Compilation of Exciting Fluorine(/Oxygen) with HDF5

exciting
1

Dear Exciting Developers,

I have been working through the tutorial for the BRIXS code but need help compiling the Exciting main code with HDF5.

Have I understood correctly? Compilation with HDF5 is a requirement to store the excitonic eigenvectors in .h5 format.

To build with HDF5 support, I have checked the preprocessor directive within the code: _HDF5_, and the include and link options for the parallel version of hdf5 I have available:

$ h5pfc -show
>> ftn -I/opt/cray/pe/hdf5-parallel/1.12.2.1/include -Wl,-rpath -Wl,/opt/cray/pe/hdf5-parallel/1.12.2.1/gnu/9.1/lib

I updated the make.inc accordingly with:

MPIF90_OPTS = -DMPI -D_HDF5_
MPI_LIBS = -I/opt/cray/pe/hdf5-parallel/1.12.2.1/include -Wl,-rpath -Wl,/opt/cray/pe/hdf5-parallel/1.12.2.1/gnu/9.1/lib

This leads to an error during compilation

../../src/src_gw/task_chi0_r.f90:236:77:

  236 |         &               chi0(1,1,iomstart,iq),(/matsizmax,matsizmax,iomstart:iomend/))
      |                                                                             1
Error: Syntax error in array constructor at (1)

that I have traced back to the following _HDF5_ block in /src/src_gw/task_chi0_r.f90 at the call on line 235:

230 #ifdef _HDF5_
231         write(cik,'(I4.4)') ik
232         path = "/qpoints/"//trim(adjustl(cik))
233         if (.not.hdf5_exist_group(fgwh5,"/qpoints",cik)) &
234         &  call hdf5_create_group(fgwh5,"/qpoints",cik)
235         call hdf5_write(fgwh5,path,"chi0", &
236         &               chi0(1,1,iomstart,iq),(/matsizmax,matsizmax,iomstart:iomend/))
237 #endif

Unfortunately, I cannot determine the error, or whether it can be mitigated with an additional compiler flag. So any help would be greatly appreciated.

As a new user to this forum I cannot upload attatchments, so I have created a GitHub repository with the output from the make command, and my make.inc file. I am compiling with GNU compilers version gcc/11.2.0.

Finally, as stated in the title of this topic, I was originally working with Exciting version Oxygen. I have also verified the same problem with compilation of Exciting version Fluorine.

Thank you very much, and best regards

Joshua Elliott

Research Scientist
Diamond Light Source
United Kingdom

2

Hi Joshua,

It’s nothing to do with compiler flags. When _HDF5_ is true, the block of code you shared is included in the source. And it looks like a bug to me.

This isn’t surprising, we don’t test with HDF5 in our CI and I doubt this has been touched for a few years.

(/matsizmax,matsizmax,iomstart:iomend/) is definitely invalid fortran, but I can’t actually work out what should be there from an initial inspection😅

Can you try commenting out lines 231 - 236 in your example? This is in GW and I doubt the RIXS code will use it. If it does, I’ll have to take a closer look.

Cheers,
Alex

3

Alex,

Thanks for your fast reply!

I understand, and commenting out this block of code has let me compile, I have also been able to generate the .h5 file required to continue with the RIXS simulation.

So that you are aware of it, I found one other instance in the gw part of the code where the same invalid FORTRAN syntax has been used

src/src_gw/task_epsilon.f90 (Line 157-164):
162 !        call hdf5_write(fgwh5,path,"epsilon", &
163 !        &               epsilon_(1,1,1,iq),(/matsizmax,matsizmax,1:freq%nomeg/))

Best regards

Josh

4

Awesome, glad to hear!

Thanks for the heads-up. There is some development to completely refactor the HDF5 outputting. At which point, I am sure we will catch many problems from the current usage in the GW and BSE modules.

Cheers,
Alex

5

Hello,

Sorry to necro the thread, but i have also had similar (albeit) different problem with compiling exciting.

my mpif90 in make.inc looks like:

 MPIF90 = mpif90
36 MPIF90_OPTS = -DMPI -D_HDF5_
37 MPI_LIBS = -I/share/pkg.7/hdf5/1.8.21/install/include -L/share/pkg.7/hdf5/1.8.21/install/lib /share/pkg.7/hdf5/1.8.21/install/lib/libhdf5hl_fortran.a /share/pkg.7/hdf5/1.8.21/install/lib/libhdf5_hl.a /share
   /pkg.7/hdf5/1.8.21/install/lib/libhdf5_fortran.a /share/pkg.7/hdf5/1.8.21/install/lib/libhdf5.a -lsz -lz -ldl -lm -Wl,-rpath -Wl,/share/pkg.7/hdf5/1.8.21/install/lib -lhdf5

yet i get the compilation error:

mpif90  -O3 -march=native -ffree-line-length-0  -cpp -DXS -DISO -DLIBXC -DMPI -D_HDF5_ -Ifinclude   -c  ../../src/src_gw/mod_hdf5.f90
../../src/src_gw/mod_hdf5.f90:43:12:

         use hdf5
            1
Fatal Error: Can't open module file ‘hdf5.mod’ for reading at (1): No such file or directory
compilation terminated.

yes, hdf5.mod is present in the location as one would hope:

~/exciting/exciting% ls /share/pkg.7/hdf5/1.8.21/install/include/hdf5*
/share/pkg.7/hdf5/1.8.21/install/include/hdf5.h  /share/pkg.7/hdf5/1.8.21/install/include/hdf5_hl.h  /share/pkg.7/hdf5/1.8.21/install/include/hdf5.mod

(among other modules)

but its unclear as to why it is throwing this error, since i believe i am linking correctly to the hdf5.mod ?

