Hi Aaditya and Johannes,
My reply might be too late to be of help. About an year ago, I ran into a
host of problems for installing dealii on Cray X50. I have posted all the
details to get a working installation here
https://groups.google.com/g/dealii/c/MCYyPrZNyjg/m/bVS1woSXBgAJ.
The workaround I figured for the issue here (atp libs) is to unload the atp
module before configuring. I faced the exact same error and this worked for
me. I hope this would be of help.
Thanks,
Vachan
On Sunday, August 30, 2020 at 5:31:47 AM UTC+5:30 jpbla...@lbl.gov wrote:
> Hi y'all,
>
> I just wanted to update y'all on what we've learned so far:
>
> 1) message("Link directories: ${CMAKE_CXX_IMPLICIT_LINK_DIRECTORIES}")
>
> Shows `/opt/cray/pe/atp/2.1.3/libApp` as one of the entries -- this is
> the home of AtpSigHandler.so, so (in theory) cmake should find it.
>
> 2) Including `find_library(ATP_SIGHANDLER_LIBRARY NAMES AtpSigHandler)`
> gives the following error:
>
> CMake Error: The following variables are used in this project, but they
> are set to NOTFOUND.
> Please set them or make sure they are set and tested correctly in the
> CMake files:
> ATP_SIGHANDLER_LIBRARY
> linked by target "deal_II.g" in directory
> /global/project/projectdirs/m2360/packagesCPFE/dealii/source
> linked by target "deal_II" in directory
> /global/project/projectdirs/m2360/packagesCPFE/dealii/source
>
> -- Configuring incomplete, errors occurred
>
> When adding `ATP_SIGHANDLER_LIBRARY` to target_link_library in
> source/CMakeLists.txt
>
> My theory is that find_library is not detecting libAtpSigHandler.so -- but
> why?
>
> Cheers,
> Johannes
>
> On Thursday, August 27, 2020 at 3:06:12 PM UTC-7 aadit...@gmail.com wrote:
>
>> 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
>>>>
>>>
--
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