[deal.II] Lapack problem during cmake

Discussion:

Praveen C

2018-12-01 02:47:12 UTC

Dear all

I am trying to install dealii from master on Windows 10 under WSL (Ubuntu 18.04).

I am using these dependencies from spack

$ spack find
==> 55 installed packages
-- linux-ubuntu18.04-x86_64 / ***@7.3.0 -------------------------
adol-***@develop ***@3.13.0 ***@1.10.4 ***@2.9.8 ***@6.1 ***@0.3.3 ***@1.5.4 superlu-***@5.4.0
arpack-***@3.6.3 ***@3.6 ***@1.11.9 ***@1.4.18 ***@4.6.1 ***@3.1.3 ***@2.7.15 ***@1.5.0
***@4.0.1 ***@1.18.1 ***@2.15.1 ***@1.5.9 netcdf-***@4.2 ***@1.1.1 ***@7.0 ***@12.12.1
***@2.69 ***@0.9.7.1 intel-***@2019.2 ***@5.1.0 ***@5.3.1 ***@2.0 ***@3.10.1 util-***@1.19.1
***@1.16.1 ***@6.1.2 ***@0.13.5 ***@5.1.1 netlib-***@2.0.2 ***@4.0.3 ***@3.25.3 ***@5.2.4
***@1.68.0 ***@4.0.0 ***@2.11 ***@2.2.6.1 ***@2.0.11 ***@5.26.2 suite-***@5.3.0 ***@1.2.11
***@1.0.6 ***@2.5 ***@2.4.6 ***@1.2.3 ***@0.18.3 ***@3.10.2 ***@3.2.1

I have openblas installed but still get this error

-- Include /home/feynman/Applications/deal.II/git/cmake/configure/configure_1_lapack.cmake
-- Performing Test DEAL_II_HAVE_FLAG_pthread
WARNING: Target "cmTC_b60c9" requests linking to directory "/opt/spack/lib/". Targets may link only to libraries. CMake is dropping the item.
-- Performing Test DEAL_II_HAVE_FLAG_pthread - Success
-- Performing Test LAPACK_SYMBOL_CHECK
WARNING: Target "cmTC_be49e" requests linking to directory "/opt/spack/lib/". Targets may link only to libraries. CMake is dropping the item.
-- Performing Test LAPACK_SYMBOL_CHECK - Failed
-- Could not find a sufficient BLAS/LAPACK installation: BLAS/LAPACK symbol check failed! Consult CMakeFiles/CMakeError.log for further information.
-- DEAL_II_WITH_LAPACK has unmet external dependencies.
CMake Error at cmake/macros/macro_configure_feature.cmake:112 (MESSAGE):

Could not find the lapack library!

Could not find a sufficient BLAS/LAPACK installation:

BLAS/LAPACK symbol check failed! This usually means that your BLAS/LAPACK
installation is incomplete or the link line is broken. Consult

CMakeFiles/CMakeError.log

for further information.

Please ensure that a suitable lapack library is installed on your computer.

If the library is not at a default location, either provide some hints for
autodetection, or set the relevant variables by hand in ccmake.

Call Stack (most recent call first):
cmake/macros/macro_configure_feature.cmake:269 (FEATURE_ERROR_MESSAGE)
cmake/configure/configure_1_lapack.cmake:84 (CONFIGURE_FEATURE)
cmake/macros/macro_verbose_include.cmake:19 (INCLUDE)
CMakeLists.txt:124 (VERBOSE_INCLUDE)

-- Configuring incomplete, errors occurred!
See also "/home/feynman/Applications/deal.II/git/build/CMakeFiles/CMakeOutput.log".
See also "/home/feynman/Applications/deal.II/git/build/CMakeFiles/CMakeError.logâ.

Also attached output from cmake.

Thanks
praveen

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Wolfgang Bangerth

2018-12-01 15:14:02 UTC

Permalink

Post by Praveen C
-- Could not find a sufficient BLAS/LAPACK installation: BLAS/LAPACK symbol
check failed! Consult CMakeFiles/CMakeError.log for further information.

