Vasp reading and writing HDF5 files

sherif542002 · January 17, 2023, 1:15pm

Dear experts and user
It is written in the vasp manual that HDF5 produces the vaspout.h5 . I compiled vasp software with the following commends but got NO vaspout.h5

This is essential for reading and writing HDF5 files, such as vaspout.h5. The HDF5 library is available for download on the HDF5 official website. To activate this feature set the following:

CPP_OPTIONS+= -DVASP_HDF5
HDF5_ROOT ?= /path/to/your/hdf5/installation
LLIBS += -L$(HDF5_ROOT)/lib -lhdf5_fortran
INCS += -I$(HDF5_ROOT)/include

Can I get some help from the community
Thanks in advance

gheber · January 17, 2023, 2:07pm

Where on your system is HDF5 installed? (Check /usr/lib or /usr/local/lib or /opt?)
When you type which h5dump in a terminal, what do you see?

G.

sherif542002 · January 17, 2023, 5:23pm

Thank you very much for your quick answer

as you advised /usr/local

[sherifyehia@192 local]$ cd hdf5/
[sherifyehia@192 hdf5]$ ls
bin include lib share
[sherifyehia@192 hdf5]$ pwd
/usr/local/hdf5
[sherifyehia@192 hdf5]$ ls
bin include lib share
[sherifyehia@192 hdf5]$

and this commend

[sherifyehia@192 ~]$ which h5dump
/opt/intel/oneapi/intelpython/latest/bin/h5dump
Can you kindly direct which is the root directory

Thank you

gheber · January 18, 2023, 1:04pm

It appears that

HDF5_ROOT ?= /usr/local/hdf5

should get you going, assuming that HDF5 version works with VASP. You can check the HDF5 version like this:

grep H5_VERS_INFO /usr/local/hdf5/include/H5public.h

G.

sherif542002 · January 18, 2023, 1:52pm

Thanks

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

#define H5_VERS_INFO “HDF5 library version: 1.12.2”

It seems anther problem with vasp. Please see some of the error in out put when I when I compile with HDF5.

pol.o wave_interpolate.o linear_response.o auger.o dmatrix.o phonon.o wannier_mats.o elphon.o core_con_mat.o embed.o extpot.o rpa_high.o fftmpiw.o fftmpi_map.o fftw3d.o fft3dlib.o main.o -Llib -ldmy -Lparser -lparser -lstdc++ -L/opt/intel/oneapi/mkl/2022.1.0/lib/intel64 -lmkl_scalapack_lp64 -lmkl_blacs_intelmpi_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -L/usr/local/hdf5/lib -lhdf5_fortran
mpiifort -qopenmp -free -names lowercase -assume byterecl -w -march=core-avx2 -O2 -I/opt/intel/oneapi/mkl/2022.1.0/include/fftw -I/usr/local/hdf5/include -c local_field.f90
vhdf5_base.o: In function vhdf5_base_mp_vh5_start_': vhdf5_base.f90:(.text+0x46): undefined reference toh5lib_mp_h5open_f_’
vhdf5_base.f90:(.text+0x52): undefined reference to h5global_mp_h5p_link_create_f_' vhdf5_base.f90:(.text+0x60): undefined reference toh5p_mp_h5pcreate_f_’
vhdf5_base.f90:(.text+0x7a): undefined reference to h5p_mp_h5pset_create_inter_group_f_' vhdf5_base.o: In functionvhdf5_base_mp_vh5_end_’:
vhdf5_base.f90:(.text+0x96): undefined reference to h5lib_mp_h5close_f_' vhdf5_base.o: In functionvhdf5_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 toh5f_mp_h5fopen_f_’
vhdf5_base.o: In function `vhdf5_base_mp_vh5_file_open_readwrite_’:

Thank you

gheber · January 18, 2023, 2:04pm

The linker can’t find certain Fortran symbols, e.g., h5lib_mp_h5open_f_, h5global_mp_h5p_link_create_f_, etc. -L/usr/local/hdf5/lib -lhdf5_fortran should take care of that, but we don’t know how that library was built. What’s output of

ls -al /usr/local/hdf5/lib

?

G.

sherif542002 · January 18, 2023, 3:32pm

Please my linker
(base) [sherifyehia@192 /]$ ls -al /usr/local/hdf5/lib
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 /]$

gheber · January 18, 2023, 5:34pm

OK. You got libhdf5_fortran.a right there, but this one might have been built with another compiler. Can you run

objdump -t /usr/local/hdf5/lib/libhdf5_fortran.a | grep h5 > symbols.txt

and send symbols.txt? (Zip the file if the attachment is too large.)

G.

sherif542002 · January 18, 2023, 8:06pm

Thanks for all the but it seems this commend is not doing anything

(base) [root@192 lib]# objdump -t /usr/local/hdf5/lib/libhdf5_fortran.a | grep h5 > symbols.txt
(base) [root@192 lib]#

sherif542002 · January 18, 2023, 8:44pm

I tried this way without the commend > symbols

It seems working h5 (181.3 KB)
Please see attached I hope I did it the right way

sherif542002 · January 18, 2023, 9:05pm

I used this commend also work with the attached file

objdump -t /usr/local/hdf5/lib/libhdf5_fortran.a | grep h5 <symbols.txtsymbols.txt (741.5 KB)

gheber · January 19, 2023, 12:27am

OK, I’m way out of my depth here about the inner workings of the linker. I can see the symbols referenced in the dump, but they are undefined. How about updating the LLIBS variable to

LLIBS += -L$(HDF5_ROOT)/lib -lhdf5_fortran -lhdf5

?

