[Trilinos-Users] [EXTERNAL] Fwd: Trilinos 12.4.2 compilation error on Mac OS X El Capitan 10.11.2

Sai P Uppati uppatis at utexas.edu
Wed Dec 23 10:28:35 EST 2015


@Andrew, thanks for the advice. I'm building Trilinos primarily for building Peridigm against the Trilinos build. I'm not sure if X11 is required for the peridigm installation. I can give turning off X11 a try and see if that helps. 
@Greg I believe the compiler is gfortran.
Sai
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On Wed, Dec 23, 2015 at 6:45 AM -0800, "Sjaardema, Gregory D" <gdsjaar at sandia.gov> wrote:

















What is the fortran compiler that is being wrapped by mpif90?
..Greg




-- 
"A supercomputer is a device for turning compute-bound problems into I/O-bound problems”








From: Trilinos-Users <trilinos-users-bounces at trilinos.org> on behalf of Sai P Uppati <uppatis at utexas.edu>

Date: Tuesday, December 22, 2015 at 7:43 PM

To: "trilinos-users at trilinos.org" <trilinos-users at trilinos.org>

Subject: [EXTERNAL] [Trilinos-Users] Fwd: Trilinos 12.4.2 compilation error on Mac OS X El Capitan 10.11.2









I'm using the following cmake configure script:





rm -rf CMakeFiles CMakeCache.txt 



MPI_HOME=/usr/local
EXTRA_ARGS=$@



cmake -D CMAKE_INSTALL_PREFIX:PATH=/usr/local/trilinos/ \
  \
  -D MPI_BASE_DIR:PATH=$MPI_HOME \
  \
  -D CMAKE_BUILD_TYPE:STRING=Debug \
  -D CMAKE_Fortran_COMPILER:FILEPATH=/usr/local/bin/mpif90 \
  -D CMAKE_CXX_FLAGS:STRING="-Wno-unused -I/usr/local/include -stdlib=libc++" \
  -D CMAKE_MACOSX_RPATH:BOOL=OFF \
  -D BUILD_SHARED_LIBS:BOOL=ON \
  -D Trilinos_WARNINGS_AS_ERRORS_FLAGS:STRING="" \
  \
  -D Trilinos_ENABLE_ALL_PACKAGES:BOOL=OFF \
  -D Trilinos_ENABLE_ALL_OPTIONAL_PACKAGES:BOOL=ON \
  -D Trilinos_ENABLE_ALL_FORWARD_DEP_PACKAGES:BOOL=ON \
  -D Trilinos_ENABLE_Teuchos:BOOL=ON \
  -D Trilinos_ENABLE_Shards:BOOL=ON \
  -D Trilinos_ENABLE_Sacado:BOOL=ON \
  -D Trilinos_ENABLE_Epetra:BOOL=ON \
  -D Trilinos_ENABLE_EpetraExt:BOOL=ON \
  -D Trilinos_ENABLE_Ifpack:BOOL=ON \
  -D Trilinos_ENABLE_AztecOO:BOOL=ON \
  -D Trilinos_ENABLE_Belos:BOOL=ON \
  -D Trilinos_ENABLE_Phalanx:BOOL=ON \
  -D Phalanx_EXPLICIT_TEMPLATE_INSTANTIATION:BOOL=ON \
  -D Trilinos_ENABLE_Zoltan:BOOL=ON \
  -D Trilinos_ENABLE_STK:BOOL=OFF \
  -D Trilinos_ENABLE_SEACAS:BOOL=ON \
  -D Trilinos_ENABLE_SECONDARY_STABLE_CODE:BOOL=ON \
  -D Trilinos_ENABLE_NOX:BOOL=ON \
  -D Trilinos_ENABLE_Intrepid:BOOL=ON \
  -D Trilinos_ENABLE_Isorropia:BOOL=ON \
  -D Trilinos_ENABLE_MueLu:BOOL=OFF \
  -D Trilinos_ENABLE_FEI:BOOL=OFF \
  -D Trilinos_ENABLE_Sundance:BOOL=OFF \
  -D Trilinos_ENABLE_Piro:BOOL=ON \
  -D Trilinos_ENABLE_Pamgen:BOOL=ON \
  -D Trilinos_ENABLE_PyTrilinos:BOOL=OFF \
  \
  -D Trilinos_ENABLE_EXAMPLES:BOOL=OFF \
  -D Trilinos_ENABLE_TESTS:BOOL=OFF \
  \
  -D TPL_ENABLE_MATLAB:BOOL=OFF \
  -D TPL_ENABLE_Matio:BOOL=OFF \
  -D TPL_ENABLE_QT:BOOL=OFF \
  -D TPL_ENABLE_GLM:BOOL=OFF \
  -D TPL_ENABLE_Netcdf:BOOL=ON \
  -D Netcdf_INCLUDE_DIRS:PATH=$MPI_HOME/netcdf/include \
  -D Netcdf_LIBRARY_DIRS:PATH=$MPI_HOME/netcdf/lib \
  -D TPL_ENABLE_MPI:BOOL=ON \
  -D TPL_ENABLE_BLAS:BOOL=ON \
  -D TPL_ENABLE_LAPACK:BOOL=ON \
  -D TPL_LAPACK_LIBRARIES:STRING=/usr/lib/liblapack.dylib \
  -D TPL_ENABLE_Boost:BOOL=ON \
  -D TPL_Boost_INCLUDE_DIRS:PATH=$MPI_HOME/include/boost \
  \
  -D CMAKE_VERBOSE_MAKEFILE:BOOL=OFF \
  -D Trilinos_VERBOSE_CONFIGURE:BOOL=OFF \
  -D Trilinos_ASSERT_MISSING_PACKAGES=OFF \
  \
  $EXTRA_ARGS \
  ..





