Re: [deal.II] Installation on cray XC50 | linking to petsc, lapack and blas libraries with different names

2020-02-11 Thread Jean-Paul Pelteret 
Hi Vachan,

If you’re still not having any luck with this, then maybe you’d consider 
investigating deal.II through Spack. There’s in fact a whole section in their 
documentation dedicated to explaining how package installation is done on Cray 
systems:
https://spack.readthedocs.io/en/latest/getting_started.html#spack-on-cray 


Best,
Jean-Paul

> On 12 Feb 2020, at 06:24, vachan potluri  wrote:
> 
> Step-1 aborts with Illegal Instruction (core dumped). The error msg gdb 
> prints is the following.
> Program received signal SIGILL, Illegal instruction.
> __static_initialization_and_destruction_0 (__initialize_p=1, __priority=65535)
> at 
> /home/ComptGasDynLab/vachanpotluri/source/dealii-9.1.1/source/numerics/time_dependent.cc:1196
> 1196   std::make_pair(0U, 
> 0.)));
> When I backtrace the error, it leads to this.
> template  
> typename TimeStepBase_Tria_Flags::RefinementFlags::CorrectionRelaxations
>   
> TimeStepBase_Tria_Flags::RefinementFlags::default_correction_relaxations(
> 1, // one element, denoting the first and all subsequent sweeps
> std::vector>(1, // one element, denoting 
> the
> // upper bound for the
> // following relaxation
>  std::make_pair(0U, 0.)));
> Not just step-1, but step.debug, affinity.debug and mpi.debug (and possibly 
> other debug tests may) also terminate with the same error and bt. Can someone 
> explain why this is happening?
> 
> -- 
> The deal.II project is located at http://www.dealii.org/ 
> 
> For mailing list/forum options, see 
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Re: [deal.II] Installation on cray XC50 | linking to petsc, lapack and blas libraries with different names

2020-02-08 Thread Daniel Arndt 
Vachan,

3. With LAPACK, the story is different. I noticed that deal.II's version of
> FindLAPACK.cmake uses the system installed cmake's FindLAPACK.cmake. And
> then I came across this question on SO:
> https://stackoverflow.com/questions/54681204/cray-cc-wrapper-cmake-find-package-blas
> and subsequently to the link
> https://gitlab.kitware.com/cmake/cmake/merge_requests/3451. So on cray
> environments, cmake's version of FindLAPACK.cmake can detect LAPACK
> library only if cmake version is >=3.16. Our system has 3.5.2. Also, the
> LAPACK library is not standalone but a part of cray's libsci module and is
> present in the library sci_gnu_61_mpi_mp along with BLAS, SCALAPACK and
> others. How can I invoke cmake such that it recognises LAPACK library as a
> part of this whole library?
>

If only an old version is the problem, I would just go ahead and download
and compile a recent version myself. I never had any issues with that and
should be quite simple.

Best,
Daniel

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[deal.II] Installation on cray XC50 | linking to petsc, lapack and blas libraries with different names

2020-02-07 Thread vachan potluri 

Hello,

I am trying to install deal.II on a cray XC50 machine. I had posted a 
question related to MPI 
here https://groups.google.com/forum/#!topic/dealii/EJm6ePrI81w.

1. Configuring with MPI was "successful" with the following cmake 
invocation.
cmake -DCMAKE_INSTALL_PREFIX=~/bin/dealii-9.1.1/ \
-DWITH_64BIT_INDICES=ON \
-DCMAKE_PREFIX_PATH=/opt/cray/pe/lib64 \
-DWITH_MPI=ON \
-DMPI_DIR=/opt/cray/pe/mpt/default/gni/mpich-gnu/5.1/ \

-DMPI_CXX_INCLUDE_PATH=/opt/cray/pe/mpt/default/gni/mpich-gnu/5.1/include/ \
-DCMAKE_CXX_COMPILER=/opt/cray/pe/craype/2.5.13/bin/CC \
-DCMAKE_C_COMPILER=/opt/cray/pe/craype/2.5.13/bin/cc \
-DCMAKE_Fortran_COMPILER=/opt/cray/pe/craype/2.5.13/bin/ftn 
\
-DWITH_BLAS=OFF \
-DWITH_LAPACK=OFF \
-DWITH_SCALAPACK=OFF \
-DWITH_PETSC=OFF \
-DWITH_P4EST=OFF -DP4EST_DIR=~/bin/p4est-2.2/ \
~/source/dealii-9.1.1