G.

byrn · January 19, 2023, 1:57pm

cmake built hdf5 linking requires all the dependent libs; fortran requires cstub require hdf5

and for autotools note that hl library has two names sometimes.

byrn · January 19, 2023, 2:05pm

Also you seem to be using mpi compilers - check if hdf5 is mpi enabled by outputting the lib/libhdf5.settings file.

sherif542002 · January 21, 2023, 11:26am

Sorry I had a crash with my Redhat I am using CentOs8
1- with LLIBS += -L$(HDF5_ROOT)/lib -lhdf5_fortran -lhdf5.
2- I am using
CPP_OPTIONS+= -DVASP_HDF5
HDF5_ROOT ?= /opt/hdf/HDF5-1.14.0-Linux/HDF_Group/HDF5/1.14.0
LLIBS += -L$(HDF5_ROOT)/lib -lhdf5_fortran -lhdf5
INCS += -I$(HDF5_ROOT)/include

But getting the error again
vhdf5_base.F(6): error #7002: Error in opening the compiled module file. Check INCLUDE paths. [HDF5]
use hdf5
------^
vhdf5_base.F(35): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T):: ih5intermediategroup_id
----------^
vhdf5_base.F(36): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T):: ih5infileid
----------^
vhdf5_base.F(37): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T):: ih5outfileid
----------^
vhdf5_base.F(38): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T):: ih5wavefileid
----------^
vhdf5_base.F(39): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T):: ih5ininputgroup_id
----------^
vhdf5_base.F(40): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T):: ih5outinputgroup_id
----------^
vhdf5_base.F(41): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T):: ih5outoriginalgroup_id
----------^
vhdf5_base.F(56): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T) :: create_inter_prop
----------^
vhdf5_base.F(203): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(out) :: fileid
------------^
vhdf5_base.F(217): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(out) :: fileid
------------^
vhdf5_base.F(231): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(out) :: fileid
------------^
vhdf5_base.F(246): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(out) :: fileid
------------^
vhdf5_base.F(262): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(out) :: fileid
------------^
vhdf5_base.F(273): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(out) :: fileid
------------^
vhdf5_base.F(315): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(in) :: fileid
------------^
vhdf5_base.F(343): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(in) :: locid
------------^
vhdf5_base.F(345): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(out) :: groupid
------------^
vhdf5_base.F(356): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(in) :: groupid
------------^
vhdf5_base.F(369): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(in) :: locid
------------^
vhdf5_base.F(371): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(out) :: groupid
------------^
vhdf5_base.F(386): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(in) :: locid
------------^
vhdf5_base.F(388): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(out) :: groupid
------------^
vhdf5_base.F(409): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(in) :: groupid
------------^
vhdf5_base.F(425): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(in) :: locid
------------^
vhdf5_base.F(450): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(in) :: groupid
------------^
vhdf5_base.F(456): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T) :: dset_id, attr_id, aspace, string_type
------------^
vhdf5_base.F(457): error #6683: A kind type parameter must be a compile-time constant. [HSIZE_T]
integer(HSIZE_T) :: dimensions(1)
------------^
vhdf5_base.F(458): error #6683: A kind type parameter must be a compile-time constant. [HSIZE_T]
integer(HSIZE_T) :: strlen
------------^
vhdf5_base.F(499): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(in) :: locid
------------^
vhdf5_base.f90(2790): catastrophic error: Too many errors, exiting
compilation aborted for vhdf5_base.f90 (code 1)
make[2]: *** [makefile:166: vhdf5_base.o] Error 1
make[2]: *** Waiting for unfinished jobs…
mpiifort -qopenmp -free -names lowercase -assume byterecl -w -march=core-avx2 -O2 -I/opt/intel/oneapi/mkl/2023.0.0/include/fftw -I/opt/hdf/HDF5-1.14.0-Linux/HDF_Group/HDF5/1.14.0/include -c command_line.f90
mpiifort -qopenmp -free -names lowercase -assume byterecl -w -march=core-avx2 -O2 -I/opt/intel/oneapi/mkl/2023.0.0/include/fftw -I/opt/hdf/HDF5-1.14.0-Linux/HDF_Group/HDF5/1.14.0/include -c vhdf5_base.f90
vhdf5_base.F(6): error #7002: Error in opening the compiled module file. Check INCLUDE paths. [HDF5]
use hdf5
------^
vhdf5_base.F(35): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T):: ih5intermediategroup_id
