I fixed the failing gmsh test case. I am reporting it here, just in case
someone else faced the same problem. It turned out that the gmsh I was
using was linking to the blas library shipped with Ubuntu, but since my
manually installed openblas appeared first on my path, gmsh wasn't picking
up the right blas library. I ended up installing gmsh on my ubuntu machine
and had deal.ii use the manually installed gmsh library, instead. Now all
deal.ii tests pass
Thanks everyone for their suggestions and help
On Wednesday, July 3, 2019 at 1:46:21 PM UTC-4, Ahmad Shahba wrote:
>
> Thanks Jean-Paul and Bruno for your input
>
> *Regarding OpenBLAS:* I installed OpenBLAS, reconfigured PETSc (to use
> OpenBLAS). Using the following CMake invocation
>
> export PREFIX_PETSC_ARCH=$PETSC_DIR/$PETSC_ARCH
>
> cmake \
> -DDEAL_II_COMPONENT_DOCUMENTATION=OFF \
> -DGSL_DIR=$HOME/workspace/gsl \
> -DHDF5_DIR=$PREFIX_PETSC_ARCH \
> -DMETIS_DIR=$PREFIX_PETSC_ARCH \
> -DP4EST_DIR=$HOME/workspace/p4est-2.2/FAST \
> -DDEAL_II_WITH_P4EST=ON \
> -DPETSC_DIR=$PETSC_DIR \
> -DPETSC_ARCH=$PETSC_ARCH \
> -DSLEPC_DIR=$SLEPC_DIR \
> -DZLIB_DIR=$PREFIX_PETSC_ARCH \
> -DDEAL_II_WITH_LAPACK=ON \
> -DLAPACK_FOUND=true \
> -DLAPACK_LIBRARIES="/opt/OpenBLAS/lib/libopenblas.so" \
> -DLAPACK_LINKER_FLAGS="-lgfortran -lpthread -lm -ldl" \
> -DDEAL_II_WITH_MPI=ON \
> -DCMAKE_INSTALL_PREFIX=$installationPath \
> ../
>
> Now I can successfully configure deal.ii and compile the library. I am
> running the post-installation tests by invoking
>
> make test
>
> I see that all the tests pass except for one related to *gmsh*. It
> produces an error
>
> This exception -- which is used in many places in the library -- usually
> indicates that some condition which the author of the code thought must be
> satisfied at a certain point in an algorithm, is not fulfilled. An example
> would be that the first part of an algorithm sorts elements of an array in
> ascending order, and a second part of the algorithm later encounters an
> element that is not larger than the previous one.
> There is usually not very much you can do if you encounter such an
> exception since it indicates an error in deal.II, not in your own program.
>
> I am going to post this issue as another question in the forum
>
> *Regarding LAPACK/BLAS in MKL: *It appears that I was missing one library
> (*libmkl_intel_lp64.so*). I reconfigured deal.ii using the following
> CMake command
>
> export PREFIX_PETSC_ARCH=$PETSC_DIR/$PETSC_ARCH
> cmake \
> -DDEAL_II_COMPONENT_DOCUMENTATION=OFF \
> -DGSL_DIR=$HOME/workspace/gsl \
> -DHDF5_DIR=$PREFIX_PETSC_ARCH \
> -DMETIS_DIR=$PREFIX_PETSC_ARCH \
> -DP4EST_DIR=$HOME/workspace/p4est-2.2/FAST \
> -DDEAL_II_WITH_P4EST=ON \
> -DPETSC_DIR=$PETSC_DIR \
> -DPETSC_ARCH=$PETSC_ARCH \
> -DSLEPC_DIR=$SLEPC_DIR \
> -DZLIB_DIR=$PREFIX_PETSC_ARCH \
> -DDEAL_II_WITH_LAPACK=ON \
> -DLAPACK_FOUND=true \
> -DLAPACK_LIBRARIES=
