Closed jhornung-gh closed 1 year ago
On centos7
submit machine lxbk0596
( should be the same for any centos7 submit node on virgo)
Commands:
dbertini@lxbk0596:~/gsi_git/mpi-sdf2opmd > . ./setup_mpi.sh -c gcc8
selected compiler = gcc8
selected vae: centos7
loading spack gcc v8 + openmpi v3.1...
General setup ->
gcc is /cvmfs/vae.gsi.de/centos7/spack-0.17/opt/linux-centos7-x86_64/gcc-4.8.5/gcc-8.1.0-nswpump2zjkpne3ipmxkqt75dq6s2g7w/bin/gcc
mpicc is /cvmfs/vae.gsi.de/centos7/spack-0.17/opt/linux-centos7-zen/gcc-8.1.0/openmpi-3.1.6-mzgrfwlfj5it47wjcnz7el56ttf6rour/bin/mpicc
python is /cvmfs/vae.gsi.de/centos7/spack-0.17/opt/linux-centos7-zen/gcc-8.1.0/python-3.8.12-27khn6eagb3ieg2mfelcpnczrdpd25bg/bin/python
Epoch setup ->
epoch1d is /lustre/rz/dbertini/plasma/epoch_dev/epoch1d/bin/epoch1d
epoch2d is /lustre/rz/dbertini/plasma/epoch_dev/epoch2d/bin/epoch2d
epoch3d is /lustre/rz/dbertini/plasma/epoch_dev/epoch3d/bin/epoch3d
and
dbertini@lxbk0596:~/gsi_git/mpi-sdf2opmd > cd ../
dbertini@lxbk0596:~/gsi_git > mkdir build_test
dbertini@lxbk0596:~/gsi_git > cd build_test
dbertini@lxbk0596:~/gsi_git/build_test > cmake ../mpi-sdf2opmd
-- The C compiler identification is GNU 8.1.0
-- The CXX compiler identification is GNU 8.1.0
-- The Fortran compiler identification is GNU 8.1.0
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Check for working C compiler: /cvmfs/vae.gsi.de/centos7/spack-0.17/opt/linux-centos7-x86_64/gcc-4.8.5/gcc-8.1.0-nswpump2zjkpne3ipmxkqt75dq6s2g7w/bin/gcc - skipped
-- Detecting C compile features
-- Detecting C compile features - done
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /cvmfs/vae.gsi.de/centos7/spack-0.17/opt/linux-centos7-x86_64/gcc-4.8.5/gcc-8.1.0-nswpump2zjkpne3ipmxkqt75dq6s2g7w/bin/g++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Check for working Fortran compiler: /cvmfs/vae.gsi.de/centos7/spack-0.17/opt/linux-centos7-x86_64/gcc-4.8.5/gcc-8.1.0-nswpump2zjkpne3ipmxkqt75dq6s2g7w/bin/gfortran - skipped
-- Checking whether /cvmfs/vae.gsi.de/centos7/spack-0.17/opt/linux-centos7-x86_64/gcc-4.8.5/gcc-8.1.0-nswpump2zjkpne3ipmxkqt75dq6s2g7w/bin/gfortran supports Fortran 90
-- Checking whether /cvmfs/vae.gsi.de/centos7/spack-0.17/opt/linux-centos7-x86_64/gcc-4.8.5/gcc-8.1.0-nswpump2zjkpne3ipmxkqt75dq6s2g7w/bin/gfortran supports Fortran 90 - yes
-- Found MPI_C: /cvmfs/vae.gsi.de/centos7/spack-0.17/opt/linux-centos7-zen/gcc-8.1.0/openmpi-3.1.6-mzgrfwlfj5it47wjcnz7el56ttf6rour/lib/libmpi.so (found version "3.1")
-- Found MPI_CXX: /cvmfs/vae.gsi.de/centos7/spack-0.17/opt/linux-centos7-zen/gcc-8.1.0/openmpi-3.1.6-mzgrfwlfj5it47wjcnz7el56ttf6rour/lib/libmpi_cxx.so (found version "3.1")
-- Found MPI_Fortran: /cvmfs/vae.gsi.de/centos7/spack-0.17/opt/linux-centos7-zen/gcc-8.1.0/openmpi-3.1.6-mzgrfwlfj5it47wjcnz7el56ttf6rour/lib/libmpi_usempif08.so (found version "3.1")
-- Found MPI: TRUE (found version "3.1")
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP_Fortran: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- MPI_INCLUDE_PATH : /cvmfs/vae.gsi.de/centos7/spack-0.17/opt/linux-centos7-zen/gcc-8.1.0/openmpi-3.1.6-mzgrfwlfj5it47wjcnz7el56ttf6rour/include