----------^
vhdf5_base.F(36): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T):: ih5infileid
----------^
vhdf5_base.F(37): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T):: ih5outfileid
----------^
vhdf5_base.F(38): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T):: ih5wavefileid
----------^
vhdf5_base.F(39): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T):: ih5ininputgroup_id
----------^
vhdf5_base.F(40): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T):: ih5outinputgroup_id
----------^
vhdf5_base.F(41): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T):: ih5outoriginalgroup_id
----------^
vhdf5_base.F(56): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T) :: create_inter_prop
----------^
vhdf5_base.F(203): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(out) :: fileid
------------^
vhdf5_base.F(217): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(out) :: fileid
------------^
vhdf5_base.F(231): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(out) :: fileid
------------^
vhdf5_base.F(246): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(out) :: fileid
------------^
vhdf5_base.F(262): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(out) :: fileid
------------^
vhdf5_base.F(273): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(out) :: fileid
------------^
vhdf5_base.F(315): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(in) :: fileid
------------^
vhdf5_base.F(343): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(in) :: locid
------------^
vhdf5_base.F(345): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(out) :: groupid
------------^
vhdf5_base.F(356): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(in) :: groupid
------------^
vhdf5_base.F(369): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(in) :: locid
------------^
vhdf5_base.F(371): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(out) :: groupid
------------^
vhdf5_base.F(386): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(in) :: locid
------------^
vhdf5_base.F(388): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(out) :: groupid
------------^
vhdf5_base.F(409): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(in) :: groupid
------------^
vhdf5_base.F(425): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(in) :: locid
------------^
vhdf5_base.F(450): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(in) :: groupid
------------^
vhdf5_base.F(456): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T) :: dset_id, attr_id, aspace, string_type
------------^
vhdf5_base.F(457): error #6683: A kind type parameter must be a compile-time constant. [HSIZE_T]
integer(HSIZE_T) :: dimensions(1)
------------^
vhdf5_base.F(458): error #6683: A kind type parameter must be a compile-time constant. [HSIZE_T]
integer(HSIZE_T) :: strlen
------------^
vhdf5_base.F(499): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(in) :: locid
------------^
vhdf5_base.f90(2790): catastrophic error: Too many errors, exiting
compilation aborted for vhdf5_base.f90 (code 1)
make[2]: *** [makefile:166: vhdf5_base.o] Error 1
make[2]: *** Waiting for unfinished jobs…
make[2]: Leaving directory ‘/home/sherifyehia/Desktop/vasp.6.3.2/build/std’
cp: cannot stat ‘vasp’: No such file or directory
make[1]: *** [makefile:129: all] Error 1
make[1]: Leaving directory ‘/home/sherifyehia/Desktop/vasp.6.3.2/build/std’
make: *** [makefile:17: std] Error 2
make: *** Waiting for unfinished jobs…
mpiifort -qopenmp -free -names lowercase -assume byterecl -w -march=core-avx2 -O2 -I/opt/intel/oneapi/mkl/2023.0.0/include/fftw -I/opt/hdf/HDF5-1.14.0-Linux/HDF_Group/HDF5/1.14.0/include -c command_line.f90
mpiifort -qopenmp -free -names lowercase -assume byterecl -w -march=core-avx2 -O2 -I/opt/intel/oneapi/mkl/2023.0.0/include/fftw -I/opt/hdf/HDF5-1.14.0-Linux/HDF_Group/HDF5/1.14.0/include -c vhdf5_base.f90
mpiifort -qopenmp -free -names lowercase -assume byterecl -w -march=core-avx2 -O2 -I/opt/intel/oneapi/mkl/2023.0.0/include/fftw -I/opt/hdf/HDF5-1.14.0-Linux/HDF_Group/HDF5/1.14.0/include -c mathtools.f90
vhdf5_base.F(6): error #7002: Error in opening the compiled module file. Check INCLUDE paths. [HDF5]
use hdf5
------^
vhdf5_base.F(35): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T):: ih5intermediategroup_id
----------^
vhdf5_base.F(36): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T):: ih5infileid
----------^
vhdf5_base.F(37): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T):: ih5outfileid
----------^
vhdf5_base.F(38): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T):: ih5wavefileid
----------^
vhdf5_base.F(39): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T):: ih5ininputgroup_id