Praveen,
this is the error line you want to investigate. There is a corresponding
"SYMBOL_CHECK" in the CMakeError.log which looks like this:
|
Run Build Command:"/usr/bin/make" "cmTC_be49e/fast"
/usr/bin/make -f CMakeFiles/cmTC_be49e.dir/build.make
CMakeFiles/cmTC_be49e.dir/build
make[1]: Entering directory
'/home/feynman/Applications/deal.II/git/build/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_be49e.dir/src.c.o
/opt/spack/bin/mpicc -DLAPACK_SYMBOL_CHECK -pthread -o
CMakeFiles/cmTC_be49e.dir/src.c.o -c
/home/feynman/Applications/deal.II/git/build/CMakeFiles/CMakeTmp/src.c
Linking C executable cmTC_be49e
/home/feynman/Applications/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.3.0/cmake-3.13.0-e5iqhy3n3hs75xojhlpto4z5a76jvg6e/bin/cmake
-E cmake_link_script CMakeFiles/cmTC_be49e.dir/link.txt --verbose=1
/opt/spack/bin/mpicc -DLAPACK_SYMBOL_CHECK -pthread -rdynamic
CMakeFiles/cmTC_be49e.dir/src.c.o -o cmTC_be49e
CMakeFiles/cmTC_be49e.dir/src.c.o: In function `main':
src.c:(.text+0xa): undefined reference to `daxpy_'
src.c:(.text+0x14): undefined reference to `dgeev_'
|

What I do find confusing is that in the "Linking C executable" line, the
lapack/blas libraries are not actually listed. But then indeed right above the
cmake output quotes above, there is this warning:

-- Performing Test LAPACK_SYMBOL_CHECK
WARNING: Target "cmTC_be49e" requests linking to directory "/opt/spack/lib/".
Targets may link only to libraries. CMake is dropping the item.

So it looks like you maybe specified a *directory* for the libraries when you
needed to provide a *path*?

Best
W.
--
------------------------------------------------------------------------
Wolfgang Bangerth email: ***@colostate.edu
www: http://www.math.colostate.edu/~bangerth/

Praveen C

2018-12-03 03:51:04 UTC

Permalink

Sorry, there was a mistake in my script in setting LAPACK_LIBRARIES. This problem goes away.

Thanks
praveen

Post by Wolfgang Bangerth

Post by Praveen C
-- Could not find a sufficient BLAS/LAPACK installation: BLAS/LAPACK symbol
check failed! Consult CMakeFiles/CMakeError.log for further information.

Praveen,
this is the error line you want to investigate. There is a corresponding
|
Run Build Command:"/usr/bin/make" "cmTC_be49e/fast"
/usr/bin/make -f CMakeFiles/cmTC_be49e.dir/build.make
CMakeFiles/cmTC_be49e.dir/build
make[1]: Entering directory
'/home/feynman/Applications/deal.II/git/build/CMakeFiles/CMakeTmp'
Building C object CMakeFiles/cmTC_be49e.dir/src.c.o
/opt/spack/bin/mpicc -DLAPACK_SYMBOL_CHECK -pthread -o
CMakeFiles/cmTC_be49e.dir/src.c.o -c
/home/feynman/Applications/deal.II/git/build/CMakeFiles/CMakeTmp/src.c
Linking C executable cmTC_be49e
/home/feynman/Applications/spack/opt/spack/linux-ubuntu18.04-x86_64/gcc-7.3.0/cmake-3.13.0-e5iqhy3n3hs75xojhlpto4z5a76jvg6e/bin/cmake
-E cmake_link_script CMakeFiles/cmTC_be49e.dir/link.txt --verbose=1
/opt/spack/bin/mpicc -DLAPACK_SYMBOL_CHECK -pthread -rdynamic
CMakeFiles/cmTC_be49e.dir/src.c.o -o cmTC_be49e
src.c:(.text+0xa): undefined reference to `daxpy_'
src.c:(.text+0x14): undefined reference to `dgeev_'
|
What I do find confusing is that in the "Linking C executable" line, the
lapack/blas libraries are not actually listed. But then indeed right above the
-- Performing Test LAPACK_SYMBOL_CHECK
WARNING: Target "cmTC_be49e" requests linking to directory "/opt/spack/lib/".
Targets may link only to libraries. CMake is dropping the item.
So it looks like you maybe specified a *directory* for the libraries when you
needed to provide a *path*?
Best
W.
--
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