.so -lpthread -I/usr/local/include -L/usr/local/lib -L/home/ubuntu/pdd_tools/gsl/lib -lgsl -lgslcblas -lm
In file included from MCDriver.h:12:0,
from Pdd.h:8,
from main.cpp:13:
/home/ubuntu/pdd_tools/deal.II/include/deal.II/base/mpi.h:29:6: error: #error "The buildsystem included an insufficient mpi.h header that does not export MPI_SEEK_SET"
# error "The buildsystem included an insufficient mpi.h header that does not export MPI_SEEK_SET"
^
compilation terminated due to -Wfatal-errors.
Best,
Matthias
Timo Heister
Aug 13, 2014, 6:21:30 PM8/13/14
to dea...@googlegroups.com
> i have installed the following with the following order:
>
> mpich (mpich3) ok
> openmpi1.6-bin ok
> openmpi1.6-common ok
> mpich3 ok
>
> mpich (mpich3) ok
> openmpi1.6-bin ok
> openmpi1.6-common ok
Why do you install mpich and openmpi? You also need the development
files (for example libmpich2-dev or libopenmpi)
> i did make -j8 all. and it was successful. Then i tried make test and it
> failed on mpi
>
> mpi.debug: RUN failed. Output:
> Hi from Hi from 0/1
> ERROR: process does not see nproc=2!
> 0/1
> ERROR: process does not see nproc=2!
compile the code.
alexandros spyrou
Aug 14, 2014, 4:49:19 AM8/14/14
to dea...@googlegroups.com
ok short update.
ubuntu@newthalis:~/pdd/src_mpi$ dpkg --get-selections | grep mpi
libmpich-dev install
libmpich10:amd64 install
mpich install
make test all 5 examples executed successfully
Test project /home/ubuntu/pdd_tools_install/deal.II/build/tests/quick_tests
Start 1: step.debug
1/5 Test #1: step.debug ....................... Passed 6.15 sec
Start 2: step.release
2/5 Test #2: step.release ..................... Passed 6.40 sec
Start 3: affinity.debug
3/5 Test #3: affinity.debug ................... Passed 6.16 sec
Start 4: mpi.debug
4/5 Test #4: mpi.debug ........................ Passed 5.12 sec
Start 5: tbb.debug
5/5 Test #5: tbb.debug ........................ Passed 5.47 sec
100% tests passed, 0 tests failed out of 5
Total Test time (real) = 29.30 sec
Built target test
but still
ubuntu@newthalis:~/pdd/src_mpi$ make
make[1]: Entering directory `/home/ubuntu/pdd/src_mpi/mba-1.1'
ar -sr lib/libmba-1.1_nopt.a lib/filterRestrict2D.o lib/MBA.o lib/MBAdata.o lib/PointAccessUtils.o lib/UCBsplines.o lib/UCBsplineSurface.o lib/UCButils.o
make[1]: Leaving directory `/home/ubuntu/pdd/src_mpi/mba-1.1'
make[1]: Entering directory `/home/ubuntu/pdd/src_mpi/Burkardt/spline'
make[1]: Nothing to be done for `default'.
make[1]: Leaving directory `/home/ubuntu/pdd/src_mpi/Burkardt/spline'
mpic++.mpich -Wfatal-errors -std=c++0x -o main.out main.cpp -I /home/ubuntu/pdd_tools/deal.II/include -I/home/ubuntu/pdd_tools/deal.II/include/deal.II -I/home/ubuntu/pdd_tools/deal.II/include/deal.II/base -I/home/ubuntu/pdd_tools/deal.II/include/lac/include -I/home/ubuntu/pdd_tools/deal.II/include/deal.II/bundled -I/home/ubuntu/pdd_tools/deal.II/include/deal.II/bundled/boost/include -I mba-1.1/include -I /home/ubuntu/pdd_tools/gsl/include Burkardt/spline/spline.o mba-1.1/lib/MBA.o mba-1.1/lib/MBAdata.o mba-1.1/lib/UCBsplineSurface.o mba-1.1/lib/UCBsplines.o mba-1.1/lib/UCButils.o /home/ubuntu/pdd_tools/deal.II/lib/libdeal_II.so -lpthread -I/usr/local/include -L/usr/local/lib -L/home/ubuntu/pdd_tools/gsl/lib -lgsl -lgslcblas -lm
In file included from MCDriver.h:12:0,
from Pdd.h:8,
from main.cpp:13:
/home/ubuntu/pdd_tools/deal.II/include/deal.II/base/mpi.h:29:6: error: #error "The buildsystem included an insufficient mpi.h header that does not export MPI_SEEK_SET"
# error "The buildsystem included an insufficient mpi.h header that does not export MPI_SEEK_SET"
^
compilation terminated due to -Wfatal-errors.