----------^
vhdf5_base.F(40): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T):: ih5outinputgroup_id
----------^
vhdf5_base.F(41): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T):: ih5outoriginalgroup_id
----------^
vhdf5_base.F(56): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T) :: create_inter_prop
----------^
vhdf5_base.F(203): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(out) :: fileid
------------^
vhdf5_base.F(217): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(out) :: fileid
------------^
vhdf5_base.F(231): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(out) :: fileid
------------^
vhdf5_base.F(246): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(out) :: fileid
------------^
vhdf5_base.F(262): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(out) :: fileid
------------^
vhdf5_base.F(273): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(out) :: fileid
------------^
vhdf5_base.F(315): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(in) :: fileid
------------^
vhdf5_base.F(343): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(in) :: locid
------------^
vhdf5_base.F(345): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(out) :: groupid
------------^
vhdf5_base.F(356): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(in) :: groupid
------------^
vhdf5_base.F(369): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(in) :: locid
------------^
vhdf5_base.F(371): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(out) :: groupid
------------^
vhdf5_base.F(386): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(in) :: locid
------------^
vhdf5_base.F(388): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(out) :: groupid
------------^
vhdf5_base.F(409): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(in) :: groupid
------------^
vhdf5_base.F(425): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(in) :: locid
------------^
vhdf5_base.F(450): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(in) :: groupid
------------^
vhdf5_base.F(456): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T) :: dset_id, attr_id, aspace, string_type
------------^
vhdf5_base.F(457): error #6683: A kind type parameter must be a compile-time constant. [HSIZE_T]
integer(HSIZE_T) :: dimensions(1)
------------^
vhdf5_base.F(458): error #6683: A kind type parameter must be a compile-time constant. [HSIZE_T]
integer(HSIZE_T) :: strlen
------------^
vhdf5_base.F(499): error #6683: A kind type parameter must be a compile-time constant. [HID_T]
integer(HID_T), intent(in) :: locid
------------^
vhdf5_base.f90(2792): catastrophic error: Too many errors, exiting
compilation aborted for vhdf5_base.f90 (code 1)
make[2]: *** [makefile:166: vhdf5_base.o] Error 1
make[2]: *** Waiting for unfinished jobs…
make[2]: Leaving directory ‘/home/sherifyehia/Desktop/vasp.6.3.2/build/gam’
cp: cannot stat ‘vasp’: No such file or directory
make[1]: *** [makefile:129: all] Error 1
make[1]: Leaving directory ‘/home/sherifyehia/Desktop/vasp.6.3.2/build/gam’
make: *** [makefile:17: gam] Error 2
make[2]: Leaving directory ‘/home/sherifyehia/Desktop/vasp.6.3.2/build/ncl’
cp: cannot stat ‘vasp’: No such file or directory
make[1]: *** [makefile:129: all] Error 1
make[1]: Leaving directory ‘/home/sherifyehia/Desktop/vasp.6.3.2/build/ncl’
make: *** [makefile:17: ncl] Error 2
[sherifyehia@192 vasp.6.3.2]$ make DEPS=1 -j4
if [ ! -d build/std ] ; then mkdir -p build/std ; fi
if [ ! -d build/gam ] ; then mkdir -p build/gam ; fi
if [ ! -d build/ncl ] ; then mkdir -p build/ncl ; fi
cp src/makefile src/.objects src/makedeps.awk makefile.include build/std
cp src/makefile src/.objects src/makedeps.awk makefile.include build/gam
cp src/makefile src/.objects src/makedeps.awk makefile.include build/ncl
make -C build/std VERSION=std check
make -C build/ncl VERSION=ncl check
make -C build/gam VERSION=gam check
make[1]: Entering directory ‘/home/sherifyehia/Desktop/vasp.6.3.2/build/std’
exit 0
make[1]: Entering directory ‘/home/sherifyehia/Desktop/vasp.6.3.2/build/ncl’
exit 0
make[1]: Entering directory ‘/home/sherifyehia/Desktop/vasp.6.3.2/build/gam’
exit 0
make[1]: Leaving directory ‘/home/sherifyehia/Desktop/vasp.6.3.2/build/std’
make -C build/std VERSION=std dependencies -j1
make[1]: Leaving directory ‘/home/sherifyehia/Desktop/vasp.6.3.2/build/ncl’
make -C build/ncl VERSION=ncl dependencies -j1
make[1]: Leaving directory ‘/home/sherifyehia/Desktop/vasp.6.3.2/build/gam’
make -C build/gam VERSION=gam dependencies -j1
make[1]: warning: -j1 forced in submake: resetting jobserver mode.
make[1]: warning: -j1 forced in submake: resetting jobserver mode.
make[1]: Entering directory ‘/home/sherifyehia/Desktop/vasp.6.3.2/build/ncl’
