My Community

Dear users and developers,
recently I got a copy of vasp-6.4.2. With the previous vasp version, I used the Intel mpi compiler - 20202.4 version and found it more effective in our institute cluster.
Our HPC service team, installed hdf5-1.14.1 with intelmpi 2020.4 compilers.

The location of hdf5-1.14.1 lib include and mod files is :
/cluster/tools/spack_20230521/opt/spack/linux-centos7-cascadelake/intel-2020.4.0/hdf5-1.14.1-2-phigtnrjfhcxobrr635hmfh2o2im2imy/mod/static/ --> for *.mod files
/cluster/tools/spack_20230521/opt/spack/linux-centos7-cascadelake/intel-2020.4.0/hdf5-1.14.1-2-phigtnrjfhcxobrr635hmfh2o2im2imy/lib ---> for libhdf5* files
/cluster/tools/spack_20230521/opt/spack/linux-centos7-cascadelake/intel-2020.4.0/hdf5-1.14.1-2-phigtnrjfhcxobrr635hmfh2o2im2imy/include ---> for *.h files

I used makefile.include.intel file from ./arch folder and added the following info for hdf5


# HDF5-support (optional but strongly recommended)
CPP_OPTIONS+= -DVASP_HDF5
HDF5_ROOT ?=/cluster/tools/spack_20230521/opt/spack/linux-centos7-cascadelake/intel-2020.4.0/hdf5-1.14.1-2-phigtnrjfhcxobrr635hmfh2o2im2imy
LLIBS += -L$(HDF5_ROOT)/lib -lhdf5_fortran
INCS += -I$(HDF5_ROOT)/mod/static -I$(HDF5_ROOT)/include


(I tried with -I$(HDF5_ROOT)/mod/shared in separate installation trial)

then I used

$make std

the compilation ends with an error message referring to hdf5 related *.h files
the error message

