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Dear Users and experts

Can any one point my mistakes in compiling vasp error with vhdf5.F

I guess this FORTRAN program is not responding to hdf5

Hdf5 compiled fine with NO ERROR

1- (base) [root@192 sherifyehia]# grep H5_VERS_INFO /usr/local/hdf5/include/H5public.h

#define H5_VERS_INFO “HDF5 library version: 1.12.2”
2- [sherifyehia@192 ~]$ which h5dump

/opt/intel/oneapi/intelpython/latest/bin/h5dump



But vasp when we switch the HDF5 key gives the following errors

Here are a sample of the given errors

vhdf5_base.o: In function `vhdf5_base_mp_vh5_start_':
vhdf5_base.f90:(.text+0x46): undefined reference to `h5lib_mp_h5open_f_'
vhdf5_base.f90:(.text+0x52): undefined reference to `h5global_mp_h5p_link_create_f_'
vhdf5_base.f90:(.text+0x60): undefined reference to `h5p_mp_h5pcreate_f_'
vhdf5_base.f90:(.text+0x7a): undefined reference to `h5p_mp_h5pset_create_inter_group_f_'
vhdf5_base.o: In function `vhdf5_base_mp_vh5_end_':
vhdf5_base.f90:(.text+0x96): undefined reference to `h5lib_mp_h5close_f_'
vhdf5_base.o: In function `vhdf5_base_mp_vh5_file_open_read_':
vhdf5_base.f90:(.text+0xa8): undefined reference to `h5global_mp_h5f_acc_rdonly_f_'
vhdf5_base.f90:(.text+0xb4): undefined reference to `h5f_mp_h5fopen_f_'
vhdf5_base.o: In function `vhdf5_base_mp_vh5_file_open_readwrite_':
vhdf5_base.f90:(.text+0xd3): undefined reference to `h5global_mp_h5f_acc_rdwr_f_'
vhdf5_base.f90:(.text+0xe5): undefined reference to `h5f_mp_h5fopen_f_'
vhdf5_base.o: In function `vhdf5_base_mp_vh5_file_close_':
vhdf5_base.f90:(.text+0xf6): undefined reference to `h5f_mp_h5fclose_f_'
vhdf5_base.o: In function `vhdf5_base_mp_vh5_file_create_':
vhdf5_base.f90:(.text+0x11e): undefined reference to `h5global_mp_h5f_acc_excl_f_'
vhdf5_base.f90:(.text+0x132): undefined reference to `h5f_mp_h5fcreate_f_'
vhdf5_base.o: In function `vhdf5_base_mp_vh5_file_create_or_overwrite_':
vhdf5_base.f90:(.text+0x15e): undefined reference to `h5global_mp_h5f_acc_trunc_f_'
vhdf5_base.f90:(.text+0x172): undefined reference to `h5f_mp_h5fcreate_f_'
vhdf5_base.o: In function `vhdf5_base_mp_vh5_file_close_writing_':
vhdf5_base.f90:(.text+0x19a): undefined reference to `h5f_mp_h5fclose_f_'
vhdf5_base.o: In function `vhdf5_base_mp_vh5_file_flush_':
vhdf5_base.f90:(.text+0x2cf): undefined reference to `h5global_mp_h5f_scope_local_f_'
vhdf5_base.f90:(.text+0x2de): undefined reference to `h5f_mp_h5fflush_f_'
vhdf5_base.o: In function `vhdf5_base_mp_vh5_group_open_':
vhdf5_base.f90:(.text+0x2fc): undefined reference to `h5g_mp_h5gopen_f_'