rsync -u …/…/src/.F …/…/src/.inc .
make[1]: warning: -j1 forced in submake: resetting jobserver mode.
make[1]: Entering directory ‘/home/sherifyehia/Desktop/vasp.6.3.2/build/std’
rsync -u …/…/src/.F …/…/src/.inc .
make[1]: Entering directory ‘/home/sherifyehia/Desktop/vasp.6.3.2/build/gam’
rsync -u …/…/src/.F …/…/src/.inc .
make depend
make depend
make depend
make[2]: Entering directory ‘/home/sherifyehia/Desktop/vasp.6.3.2/build/std’
awk -f makedeps.awk c2f_interface.f90 nccl2for.f90 simd.f90 base.f90 profiling.f90 string.f90 tutor.f90 version.f90 command_line.f90 vhdf5_base.f90 incar_reader.f90 reader_base.f90 openmp.f90 openacc_struct.f90 mpi.f90 mpi_shmem.f90 mathtools.f90 hamil_struct.f90 radial_struct.f90 pseudo_struct.f90 mgrid_struct.f90 wave_struct.f90 nl_struct.f90 mkpoints_struct.f90 poscar_struct.f90 afqmc_struct.f90 fock_glb.f90 chi_glb.f90 smart_allocate.f90 xml.f90 extpot_glb.f90 constant.f90 ml_ff_c2f_interface.f90 ml_ff_prec.f90 ml_ff_constant.f90 ml_ff_taglist.f90 ml_ff_struct.f90 ml_ff_mpi_help.f90 ml_ff_mpi_shmem.f90 vdwforcefield_glb.f90 jacobi.f90 main_mpi.f90 openacc.f90 scala.f90 asa.f90 lattice.f90 poscar.f90 ini.f90 mgrid.f90 ml_ff_error.f90 ml_ff_mpi.f90 ml_ff_helper.f90 ml_ff_logfile.f90 ml_ff_math.f90 ml_ff_iohandle.f90 ml_ff_memory.f90 ml_ff_abinitio.f90 ml_ff_ff.f90 ml_ff_mlff.f90 setex_struct.f90 xclib.f90 vdw_nl.f90 xclib_grad.f90 setex.f90 radial.f90 pseudo.f90 gridq.f90 ebs.f90 symlib.f90 mkpoints.f90 random.f90 wave.f90 wave_mpi.f90 wave_high.f90 bext.f90 spinsym.f90 symmetry.f90 lattlib.f90 nonl.f90 nonlr.f90 nonl_high.f90 dfast.f90 choleski2.f90 mix.f90 hamil.f90 xcgrad.f90 xcspin.f90 potex1.f90 potex2.f90 constrmag.f90 cl_shift.f90 relativistic.f90 LDApU.f90 paw_base.f90 metagga.f90 egrad.f90 pawsym.f90 pawfock.f90 pawlhf.f90 diis.f90 rhfatm.f90 hyperfine.f90 fock_ace.f90 paw.f90 mkpoints_full.f90 charge.f90 Lebedev-Laikov.f90 stockholder.f90 dipol.f90 solvation.f90 scpc.f90 pot.f90 tet.f90 dos.f90 elf.f90 hamil_rot.f90 chain.f90 dyna.f90 fileio.f90 vhdf5.f90 sphpro.f90 us.f90 core_rel.f90 aedens.f90 wavpre.f90 wavpre_noio.f90 broyden.f90 dynbr.f90 reader.f90 writer.f90 xml_writer.f90 brent.f90 stufak.f90 opergrid.f90 stepver.f90 fast_aug.f90 fock_multipole.f90 fock.f90 fock_dbl.f90 fock_frc.f90 mkpoints_change.f90 subrot_cluster.f90 sym_grad.f90 mymath.f90 npt_dynamics.f90 subdftd3.f90 subdftd4.f90 internals.f90 dynconstr.f90 dimer_heyden.f90 dvvtrajectory.f90 vdwforcefield.f90 nmr.f90 pead.f90 k-proj.f90 subrot.f90 subrot_scf.f90 paircorrection.f90 rpa_force.f90 ml_reader.f90 ml_interface.f90 force.f90 pwlhf.f90 gw_model.f90 optreal.f90 steep.f90 rmm-diis.f90 davidson.f90 david_inner.f90 root_find.f90 lcao_bare.f90 locproj.f90 electron_common.f90 electron.f90 rot.f90 electron_all.f90 shm.f90 pardens.f90 optics.f90 constr_cell_relax.f90 stm.f90 finite_diff.f90 elpol.f90 hamil_lr.f90 rmm-diis_lr.f90 subrot_lr.f90 lr_helper.f90 hamil_lrf.f90 elinear_response.f90 ilinear_response.f90 linear_optics.f90 setlocalpp.f90 wannier.f90 electron_OEP.f90 electron_lhf.f90 twoelectron4o.f90 gauss_quad.f90 m_unirnk.f90 minimax_ini.f90 minimax_dependence.f90 minimax_functions1D.f90 minimax_functions2D.f90 minimax_struct.f90 minimax_varpro.f90 minimax.f90 umco.f90 mlwf.f90 ratpol.f90 pade_fit.f90 screened_2e.f90 wave_cacher.f90 crpa.f90 chi_base.f90 wpot.f90 local_field.f90 ump2.f90 ump2kpar.f90 fcidump.f90 ump2no.f90 bse_te.f90 bse.f90 time_propagation.f90 acfdt.f90 afqmc.f90 rpax.f90 chi.f90 acfdt_GG.f90 dmft.f90 GG_base.f90 greens_orbital.f90 lt_mp2.f90 rnd_orb_mp2.f90 greens_real_space.f90 chi_GG.f90 chi_super.f90 sydmat.f90 rmm-diis_mlr.f90 linear_response_NMR.f90 wannier_interpol.f90 wave_interpolate.f90 linear_response.f90 auger.f90 dmatrix.f90 phonon.f90 wannier_mats.f90 elphon.f90 core_con_mat.f90 embed.f90 extpot.f90 rpa_high.f90 fftmpiw.f90 fftmpi_map.f90 fftw3d.f90 fft3dlib.f90 main.f90 > .depend
make[2]: Entering directory ‘/home/sherifyehia/Desktop/vasp.6.3.2/build/ncl’
awk -f makedeps.awk c2f_interface.f90 nccl2for.f90 simd.f90 base.f90 profiling.f90 string.f90 tutor.f90 version.f90 command_line.f90 vhdf5_base.f90 incar_reader.f90 reader_base.f90 openmp.f90 openacc_struct.f90 mpi.f90 mpi_shmem.f90 mathtools.f90 hamil_struct.f90 radial_struct.f90 pseudo_struct.f90 mgrid_struct.f90 wave_struct.f90 nl_struct.f90 mkpoints_struct.f90 poscar_struct.f90 afqmc_struct.f90 fock_glb.f90 chi_glb.f90 smart_allocate.f90 xml.f90 extpot_glb.f90 constant.f90 ml_ff_c2f_interface.f90 ml_ff_prec.f90 ml_ff_constant.f90 ml_ff_taglist.f90 ml_ff_struct.f90 ml_ff_mpi_help.f90 ml_ff_mpi_shmem.f90 vdwforcefield_glb.f90 jacobi.f90 main_mpi.f90 openacc.f90 scala.f90 asa.f90 lattice.f90 poscar.f90 ini.f90 mgrid.f90 