mpiifort -free - ....
....
...
mpiifort -free -names lowercase -assume byterecl -w -xHOST -O2 -I/cluster/compilers/intel/2020.4/compilers_and_libraries_2020.4.304/linux/mkl/include/fftw -I/cluster/tools/spack_20230521/opt/spack/linux-centos7-cascadelake/intel-2020.4.0/hdf5-1.14.1-2-phigtnrjfhcxobrr635hmfh2o2im2imy/include -I/cluster/tools/spack_20230521/opt/spack/linux-centos7-cascadelake/intel-2020.4.0/hdf5-1.14.1-2-phigtnrjfhcxobrr635hmfh2o2im2imy/mod/shared -I/cluster/tools/spack_20230521/opt/spack/linux-centos7-cascadelake/intel-2020.4.0/hdf5-1.14.1-2-phigtnrjfhcxobrr635hmfh2o2im2imy/mod/static -I/cluster/tools/spack_20230521/opt/spack/linux-centos7-cascadelake/intel-2020.4.0/hdf5-1.14.1-2-phigtnrjfhcxobrr635hmfh2o2im2imy/include/ -c vhdf5_base.f90
vhdf5_base.F(7): error #7002: Error in opening the compiled module file. Check INCLUDE paths. [H5ES]
use hdf5
------^
vhdf5_base.F(550): error #6632: Keyword arguments are invalid without an explicit interface. [LCPL_ID]
call h5dcreate_f(locid, dataset_name, H5T_IEEE_F32LE, dspace, dset, ierr, lcpl_id = create_inter_prop); if (ierr/=0) return
---------------------------------------------------------------------------------^
vhdf5_base.F(701): error #6632: Keyword arguments are invalid without an explicit interface. [LCPL_ID]
call h5dcreate_f(locid, dataset_name, H5T_IEEE_F32LE, dspace, dset, ierr, lcpl_id = create_inter_prop); if (ierr/=0) return
--------------------------------------------------------------------------------^
vhdf5_base.F(725): error #6632: Keyword arguments are invalid without an explicit interface. [LCPL_ID]
call h5dcreate_f(locid, dataset_name, H5T_IEEE_F32LE, dspace, dset, ierr, lcpl_id = create_inter_prop); if (ierr/=0) return
------------------------------------------------------------------------------^
vhdf5_base.F(790): error #6632: Keyword arguments are invalid without an explicit interface. [LCPL_ID]
call h5dcreate_f(locid, dataset_name, H5T_IEEE_F32LE, dspace, dset, ierr, lcpl_id = create_inter_prop); if (ierr/=0) return
------------------------------------------------------------------------------^
vhdf5_base.F(908): error #6632: Keyword arguments are invalid without an explicit interface. [LCPL_ID]
call h5dcreate_f(locid, dataset_name, H5T_IEEE_F64LE, dspace, dset, ierr, lcpl_id = create_inter_prop); if (ierr/=0) return
--------------------------------------------------------------------------------^
vhdf5_base.F(948): error #6632: Keyword arguments are invalid without an explicit interface. [LCPL_ID]
call h5dcreate_f(locid, dataset_name, H5T_IEEE_F64LE, dspace, dset, ierr, crp_list, lcpl_id = create_inter_prop); if (ierr/=0) return
--------------------------------------------------------------------------------------------^
vhdf5_base.F(951): error #6632: Keyword arguments are invalid without an explicit interface. [LCPL_ID]
call h5dcreate_f(locid, dataset_name, H5T_IEEE_F64LE, dspace, dset, ierr, lcpl_id = create_inter_prop); if (ierr/=0) return
----------------------------------------------------------------------------------^
vhdf5_base.F(1025): error #6632: Keyword arguments are invalid without an explicit interface. [LCPL_ID]
call h5dcreate_f(locid, dataset_name, H5T_IEEE_F64LE, dspace, dset, ierr, lcpl_id = create_inter_prop); if (ierr/=0) return
--------------------------------------------------------------------------------^
vhdf5_base.F(1786): error #6632: Keyword arguments are invalid without an explicit interface. [LCPL_ID]
call h5dcreate_f(locid, dataset_name, H5T_STD_I32LE, dspace, dset, ierr, lcpl_id = create_inter_prop); if (ierr/=0) return
-------------------------------------------------------------------------------^
vhdf5_base.F(1818): error #6632: Keyword arguments are invalid without an explicit interface. [LCPL_ID]
call h5dcreate_f(locid, dataset_name, H5T_STD_I32LE, dspace, dset, ierr, lcpl_id = create_inter_prop); if (ierr/=0) return
-------------------------------------------------------------------------------^
vhdf5_base.F(2152): error #6632: Keyword arguments are invalid without an explicit interface. [LCPL_ID]
call h5dcreate_f(locid, dataset_name, string_type, dspace, dset, ierr, lcpl_id = create_inter_prop); if (ierr/=0) return
-----------------------------------------------------------------------------^
vhdf5_base.F(2189): error #6632: Keyword arguments are invalid without an explicit interface. [LCPL_ID]
call h5dcreate_f(locid, dataset_name, string_type, dspace, dset, ierr, lcpl_id = create_inter_prop); if (ierr/=0) return
-----------------------------------------------------------------------------^
compilation aborted for vhdf5_base.f90 (code 1)
make[2]: *** [vhdf5_base.o] Error 1
make[2]: Leaving directory `/home/mv27lepe/opt/vasp/vasp6.4.2/build/std'
cp: cannot stat 'vasp': No such file or directory
make[1]: *** [all] Error 1
make[1]: Leaving directory `/home/mv27lepe/opt/vasp/vasp6.4.2/build/std'
make: *** [std] Error 2


