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

Sjaardema, Gregory D gdsjaar at sandia.gov
Wed Dec 23 10:54:21 EST 2015 

Ok.  The issue is that there are a few of the SEACAS libraries that are related to the graphics device drivers (libsvdi_cgi is one of these) that do not work correctly as shareable libraries on some or all platforms.

Roscoe Bartlett is working on a patch for TriBits that will allow some of the libraries to be built as archive/static libraries even when the “BUILD_SHARED_LIBS” is enabled.  If you are building with shared libs, then you will have to disable the graphics device driver build for SEACAS and the easiest way to do this is to turn off the X11 support.   You should also be able to disable it by using
“-DTrilinos_ENABLE_SEACASSVDI:BOOL=OFF”.  If you do need the SEACAS graphics programs (blot, fastq), then for now you will have to build with BUILD_SHARED_LIBS set to OFF.

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

From: Sai P Uppati <uppatis at utexas.edu<mailto:uppatis at utexas.edu>>
Date: Wednesday, December 23, 2015 at 10:28 AM
To: "Sjaardema, Gregory D" <gdsjaar at sandia.gov<mailto:gdsjaar at sandia.gov>>, "trilinos-users at trilinos.org<mailto:trilinos-users at trilinos.org>" <trilinos-users at trilinos.org<mailto:trilinos-users at trilinos.org>>
Subject: Re: [EXTERNAL] [Trilinos-Users] Fwd: Trilinos 12.4.2 compilation error on Mac OS X El Capitan 10.11.2

@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

Sent from Outlook Mobile<https://aka.ms/qtex0l>




On Wed, Dec 23, 2015 at 6:45 AM -0800, "Sjaardema, Gregory D" <gdsjaar at sandia.gov<mailto: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<mailto:trilinos-users-bounces at trilinos.org>> on behalf of Sai P Uppati <uppatis at utexas.edu<mailto:uppatis at utexas.edu>>
Date: Tuesday, December 22, 2015 at 7:43 PM
To: "trilinos-users at trilinos.org<mailto:trilinos-users at trilinos.org>" <trilinos-users at trilinos.org<mailto: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
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