ml_ff_error.f90 ml_ff_mpi.f90 ml_ff_helper.f90 ml_ff_logfile.f90 ml_ff_math.f90 ml_ff_iohandle.f90 ml_ff_memory.f90 ml_ff_abinitio.f90 ml_ff_ff.f90 ml_ff_mlff.f90 setex_struct.f90 xclib.f90 vdw_nl.f90 xclib_grad.f90 setex.f90 radial.f90 pseudo.f90 gridq.f90 ebs.f90 symlib.f90 mkpoints.f90 random.f90 wave.f90 wave_mpi.f90 wave_high.f90 bext.f90 spinsym.f90 symmetry.f90 lattlib.f90 nonl.f90 nonlr.f90 nonl_high.f90 dfast.f90 choleski2.f90 mix.f90 hamil.f90 xcgrad.f90 xcspin.f90 potex1.f90 potex2.f90 constrmag.f90 cl_shift.f90 relativistic.f90 LDApU.f90 paw_base.f90 metagga.f90 egrad.f90 pawsym.f90 pawfock.f90 pawlhf.f90 diis.f90 rhfatm.f90 hyperfine.f90 fock_ace.f90 paw.f90 mkpoints_full.f90 charge.f90 Lebedev-Laikov.f90 stockholder.f90 dipol.f90 solvation.f90 scpc.f90 pot.f90 tet.f90 dos.f90 elf.f90 hamil_rot.f90 chain.f90 dyna.f90 fileio.f90 vhdf5.f90 sphpro.f90 us.f90 core_rel.f90 aedens.f90 wavpre.f90 wavpre_noio.f90 broyden.f90 dynbr.f90 reader.f90 writer.f90 xml_writer.f90 brent.f90 stufak.f90 opergrid.f90 stepver.f90 fast_aug.f90 fock_multipole.f90 fock.f90 fock_dbl.f90 fock_frc.f90 mkpoints_change.f90 subrot_cluster.f90 sym_grad.f90 mymath.f90 npt_dynamics.f90 subdftd3.f90 subdftd4.f90 internals.f90 dynconstr.f90 dimer_heyden.f90 dvvtrajectory.f90 vdwforcefield.f90 nmr.f90 pead.f90 k-proj.f90 subrot.f90 subrot_scf.f90 paircorrection.f90 rpa_force.f90 ml_reader.f90 ml_interface.f90 force.f90 pwlhf.f90 gw_model.f90 optreal.f90 steep.f90 rmm-diis.f90 davidson.f90 david_inner.f90 root_find.f90 lcao_bare.f90 locproj.f90 electron_common.f90 electron.f90 rot.f90 electron_all.f90 shm.f90 pardens.f90 optics.f90 constr_cell_relax.f90 stm.f90 finite_diff.f90 elpol.f90 hamil_lr.f90 rmm-diis_lr.f90 subrot_lr.f90 lr_helper.f90 hamil_lrf.f90 elinear_response.f90 ilinear_response.f90 linear_optics.f90 setlocalpp.f90 wannier.f90 electron_OEP.f90 electron_lhf.f90 twoelectron4o.f90 gauss_quad.f90 m_unirnk.f90 minimax_ini.f90 minimax_dependence.f90 minimax_functions1D.f90 minimax_functions2D.f90 minimax_struct.f90 minimax_varpro.f90 minimax.f90 umco.f90 mlwf.f90 ratpol.f90 pade_fit.f90 screened_2e.f90 wave_cacher.f90 crpa.f90 chi_base.f90 wpot.f90 local_field.f90 ump2.f90 ump2kpar.f90 fcidump.f90 ump2no.f90 bse_te.f90 bse.f90 time_propagation.f90 acfdt.f90 afqmc.f90 rpax.f90 chi.f90 acfdt_GG.f90 dmft.f90 GG_base.f90 greens_orbital.f90 lt_mp2.f90 rnd_orb_mp2.f90 greens_real_space.f90 chi_GG.f90 chi_super.f90 sydmat.f90 rmm-diis_mlr.f90 linear_response_NMR.f90 wannier_interpol.f90 wave_interpolate.f90 linear_response.f90 auger.f90 dmatrix.f90 phonon.f90 wannier_mats.f90 elphon.f90 core_con_mat.f90 embed.f90 extpot.f90 rpa_high.f90 fftmpiw.f90 fftmpi_map.f90 fftw3d.f90 fft3dlib.f90 main.f90 > .depend
make[2]: Entering directory ‘/home/sherifyehia/Desktop/vasp.6.3.2/build/gam’
awk -f makedeps.awk c2f_interface.f90 nccl2for.f90 simd.f90 base.f90 profiling.f90 string.f90 tutor.f90 version.f90 command_line.f90 vhdf5_base.f90 incar_reader.f90 reader_base.f90 openmp.f90 openacc_struct.f90 mpi.f90 mpi_shmem.f90 mathtools.f90 hamil_struct.f90 radial_struct.f90 pseudo_struct.f90 mgrid_struct.f90 wave_struct.f90 nl_struct.f90 mkpoints_struct.f90 poscar_struct.f90 afqmc_struct.f90 fock_glb.f90 chi_glb.f90 smart_allocate.f90 xml.f90 extpot_glb.f90 constant.f90 ml_ff_c2f_interface.f90 ml_ff_prec.f90 ml_ff_constant.f90 ml_ff_taglist.f90 ml_ff_struct.f90 ml_ff_mpi_help.f90 ml_ff_mpi_shmem.f90 vdwforcefield_glb.f90 jacobi.f90 main_mpi.f90 openacc.f90 scala.f90 asa.f90 lattice.f90 poscar.f90 ini.f90 mgrid.f90 ml_ff_error.f90 ml_ff_mpi.f90 ml_ff_helper.f90 ml_ff_logfile.f90 ml_ff_math.f90 ml_ff_iohandle.f90 ml_ff_memory.f90 ml_ff_abinitio.f90 ml_ff_ff.f90 ml_ff_mlff.f90 setex_struct.f90 xclib.f90 vdw_nl.f90 xclib_grad.f90 setex.f90 radial.f90 pseudo.f90 gridq.f90 ebs.f90 symlib.f90 mkpoints.f90 random.f90 wave.f90 wave_mpi.f90 wave_high.f90 bext.f90 spinsym.f90 symmetry.f90 lattlib.f90 nonl.f90 nonlr.f90 nonl_high.f90 dfast.f90 choleski2.f90 mix.f90 hamil.f90 xcgrad.f90 xcspin.f90 potex1.f90 potex2.f90 constrmag.f90 cl_shift.f90 relativistic.f90 LDApU.f90 paw_base.f90 metagga.f90 egrad.f90 pawsym.f90 pawfock.f90 pawlhf.f90 diis.f90 rhfatm.f90 hyperfine.f90 fock_ace.f90 paw.f90 mkpoints_full.f90 charge.f90 Lebedev-Laikov.f90 stockholder.f90 dipol.f90 solvation.f90 scpc.f90 pot.f90 tet.f90 dos.f90 elf.f90 hamil_rot.f90 chain.f90 dyna.f90 fileio.f90 vhdf5.f90 sphpro.f90 us.f90 core_rel.f90 aedens.f90 wavpre.f90 wavpre_noio.f90 broyden.f90 dynbr.f90 reader.f90 writer.f90 xml_writer.f90 brent.f90 stufak.f90 opergrid.f90 stepver.f90 fast_aug.f90 fock_multipole.f90 fock.f90 fock_dbl.f90 fock_frc.f90 mkpoints_change.f90 subrot_cluster.f90 sym_grad.f90 mymath.f90 npt_dynamics.f90 subdftd3.f90 