using ldd command i see

$ ldd /cluster/tools/spack_20230521/opt/spack/linux-centos7-cascadelake/intel-2020.4.0/hdf5-1.14.1-2-phigtnrjfhcxobrr635hmfh2o2im2imy/lib/libhdf5.so
linux-vdso.so.1 => (0x00007fff8379f000)
libm.so.6 => /lib64/libm.so.6 (0x00002b3110af8000)
libdl.so.2 => /lib64/libdl.so.2 (0x00002b3110dfa000)
libmpifort.so.12 => /cluster/compilers/intel/2020.4/compilers_and_libraries_2020.4.304/linux/mpi/intel64/lib/libmpifort.so.12 (0x00002b3110ffe000)
libmpi.so.12 => /cluster/compilers/intel/2020.4/compilers_and_libraries_2020.4.304/linux/mpi/intel64/lib/release/libmpi.so.12 (0x00002b31113bc000)
librt.so.1 => /lib64/librt.so.1 (0x00002b311271c000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00002b3112924000)
libz.so.1 => /cluster/tools/spack_20230521/opt/spack/linux-centos7-cascadelake/intel-2020.4.0/zlib-1.2.13-pyyhme3w754c3gryixx6r4lktjh74p2t/lib/libz.so.1 (0x00002b3112b40000)
libimf.so => /cluster/compilers/intel/2020.4/compilers_and_libraries_2020.4.304/linux/compiler/lib/intel64_lin/libimf.so (0x00002b3112d60000)
libsvml.so => /cluster/compilers/intel/2020.4/compilers_and_libraries_2020.4.304/linux/compiler/lib/intel64_lin/libsvml.so (0x00002b31133e3000)
libirng.so => /cluster/compilers/intel/2020.4/compilers_and_libraries_2020.4.304/linux/compiler/lib/intel64_lin/libirng.so (0x00002b3114eb3000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00002b311521e000)
libintlc.so.5 => /cluster/compilers/intel/2020.4/compilers_and_libraries_2020.4.304/linux/compiler/lib/intel64_lin/libintlc.so.5 (0x00002b3115434000)
libc.so.6 => /lib64/libc.so.6 (0x00002b31156ac000)
/lib64/ld-linux-x86-64.so.2 (0x00002b3110133000)
libfabric.so.1 => /cluster/compilers/intel/2020.4/compilers_and_libraries_2020.4.304/linux/mpi/intel64/libfabric/lib/libfabric.so.1 (0x00002b3115a7a000)

and

$ module li
Currently Loaded Modulefiles:
1) python/gcc/9.1.0/3.7.4 2) gnuplot/gcc/9.1.0/5.2.5 3) intel/2020.4 4) intelmpi/2020.4 5) hdf5/intel/2020.4/1.14.1


Even though using the same compiler I see the error message related to finding the *mod and *h files.

did anyone face such an issue?

what could be done here to resolve this issue?

Why the VASP compilation is not able to link *mod and *.h files though I use the correct path setting in the makefile.include?

Any suggestion are highly appreciated !!!

Thank you

Best regards,
Muthu,
Researcher
TU Freiberg, Germany

Dear users and developers,
did anyone face such issues with linking vasp with hdf5*.mod?
Again I cross-verified with the cluster administration that the hdf5 are compiled with intelmpi-2020.4 .
your comments are highly appreciated !!

Dear Muthu,

at first glance I cannot find any mistakes in the way you set up your makefile.include and compiled VASP. I will investigate and try the same toolchain you suggested. Maybe the problem is related to recent changes in the HDF5 API (see the notes here: https://www.hdfgroup.org/downloads/hdf5). As far as I know we did not yet test HDF5 1.14, the last version we used in our tests is 1.13. Please stay tuned...

Best,
Andreas Singraber

Dear Muthu,

unfortunately, I do not have the Intel 2020.4 compiler available, so I could not test exactly the same toolchain. However, I tried with Intel 2024.0 and HDF5 1.14 and was able to successfully compile VASP and run the testsuite. Hence, I believe that in principle also your combination should work.

From the error messages you posted it seems that the hdf5.mod file was not found. However, you mentioned that it should be present in the $(HDF5_ROOT)/mod/static because your system administrators verified that they built HDF5 for this compiler. The files necessary (hdf5.mod, libhdf5_fortran.a/.so) for a VASP build are only produced if HDF5 is compiled with the flag --enable-fortran. So, to ensure that they are really there could you please post the contents of the static/mod, include and lib directory within the $(HDF5_ROOT) folder? If the hdf5.mod file is present, could you please attach it to your message?

Thank you!

Best,
Andreas Singraber