Any insight? I am very interested in doing these RIXS calculations as well.

6

So this error i found was due to an older version of hdf5 which was compiled for an older version of gfortran.

I now have a version of hdf5 compiled with gfortran8.5
The openmpi and hdf5 versions are

 openmpi/4.1.5   2) hdf5/1.10.10```

but now i am getting an mpi_bcast error when trying to compile exciting with mpi and smp


```bash 

mpif90    -O3 -march=broadwell -mtune=intel -ffree-line-length-0  -cpp -DXS -DISO -DLIBXC -fopenmp -DUSEOMP -DMPI -D_HDF5_ -I/share/pkg.8/hdf5/1.10.10/install/include -Ifinclude   -c     ../../src/src_xs/m_putgetexcitons.f90
../../src/src_xs/m_putgetexcitons.f90:427:96:

       call mpi_bcast(vqlmt_,shape(vqlmt_), MPI_DOUBLE_PRECISION,0,mpiglobal%comm,mpiglobal%ierr)
                                                                                                1
Error: There is no specific subroutine for the generic ‘mpi_bcast’ at (1)
../../src/src_xs/m_putgetexcitons.f90:428:89:

       call mpi_bcast(ngridk_,shape(ngridk_), MPI_INTEGER,0,mpiglobal%comm,mpiglobal%ierr)
                                                                                         1
Error: There is no specific subroutine for the generic ‘mpi_bcast’ at (1)
../../src/src_xs/m_putgetexcitons.f90:502:87:

       call mpi_bcast(ikmap_,shape(ikmap_), MPI_INTEGER,0,mpiglobal%comm,mpiglobal%ierr)
                                                                                       1
Error: There is no specific subroutine for the generic ‘mpi_bcast’ at (1)
../../src/src_xs/m_putgetexcitons.f90:503:95:

       call mpi_bcast(ik2ikqmtm_,shape(ik2ikqmtm_), MPI_INTEGER,0,mpiglobal%comm,mpiglobal%ierr)
                                                                                               1
Error: There is no specific subroutine for the generic ‘mpi_bcast’ at (1)
../../src/src_xs/m_putgetexcitons.f90:504:95:

       call mpi_bcast(ik2ikqmtp_,shape(ik2ikqmtm_), MPI_INTEGER,0,mpiglobal%comm,mpiglobal%ierr)
                                                                                               1
Error: There is no specific subroutine for the generic ‘mpi_bcast’ at (1)
../../src/src_xs/m_putgetexcitons.f90:505:91:

       call mpi_bcast(kousize_,shape(kousize_), MPI_INTEGER,0,mpiglobal%comm,mpiglobal%ierr)
                                                                                           1
Error: There is no specific subroutine for the generic ‘mpi_bcast’ at (1)
../../src/src_xs/m_putgetexcitons.f90:506:91:

       call mpi_bcast(koulims_,shape(koulims_), MPI_INTEGER,0,mpiglobal%comm,mpiglobal%ierr)
                                                                                           1
Error: There is no specific subroutine for the generic ‘mpi_bcast’ at (1)
../../src/src_xs/m_putgetexcitons.f90:507:85:

       call mpi_bcast(smap_,shape(smap_), MPI_INTEGER,0,mpiglobal%comm,mpiglobal%ierr)
                                                                                     1
Error: There is no specific subroutine for the generic ‘mpi_bcast’ at (1)
../../src/src_xs/m_putgetexcitons.f90:508:93:

       call mpi_bcast(smap_rel_,shape(smap_rel_), MPI_INTEGER,0,mpiglobal%comm,mpiglobal%ierr)
                                                                                             1
Error: There is no specific subroutine for the generic ‘mpi_bcast’ at (1)
../../src/src_xs/m_putgetexcitons.f90:509:82:

       call mpi_bcast(vkl0_,shape(vkl0_), MPI_REAL,0,mpiglobal%comm,mpiglobal%ierr)
                                                                                  1
Error: There is no specific subroutine for the generic ‘mpi_bcast’ at (1)
../../src/src_xs/m_putgetexcitons.f90:510:80:

       call mpi_bcast(vkl_,shape(vkl_), MPI_REAL,0,mpiglobal%comm,mpiglobal%ierr)
                                                                                1
Error: There is no specific subroutine for the generic ‘mpi_bcast’ at (1)
../../src/src_xs/m_putgetexcitons.f90:511:88:

       call mpi_bcast(evalstmp,shape(evalstmp), MPI_REAL,0,mpiglobal%comm,mpiglobal%ierr)
                                                                                        1
Error: There is no specific subroutine for the generic ‘mpi_bcast’ at (1)
../../src/src_xs/m_putgetexcitons.f90:598:94:

     call mpi_bcast(evals_, shape(evals_), MPI_DOUBLE_COMPLEX,0, mpiglobal%comm,mpiglobal%ierr)
                                                                                              1
Error: There is no specific subroutine for the generic ‘mpi_bcast’ at (1)
../../src/src_xs/m_putgetexcitons.f90:599:92:

     call mpi_bcast(rvec_, shape(rvec_), MPI_DOUBLE_COMPLEX,0, mpiglobal%comm,mpiglobal%ierr)
                                                                                            1
Error: There is no specific subroutine for the generic ‘mpi_bcast’ at (1)
../../src/src_xs/m_putgetexcitons.f90:602:89:

     call mpi_bcast(koulims_,shape(koulims_), MPI_INTEGER,0,mpiglobal%comm,mpiglobal%ierr)
                                                                                         1
Error: There is no specific subroutine for the generic ‘mpi_bcast’ at (1)

any idea how to fix?