subdftd4.f90 internals.f90 dynconstr.f90 dimer_heyden.f90 dvvtrajectory.f90 vdwforcefield.f90 nmr.f90 pead.f90 k-proj.f90 subrot.f90 subrot_scf.f90 paircorrection.f90 rpa_force.f90 ml_reader.f90 ml_interface.f90 force.f90 pwlhf.f90 gw_model.f90 optreal.f90 steep.f90 rmm-diis.f90 davidson.f90 david_inner.f90 root_find.f90 lcao_bare.f90 locproj.f90 electron_common.f90 electron.f90 rot.f90 electron_all.f90 shm.f90 pardens.f90 optics.f90 constr_cell_relax.f90 stm.f90 finite_diff.f90 elpol.f90 hamil_lr.f90 rmm-diis_lr.f90 subrot_lr.f90 lr_helper.f90 hamil_lrf.f90 elinear_response.f90 ilinear_response.f90 linear_optics.f90 setlocalpp.f90 wannier.f90 electron_OEP.f90 electron_lhf.f90 twoelectron4o.f90 gauss_quad.f90 m_unirnk.f90 minimax_ini.f90 minimax_dependence.f90 minimax_functions1D.f90 minimax_functions2D.f90 minimax_struct.f90 minimax_varpro.f90 minimax.f90 umco.f90 mlwf.f90 ratpol.f90 pade_fit.f90 screened_2e.f90 wave_cacher.f90 crpa.f90 chi_base.f90 wpot.f90 local_field.f90 ump2.f90 ump2kpar.f90 fcidump.f90 ump2no.f90 bse_te.f90 bse.f90 time_propagation.f90 acfdt.f90 afqmc.f90 rpax.f90 chi.f90 acfdt_GG.f90 dmft.f90 GG_base.f90 greens_orbital.f90 lt_mp2.f90 rnd_orb_mp2.f90 greens_real_space.f90 chi_GG.f90 chi_super.f90 sydmat.f90 rmm-diis_mlr.f90 linear_response_NMR.f90 wannier_interpol.f90 wave_interpolate.f90 linear_response.f90 auger.f90 dmatrix.f90 phonon.f90 wannier_mats.f90 elphon.f90 core_con_mat.f90 embed.f90 extpot.f90 rpa_high.f90 fftmpiw.f90 fftmpi_map.f90 fftw3d.f90 fft3dlib.f90 main.f90 > .depend
make[2]: Leaving directory ‘/home/sherifyehia/Desktop/vasp.6.3.2/build/std’
make[1]: Leaving directory ‘/home/sherifyehia/Desktop/vasp.6.3.2/build/std’
make -C build/std VERSION=std all
make[2]: Leaving directory ‘/home/sherifyehia/Desktop/vasp.6.3.2/build/ncl’
make[1]: Leaving directory ‘/home/sherifyehia/Desktop/vasp.6.3.2/build/ncl’
make -C build/ncl VERSION=ncl all
make[1]: Entering directory ‘/home/sherifyehia/Desktop/vasp.6.3.2/build/std’
rsync -ru …/…/src/lib .
rsync -ru …/…/src/parser .
make[1]: Entering directory ‘/home/sherifyehia/Desktop/vasp.6.3.2/build/ncl’
rsync -ru …/…/src/lib .
cp makefile.include lib
cp makefile.include parser
make[2]: Leaving directory ‘/home/sherifyehia/Desktop/vasp.6.3.2/build/gam’
make[1]: Leaving directory ‘/home/sherifyehia/Desktop/vasp.6.3.2/build/gam’
make -C build/gam VERSION=gam all
make -C lib -j1
make -C parser -j1
cp makefile.include lib
make[2]: Entering directory ‘/home/sherifyehia/Desktop/vasp.6.3.2/build/std’
make[2]: warning: -j1 forced in submake: resetting jobserver mode.
make[2]: Entering directory ‘/home/sherifyehia/Desktop/vasp.6.3.2/build/std’
make[2]: warning: -j1 forced in submake: resetting jobserver mode.
make libdmy.a
make libparser.a
make[3]: Entering directory ‘/home/sherifyehia/Desktop/vasp.6.3.2/build/std/lib’
make[3]: ‘libdmy.a’ is up to date.
make[3]: Leaving directory ‘/home/sherifyehia/Desktop/vasp.6.3.2/build/std/lib’
make[2]: Leaving directory ‘/home/sherifyehia/Desktop/vasp.6.3.2/build/std/lib’
rsync -ru …/…/src/parser .
make -C lib -j1
make[3]: Entering directory ‘/home/sherifyehia/Desktop/vasp.6.3.2/build/std/parser’
make[3]: ‘libparser.a’ is up to date.
make[3]: Leaving directory ‘/home/sherifyehia/Desktop/vasp.6.3.2/build/std/parser’
make[1]: Entering directory ‘/home/sherifyehia/Desktop/vasp.6.3.2/build/gam’
rsync -ru …/…/src/lib .
make[2]: Leaving directory ‘/home/sherifyehia/Desktop/vasp.6.3.2/build/std/parser’
cp makefile.include parser
rsync -ru …/…/src/fftlib .
make[2]: Entering directory ‘/home/sherifyehia/Desktop/vasp.6.3.2/build/ncl’
make[2]: warning: -j1 forced in submake: resetting jobserver mode.
make libdmy.a
make -C parser -j1
cp makefile.include fftlib
make[2]: Entering directory ‘/home/sherifyehia/Desktop/vasp.6.3.2/build/ncl’
make[2]: warning: -j1 forced in submake: resetting jobserver mode.
cp makefile.include lib
make[3]: Entering directory ‘/home/sherifyehia/Desktop/vasp.6.3.2/build/ncl/lib’
make[3]: ‘libdmy.a’ is up to date.
make[3]: Leaving directory ‘/home/sherifyehia/Desktop/vasp.6.3.2/build/ncl/lib’
make[2]: Leaving directory ‘/home/sherifyehia/Desktop/vasp.6.3.2/build/ncl/lib’
rsync -u …/…/src/.F …/…/src/.inc .
make libparser.a
make -C fftlib -j1
make[3]: Entering directory ‘/home/sherifyehia/Desktop/vasp.6.3.2/build/ncl/parser’
make[3]: ‘libparser.a’ is up to date.
make[3]: Leaving directory ‘/home/sherifyehia/Desktop/vasp.6.3.2/build/ncl/parser’
make[2]: Leaving directory ‘/home/sherifyehia/Desktop/vasp.6.3.2/build/ncl/parser’
rsync -ru …/…/src/fftlib .
make[2]: Entering directory ‘/home/sherifyehia/Desktop/vasp.6.3.2/build/std’
make[2]: warning: -j1 forced in submake: resetting jobserver mode.
make -C lib -j1
make fftlib.o