Please see my linker

total 20340
drwxr-xr-x. 2 root root 4096 Jan 18 15:32 .
drwxr-xr-x. 6 root root 56 Jan 18 15:32 …
-rw-r–r--. 1 root root 11791634 Jan 18 15:31 libhdf5.a
-rw-r–r--. 1 root root 1369916 Jan 18 15:31 libhdf5_cpp.a
-rwxr-xr-x. 1 root root 992 Jan 18 15:31 libhdf5_cpp.la
lrwxrwxrwx. 1 root root 22 Jan 18 15:31 libhdf5_cpp.so -> libhdf5_cpp.so.200.2.0
lrwxrwxrwx. 1 root root 22 Jan 18 15:31 libhdf5_cpp.so.200 -> libhdf5_cpp.so.200.2.0
-rwxr-xr-x. 1 root root 549232 Jan 18 15:31 libhdf5_cpp.so.200.2.0
-rw-r–r--. 1 root root 543800 Jan 18 15:32 libhdf5_fortran.a
-rwxr-xr-x. 1 root root 1020 Jan 18 15:32 libhdf5_fortran.la
lrwxrwxrwx. 1 root root 26 Jan 18 15:32 libhdf5_fortran.so -> libhdf5_fortran.so.200.1.1
lrwxrwxrwx. 1 root root 26 Jan 18 15:32 libhdf5_fortran.so.200 -> libhdf5_fortran.so.200.1.1
-rwxr-xr-x. 1 root root 482024 Jan 18 15:32 libhdf5_fortran.so.200.1.1
-rw-r–r--. 1 root root 284340 Jan 18 15:32 libhdf5_hl.a
-rw-r–r--. 1 root root 18232 Jan 18 15:32 libhdf5_hl_cpp.a
-rwxr-xr-x. 1 root root 1082 Jan 18 15:32 libhdf5_hl_cpp.la
lrwxrwxrwx. 1 root root 25 Jan 18 15:32 libhdf5_hl_cpp.so -> libhdf5_hl_cpp.so.200.1.0
lrwxrwxrwx. 1 root root 25 Jan 18 15:32 libhdf5_hl_cpp.so.200 -> libhdf5_hl_cpp.so.200.1.0
-rwxr-xr-x. 1 root root 19192 Jan 18 15:32 libhdf5_hl_cpp.so.200.1.0
lrwxrwxrwx. 1 root root 19 Jan 18 15:32 libhdf5_hl_fortran.a -> libhdf5hl_fortran.a
-rw-r–r--. 1 root root 250566 Jan 18 15:32 libhdf5hl_fortran.a
-rwxr-xr-x. 1 root root 1107 Jan 18 15:32 libhdf5hl_fortran.la
lrwxrwxrwx. 1 root root 20 Jan 18 15:32 libhdf5_hl_fortran.so -> libhdf5hl_fortran.so
lrwxrwxrwx. 1 root root 28 Jan 18 15:32 libhdf5hl_fortran.so -> libhdf5hl_fortran.so.200.0.2
lrwxrwxrwx. 1 root root 28 Jan 18 15:32 libhdf5hl_fortran.so.200 -> libhdf5hl_fortran.so.200.0.2
-rwxr-xr-x. 1 root root 217072 Jan 18 15:32 libhdf5hl_fortran.so.200.0.2
-rwxr-xr-x. 1 root root 994 Jan 18 15:32 libhdf5_hl.la
lrwxrwxrwx. 1 root root 21 Jan 18 15:32 libhdf5_hl.so -> libhdf5_hl.so.200.1.0
lrwxrwxrwx. 1 root root 21 Jan 18 15:32 libhdf5_hl.so.200 -> libhdf5_hl.so.200.1.0
-rwxr-xr-x. 1 root root 155640 Jan 18 15:32 libhdf5_hl.so.200.1.0
-rwxr-xr-x. 1 root root 942 Jan 18 15:31 libhdf5.la
-rw-r–r--. 1 root root 4307 Jan 18 15:31 libhdf5.settings
lrwxrwxrwx. 1 root root 18 Jan 18 15:31 libhdf5.so -> libhdf5.so.200.2.0
lrwxrwxrwx. 1 root root 18 Jan 18 15:31 libhdf5.so.200 -> libhdf5.so.200.2.0
-rwxr-xr-x. 1 root root 5087776 Jan 18 15:31 libhdf5.so.200.2.0
(base) [sherifyehia@192 /]$

