Hi Matthias,
I tried the cmake and make on the login and interactive compute nodes
with other versions of zlib modules. In all cases I obtain the same error
as I did earlier :
[100%] Building CXX object source/CMakeFiles/deal_II.dir/dummy.cc.o
[100%] Linking CXX shared library ../lib/libdeal_II.so
/usr/bin/ld: cannot find -lAtpSigHandler
/usr/bin/ld: cannot find -lAtpSigHCommData
make[2]: *** [source/CMakeFiles/deal_II.dir/build.make:1274:
lib/libdeal_II.so] Error 1
make[1]: *** [CMakeFiles/Makefile2:2879: source/CMakeFiles/deal_II.dir/all]
Error 2
make[1]: *** Waiting for unfinished jobs....
For all the versions of zlib modules loaded, in the 'detailed.log' file the
lines involving zlib dependencies are as follows :
# DEAL_II_WITH_ZLIB set up with external dependencies
# ZLIB_VERSION = 1.2.11
# ZLIB_INCLUDE_DIRS = /usr/include
# ZLIB_LIBRARIES = /usr/lib64/libz.so
I performed a make clean and deleted the files in the build directory
before running cmake with a different zlib module.
Based on one of your earlier suggestions I included the following
lines(with help from Johannes) in 'CMakeLists.txt' :
---------------------------------------------------------------------------------------------------
ENABLE_LANGUAGE_OPTIONAL(Fortran)
# Modification start - Lines included based on Matthias suggestion
message("Link directories: ${CMAKE_CXX_IMPLICIT_LINK_DIRECTORIES}")
message("Link libraries: ${CMAKE_CXX_IMPLICIT_LINK_LIBRARIES}")
message(FATAL_ERROR "exit")
# Modification end
#-------------------------------------------
VERBOSE_INCLUDE(${CMAKE_SOURCE_DIR}/cmake/setup_deal_ii.cmake)
---------------------------------------------------------------------------------------------------
and then executing cmake from the main build directory resulted in the
following output just before exiting :
Link directories:
/opt/cray/pe/hdf5/1.10.2.0/intel/16.0/lib;/opt/cray/dmapp/default/lib64;/opt/cray/pe/mpt/7.7.14/gni/mpich-intel/16.0/lib;/global/common/sw/cray/sles15/x86_64/zlib/1.2.11/gcc/8.2.0/pep2pal/lib;/opt/cray/pe/atp/2.1.3/libApp;/global/common/sw/cray/cnl7/haswell/petsc/3.11.2/intel/19.0.3.199/hocbntp/lib;/global/common/sw/cray/cnl7/haswell/hypre/2.15.1/intel/19.0.3.199/2jbygqt/lib;/global/common/sw/cray/cnl7/haswell/superlu-dist/6.1.1/intel/19.0.3.199/vnkv5xn/lib;/global/common/sw/cray/cnl7/haswell/metis/5.1.0/intel/19.0.3.199/fpy6uzj/lib;/global/common/sw/cray/cnl7/haswell/hypre/2.15.1/intel/19.0.3.199/j73evxt/lib;/global/common/sw/cray/cnl7/haswell/superlu-dist/6.1.1/intel/19.0.3.199/4m7cu62/lib;/global/common/sw/cray/cnl7/haswell/metis/5.1.0/intel/19.0.3.199/dkb63mv/lib;/opt/intel/compilers_and_libraries_2019.3.199/linux/compiler/lib/intel64;/opt/intel/compilers_and_libraries_2019.3.199/linux/mkl/lib/intel64;/opt/intel/compilers_and_libraries_2019.3.199/linux/compiler/lib/intel64_lin;/usr/lib64/gcc/x86_64-suse-linux/7;/usr/lib64;/lib64;/usr/x86_64-suse-linux/lib;/lib;/usr/lib
Link libraries:
hugetlbfs;AtpSigHandler;AtpSigHCommData;z;hdf5_hl;hdf5;hdf5_hl_cpp;hdf5_cpp;mpich_intel;mpichcxx_intel;stdc++;imf;m;ifcoremt;ifport;pthread;imf;svml;irng;stdc++;m;ipgo;decimal;cilkrts;stdc++;gcc;gcc_s;irc;svml;c;gcc;gcc_s;irc_s;dl;c
CMake Error at CMakeLists.txt:102 (message):
exit
-- Configuring incomplete, errors occurred!
>From the Link libraries output it looks like AtpSigHandler and
AtpSigHCommData are picked up. Is there anything else I can try? Thank you.
Best,
Aaditya
On Wednesday, August 26, 2020 at 5:31:53 PM UTC-4 Aaditya Lakshmanan wrote:
> Hi,
> Compiling deal.ii with DEAL_II_WITH_ZLIB=OFF and subsequently make -j 32
> install gives the same error as earlier :
>
> [100%] Building CXX object source/CMakeFiles/deal_II.dir/dummy.cc.o
> [100%] Linking CXX shared library ../lib/libdeal_II.so
> /usr/bin/ld: cannot find -lAtpSigHandler
> /usr/bin/ld: cannot find -lAtpSigHCommData
> make[2]: *** [source/CMakeFiles/deal_II.dir/build.make:1274:
> lib/libdeal_II.so] Error 1
> make[1]: *** [CMakeFiles/Makefile2:2879:
> source/CMakeFiles/deal_II.dir/all] Error 2
> make[1]: *** Waiting for unfinished jobs....
>
> So I will try with another zlib module than the one originally used. I
> have attached the 'detalied.log' file for my most recent attempt.
>
> Best,
> Aaditya
>
> On Wednesday, August 26, 2020 at 3:07:24 PM UTC-4 Matthias Maier wrote:
>
>>
>> On Wed, Aug 26, 2020, at 12:46 CDT, Johannes Blaschke <jpbla...@lbl.gov>
>> wrote:
>>
>> > HI Matthias,
>> >
>> > thanks for your input -- you might be onto something RE ld
>> >
>> > We use a wrapper script for ld:
>> > ```
>> > blaschke@cori06:~> which ld
>> > /global/common/cori/software/altd/2.0/bin/ld
>> > ```
>> > which is managed by the ALTD module (Automatic Library Tracking
>> Database).
>> > Using the system linker (which is what cmake is picking up) isn't
>> usually a
>> > problem, but in this case it might be. I checked Aaditya's loaded
>> modules
>> > and ALTD is in there, so CMake should be picking it up. How does CMake
>> > detect the linker? Is it just a question of adding
>> `-DCMAKE_LINKER=$(which
>> > ld)`?
>>
>> Yes, setting CMAKE_LINKER would be an option. But typically CMake just
>> invokes the compiler wrapper which should do the right thing...
>>
>> Best,
>> Matthias
>>
>
--
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/24978d8f-141e-424c-b98c-d0ec61395cd8n%40googlegroups.com.
