Precompiler error with GNU compiler
Posted: Mon Jun 13, 2022 6:31 pm
Hello forum and developers.
I am a system administrator of an HPC, and I am trying to install yambo in our cluster. I am getting an error in the "configure" phase.
Compiler: GNU 9.3.0 and OpenMPI 4.0.4
Architecture: AMD x86_64. AMD EPYC 7702 dual 64-Core Processors
Full details about the cluster
https://www.ni-hpc.ac.uk/
Compiling in parallel
Yambo version 5.1.0
Procedure to get the error:
Load necessary modules and dependencies:
$ module load apps/cmake/3.18.4/gcc-9.3.0
$ module load compilers/gcc/9.3.0
$ module load mpi/openmpi/4.0.4/gcc-9.3.0+ucx-1.8.0
$ module load libs/blas/3.8.0/gcc-9.3.0
$ module load libs/lapack/3.9.0/gcc-9.3.0
$ module load libs/fftw3_double/3.3.10/gcc-9.3.0+openmpi-4.0.4
$ module load libs/fftw3_float/3.3.10/gcc-9.3.0+openmpi-4.0.4
$ module load petsc/3.17.2/gcc-9.3.0+openmpi-4.0.4+blas-3.8.0+lapack-3.9.0
$ module load apps/hdf5_mpi/1.12.2/gcc-9.3.0+openmpi-4.0.4
Precompiling command:
$ CC=/opt/gridware/depots/54e7fb3c/el7/pkg/compilers/gcc/9.3.0/bin/gcc \
> FC=/opt/gridware/depots/54e7fb3c/el7/pkg/compilers/gcc/9.3.0/bin/gfortran \
> F77=/opt/gridware/depots/54e7fb3c/el7/pkg/compilers/gcc/9.3.0/bin/gfortran \
> MPICC=/opt/gridware/depots/54e7fb3c/el7/pkg/mpi/openmpi/4.0.4/gcc-9.3.0+ucx-1.8.0/bin/mpicc \
> MPIF90=/opt/gridware/depots/54e7fb3c/el7/pkg/mpi/openmpi/4.0.4/gcc-9.3.0+ucx-1.8.0/bin/mpif90 \
> MPIF77=/opt/gridware/depots/54e7fb3c/el7/pkg/mpi/openmpi/4.0.4/gcc-9.3.0+ucx-1.8.0/bin/mpif77 \
> ./configure --prefix=/opt/apps/yambo/5.1.0/gcc-9.3.0+openmpi-4.0.4+blas-3.8.0+lapack-3.9.0+fftw3-3.3.10+hdf5-1.12.2+petsc-3.17.2 \
> --with-mpi-path=/opt/gridware/depots/54e7fb3c/el7/pkg/mpi/openmpi/4.0.4/gcc-9.3.0+ucx-1.8.0 \
> --with-blas-libs=/opt/gridware/depots/54e7fb3c/el7/pkg/libs/blas/3.8.0/gcc-9.3.0/libblas.a \
> --with-lapack-libs=/opt/gridware/depots/54e7fb3c/el7/pkg/libs/lapack/3.9.0/gcc-9.3.0/lib64/liblapack.a \
> --with-fft-path=/opt/gridware/depots/54e7fb3c/el7/pkg/libs/fftw3_double/3.3.10/gcc-9.3.0+openmpi-4.0.4 \
> --with-petsc-path=/opt/apps/petsc/3.17.2/gcc-9.3.0+openmpi-4.0.4+blas-3.8.0+lapack-3.9.0 \
> --with-hdf5-path=/opt/gridware/depots/54e7fb3c/el7/pkg/apps/hdf5_mpi/1.12.2/gcc-9.3.0+openmpi-4.0.4
Error:
[yambo] Compilation Precision check
make[4]: Nothing to be done for `all'.
[lib/qe_pseudo] qe_pseudo (checking work to be done)
objects.mk:8: *** missing separator (did you mean TAB instead of 8 spaces?). Stop.
make[3]: *** [qe_pseudo] Error 2
[lib/slatec] slatec (checking work to be done)
objects.mk:9: *** missing separator (did you mean TAB instead of 8 spaces?). Stop.
make[3]: *** [slatec] Error 2
[lib/math77] math77 (checking work to be done)
[lib/local] local (checking work to be done)
[lib/yambo/driver/src/interface] interface (checking work to be done)
[lib/yambo/driver/src/main] main (checking work to be done)
[lib/yambo/driver/src/options] options (checking work to be done)
make[2]: *** No rule to make target `lib'. Stop.
make[1]: *** [yambo] Error 2
yambo build failed
It looks like it is related to the precompiler, it is not building the Makefile properly.
Has anyone compiled yambo with the GNU compiler suite?