How to fix that

Thanks all

Dear Experts

I getting error when I switch CPP_OPTIONS in the makefile.include

# HDF5-support (optional but strongly recommended)
CPP_OPTIONS += -DVASP_HDF5
HDF5_ROOT ?= /usr/local/hdf5
LLIBS += -L$(HDF5_ROOT)/lib -lhdf5_fortran -lhdf5
INCS += -I$(HDF5_ROOT)/include

Please see the portion the error

vhdf5_base.o: In function `vhdf5_base_mp_vh5_start_':
vhdf5_base.f90:(.text+0x46): undefined reference to `h5lib_mp_h5open_f_'
vhdf5_base.f90:(.text+0x52): undefined reference to `h5global_mp_h5p_link_create_f_'
vhdf5_base.f90:(.text+0x60): undefined reference to `h5p_mp_h5pcreate_f_'
vhdf5_base.f90:(.text+0x7a): undefined reference to `h5p_mp_h5pset_create_inter_group_f_'
vhdf5_base.o: In function `vhdf5_base_mp_vh5_end_':
vhdf5_base.f90:(.text+0x96): undefined reference to `h5lib_mp_h5close_f_'

Can you help me out
Thank you

I expect that if you run in your VASP directory, you will see something like among the list of linked libraries.

If that is the case then you need to set your LD_LIBRARY_PATH to include the path to your libhdf5.

If the error happens already during the linking step in the compilation then your HDF5_ROOT is not set appropriately.

Thank for your quick answer

As you advice

[sherifyehia@192 vasp.6.3.2]$ ldd bin/vasp_std
linux-vdso.so.1 (0x00007ffcb7777000)
libmkl_intel_lp64.so.2 => /opt/intel/oneapi/mkl/2023.0.0/lib/intel64/libmkl_intel_lp64.so.2 (0x00007f3b3098e000)
libmkl_intel_thread.so.2 => /opt/intel/oneapi/mkl/2023.0.0/lib/intel64/libmkl_intel_thread.so.2 (0x00007f3b2d1f5000)
libmkl_core.so.2 => /opt/intel/oneapi/mkl/2023.0.0/lib/intel64/libmkl_core.so.2 (0x00007f3b28e13000)
libiomp5.so => /opt/intel/oneapi/compiler/2023.0.0/linux/compiler/lib/intel64_lin/libiomp5.so (0x00007f3b289cd000)
libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007f3b28638000)
libmkl_scalapack_lp64.so.2 => /opt/intel/oneapi/mkl/2023.0.0/lib/intel64/libmkl_scalapack_lp64.so.2 (0x00007f3b27f0b000)
libmkl_blacs_intelmpi_lp64.so.2 => /opt/intel/oneapi/mkl/2023.0.0/lib/intel64/libmkl_blacs_intelmpi_lp64.so.2 (0x00007f3b31d8d000)
libm.so.6 => /lib64/libm.so.6 (0x00007f3b27b89000)
libdl.so.2 => /lib64/libdl.so.2 (0x00007f3b27985000)
libmpifort.so.12 => /opt/intel/oneapi/mpi/2021.8.0/lib/libmpifort.so.12 (0x00007f3b275d1000)
libmpi.so.12 => /opt/intel/oneapi/mpi/2021.8.0/lib/release/libmpi.so.12 (0x00007f3b25cb4000)
librt.so.1 => /lib64/librt.so.1 (0x00007f3b25aac000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f3b2588c000)
libc.so.6 => /lib64/libc.so.6 (0x00007f3b254c7000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f3b252af000)
/lib64/ld-linux-x86-64.so.2 (0x00007f3b31bba000)

Could you help me to point my mistake

Thanks very much

Well, there is no HDF5 library on that list. Could that be an executable from a previous compilation? I suspect that you did not set the HDF5_ROOT correctly in your makefile.include.