The configuration seems to complete fine. Once the build files are generated, I start compiling with:



make -j8



Around 12% of the compilation, I get the following error:




[ 12%] Linking Fortran shared library libsvdi_cgi.dylib
[ 12%] Building C object packages/seacas/libraries/exodus/cbind/CMakeFiles/exodus.dir/src/ex_int_get_block_param.c.o
[ 12%] Building C object packages/zoltan/src/CMakeFiles/zoltan.dir/reftree/reftree_coarse_path.c.o
[ 12%] Building C object packages/seacas/libraries/exodus/cbind/CMakeFiles/exodus.dir/src/ex_ne_util.c.o
Undefined symbols for architecture x86_64:
  "_cdr1ch_", referenced from:
      _wpstkl_ in pst_vdipst.f.o
      _wmet05_ in met_vdimet.f.o
      _wmetkl_ in met_vdimet.f.o
  "_cdra2c_", referenced from:
      _wpstix_ in pst_vdipst.f.o
  "_cdrcvt_", referenced from:
      _wpstkl_ in pst_vdipst.f.o
      _wmet05_ in met_vdimet.f.o
      _wmetkl_ in met_vdimet.f.o
  "_cdrela_", referenced from:
      _master.1.wpstmo_ in pst_vdipst.f.o
      _master.1.wmetmo_ in met_vdimet.f.o
  "_cdrgnm_", referenced from:
      _wpstgn_ in pst_vdipst.f.o
      _wmetgn_ in met_vdimet.f.o
  "_cdri2c_", referenced from:
      _wpst13_ in pst_vdipst.f.o
      _wpstcs_ in pst_vdipst.f.o
      _wpstlw_ in pst_vdipst.f.o
      _master.2.wpstls_ in pst_vdipst.f.o
      _wpstii_ in pst_vdipst.f.o
  "_cdrmon_", referenced from:
      _master.1.wpstmo_ in pst_vdipst.f.o
      _master.1.wmetmo_ in met_vdimet.f.o
  "_cdrtbk_", referenced from:
      _wpstle_ in pst_vdipst.f.o
      _wmetle_ in met_vdimet.f.o
ld: symbol(s) not found for architecture x86_64
collect2: error: ld returned 1 exit status
make[2]: *** [packages/seacas/libraries/svdi/libsvdi_cgi.12.4.2.dylib] Error 1
make[1]: *** [packages/seacas/libraries/svdi/CMakeFiles/svdi_cgi.dir/all] Error 2
make[1]: *** Waiting for unfinished jobs....
[ 12%] Building CXX object packages/pamgen/src/CMakeFiles/pamgen.dir/radial_trisection_inline_mesh_desc.C.o
[ 12%] Building C object packages/seacas/libraries/exodus/cbind/CMakeFiles/exodus.dir/src/ex_open.c.o




I'm not sure what to make of it. I have the following dependencies installed:



1. boost 1.59.0
2. hdf5 1.8.16
3. netcdf 4.3.3.1



Any advice on this issue is appreciated. Thanks!



--
Sai Uppati
UT Austin

ᐧ




ᐧ










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