[petsc-users] configure error with netcdf
fdkong
fd.kong at siat.ac.cn
Fri Sep 7 18:41:46 CDT 2012
Hi all,
There are anyone who know how to install netcdf with cross compile? I configured petsc with netcdf, but got error below:
===============================================================================
Configuring PETSc to compile on your system
===============================================================================
=============================================================================== ***** WARNING: MPI_DIR found in enviornment variables - ignoring ****** =============================================================================== =============================================================================== WARNING! Compiling PETSc with no debugging, this should only be done for timing and production runs. All development should be done when configured using --with-debugging=1 =============================================================================== =============================================================================== Configuring NetCDF; this may take several minutes =============================================================================== *******************************************************************************
UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for details):
-------------------------------------------------------------------------------
Error running make on NetCDF: Could not execute "cd /projects/fako9399/petsc-3.3-p3/externalpackages/netcdf-4.1.1 && AR="/usr/bin/ar" ARFLAGS="cr" CC="/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/bin/mpicc" CFLAGS=" -fPIC -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -O -I/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/include -I/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/include -I." CXX="/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/bin/mpicxx" CXXFLAGS=" -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -O -fPIC -I/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/include -I/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/include -I." FC="/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/bin/mpif90" FCFLAGS=" -fPIC -Wno-unused-variable -O -I/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/include -I/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/include -I." F90="/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/bin/mpif90" ./configure --prefix=/projects/fako9399/petsc-3.3-p3/arch-linux264-cxx-opt --libdir=/projects/fako9399/petsc-3.3-p3/arch-linux264-cxx-opt/lib --disable-dap --enable-shared":
configure: netCDF 4.1.1
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
configure: checking user options
checking whether CXX is set to ''... no
checking whether FC is set to ''... no
checking whether F90 is set to ''... no
checking whether a NCIO_MINBLOCKSIZE was specified... 256
checking whether udunits is to be built... no
checking if fsync support is enabled... yes
checking whether extra valgrind tests should be run... no
checking whether libcf is to be built... no
checking whether reading of HDF4 SD files is to be enabled... no
checking whether to fetch some sample HDF4 files from Unidata ftp site to test HDF4 reading (requires wget)... no
checking whether parallel I/O for classic and 64-bit offset files using parallel-netcdf is to be enabled... no
checking whether a location for the parallel-netcdf library was specified... no
checking whether new netCDF-4 C++ API is to be built... no
checking whether extra example tests should be run... no
checking whether parallel IO tests should be run... no
checking whether a location for the HDF5 library was specified...
checking whether a location for the ZLIB library was specified...
checking whether a location for the SZLIB library was specified...
checking whether a location for the HDF4 library was specified...
checking whether a default chunk size in bytes was specified... 4194304
checking whether a maximum per-variable cache size for HDF5 was specified... 67108864
checking whether a number of chunks for the default per-variable cache was specified... 10
checking whether a default file cache size for HDF5 was specified... 4194304
checking whether a default file cache maximum number of elements for HDF5 was specified... 1009
checking whether a default cache preemption for HDF5 was specified... 0.75
checking whether netCDF-4 logging is enabled... no
checking whether a path for curl-config was specified... no
checking whether a location for curl installation was specified... no
configure: checking whether a location for curl-config is in PATH... yes
checking whether DAP client is to be built... no
checking whether dap remote testing should be enabled (default on)... no
checking whether the time-consuming dap tests should be enabled (default off)... no
checking whether a location for liboc was specified... no
checking whether netCDF extra tests should be run (developers only)... no
checking whether Fortran compiler(s) should be tested during configure... yes
checking whether FFIO will be used... no
checking whether to skip C++, F77, or F90 APIs if compiler is broken... yes
checking whether only the C library is desired... no
checking whether examples should be built... yes
checking whether F77 API is desired... yes
checking whether any Fortran API is desired... yes
checking whether F90 API is desired... yes
checking whether fortran type sizes should be checked... yes
checking whether C API is desired... yes
checking where to get netCDF C-only library for separate fortran libraries...
checking whether CXX API is desired... yes
checking whether v2 netCDF API should be built... yes
checking whether the ncgen/ncdump should be built... yes
checking whether large file (> 2GB) tests should be run... no
checking whether benchmaks should be run (experimental)... no
checking whether extreme numbers should be used in tests... yes
checking where to put large temp files if large file tests are run... .
checking whether a win32 DLL is desired... no
checking whether separate fortran libs are desired... yes
configure: finding C compiler
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... configure: error: in `/projects/fako9399/petsc-3.3-p3/externalpackages/netcdf-4.1.1':
configure: error: cannot run C compiled programs.
If you meant to cross compile, use `--host'.
See `config.log' for more details.
*******************************************************************************
The configure script is:
./configure --with-clanguage=cxx --with-shared-libraries=1 --with-dynamic-loading=1 --download-f-blas-lapack=1 --with-mpi-dir=$MPI_DIR --known-mpi-shared-libraries=0 --with-batch=1 --download-parmetis=1 --download-metis=1 --with-64-bit-indices=1 --download-netcdf=1 --download-exodusii=1 --with-debugging=no --download-ptscotch=1
I also attached the file configure.log
------------------
Fande Kong
ShenZhen Institutes of Advanced Technology
Chinese Academy of Sciences
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