Thanks for your reply

Kindly see below a copy of my makefile.include which gives error.
Please pay attention that when switching the option "CPP_OPTIONS+= -DVASP_HDF5" (On)
shows no error, other wise, there is error i.e. no executable file under bin.



# Default precompiler options
CPP_OPTIONS = -DHOST=\"LinuxIFC\" \
-DMPI -DMPI_BLOCK=8000 -Duse_collective \
-DscaLAPACK \
-DCACHE_SIZE=4000 \
-Davoidalloc \
-Dvasp6 \
-Duse_bse_te \
-Dtbdyn \
-Dfock_dblbuf \
-D_OPENMP

CPP = fpp -f_com=no -free -w0 $*$(FUFFIX) $*$(SUFFIX) $(CPP_OPTIONS)

FC = mpiifort -qopenmp
FCL = mpiifort

FREE = -free -names lowercase

FFLAGS = -assume byterecl -w

OFLAG = -O2
OFLAG_IN = $(OFLAG)
DEBUG = -O0

OBJECTS = fftmpiw.o fftmpi_map.o fftw3d.o fft3dlib.o
OBJECTS_O1 += fftw3d.o fftmpi.o fftmpiw.o
OBJECTS_O2 += fft3dlib.o

# For what used to be vasp.5.lib
CPP_LIB = $(CPP)
FC_LIB = $(FC)
CC_LIB = icc
CFLAGS_LIB = -O
FFLAGS_LIB = -O1
FREE_LIB = $(FREE)

OBJECTS_LIB = linpack_double.o

# For the parser library
CXX_PARS = icpc
LLIBS = -lstdc++

##
## Customize as of this point! Of course you may change the preceding
## part of this file as well if you like, but it should rarely be
## necessary ...
##

# When compiling on the target machine itself, change this to the
# relevant target when cross-compiling for another architecture
VASP_TARGET_CPU ?= -march=core-avx2
FFLAGS += $(VASP_TARGET_CPU)

# Intel MKL (FFTW, BLAS, LAPACK, and scaLAPACK)
# (Note: for Intel Parallel Studio's MKL use -mkl instead of -qmkl)
FCL += -qmkl
MKLROOT ?= /opt/intel/oneapi/mkl/2023.0.0/lib/intel64
LLIBS += -L$(MKLROOT)/lib/intel64 -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64 -lmkl_intel_lp64 -lmkl_intel_thread
INCS =-I$(MKLROOT)/include/fftw

# HDF5-support (optional but strongly recommended)
CPP_OPTIONS+= -DVASP_HDF5
HDF5_ROOT ?= /home/sherifyehia/hdf5-1.8.14
LLIBS += -L$(HDF5_ROOT)/lib -lhdf5_fortran -lhdf5
INCS += -I$(HDF5_ROOT)/include

# For the VASP-2-Wannier90 interface (optional)
#CPP_OPTIONS += -DVASP2WANNIER90
#WANNIER90_ROOT ?= /path/to/your/wannier90/installation
#LLIBS += -L$(WANNIER90_ROOT)/lib -lwannier

# For the fftlib library (hardly any benefit in combination with MKL's FFTs)
FCL = mpiifort fftlib.o -qmkl
CXX_FFTLIB = icpc -qopenmp -std=c++11 -DFFTLIB_USE_MKL -DFFTLIB_THREADSAFE
INCS_FFTLIB = -I./include -I$(MKLROOT)/include/fftw
LIBS += fftlib

Here are a couple of things you can try:

• Please check whether the directory /home/sherifyehia/hdf5-1.8.14 contains the libraries libhdf5_fortran and libhdf5. If only the former is missing you need to reconfigure the HDF5 installation to enable the Fortran library
• Verify that no other HDF5_ROOT is defined

  Code: Select all

  env | grep HDF5

• Start a clean installation, i.e.,

  Code: Select all

  make veryclean
  make all

• Our recommended list of toolchains uses more recent version of the HDF5 library. Please verify the older version is compatible or upgrade to a newer version.