Some help will be very appreciated.
Thank you.
Luis.
I am a system administrator of an HPC, and I am trying to install yambo in our cluster. I am getting an error in the "configure" phase.
Compiler: GNU 9.3.0 and OpenMPI 4.0.4
Architecture: AMD x86_64. AMD EPYC 7702 dual 64-Core Processors
Full details about the cluster
https://www.ni-hpc.ac.uk/
Compiling in parallel
Yambo version 5.1.0
Procedure to get the error:
Load necessary modules and dependencies:
$ module load apps/cmake/3.18.4/gcc-9.3.0
$ module load compilers/gcc/9.3.0
$ module load mpi/openmpi/4.0.4/gcc-9.3.0+ucx-1.8.0
$ module load libs/blas/3.8.0/gcc-9.3.0
$ module load libs/lapack/3.9.0/gcc-9.3.0
$ module load libs/fftw3_double/3.3.10/gcc-9.3.0+openmpi-4.0.4
$ module load libs/fftw3_float/3.3.10/gcc-9.3.0+openmpi-4.0.4
$ module load petsc/3.17.2/gcc-9.3.0+openmpi-4.0.4+blas-3.8.0+lapack-3.9.0
$ module load apps/hdf5_mpi/1.12.2/gcc-9.3.0+openmpi-4.0.4
Precompiling command:
$ CC=/opt/gridware/depots/54e7fb3c/el7/pkg/compilers/gcc/9.3.0/bin/gcc \
> FC=/opt/gridware/depots/54e7fb3c/el7/pkg/compilers/gcc/9.3.0/bin/gfortran \
> F77=/opt/gridware/depots/54e7fb3c/el7/pkg/compilers/gcc/9.3.0/bin/gfortran \
> MPICC=/opt/gridware/depots/54e7fb3c/el7/pkg/mpi/openmpi/4.0.4/gcc-9.3.0+ucx-1.8.0/bin/mpicc \
> MPIF90=/opt/gridware/depots/54e7fb3c/el7/pkg/mpi/openmpi/4.0.4/gcc-9.3.0+ucx-1.8.0/bin/mpif90 \
> MPIF77=/opt/gridware/depots/54e7fb3c/el7/pkg/mpi/openmpi/4.0.4/gcc-9.3.0+ucx-1.8.0/bin/mpif77 \
> ./configure --prefix=/opt/apps/yambo/5.1.0/gcc-9.3.0+openmpi-4.0.4+blas-3.8.0+lapack-3.9.0+fftw3-3.3.10+hdf5-1.12.2+petsc-3.17.2 \
> --with-mpi-path=/opt/gridware/depots/54e7fb3c/el7/pkg/mpi/openmpi/4.0.4/gcc-9.3.0+ucx-1.8.0 \
> --with-blas-libs=/opt/gridware/depots/54e7fb3c/el7/pkg/libs/blas/3.8.0/gcc-9.3.0/libblas.a \
> --with-lapack-libs=/opt/gridware/depots/54e7fb3c/el7/pkg/libs/lapack/3.9.0/gcc-9.3.0/lib64/liblapack.a \
> --with-fft-path=/opt/gridware/depots/54e7fb3c/el7/pkg/libs/fftw3_double/3.3.10/gcc-9.3.0+openmpi-4.0.4 \
> --with-petsc-path=/opt/apps/petsc/3.17.2/gcc-9.3.0+openmpi-4.0.4+blas-3.8.0+lapack-3.9.0 \
> --with-hdf5-path=/opt/gridware/depots/54e7fb3c/el7/pkg/apps/hdf5_mpi/1.12.2/gcc-9.3.0+openmpi-4.0.4
Error:
[yambo] Compilation Precision check
make[4]: Nothing to be done for `all'.
[lib/qe_pseudo] qe_pseudo (checking work to be done)
objects.mk:8: *** missing separator (did you mean TAB instead of 8 spaces?). Stop.
make[3]: *** [qe_pseudo] Error 2
[lib/slatec] slatec (checking work to be done)
objects.mk:9: *** missing separator (did you mean TAB instead of 8 spaces?). Stop.
make[3]: *** [slatec] Error 2
[lib/math77] math77 (checking work to be done)
[lib/local] local (checking work to be done)
[lib/yambo/driver/src/interface] interface (checking work to be done)
[lib/yambo/driver/src/main] main (checking work to be done)
[lib/yambo/driver/src/options] options (checking work to be done)
make[2]: *** No rule to make target `lib'. Stop.
make[1]: *** [yambo] Error 2
yambo build failed
It looks like it is related to the precompiler, it is not building the Makefile properly.
Has anyone compiled yambo with the GNU compiler suite?
Some help will be very appreciated.
Thank you.
Luis.