FLUSI compiling issue

[balbir1313]

balbir@quanta:~/FLUSI$ make -j1
mkdir -p obj
mpif90 -g -Jobj -Wuninitialized -fimplicit-none -fbounds-check -g -ggdb -fbacktrace -O3 -I/home/balbir/src/p3dfft-2.7.9/include -I/home/balbir/src/fftw-3.3.9/include -cpp -I/home/balbir/src/hdf5-1.12.1/include -c -o obj/module_timing.o src/module_timing.f90 -L/home/balbir/src/p3dfft-2.7.9/lib -lp3dfft -L/home/balbir/src/fftw-3.3.9/lib -lfftw3 -L/home/balbir/src/hdf5-1.12.1/lib -lhdf5_fortran -lhdf5 -llapack -lblas -lz -ldl -lm
mpif90 -g -Jobj -Wuninitialized -fimplicit-none -fbounds-check -g -ggdb -fbacktrace -O3 -I/home/balbir/src/p3dfft-2.7.9/include -I/home/balbir/src/fftw-3.3.9/include -cpp -I/home/balbir/src/hdf5-1.12.1/include -c -o obj/vars.o src/vars.f90 -L/home/balbir/src/p3dfft-2.7.9/lib -lp3dfft -L/home/balbir/src/fftw-3.3.9/lib -lfftw3 -L/home/balbir/src/hdf5-1.12.1/lib -lhdf5_fortran -lhdf5 -llapack -lblas -lz -ldl -lm
mpif90 -g -Jobj -Wuninitialized -fimplicit-none -fbounds-check -g -ggdb -fbacktrace -O3 -I/home/balbir/src/p3dfft-2.7.9/include -I/home/balbir/src/fftw-3.3.9/include -cpp -I/home/balbir/src/hdf5-1.12.1/include -c -o obj/module_helpers.o src/module_helpers.f90 -L/home/balbir/src/p3dfft-2.7.9/lib -lp3dfft -L/home/balbir/src/fftw-3.3.9/lib -lfftw3 -L/home/balbir/src/hdf5-1.12.1/lib -lhdf5_fortran -lhdf5 -llapack -lblas -lz -ldl -lm
mpif90 -g -Jobj -Wuninitialized -fimplicit-none -fbounds-check -g -ggdb -fbacktrace -O3 -I/home/balbir/src/p3dfft-2.7.9/include -I/home/balbir/src/fftw-3.3.9/include -cpp -I/home/balbir/src/hdf5-1.12.1/include -c -o obj/cof_p3dfft.o src/cof_p3dfft.f90 -L/home/balbir/src/p3dfft-2.7.9/lib -lp3dfft -L/home/balbir/src/fftw-3.3.9/lib -lfftw3 -L/home/balbir/src/hdf5-1.12.1/lib -lhdf5_fortran -lhdf5 -llapack -lblas -lz -ldl -lm
mpif90 -g -Jobj -Wuninitialized -fimplicit-none -fbounds-check -g -ggdb -fbacktrace -O3 -I/home/balbir/src/p3dfft-2.7.9/include -I/home/balbir/src/fftw-3.3.9/include -cpp -I/home/balbir/src/hdf5-1.12.1/include -c -o obj/ghostpoints.o src/ghostpoints.f90 -L/home/balbir/src/p3dfft-2.7.9/lib -lp3dfft -L/home/balbir/src/fftw-3.3.9/lib -lfftw3 -L/home/balbir/src/hdf5-1.12.1/lib -lhdf5_fortran -lhdf5 -llapack -lblas -lz -ldl -lm
mpif90 -g -Jobj -Wuninitialized -fimplicit-none -fbounds-check -g -ggdb -fbacktrace -O3 -I/home/balbir/src/p3dfft-2.7.9/include -I/home/balbir/src/fftw-3.3.9/include -cpp -I/home/balbir/src/hdf5-1.12.1/include -c -o obj/basic_operators.o src/basic_operators.f90 -L/home/balbir/src/p3dfft-2.7.9/lib -lp3dfft -L/home/balbir/src/fftw-3.3.9/lib -lfftw3 -L/home/balbir/src/hdf5-1.12.1/lib -lhdf5_fortran -lhdf5 -llapack -lblas -lz -ldl -lm
mpif90 -g -Jobj -Wuninitialized -fimplicit-none -fbounds-check -g -ggdb -fbacktrace -O3 -I/home/balbir/src/p3dfft-2.7.9/include -I/home/balbir/src/fftw-3.3.9/include -cpp -I/home/balbir/src/hdf5-1.12.1/include -c -o obj/interpolation.o src/interpolation.f90 -L/home/balbir/src/p3dfft-2.7.9/lib -lp3dfft -L/home/balbir/src/fftw-3.3.9/lib -lfftw3 -L/home/balbir/src/hdf5-1.12.1/lib -lhdf5_fortran -lhdf5 -llapack -lblas -lz -ldl -lm
src/interpolation.f90:78:0:

end function

Warning: ‘__result_delta’ may be used uninitialized in this function [-Wmaybe-uninitialized]
src/interpolation.f90:57:0:

real (kind=pr) function delta(x,dx1)

note: ‘__result_delta’ was declared here
src/interpolation.f90:43:0:

         value = value + delx*dely*delz*field( per(ix,nx),per(iy,ny),per(iz,nz) )

Warning: ‘__result_delta’ may be used uninitialized in this function [-Wmaybe-uninitialized]
mpif90 -g -Jobj -Wuninitialized -fimplicit-none -fbounds-check -g -ggdb -fbacktrace -O3 -I/home/balbir/src/p3dfft-2.7.9/include -I/home/balbir/src/fftw-3.3.9/include -cpp -I/home/balbir/src/hdf5-1.12.1/include -c -o obj/ini_files_parser.o src/ini_files_parser.f90 -L/home/balbir/src/p3dfft-2.7.9/lib -lp3dfft -L/home/balbir/src/fftw-3.3.9/lib -lfftw3 -L/home/balbir/src/hdf5-1.12.1/lib -lhdf5_fortran -lhdf5 -llapack -lblas -lz -ldl -lm
mpif90 -g -Jobj -Wuninitialized -fimplicit-none -fbounds-check -g -ggdb -fbacktrace -O3 -I/home/balbir/src/p3dfft-2.7.9/include -I/home/balbir/src/fftw-3.3.9/include -cpp -I/home/balbir/src/hdf5-1.12.1/include -c -o obj/ini_files_parser_mpi.o src/ini_files_parser_mpi.f90 -L/home/balbir/src/p3dfft-2.7.9/lib -lp3dfft -L/home/balbir/src/fftw-3.3.9/lib -lfftw3 -L/home/balbir/src/hdf5-1.12.1/lib -lhdf5_fortran -lhdf5 -llapack -lblas -lz -ldl -lm
mpif90 -g -Jobj -Wuninitialized -fimplicit-none -fbounds-check -g -ggdb -fbacktrace -O3 -I/home/balbir/src/p3dfft-2.7.9/include -I/home/balbir/src/fftw-3.3.9/include -cpp -I/home/balbir/src/hdf5-1.12.1/include -c -o obj/module_insects_integration_flusi_wabbit.o src/insects/module_insects_integration_flusi_wabbit.f90 -L/home/balbir/src/p3dfft-2.7.9/lib -lp3dfft -L/home/balbir/src/fftw-3.3.9/lib -lfftw3 -L/home/balbir/src/hdf5-1.12.1/lib -lhdf5_fortran -lhdf5 -llapack -lblas -lz -ldl -lm
mpif90 -Isrc/insects/ -g -Jobj -Wuninitialized -fimplicit-none -fbounds-check -g -ggdb -fbacktrace -O3 -I/home/balbir/src/p3dfft-2.7.9/include -I/home/balbir/src/fftw-3.3.9/include -cpp -I/home/balbir/src/hdf5-1.12.1/include -c -o obj/module_insects.o src/insects/module_insects.f90 -L/home/balbir/src/p3dfft-2.7.9/lib -lp3dfft -L/home/balbir/src/fftw-3.3.9/lib -lfftw3 -L/home/balbir/src/hdf5-1.12.1/lib -lhdf5_fortran -lhdf5 -llapack -lblas -lz -ldl -lm
body_motion.f90:244:0:

Warning: ‘psi_dt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
body_motion.f90:246:0:

Warning: ‘gamma_dt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
body_motion.f90:245:0:

Warning: ‘beta_dt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
mpif90 -Isrc/solid_solver/ -g -Jobj -Wuninitialized -fimplicit-none -fbounds-check -g -ggdb -fbacktrace -O3 -I/home/balbir/src/p3dfft-2.7.9/include -I/home/balbir/src/fftw-3.3.9/include -cpp -I/home/balbir/src/hdf5-1.12.1/include -c -o obj/solid_solver.o src/solid_solver/solid_solver.f90 -L/home/balbir/src/p3dfft-2.7.9/lib -lp3dfft -L/home/balbir/src/fftw-3.3.9/lib -lfftw3 -L/home/balbir/src/hdf5-1.12.1/lib -lhdf5_fortran -lhdf5 -llapack -lblas -lz -ldl -lm
plate_geometry.f90:218:0:

Warning: ‘__result_z_bottom’ may be used uninitialized in this function [-Wmaybe-uninitialized]
plate_geometry.f90:172:0:

note: ‘__result_z_bottom’ was declared here
plate_geometry.f90:168:0:

Warning: ‘__result_z_top’ may be used uninitialized in this function [-Wmaybe-uninitialized]
plate_geometry.f90:123:0:

note: ‘__result_z_top’ was declared here
mpif90 -Isrc/flexible_solver/ -g -Jobj -Wuninitialized -fimplicit-none -fbounds-check -g -ggdb -fbacktrace -O3 -I/home/balbir/src/p3dfft-2.7.9/include -I/home/balbir/src/fftw-3.3.9/include -cpp -I/home/balbir/src/hdf5-1.12.1/include -c -o obj/flexible_solver.o src/flexible_solver/flexible_solver.f90 -L/home/balbir/src/p3dfft-2.7.9/lib -lp3dfft -L/home/balbir/src/fftw-3.3.9/lib -lfftw3 -L/home/balbir/src/hdf5-1.12.1/lib -lhdf5_fortran -lhdf5 -llapack -lblas -lz -ldl -lm
mpif90 -g -Jobj -Wuninitialized -fimplicit-none -fbounds-check -g -ggdb -fbacktrace -O3 -I/home/balbir/src/p3dfft-2.7.9/include -I/home/balbir/src/fftw-3.3.9/include -cpp -I/home/balbir/src/hdf5-1.12.1/include -c -o obj/turbulent_inlet.o src/turbulent_inlet.f90 -L/home/balbir/src/p3dfft-2.7.9/lib -lp3dfft -L/home/balbir/src/fftw-3.3.9/lib -lfftw3 -L/home/balbir/src/hdf5-1.12.1/lib -lhdf5_fortran -lhdf5 -llapack -lblas -lz -ldl -lm
mpif90 -g -Jobj -Wuninitialized -fimplicit-none -fbounds-check -g -ggdb -fbacktrace -O3 -I/home/balbir/src/p3dfft-2.7.9/include -I/home/balbir/src/fftw-3.3.9/include -cpp -I/home/balbir/src/hdf5-1.12.1/include -c -o obj/passive_scalar.o src/passive_scalar.f90 -L/home/balbir/src/p3dfft-2.7.9/lib -lp3dfft -L/home/balbir/src/fftw-3.3.9/lib -lfftw3 -L/home/balbir/src/hdf5-1.12.1/lib -lhdf5_fortran -lhdf5 -llapack -lblas -lz -ldl -lm
mpif90 -Isrc/wavelets/ -g -Jobj -Wuninitialized -fimplicit-none -fbounds-check -g -ggdb -fbacktrace -O3 -I/home/balbir/src/p3dfft-2.7.9/include -I/home/balbir/src/fftw-3.3.9/include -cpp -I/home/balbir/src/hdf5-1.12.1/include -c -o obj/wavelet_library.o src/wavelets/wavelet_library.f90 -L/home/balbir/src/p3dfft-2.7.9/lib -lp3dfft -L/home/balbir/src/fftw-3.3.9/lib -lfftw3 -L/home/balbir/src/hdf5-1.12.1/lib -lhdf5_fortran -lhdf5 -llapack -lblas -lz -ldl -lm
IWT3_PO.f90:186:0:

Warning: ‘iy’ may be used uninitialized in this function [-Wmaybe-uninitialized]
IWT3_PO.f90:186:0:

Warning: ‘iy’ may be used uninitialized in this function [-Wmaybe-uninitialized]
IWT3_PO.f90:179:0:

note: ‘iy’ was declared here
mpif90 -g -Jobj -Wuninitialized -fimplicit-none -fbounds-check -g -ggdb -fbacktrace -O3 -I/home/balbir/src/p3dfft-2.7.9/include -I/home/balbir/src/fftw-3.3.9/include -cpp -I/home/balbir/src/hdf5-1.12.1/include -c -o obj/krylov_time_stepper.o src/krylov_time_stepper.f90 -L/home/balbir/src/p3dfft-2.7.9/lib -lp3dfft -L/home/balbir/src/fftw-3.3.9/lib -lfftw3 -L/home/balbir/src/hdf5-1.12.1/lib -lhdf5_fortran -lhdf5 -llapack -lblas -lz -ldl -lm
mpif90 -g -Jobj -Wuninitialized -fimplicit-none -fbounds-check -g -ggdb -fbacktrace -O3 -I/home/balbir/src/p3dfft-2.7.9/include -I/home/balbir/src/fftw-3.3.9/include -cpp -I/home/balbir/src/hdf5-1.12.1/include -c -o obj/hdf5_wrapper.o src/file_io/hdf5_wrapper.f90 -L/home/balbir/src/p3dfft-2.7.9/lib -lp3dfft -L/home/balbir/src/fftw-3.3.9/lib -lfftw3 -L/home/balbir/src/hdf5-1.12.1/lib -lhdf5_fortran -lhdf5 -llapack -lblas -lz -ldl -lm
src/file_io/hdf5_wrapper.f90:5:6:

use hdf5
1
Fatal Error: Can't open module file ‘hdf5.mod’ for reading at (1): No such file or directory
compilation terminated.
Makefile:247: recipe for target 'obj/hdf5_wrapper.o' failed
make: *** [obj/hdf5_wrapper.o] Error 1
balbir@quanta:~/FLUSI$

[balbir1313]

I am not able to compile FLUSI. This is the make -j1 result. I am using HDF5 version 1.12.1 which is the latest one.

[dkolom]

Dear Balbir, It seems that 'make' does not see the HDF5 library. Please make sure that you have set up the path to HDF5 library files in .bashrc or equivalent. I hope this helps. Kind regards, Dmitry

…

On Thu, Jul 29, 2021 at 8:27 AM Balbir Singh ***@***.***> wrote: I am not able to compile FLUSI. This is the make -j1 result. I am using HDF5 version 1.12.1 which is the latest one. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#26 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABENQFBRKYS2UWR2BJNM4WDT2DRD3ANCNFSM5BFWR2YQ> .

[balbir1313]

Thanks for your reply, Dmitry. I think I am setting it correctly in .bashrc as:

export HDF_ROOT=$HOME/src/hdf5-1.12.1
echo "export HDF_ROOT=$HOME/src/hdf5-1.12.1" >> $HOME/.bashrc
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:${HDF_ROOT}/lib

I don't know if I have to take some other approach. Also, I didn't find the hdf5.mod file in the #include. I also tried with old versions of hdf5 like 1.8 but still getting the same error.

Let me try once again

Best wishes

Balbir

[balbir1313]

I have seen that the directory /include in HDF5 does not contain any module files because of which the FLUSI is not getting compiled and shows an error. Can you guide why? make and make check in case of HDF5 does not show any error!