If none of that works, store the output of the complete build in a file and share it here.

Thanks for your reply
unfortunately nothing work followed your advise in 1 and the site recommendation in 2 to update HDF5 root@192 hdf5-1.13.2] and the locate library in 3 Please see attached the error out of vasp
1- [root@192 vasp.6.3.2]# env | grep HDF5
HDF5_MPI=ON
2- locate libhdf5.a
/opt/intel/oneapi/intelpython/python3.9/pkgs/hdf5-1.10.6-hb1b8bf9_0/lib/libhdf5.a
/opt/intel/oneapi/mkl/2023.0.0/lib/intel64/libhdf5.a
/opt/intel/oneapi/mpi/2021.8.0/lib/libhdf5.a
/opt/intel/oneapi/tensorflow/2.9.1.1/lib/libhdf5.a
/usr/local/hdf5/lib/libhdf5.a
3-root@192 vasp.6.3.2]# ls /usr/local/hdf5/lib
libhdf5.a libhdf5hl_fortran.la libhdf5_hl.so.9
libhdf5_fortran.a libhdf5_hl_fortran.so libhdf5_hl.so.9.0.0
libhdf5_fortran.la libhdf5hl_fortran.so libhdf5.la
libhdf5_fortran.so libhdf5hl_fortran.so.300 libhdf5.settings
libhdf5_fortran.so.300 libhdf5hl_fortran.so.300.0.2 libhdf5.so
libhdf5_fortran.so.300.0.2 libhdf5hl_fortran.so.9 libhdf5.so.302
libhdf5_fortran.so.9 libhdf5hl_fortran.so.9.0.0 libhdf5.so.302.0.0
libhdf5_fortran.so.9.0.0 libhdf5_hl.la libhdf5.so.9
libhdf5_hl.a libhdf5_hl.so libhdf5.so.9.0.0
libhdf5_hl_fortran.a libhdf5_hl.so.300
libhdf5hl_fortran.a libhdf5_hl.so.300.0.2

Thank you very much for all your kind effort

Please disregard my previous attachment for error
The right one is here
Sorry for the inconvenience

Thanks again

There is still a mismatch in the HDF_ROOT. In your makefile.include you set it to /home/sherifyehia/hdf5-1.13.2/ but you check for the installed libraries in Please try whether setting HDF5_ROOT to /usr/local/hdf5 works or check whether /home/sherifyehia/hdf5-1.13.2/lib contains the required libhdf5_fortran.

One more thing, from the output it looks like you removed the -lhdf5 from the LLIBS variable. Please check whether this is still set correctly.

Thanks for the advice

Please see
1- (base) [sherifyehia@192 ~]$ ls /usr/local/hdf5/lib
libhdf5.a libhdf5hl_fortran.la libhdf5_hl.so.9
libhdf5_fortran.a libhdf5_hl_fortran.so libhdf5_hl.so.9.0.0
libhdf5_fortran.la libhdf5hl_fortran.so libhdf5.la
libhdf5_fortran.so libhdf5hl_fortran.so.300 libhdf5.settings
libhdf5_fortran.so.300 libhdf5hl_fortran.so.300.0.2 libhdf5.so
libhdf5_fortran.so.300.0.2 libhdf5hl_fortran.so.9 libhdf5.so.302
libhdf5_fortran.so.9 libhdf5hl_fortran.so.9.0.0 libhdf5.so.302.0.0
libhdf5_fortran.so.9.0.0 libhdf5_hl.la libhdf5.so.9
libhdf5_hl.a libhdf5_hl.so libhdf5.so.9.0.0
libhdf5_hl_fortran.a libhdf5_hl.so.300
libhdf5hl_fortran.a libhdf5_hl.so.300.0.2