2. Configuring with PETSC was also successful, but I had to make the 
following change in cmake/modules/FindPETSC.cmake because the petsc 
libraries had a different name.
DEAL_II_FIND_LIBRARY(PETSC_LIBRARY
  #NAMES petsc libpetsc
  NAMES craypetsc_gnu_real-64 craypetsc_gnu_53_real-64
  HINTS ${PETSC_DIR} ${PETSC_DIR}/${PETSC_ARCH}
  PATH_SUFFIXES lib${LIB_SUFFIX} lib64 lib
  )
With -DWITH_PETSC=ON option, configuring with petsc was also "successful" 
but the libraries optionally used by petsc were not detected, as stated in 
this snippet of the output:
-- Include 
/home/ComptGasDynLab/vachanpotluri/source/dealii-9.1.1/cmake/configure/configure_3_petsc.cmake
-- Found PETSC_LIBRARY
-- Found PETSC_INCLUDE_DIR_ARCH
-- Found PETSC_INCLUDE_DIR_COMMON
-- Found PETSC_PETSCVARIABLES
-- PETSC_LIBRARY_superlu_dist-64 not found! Call:
-- FIND_LIBRARY(PETSC_LIBRARY_superlu_dist-64 NAMES superlu_dist-64 
HINTS /opt/cray/pe/petsc/3.7.6.2/real/GNU64/5.3/x86_64/lib 
/opt/cray/pe/hdf5-parallel/1.10.1.1/GNU/5.1/lib)
-- PETSC_LIBRARY_parmetis-64 not found! Call:
-- FIND_LIBRARY(PETSC_LIBRARY_parmetis-64 NAMES parmetis-64 HINTS 
/opt/cray/pe/petsc/3.7.6.2/real/GNU64/5.3/x86_64/lib 
/opt/cray/pe/hdf5-parallel/1.10.1.1/GNU/5.1/lib)
-- PETSC_LIBRARY_metis-64 not found! Call:
-- FIND_LIBRARY(PETSC_LIBRARY_metis-64 NAMES metis-64 HINTS 
/opt/cray/pe/petsc/3.7.6.2/real/GNU64/5.3/x86_64/lib 
/opt/cray/pe/hdf5-parallel/1.10.1.1/GNU/5.1/lib)
-- PETSC_LIBRARY_HYPRE-64 not found! Call:
-- FIND_LIBRARY(PETSC_LIBRARY_HYPRE-64 NAMES HYPRE-64 HINTS 
/opt/cray/pe/petsc/3.7.6.2/real/GNU64/5.3/x86_64/lib 
/opt/cray/pe/hdf5-parallel/1.10.1.1/GNU/5.1/lib)
-- PETSC_LIBRARY_sci_gnu_mpi_mp not found! Call:
-- FIND_LIBRARY(PETSC_LIBRARY_sci_gnu_mpi_mp NAMES sci_gnu_mpi_mp HINTS 
/opt/cray/pe/petsc/3.7.6.2/real/GNU64/5.3/x86_64/lib 
/opt/cray/pe/hdf5-parallel/1.10.1.1/GNU/5.1/lib)
-- PETSC_LIBRARY_sci_gnu_mp not found! Call:
-- FIND_LIBRARY(PETSC_LIBRARY_sci_gnu_mp NAMES sci_gnu_mp HINTS 
/opt/cray/pe/petsc/3.7.6.2/real/GNU64/5.3/x86_64/lib 
/opt/cray/pe/hdf5-parallel/1.10.1.1/GNU/5.1/lib)
-- PETSC_LIBRARY_ptscotch-64 not found! Call:
-- FIND_LIBRARY(PETSC_LIBRARY_ptscotch-64 NAMES ptscotch-64 HINTS 
/opt/cray/pe/petsc/3.7.6.2/real/GNU64/5.3/x86_64/lib 
/opt/cray/pe/hdf5-parallel/1.10.1.1/GNU/5.1/lib)
-- PETSC_LIBRARY_scotch-64 not found! Call:
-- FIND_LIBRARY(PETSC_LIBRARY_scotch-64 NAMES scotch-64 HINTS 
/opt/cray/pe/petsc/3.7.6.2/real/GNU64/5.3/x86_64/lib 
/opt/cray/pe/hdf5-parallel/1.10.1.1/GNU/5.1/lib)
-- PETSC_LIBRARY_ptscotcherr-64 not found! Call:
-- FIND_LIBRARY(PETSC_LIBRARY_ptscotcherr-64 NAMES ptscotcherr-64 HINTS 
/opt/cray/pe/petsc/3.7.6.2/real/GNU64/5.3/x86_64/lib 
/opt/cray/pe/hdf5-parallel/1.10.1.1/GNU/5.1/lib)
-- PETSC_LIBRARY_scotcherr-64 not found! Call:
-- FIND_LIBRARY(PETSC_LIBRARY_scotcherr-64 NAMES scotcherr-64 HINTS 
/opt/cray/pe/petsc/3.7.6.2/real/GNU64/5.3/x86_64/lib 
/opt/cray/pe/hdf5-parallel/1.10.1.1/GNU/5.1/lib)
-- Found PETSC_LIBRARY_hdf5_parallel
-- Found PETSC_LIBRARY_z
-- Performing Test PETSC_LIBRARY_dl
-- Performing Test PETSC_LIBRARY_dl - Success
--   PETSC_VERSION: 3.7.6.0
--   PETSC_LIBRARIES: 
/opt/cray/pe/petsc/3.7.6.2/real/GNU64/5.3/x86_64/lib/libcraypetsc_gnu_real-64.so;/opt/cray/pe/hdf5-parallel/1.10.1.1/GNU/5.1/lib/libhdf5_parallel.so;/usr/lib64/libz.so;dl;dl
--   PETSC_INCLUDE_DIRS: 
/opt/cray/pe/petsc/3.7.6.2/real/GNU64/5.3/x86_64/include;/opt/cray/pe/petsc/3.7.6.2/real/GNU64/5.3/x86_64/include;${PETSC_DIR}/include;${PETSC_DIR}/include;/opt/cray/pe/hdf5-parallel/1.10.1.1/GNU/5.1/include
--   PETSC_USER_INCLUDE_DIRS: 
/opt/cray/pe/petsc/3.7.6.2/real/GNU64/5.3/x86_64/include;/opt/cray/pe/petsc/3.7.6.2/real/GNU64/5.3/x86_64/include;${PETSC_DIR}/include;${PETSC_DIR}/include;/opt/cray/pe/hdf5-parallel/1.10.1.1/GNU/5.1/include
-- Found PETSC
-- DEAL_II_WITH_PETSC successfully set up with external dependencies.
The reason is that these libraries also have different names. For example, 
the GNU compiled metis-64 is named metis-