<div>Thank you Matt. I added MPI shared libraries to my LD_LIBRARY_PATH. The error disappeared. But other errors happened. Please find the attached files!</div><div><div style="font-size:14px;font-family:Verdana;color:#000;">
</div></div><div> </div><div><includetail><div><br></div><div><br></div><div style="font-size: 12px;font-family: Arial Narrow;padding:2px 0 2px 0;">------------------ Original ------------------</div><div style="font-size: 12px;background:#efefef;padding:8px;"><div><b>From: </b> "knepley"<knepley@gmail.com>;</div><div><b>Date: </b> Sat, Sep 8, 2012 12:30 PM</div><div><b>To: </b> "fdkong"<fd.kong@siat.ac.cn>; <wbr></div><div><b>Cc: </b> "petsc-users"<petsc-users@mcs.anl.gov>; <wbr></div><div><b>Subject: </b> Re: configure error with netcdf</div></div><div><br></div>On Fri, Sep 7, 2012 at 11:28 PM, fdkong <span dir="ltr"><<a href="mailto:fd.kong@siat.ac.cn" target="_blank">fd.kong@siat.ac.cn</a>></span> wrote:<br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>>> Hi all,</div><div>>></div><div>>> There are anyone who know how to install netcdf with cross compile? I</div><div>>> configured petsc with netcdf, but got error below:</div><div>>></div>
<div><br></div><div>>Send externalpackages./netcdf*/config.log</div><div><br></div><div>> Thanks,</div><div><br></div><div>> Matt</div><div><br></div><div>I attached the file config.log. </div></blockquote><div>
<br></div><div>Your MPI shared libraries are not in your LD_LIBRARY_PATH</div><div><br></div><div><span style="font-family:monospace;font-size:13.333333015441895px;background-color:rgb(255,255,255)">configure:5252: checking whether we are cross compiling</span><br style="font-family:monospace;font-size:13.333333015441895px">
<span style="font-family:monospace;font-size:13.333333015441895px;background-color:rgb(255,255,255)">configure:5260: /curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/bin/mpicc -o conftest -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. conftest.c >&5</span><br style="font-family:monospace;font-size:13.333333015441895px">
<span style="font-family:monospace;font-size:13.333333015441895px;background-color:rgb(255,255,255)">configure:5264: $? = 0</span><br style="font-family:monospace;font-size:13.333333015441895px"><span style="font-family:monospace;font-size:13.333333015441895px;background-color:rgb(255,255,255)">configure:5271: ./conftest</span><br style="font-family:monospace;font-size:13.333333015441895px">
<span style="font-family:monospace;font-size:13.333333015441895px;background-color:rgb(255,255,255)">./conftest: error while loading shared libraries: libmpi.so.0: cannot open shared object file: No such file or directory</span><br style="font-family:monospace;font-size:13.333333015441895px">
<span style="font-family:monospace;font-size:13.333333015441895px;background-color:rgb(255,255,255)">configure:5275: $? = 127</span></div><div><span style="font-family:monospace;font-size:13.333333015441895px;background-color:rgb(255,255,255)"><br>
</span></div><div><span style="font-family:monospace;font-size:13.333333015441895px;background-color:rgb(255,255,255)"> Matt</span></div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>>></div><div>>> >===========================================================================>====</div><div>>> Configuring PETSc to compile on your system</div><div>>></div>
<div>>></div><div>>> >===========================================================================>====</div><div>> >===========================================================================>====</div>
<div>>></div><div>>> ***** WARNING: MPI_DIR</div><div>>> found in enviornment variables - ignoring ******</div><div>>>></div><div>>></div>
<div>>> >===========================================================================>====</div><div>>></div><div>>></div><div>>> ===============================================================================</div>
<div>>></div><div>>> WARNING!</div><div>>> Compiling PETSc with no debugging, this should</div><div>>></div><div>>> only be done for timing and</div>
<div>>> production runs. All development should</div><div>>></div><div>>> be done when configured using --with-debugging=1</div><div>></div><div>></div><div>> ===============================================================================</div>