-- C++ compiler is : /cvmfs/vae.gsi.de/centos7/spack-0.17/opt/linux-centos7-x86_64/gcc-4.8.5/gcc-8.1.0-nswpump2zjkpne3ipmxkqt75dq6s2g7w/bin/g++
-- C++ compiler Flags are : -fPIC -Wshadow -Wall -W -Woverloaded-virtual -fsigned-char -Wextra -std=c++17 -g
-- C++ compiler identification is : GNU
-- EPOCH PATH is : /lustre/rz/dbertini/plasma/epoch_dev
-- EPOCH SDF PATH is : /lustre/rz/dbertini/plasma/epoch_dev/SDF/FORTRAN
-- MPI_INCLUDE_PATH : /cvmfs/vae.gsi.de/centos7/spack-0.17/opt/linux-centos7-zen/gcc-8.1.0/openmpi-3.1.6-mzgrfwlfj5it47wjcnz7el56ttf6rour/include
-- ROOT_INCLUDE_PATH :
-- C++ compiler is : /cvmfs/vae.gsi.de/centos7/spack-0.17/opt/linux-centos7-x86_64/gcc-4.8.5/gcc-8.1.0-nswpump2zjkpne3ipmxkqt75dq6s2g7w/bin/g++
-- C++ compiler Flags are : -fPIC -Wshadow -Wall -W -Woverloaded-virtual -fsigned-char -Wextra -std=c++17 -g
-- C++ compiler identification is : GNU
-- EPOCH PATH is : /lustre/rz/dbertini/plasma/epoch_dev
-- EPOCH SDF PATH is : /lustre/rz/dbertini/plasma/epoch_dev/SDF/FORTRAN
-- Found HDF5: hdf5-shared (found version "1.10.7")
-- Found ADIOS2: /lustre/rz/dbertini/soft/adios2/lib64/cmake/adios2/adios2-config.cmake (found version "2.8.3") found components: C CXX Fortran MPI
-- Configuring done
-- Generating done
-- Build files have been written to: /u/dbertini/gsi_git/build_test
So could you cross-check your build using . ./setup_mpi.sh -c gcc8
instead ?
BTW trying without source the setup script ( ./setup_mpi.sh -c gcc8
) gives me immediately the following problem:
dbertini@lxbk0595:~/gsi_git/mpi-sdf2opmd > ./setup_mpi.sh -c gcc8
selected compiler = gcc8
selected vae: centos7
loading spack gcc v8 + openmpi v3.1...
General setup ->
gcc is /cvmfs/vae.gsi.de/centos7/spack-0.17/opt/linux-centos7-x86_64/gcc-4.8.5/gcc-8.1.0-nswpump2zjkpne3ipmxkqt75dq6s2g7w/bin/gcc
mpicc is /cvmfs/vae.gsi.de/centos7/spack-0.17/opt/linux-centos7-zen/gcc-8.1.0/openmpi-3.1.6-mzgrfwlfj5it47wjcnz7el56ttf6rour/bin/mpicc
python is /cvmfs/vae.gsi.de/centos7/spack-0.17/opt/linux-centos7-zen/gcc-8.1.0/python-3.8.12-27khn6eagb3ieg2mfelcpnczrdpd25bg/bin/python
Epoch setup ->
epoch1d is /lustre/rz/dbertini/plasma/epoch_dev/epoch1d/bin/epoch1d
epoch2d is /lustre/rz/dbertini/plasma/epoch_dev/epoch2d/bin/epoch2d
epoch3d is /lustre/rz/dbertini/plasma/epoch_dev/epoch3d/bin/epoch3d
dbertini@lxbk0595:~/gsi_git/mpi-sdf2opmd > ls
CMakeLists.txt LICENSE README.md sdf2opmd_1d/ sdf2opmd_2d/ sdf2opmd_3d/ setup_mpi.sh*
dbertini@lxbk0595:~/gsi_git/mpi-sdf2opmd > cd ..
dbertini@lxbk0595:~/gsi_git > mkdir build-test
dbertini@lxbk0595:~/gsi_git > cd build-test/
dbertini@lxbk0595:~/gsi_git/build-test > cmake ../mpi-sdf2opmd
CMake Error at CMakeLists.txt:1 (cmake_minimum_required):
CMake 3.2 or higher is required. You are running version 2.8.12.2
-- Configuring incomplete, errors occurred!
I am wondering why in you case you do not see the CMake
version problem, user-defined profile ?
I have this issue if I don't load the modulefiles from cvmfs.