make: *** [main.o] Error 1
sudo find / -name "mpi.h"
ubuntu@newthalis:~/pdd/src_mpi$ sudo find / -name "mpi.h"
/home/ubuntu/pdd_tools_install/deal.II/include/deal.II/base/mpi.h
/home/ubuntu/pdd_tools/deal.II/include/deal.II/base/mpi.h
/usr/src/linux-headers-3.13.0-32/include/linux/mpi.h
/usr/src/linux-headers-3.13.0-32-generic/include/linux/mpi.h
/usr/include/mpich/mpi.h
Matthias Maier
Aug 14, 2014, 5:29:50 AM8/14/14
to dea...@googlegroups.com
Can you please post the detailed.log for the working configuration?
Am 14. Aug 2014, 10:49 schrieb alexandros spyrou <alexandr...@gmail.com>:
> mpic++.mpich -Wfatal-errors -std=c++0x -o main.out main.cpp -I /home
> /ubuntu/pdd_tools/deal.II/include -I/home/ubuntu/pdd_tools/deal.II/
> include/deal.II -I/home/ubuntu/pdd_tools/deal.II/include/deal.II/
> base -I/home/ubuntu/pdd_tools/deal.II/include/lac/include -I/home
> /ubuntu/pdd_tools/deal.II/include/deal.II/bundled -I/home/ubuntu/
> pdd_tools/deal.II/include/deal.II/bundled/boost/include -I mba-1.1/
> include -I /home/ubuntu/pdd_tools/gsl/include Burkardt/spline/
> spline.o mba-1.1/lib/MBA.o mba-1.1/lib/MBAdata.o mba-1.1/lib/
> UCBsplineSurface.o mba-1.1/lib/UCBsplines.o mba-1.1/lib/UCButils.o
> /home/ubuntu/pdd_tools/deal.II/lib/libdeal_II.so -lpthread -I/usr/
> local/include -L/usr/local/lib -L/home/ubuntu/pdd_tools/gsl/lib
> -lgsl -lgslcblas -lm
How is this compile statement put together? By hand?
It is missing the include path statements for external projects. And
therefore, very likely picks up the wrong mpi headers.
Best,
Matthias
Am 14. Aug 2014, 10:49 schrieb alexandros spyrou <alexandr...@gmail.com>:
> mpic++.mpich -Wfatal-errors -std=c++0x -o main.out main.cpp -I /home
> /ubuntu/pdd_tools/deal.II/include -I/home/ubuntu/pdd_tools/deal.II/
> include/deal.II -I/home/ubuntu/pdd_tools/deal.II/include/deal.II/
> base -I/home/ubuntu/pdd_tools/deal.II/include/lac/include -I/home
> /ubuntu/pdd_tools/deal.II/include/deal.II/bundled -I/home/ubuntu/
> pdd_tools/deal.II/include/deal.II/bundled/boost/include -I mba-1.1/
> include -I /home/ubuntu/pdd_tools/gsl/include Burkardt/spline/
> spline.o mba-1.1/lib/MBA.o mba-1.1/lib/MBAdata.o mba-1.1/lib/
> UCBsplineSurface.o mba-1.1/lib/UCBsplines.o mba-1.1/lib/UCButils.o
> /home/ubuntu/pdd_tools/deal.II/lib/libdeal_II.so -lpthread -I/usr/
> local/include -L/usr/local/lib -L/home/ubuntu/pdd_tools/gsl/lib
> -lgsl -lgslcblas -lm
It is missing the include path statements for external projects. And
therefore, very likely picks up the wrong mpi headers.