<div>>></div><div>>></div><div>>> ===============================================================================</div><div>>></div><div>>> Configuring NetCDF; this</div>
<div>>> may take several minutes</div><div>>></div><div>>></div><div>>> ===============================================================================</div><div>>></div><div>>></div><div>
>></div><div>>></div><div>>></div><div>>> *******************************************************************************</div><div>>> UNABLE to CONFIGURE with GIVEN OPTIONS (see configure.log for</div>
<div>>> details):</div><div>>></div><div>>> -------------------------------------------------------------------------------</div><div>>> Error running make on NetCDF: Could not execute "cd</div>
<div>>> /projects/fako9399/petsc-3.3-p3/externalpackages/netcdf-4.1.1 &&</div><div>>> AR="/usr/bin/ar" ARFLAGS="cr"</div><div>>> CC="/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/bin/mpicc" CFLAGS="</div>
<div>>> -fPIC -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -O</div><div>>> -I/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/include</div><div>>> -I/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/include -I."</div>
<div>>> CXX="/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/bin/mpicxx"</div><div>>> CXXFLAGS=" -Wwrite-strings -Wno-strict-aliasing -Wno-unknown-pragmas -O</div><div>>> -fPIC -I/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/include</div>
<div>>> -I/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/include -I."</div><div>>> FC="/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/bin/mpif90" FCFLAGS="</div><div>>> -fPIC -Wno-unused-variable -O</div>
<div>>> -I/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/include</div><div>>> -I/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/include -I."</div><div>>> F90="/curc/tools/free/redhat_5_x86_64/openmpi-1.4.3_ib/bin/mpif90"</div>
<div>>> ./configure --prefix=/projects/fako9399/petsc-3.3-p3/arch-linux264-cxx-opt</div><div>>> --libdir=/projects/fako9399/petsc-3.3-p3/arch-linux264-cxx-opt/lib</div><div>>> --disable-dap --enable-shared":</div>
<div>>> configure: netCDF 4.1.1</div><div>>> checking build system type... x86_64-unknown-linux-gnu</div><div>>> checking host system type... x86_64-unknown-linux-gnu</div><div>>> checking for a BSD-compatible install... /usr/bin/install -c</div>
<div>>> checking whether build environment is sane... yes</div><div>>> checking for a thread-safe mkdir -p... /bin/mkdir -p</div><div>>> checking for gawk... gawk</div><div>>> checking whether make sets $(MAKE)... yes</div>
<div>>> configure: checking user options</div><div>> >checking whether CXX is set to ''... no</div><div>>> checking whether FC is set to ''... no</div><div>>> checking whether F90 is set to ''... no</div>
<div>>> checking whether a NCIO_MINBLOCKSIZE was specified... 256</div><div>>> checking whether udunits is to be built... no</div><div>> >checking if fsync support is enabled... yes</div><div>>> checking whether extra valgrind tests should be run... no</div>
<div>>> checking whether libcf is to be built... no</div><div>>> checking whether reading of HDF4 SD files is to be enabled... no</div><div>>> checking whether to fetch some sample HDF4 files from Unidata ftp site to</div>
<div>> >test HDF4 reading (requires wget)... no</div><div>>> checking whether parallel I/O for classic and 64-bit offset files using</div><div>>> parallel-netcdf is to be enabled... no</div><div>> >checking whether a location for the parallel-netcdf library was</div>
<div>>> specified... no</div><div>>> checking whether new netCDF-4 C++ API is to be built... no</div><div>> >checking whether extra example tests should be run... no</div><div>> >checking whether parallel IO tests should be run... no</div>
<div>> >checking whether a location for the HDF5 library was specified...</div><div>>> checking whether a location for the ZLIB library was specified...</div><div>>> checking whether a location for the SZLIB library was specified...</div>
<div>>> checking whether a location for the HDF4 library was specified...</div><div>>> checking whether a default chunk size in bytes was specified... 4194304</div><div>> >checking whether a maximum per-variable cache size for HDF5 was</div>
