Re: [deal.II] deal.ii Installation : expand_instantiations Error

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

Re: [deal.II] deal.ii Installation : expand_instantiations Error

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

Re: [deal.II] deal.ii Installation : expand_instantiations Error

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

Re: [deal.II] deal.ii Installation : expand_instantiations Error

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

Re: [deal.II] deal.ii Installation : expand_instantiations Error

On Wed, Aug 26, 2020, at 12:46 CDT, Johannes Blaschke 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

Re: [deal.II] deal.ii Installation : expand_instantiations Error

On Wed, Aug 26, 2020, at 13:01 CDT, Aaditya Lakshmanan wrote: > Hi, > zlib(version 1.2.11) was already loaded as a module in all my previous > compilation attempts. I will try it by setting DEAL_II_WITH_ZLIB=OFF but I > am not sure why the path to zlib libraries is picked up from /usr .

Re: [deal.II] deal.ii Installation : expand_instantiations Error

Hi, zlib(version 1.2.11) was already loaded as a module in all my previous compilation attempts. I will try it by setting DEAL_II_WITH_ZLIB=OFF but I am not sure why the path to zlib libraries is picked up from /usr . Thanks for the suggestion. Best, Aaditya On Wednesday, August 26, 2020

Re: [deal.II] deal.ii Installation : expand_instantiations Error

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

Re: [deal.II] deal.ii Installation : expand_instantiations Error

Thanks. This looks mostly good. In particular, the Lapack CMake module seems to pick up "AtpSigHandler" and "AtpSigHCommData": 55 #DEAL_II_WITH_LAPACK set up with external dependencies 56 #LAPACK_WITH_64BIT_BLAS_INDICES = OFF

Re: [deal.II] deal.ii Installation : expand_instantiations Error

Hi Matthias, I have attached the 'detailed.log' file here. I will attempt what you suggested. Thank you. Best, Aaditya On Tuesday, August 25, 2020 at 5:10:30 PM UTC-4 Matthias Maier wrote: > > On Tue, Aug 25, 2020, at 00:07 CDT, Johannes Blaschke > wrote: > > > But I am available to work

Re: [deal.II] deal.ii Installation : expand_instantiations Error

On Tue, Aug 25, 2020, at 00:07 CDT, Johannes Blaschke wrote: > But I am available to work with you directly -- however I cannot debug this > on my own (as the cmake setup is pretty huge!). Please have a look at the file `detailed.log` found in the build directory. It spells out the

Re: [deal.II] deal.ii Installation : expand_instantiations Error

Would you mind quickly sending us the file `detailed.log` that you can find in the build directory? This would help us a lot. On Mon, Aug 24, 2020, at 16:40 CDT, Aaditya Lakshmanan wrote: > [100%] Built target obj_fe_debug > [100%] Linking CXX shared library ../lib/libdeal_II.g.so >

Re: [deal.II] deal.ii Installation : expand_instantiations Error

Hi all y'all I am the consultant helping Aaditya compile deal.II on NERSC's Cori system. Let me start by trying to address Wolfgang's questions: > that would help, but the question is why that is necessary Good question! I've never had to do this myself (the cray compiler wrappers usually

Re: [deal.II] deal.ii Installation : expand_instantiations Error

On 8/24/20 3:40 PM, Aaditya Lakshmanan wrote: I am not sure what the above means. I contacted support at NERSC for help and he responded as follows : - The problem is that somewhere in the

Re: [deal.II] deal.ii Installation : expand_instantiations Error

Hi Matthias, I followed the steps you suggested so that expand_instantiations gave the output : Usage: expand_instantiations class_list_files < in_file > out_file after which I changed to the regular build directory for building(all performed on an interactive compute node ) as cmake

Re: [deal.II] deal.ii Installation : expand_instantiations Error

Hi, CMake's cross compilation features are unfortunately a bit limited. To work around this you have to create an executable "expand_instantiations" separately by doing for example the following in the source directory: $ mkdir build-executable $ cd build-executable $ cmake .. $ make

Re: [deal.II] deal.ii Installation : expand_instantiations Error

I tried compilation on the compute node with PrgEnv-intel loaded and including CMAKE_SYSTEM_NAME=CrayLinuxEnvironment in the cmake line. Upon make install it yielded the same error that I got earlier : Scanning dependencies of target obj_numerics_inst [ 41%] Generating data_out_dof_data.inst

Re: [deal.II] deal.ii Installation : expand_instantiations Error

Hi Timo, Thank you for sharing the link for cross-compilation of dealii. In the same webpage there is a link to information about cmake toolchain information and in that webpage I found the following : Cross Compiling

Re: [deal.II] deal.ii Installation : expand_instantiations Error

Hi Aaditya, it looks like you are cross compiling due to the cray system you are on? I don't have first-hand experience, but I know some users have had success with it in the past. The error message stems from the fact that we build a small tool "expand_instantiations" during the build process.

Re: [deal.II] deal.ii Installation : expand_instantiations Error

Hi Jean-Paul, I cleaned the previous installation, deleted all the files generated in the build directory and attempted a fresh build process as follows : cmake -DCMAKE_SYSTEM_NAME=CrayLinuxEnvironment -DCMAKE_C_COMPILER=cc -DCMAKE_CXX_COMPILER=CC -DCMAKE_Fortran_COMPILER=ftn

Re: [deal.II] deal.ii Installation : expand_instantiations Error

Hi Aaditya, Great, let us know if that works for you. You should see the expand_instantiations binary appear in the “bin” sub-directory with your build folder. If it still doesn’t appear there, then perhaps you could create a new build directory and then post the configuration and full build

Re: [deal.II] deal.ii Installation : expand_instantiations Error

Hi Jean-Paul, Thank you for your suggestion. I shall try the installation process with fewer processors(perhaps 4) and if even that doesn't work, then I will try it in serial. Best, Aaditya On Friday, August 21, 2020 at 1:07:54 PM UTC-4 Jean-Paul Pelteret wrote: > Hi Aaditaya, > > I don’t

Re: [deal.II] deal.ii Installation : expand_instantiations Error

Hi Aaditaya, I don’t think that I’ve ever seen anyone have this problem before. We build the expand_instantiations binary, and its supposed to be used when expanding files in which we define various combinations of template parameters to instantiate templates within the library. If you’re