> "${MKLROOT}/lib/intel64/libmkl_blas95_lp64.a;${MKLROOT}/lib/intel64/libmkl_lapack95_lp64.a;${MKLROOT}/lib/intel64/libmkl_gf_lp64.a;${MKLROOT}/lib/intel64/libmkl_intel_lp64.so;${MKLROOT}/lib/intel64/libmkl_sequential.so;${MKLROOT}/lib/intel64/libmkl_core.so"
>
> \
> -DLAPACK_LINKER_FLAGS="-lgfortran -lpthread -lm -ldl" \
> -DDEAL_II_WITH_BLAS=ON \
> -DBLAS_FOUND=true \
> -DBLAS_LIBRARIES=
> "${MKLROOT}/lib/intel64/libmkl_blas95_lp64.a;${MKLROOT}/lib/intel64/libmkl_lapack95_lp64.a;${MKLROOT}/lib/intel64/libmkl_gf_lp64.a;${MKLROOT}/lib/intel64/libmkl_intel_lp64.so;${MKLROOT}/lib/intel64/libmkl_sequential.so;${MKLROOT}/lib/intel64/libmkl_core.so"
>
> \
> -DBLAS_LINKER_FLAGS="-lgfortran -lpthread -lm -ldl" \
> -DSCALAPACK_DIR==$PREFIX_PETSC_ARCH \
> -DDEAL_II_WITH_MPI=ON \
> -DCMAKE_INSTALL_PREFIX=$installationPath \
> ../
>
> CMake still fails to locate LAPACK/BLAS. The *CMakeError.Log* file is
> attached. Bruno's comment and previous post
> <https://groups.google.com/forum/#!topic/dealii/W9roLJ9r71g> made me
> think of something. The LAPACK and BLAS libraries provided in MKL are
> static .a libraries. Could this be the reason why CMake cannot locate
> them?
>
>
> On Wednesday, July 3, 2019 at 9:49:40 AM UTC-4, Bruno Turcksin wrote:
>>
>> Ahmad,
>>
>> The first thing is that you should not try to set the flags yourself. You
>> should let CMake take care of that. You should just set the paths (BLAS_DIR
>> and LAPACK_DIR) and let CMake do the rest. The second thing is that I am
>> not sure sure that you are using the right MKL libraries. You can go here
>> <https://software.intel.com/en-us/articles/intel-mkl-link-line-advisor>
>> to check what you need.
>>
>> Best,
>>
>> Bruno
>>
>> On Tuesday, July 2, 2019 at 7:18:40 PM UTC-4, Ahmad Shahba wrote:
>>>
>>> I am trying to compile deal.ii (version 9.1.1) on my Ubuntu laptop with
>>> gcc compilers. I have tried two methods to configure deal.ii with
>>> LAPACK/BLAS and both failed in a similar manner.
>>>
>>> *method 1: Using LAPACK/BLAS in my PETSc (version 3.9) installation*
>>> Motivated by the instructions given here
>>> <https://dealii.org/developer/users/cmake.html#advanced>, I use the
>>> following CMake command
>>>
>>>
>>> export PREFIX_PETSC_ARCH=$PETSC_DIR/$PETSC_ARCH
>>>
>>> cmake \
>>> -DDEAL_II_COMPONENT_DOCUMENTATION=OFF \
>>> -DGSL_DIR=$HOME/workspace/gsl \
>>> -DHDF5_DIR=$PREFIX_PETSC_ARCH \
>>> -DMETIS_DIR=$PREFIX_PETSC_ARCH \
>>> -DP4EST_DIR=$HOME/workspace/p4est-2.2/FAST \
>>> -DDEAL_II_WITH_P4EST=ON \
>>> -DPETSC_DIR=$PETSC_DIR \
>>> -DPETSC_ARCH=$PETSC_ARCH \
>>> -DSLEPC_DIR=$SLEPC_DIR \
>>> -DZLIB_DIR=$PREFIX_PETSC_ARCH \
>>> -DDEAL_II_WITH_LAPACK=ON \
>>> -DLAPACK_FOUND=true \
>>>
>>>
>>> -DLAPACK_LIBRARIES="$PREFIX_PETSC_ARCH/lib/libflapack.a;$PREFIX_PETSC_ARCH/lib/libfblas.a"
>>>
>>> \
>>> -DLAPACK_LINKER_FLAGS="-lgfortran -lm" \
>>> -DDEAL_II_WITH_MPI=ON \
>>> -DCMAKE_INSTALL_PREFIX=path/to/some/installation/directory \
>>> ../
>>>
>>> The configuration fails with prints an error message like
>>>
>>> BLAS/LAPACK symbol check failed! This usually means that your BLAS/LAPACK
>>> installation is incomplete or the link line is broken.