2- (base) [sherifyehia@192 ~]$ ls /home/sherifyehia/hdf5-1.13.2/lib
libhdf5.a libhdf5_fortran.so libhdf5.la libhdf5.so.302
libhdf5_fortran.a libhdf5_fortran.so.300 libhdf5.settings libhdf5.so.302.0.0
libhdf5_fortran.la libhdf5_fortran.so.300.0.2 libhdf5.so libhdf5.so.9.0.0

I made the run Root /home/sherifyehia/hdf5-1.13.2

Same error and no executable file at bin ONLY when I switch CPP_OPTIONS+= -DVASP_HDF5 OFF
Was this problem seen before
Please waiting for your advice

Can you check the symbols defined in the hdf5 library? This should print a list of all things defined in the library. You can grep for one of the functions If this does not print anything, something went wrong with the installation of the HDF5 library.

For the record, here is a script that I used many times to install HDF5 with the Intel compiler Assuming I'm in the source directory of VASP, I can then install VASP with I did not try this with the most recent oneAPI compiler, so it would be good to know if anything failed here.

Thanks for sending those great codes 1&2

Here is what happened when I run the first one I got the following error

configure: error: cannot run C compiled programs.
If you meant to cross compile, use `--host'.
See `config.log' for more details
make: *** [Makefile:32: _config] Error 1
I put in the 3 lines of the first code as you recomend before
export CFLAGS='-march=core-avx2'
export CXXFLAGS='-march=core-avx2'
export FCFLAGS='-march=core-avx2'
Instead
export CFLAGS='-O3 -xHost -ip'
export CXXFLAGS='-O3 -xHost -ip'
export FCFLAGS='-O3 -xHost -ip'

It workks fine but in the installation part names became hdf5-1.12.2 NOT hdf5
(base) [sherifyehia@192 ~]$ cd /usr/local/hdf5-1.12.2/
(base) [sherifyehia@192 hdf5-1.12.2]$ ls
bin include lib share
(base) [sherifyehia@192 hdf5-1.12.2]$

and no lib on the main installation part
(base) [sherifyehia@192 hdf5-1.12.2]$ ls /home/sherifyehia/hdf5-1.12.2/lib
ls: cannot access '/home/sherifyehia/hdf5-1.12.2/lib': No such file or directory
(base) [sherifyehia@192 hdf5-1.12.2]$

I tried now the second code to Install vasp and put it in the same directory I got the error

checking whether we are cross compiling... configure: error: in `/home/sherifyehia/hdf5-1.12.2':
configure: error: cannot run C compiled programs.
If you meant to cross compile, use `--host'.

Well I changed the flags in the makefile.include file i.e. put '-march=core-avx2' instead of '-O3 -xHost -ip' I get
The same old error
opt/intel/oneapi/mkl/2023.0.0/lib/intel64 -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64 -L/usr/local/hdf5-/lib -lhdf5_fortran
vhdf5_base.o: In function `vhdf5_base_mp_vh5_start_':
vhdf5_base.f90:(.text+0x46): undefined reference to `h5lib_mp_h5open_f_'
vhdf5_base.f90:(.text+0x52): undefined reference to `h5global_mp_h5p_link_create_f_'
vhdf5_base.f90:(.text+0x60): undefined reference to `h5p_mp_h5pcreate_f_'
vhdf5_base.f90:(.text+0x7a): undefined reference to `h5p_mp_h5pset_create_inter_group_f_'

I hope I explained the problem clear and not doing big mistake
Thanks very much appreciate you very kind help

Further to my previous post to clarify the existence of the libhdf5_fortran.so

with the code nm /usr/local/hdf5-1.12.2/lib/libhdf5_fortran.so
and the grep order

"grep h5f_mp_h5fopen"

Please see attached the zip file to indicate that this library is there

Thank you

The second part (the installation of VASP) will not work if the first part (the installation of HDF5) fails. If you can provide the output of the HDF5 installation, I can have a quick look into that but we can only support the installation of VASP. You also need to run both parts in the same shell otherwise the environment variables are not set appropriately. Alternatively, you can put the things in your .bashrc.