Best,
Matthias
alexandros spyrou
Aug 14, 2014, 5:43:29 AM8/14/14
to dea...@googlegroups.com
detailed log.
------------------
also the makefile....
.PHONY: default opt debug clean clean_output
#CXX = g++
CXX = mpic++
LD = mpic++.mpich
moredir = more
splinedir = Burkardt/spline
splineobj = ${splinedir}/spline.o
MBAdir = mba-1.1
MBAlibdir = ${MBAdir}/lib
MBAinclude = ${MBAdir}/include
MBAo = MBA.o MBAdata.o UCBsplineSurface.o UCBsplines.o UCButils.o
MBAobj = $(patsubst %, ${MBAlibdir}/%, ${MBAo})
GSL_DIR = /home/ubuntu/pdd_tools/gsl
DEALIIdir = /home/ubuntu/pdd_tools/deal.II
DEALIIinclude = $(patsubst %, ${DEALIIdir}/include/%, deal.II deal.II/base lac/include deal.II/bundled deal.II/bundled/boost/include )
DEALIIlibdir = ${DEALIIdir}/lib
DEALIIlibfiles = libdeal_II
LINK = -lpthread -I/usr/local/include -L/usr/local/lib -L${GSL_DIR}/lib -lgsl -lgslcblas -lm
default: DEALIIlib = $(patsubst %, ${DEALIIlibdir}/%.so, ${DEALIIlibfiles})
default: CCFLAGS = -Wfatal-errors #-Wall
default: MBA_MODE = nopt
default: main.o
opt: DEALIIlib = $(patsubst %, ${DEALIIlibdir}/%.so, ${DEALIIlibfiles})
opt: CCFLAGS = -O2 -Wfatal-errors #-Wall
opt: MBA_MODE = opt
opt: main.o
debug: DEALIIlib = $(patsubst %, ${DEALIIlibdir}/%.g.so, ${DEALIIlibfiles})
debug: CCFLAGS = -Wall
debug: MBA_MODE = nopt
debug: main.o
#main ===========================================
main.o: main.cpp ${splineo}
main.o: dd.h Problem.h Pdd.h MCDriver.h Inter3DDriver.h LaplaceDriver.h LaplaceSolve.h ${moredir}/Ranq1.h ${moredir}/Vdcbin.h
@make lib MODE=${MBA_MODE} --directory=${MBAdir} -f Makefile CCFLAGS=${CCFLAGS}
@make --directory=${splinedir} -f makefile CCFLAGS=${CCFLAGS}
${LD} ${CCFLAGS} -std=c++0x -o main.out main.cpp -I ${DEALIIdir}/include $(patsubst %, -I% , ${DEALIIinclude}) -I ${MBAinclude} -I ${GSL_DIR}/include ${splineobj} ${MBAobj} ${DEALIIlib} ${LINK}
#more ==========================================
clean:
@make --directory=${MBAdir} -f Makefile clean
@make --directory=${splinedir} -f makefile clean
rm -rf *.o *~ main.out gmon.out
clean_output:
rm -rf ../solution/*.gnuplot ../solution/*.tecplot ../solution/*.dx ../solution/*.povray
Matthias Maier
Aug 14, 2014, 6:08:17 AM8/14/14
to dea...@googlegroups.com
> .PHONY: default opt debug clean clean_output
>
> #CXX = g++
> CXX = mpic++
It sounds reasonable to also use mpic++.mpich here.
> DEALIIinclude = $(patsubst %, ${DEALIIdir}/include/%, deal.II deal.II
> /base lac/include deal.II/bundled deal.II/bundled/boost/include )
This is insufficient. Have a look at common/Make.global_options in your
(install, or build directory, depending on what ${DEALIIdir} is).