Not sure what exactly the problem was, if it was the use of quotes for the "gcc8" or if I am not allowed to call cmake within the base folder and I have to create a build folder. Now the compilation works.
Thank you! I will try to run it after lunch.
great !
Hi Denis, it seems like you changed the directory of the epoch installation which affects the sdf2opmd converter. Can you tell me the path of the new "/lustre/rz/dbertini/plasma/epoch_dev" directory which I should include?
I tried to exchange it by "/lustre/rz/dbertini/plasma/epoch_git" but I only get warnings of non-existing include directories and I cannot build the fortran code using "make" in the "sdf2opmd_2d" subfolder. Running cmake on "mpi-sdf2opmd" works fine.
Cheers,
Johannes
Sorry for that, i recreated the link epoch_dev to
bertini@lxbk0596:/lustre/rz/dbertini/plasma > ls -al epoch_dev
lrwxrwxrwx. 1 dbertini 14 Feb 20 13:03 epoch_dev -> epoch-4.17.13//
Tell me if this works now
Unfortunately not. I tried it with "epoch_dev" and by exchanging it to "epoch-4.17.13", however I always get an error when trying to compile the fortran code. See the attached image.
Running the setup_mpi.sh and performing cmake runs without errors.
Sorry my mistake ! Should be fixed now ! Just now, compilation ran ok:
dbertini@lxbk0596:~/gsi_git/sdf2opmd-build > make clean
dbertini@lxbk0596:~/gsi_git/sdf2opmd-build > make
[ 14%] Building Fortran object sdf2opmd_2d/CMakeFiles/SDFOPMD2D.dir/src/sdf_reader.f90.o
f951: Warning: Nonexistent include directory '/u/dbertini/gsi_git/mpi-sdf2opmd/sdf2opmd_2d/include' [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory '/u/dbertini/gsi_git/mpi-sdf2opmd/sdf2opmd_2d/}' [-Wmissing-include-dirs]
f951: Warning: command line option '-fpermissive' is valid for C++/ObjC++ but not for Fortran
[ 28%] Building Fortran object sdf2opmd_2d/CMakeFiles/SDFOPMD2D.dir/src/sdf_interface.f90.o
f951: Warning: Nonexistent include directory '/u/dbertini/gsi_git/mpi-sdf2opmd/sdf2opmd_2d/include' [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory '/u/dbertini/gsi_git/mpi-sdf2opmd/sdf2opmd_2d/}' [-Wmissing-include-dirs]
f951: Warning: command line option '-fpermissive' is valid for C++/ObjC++ but not for Fortran
[ 42%] Linking CXX shared library libSDFOPMD2D.so
[ 42%] Built target SDFOPMD2D
[ 57%] Building CXX object sdf2opmd_2d/converter/CMakeFiles/sdf2opmd_2d.dir/sdf2opmd_2d.cxx.o
/u/dbertini/gsi_git/mpi-sdf2opmd/sdf2opmd_2d/converter/sdf2opmd_2d.cxx: In function 'int main(int, char**)':
/u/dbertini/gsi_git/mpi-sdf2opmd/sdf2opmd_2d/converter/sdf2opmd_2d.cxx:372:8: warning: unused variable 'mpi_size' [-Wunused-variable]
auto mpi_size = static_cast<uint64_t>(mpi_s);
^~~~~~~~
/u/dbertini/gsi_git/mpi-sdf2opmd/sdf2opmd_2d/converter/sdf2opmd_2d.cxx:373:8: warning: unused variable 'mpi_rank' [-Wunused-variable]
auto mpi_rank = static_cast<uint64_t>(mpi_r);
^~~~~~~~
[ 71%] Linking CXX executable sdf2opmd_2d
[ 71%] Built target sdf2opmd_2d
[ 85%] Building CXX object sdf2opmd_2d/reader/CMakeFiles/opmd_reader_2d.dir/opmd_reader_2d.cxx.o
[100%] Linking CXX executable opmd_reader_2d
[100%] Built target opmd_reader_2d
Thanks for the help, now it is working again :)
Cheers
Great !
Hi,
I have some difficulties with the installation. Step by step I am
This results in the output![attachment_1](https://user-images.githubusercontent.com/85337548/213647056-5c85f3c8-4754-4feb-9b72-d7a7e7728d30.PNG)
This results in the following output and error![attachment_2](https://user-images.githubusercontent.com/85337548/213647303-0dca765e-8832-443b-b3d2-1cc78df40858.PNG)
I also attached the CMake Error and Output files.
CMakeOutput.log CMakeError.log
Am I doing something wrong?
Thanks,
Johannes