<div>> >specified... 67108864</div><div>> >checking whether a number of chunks for the default per-variable cache was</div><div>>> specified... 10</div><div>>> checking whether a default file cache size for HDF5 was specified...</div>
<div>> >4194304</div><div>> >checking whether a default file cache maximum number of elements for HDF5</div><div>> >was specified... 1009</div><div>> >checking whether a default cache preemption for HDF5 was specified... 0.75</div>
<div>> >checking whether netCDF-4 logging is enabled... no</div><div>> >checking whether a path for curl-config was specified... no</div><div>> >checking whether a location for curl installation was specified... no</div>
<div>> >configure: checking whether a location for curl-config is in PATH... yes</div><div>> >checking whether DAP client is to be built... no</div><div>> >checking whether dap remote testing should be enabled (default on)... no</div>
<div>> >checking whether the time-consuming dap tests should be enabled (default</div><div>> >off)... no</div><div>> >checking whether a location for liboc was specified... no</div><div>>> checking whether netCDF extra tests should be run (developers only)... no</div>
<div>> >checking whether Fortran compiler(s) should be tested during configure...</div><div>> >yes</div><div>> >checking whether FFIO will be used... no</div><div>> >checking whether to skip C++, F77, or F90 APIs if compiler is broken... yes</div>
<div>> >checking whether only the C library is desired... no</div><div>>> checking whether examples should be built... yes</div><div>>> checking whether F77 API is desired... yes</div><div>> >checking whether any Fortran API is desired... yes</div>
<div>> >checking whether F90 API is desired... yes</div><div>> >checking whether fortran type sizes should be checked... yes</div><div>>> checking whether C API is desired... yes</div><div>>> checking where to get netCDF C-only library for separate fortran</div>
<div>>> libraries...</div><div>> >checking whether CXX API is desired... yes</div><div>> >checking whether v2 netCDF API should be built... yes</div><div>> >checking whether the ncgen/ncdump should be built... yes</div>
<div>>> checking whether large file (> 2GB) tests should be run... no</div><div>> >checking whether benchmaks should be run (experimental)... no</div><div>>> checking whether extreme numbers should be used in tests... yes</div>
<div>> >checking where to put large temp files if large file tests are run... .</div><div>> >checking whether a win32 DLL is desired... no</div><div>> >checking whether separate fortran libs are desired... yes</div>
<div>>> configure: finding C compiler</div><div>> >checking whether the C compiler works... yes</div><div>>> checking for C compiler default output file name... a.out</div><div>> >checking for suffix of executables...</div>
<div>> >checking whether we are cross compiling... configure: error: in</div><div>>> `/projects/fako9399/petsc-3.3-p3/externalpackages/netcdf-4.1.1':</div><div>> >configure: error: cannot run C compiled programs.</div>
<div>> >If you meant to cross compile, use `--host'.</div><div>> >See `config.log' for more details.</div><div>>></div><div>>> *******************************************************************************</div>
<div>>></div><div>> >The configure script is:</div><div>>></div><div>> > ./configure --with-clanguage=cxx --with-shared-libraries=1</div><div>>> --with-dynamic-loading=1 --download-f-blas-lapack=1 --with-mpi-dir=$MPI_DIR</div>
<div>>> --known-mpi-shared-libraries=0 --with-batch=1 --download-parmetis=1</div><div>> >--download-metis=1 --with-64-bit-indices=1 --download-netcdf=1</div><div>> >--download-exodusii=1 --with-debugging=no --download-ptscotch=1</div>
<div>>></div><div>>> I also attached the file configure.log</div><div>>></div><div>> >------------------</div><div>> >Fande Kong</div><div>>> ShenZhen Institutes of Advanced Technology</div>
<div>> >Chinese Academy of Sciences</div><div>>></div><div>>></div><div><br></div></blockquote></div><br><br clear="all"><div><br></div>-- <br>What most experimenters take for granted before they begin their experiments is infinitely more interesting than any results to which their experiments lead.<br>
-- Norbert Wiener<br></includetail></div>