Make.global_options has a line that defines an INCLUDE. You need all of
those include statements.
> LINK = -lpthread -I/usr/local/include -L/usr/local/lib -L${GSL_DIR}/
> lib -lgsl -lgslcblas -lm
compile line CXXFLAGS.(g|o) in order to have matchin compile flags and
compile definitions.
Alternatively, have a look at the CMake documentation [1].
Best,
Matthias
[1] http://www.dealii.org/developer/users/cmakelists.html
alexandros spyrou
Aug 14, 2014, 1:52:57 PM8/14/14
to dea...@googlegroups.com
Hi Matthias,
i installed gsl with sudo apt-get install and i changed the makefile as follows and it is working now:
--------------------------------
.PHONY: default opt debug clean clean_output
#CXX = g++
CXX = mpic++
LD = mpic++
moredir = more
splinedir = Burkardt/spline
splineobj = ${splinedir}/spline.o
MBAdir = mba-1.1
MBAlibdir = ${MBAdir}/lib
MBAinclude = ${MBAdir}/include
MBAo = MBA.o MBAdata.o UCBsplineSurface.o UCBsplines.o UCButils.o
MBAobj = $(patsubst %, ${MBAlibdir}/%, ${MBAo})
DEALIIdir = /home/ubuntu/pdd_tools/deal.II
DEALIIinclude = $(DEALIIdir)/include $(DEALIIdir)/../deal.II/include
DEALIIlibdir = ${DEALIIdir}/lib
DEALIIlibfiles = libdeal_II
LINK = -lpthread -lm `pkg-config --libs --cflags gsl` #-ltbb
CXXFLAGS += $(patsubst %, -I%, ${DEALIIinclude}) -I ${MBAinclude} -I /home/ubuntu/pdd_tools/deal.II/include/deal.II/bundled -Wall -std=c++11
all: default
# This is the config for default and opt. Debug simply overwrites it.
DEALIIlib = $(patsubst %, ${DEALIIlibdir}/%.g.so, ${DEALIIlibfiles})
#default: DEALIIlib = $(patsubst %, ${DEALIIlibdir}/%.so, ${DEALIIlibfiles})
#default: CXXFLAGS = -Wall -Wno-unused-variable
default: MBA_MODE = nopt
default: main.out
#opt: DEALIIlib = $(patsubst %, ${DEALIIlibdir}/%.so, ${DEALIIlibfiles})
#opt: CXXFLAGS = -O2 -Wall -Wno-unused-variable
opt: MBA_MODE = opt
opt: main.out
debug: DEALIIlib = $(patsubst %, ${DEALIIlibdir}/%.g.so, ${DEALIIlibfiles})
debug: CXXFLAGS += -pg
debug: MBA_MODE = nopt
debug: main.out
#main ===========================================
main.o: main.cpp MPIHelper.h dd.h Problem.h Pdd.h MCDriver.h Inter3DDriver.h LaplaceDriver.h LaplaceSolve.h ${moredir}/Ranq1.h ${moredir}/Vdcbin.h
main.out: main.o MPIHelper.o ${splineobj}
@make lib MODE=${MBA_MODE} --directory=${MBAdir} -f Makefile CXXFLAGS="${CXXFLAGS}"
@make --directory=${splinedir} -f makefile CXXFLAGS="${CXXFLAGS}"
${LD} ${CXXFLAGS} -o main.out main.o MPIHelper.o ${splineobj} ${MBAobj} ${DEALIIlib} ${LINK}
#more ==========================================
clean:
@make --directory=${MBAdir} -f Makefile clean
@make --directory=${splinedir} -f makefile clean
rm -rf *.o *~ main.out gmon.out
clean_output:
rm -rf ./solution/*.gnuplot ./solution/*.tecplot ./solution/*.dx ./solution/*.povray
THx for all the help you provided all of you....
BRs,
Alex.
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