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-64_gnu_61 and sci_gnu_mpi_mp is
named sci_gnu_61_mpi_mp. I had a look at FindPETSC.cmake and noticed that
there is no explicit listing of these libraries where I could change their
names as I did for petsc itself (see beginning of 2nd point). Is there a
way I can tackle this issue?
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?
Thanks
--
The deal.II project is located at http://www.dealii.org/
For mailing list/forum options, see
https://groups.google.com/d/forum/dealii?hl=en
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