>>>
>>> I am attaching some CMake log and error files.
>>>
>>> *method 2:Linking to the LAPACK/BLAS whick comes with MKL*
>>> For another project, I had use gfortran to compile LAPACK/BLAS which
>>> comes with Intel MKL. Linking to these libraries also failed in the same
>>> manner. Here is the CMake command
>>>
>>> export PREFIX_PETSC_ARCH=$PETSC_DIR/$PETSC_ARCH
>>>
>>> cmake \
>>> -DDEAL_II_COMPONENT_DOCUMENTATION=OFF \
>>> -DGSL_DIR=$HOME/workspace/gsl \
>>> -DHDF5_DIR=$PREFIX_PETSC_ARCH \
>>> -DMETIS_DIR=$PREFIX_PETSC_ARCH \
>>> -DP4EST_DIR=$HOME/workspace/p4est-2.2/FAST \
>>> -DDEAL_II_WITH_P4EST=ON \
>>> -DPETSC_DIR=$PETSC_DIR \
>>> -DPETSC_ARCH=$PETSC_ARCH \
>>> -DSLEPC_DIR=$SLEPC_DIR \
>>> -DZLIB_DIR=$PREFIX_PETSC_ARCH \
>>> -DDEAL_II_WITH_LAPACK=ON \
>>> -DLAPACK_FOUND=true \
>>>
>>>
>>> -DLAPACK_LIBRARIES="${myInstallations}/lib/intel64/libmkl_blas95_lp64.a;${myInstallations}/lib/intel64/libmkl_lapack95_lp64.a;${MKLROOT}/lib/intel64/libmkl_gf_lp64.a;${MKLROOT}/lib/intel64/libmkl_sequential.a;${MKLROOT}/lib/intel64/libmkl_core.a"
>>>
>>> \
>>> -DLAPACK_LINKER_FLAGS="-lgfortran -lpthread -lm -ldl" \
>>> -DDEAL_II_WITH_BLAS=ON \
>>> -DBLAS_FOUND=true \
>>>
>>>
>>> -DBLAS_LIBRARIES="${myInstallations}/lib/intel64/libmkl_blas95_lp64.a;${myInstallations}/lib/intel64/libmkl_lapack95_lp64.a;${MKLROOT}/lib/intel64/libmkl_gf_lp64.a;${MKLROOT}/lib/intel64/libmkl_sequential.a;${MKLROOT}/lib/intel64/libmkl_core.a"
>>>
>>> \
>>> -DBLAS_LINKER_FLAGS="-lgfortran -lpthread -lm -ldl" \
>>> -DSCALAPACK_DIR==$PREFIX_PETSC_ARCH \
>>> -DDEAL_II_WITH_MPI=ON \
>>> -DCMAKE_INSTALL_PREFIX=path/to/some/installation/directory \
>>> ../
>>>
>>>
>>> Any thoughts how I can get this done?
>>> Thanks in advance,
>>> Ahmad
>>>
>>>
>>
--
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
---
You received this message because you are subscribed to the Google Groups
"deal.II User Group" group.
To unsubscribe from this group and stop receiving emails from it, send an email
to dealii+unsubscr...@googlegroups.com.
To view this discussion on the web visit
https://groups.google.com/d/msgid/dealii/7dbb9aa7-6b50-44fc-bb91-8dd6fcbf3456%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.