gheber · January 21, 2023, 3:45pm

That’s the problem & everything else is just noise. What’s in this directory?

$(HDF5_ROOT)/include

?

G.

sherif542002 · January 21, 2023, 4:00pm

Thank you

[root@192 include]# ls
aec_config.h H5DxferProp.h H5AbstractDs.h H5EnumType.h H5ACpublic.h H5Epubgen.h H5Alltypes.h H5Epublic.h H5api_adpt.h H5ESdevelop.h H5Apublic.h H5ESpublic.h H5ArrayType.h H5Exception.h H5AtomType.h H5f90.h H5Attribute.h H5f90i_gen.h H5Classes.h H5f90i.h H5CommonFG.h H5f90proto.h H5CompType.h H5FaccProp.h H5CppDoc.h H5FcreatProp.h H5Cpp.h H5FDcore.h H5Cpublic.h H5FDdevelop.h H5DaccProp.h H5FDdirect.h H5DataSet.h H5FDfamily.h H5DataSpace.h H5FDhdfs.h H5DataType.h H5FDioc.h H5DcreatProp.h H5FDlog.h H5DOpublic.h H5FDmirror.h H5Dpublic.h H5FDmpi.h H5DSpublic.h H5FDmpio.h H5FDmulti.h H5LcreatProp.h H5Spublic.h
H5FDonion.h H5Ldevelop.h H5StrType.h
H5FDpublic.h H5LDpublic.h H5TBpublic.h
H5FDros3.h H5Library.h H5Tdevelop.h
H5FDs3comms.h H5Location.h H5Tpublic.h
H5FDsec2.h H5Lpublic.h H5TSdevelop.h
H5FDsplitter.h H5LTpublic.h H5VarLenType.h
H5FDstdio.h H5MMpublic.h H5version.h
H5FDsubfiling.h H5Mpublic.h H5VLconnector.h
H5FDwindows.h H5Object.h H5VLconnector_passthru.h
H5File.h H5OcreatProp.h H5VLnative.h
H5FloatType.h H5Opublic.h H5VLpassthru.h
H5fortran_types.F90 H5overflow.h H5VLpublic.h
H5Fpublic.h H5PacketTable.h H5Zdevelop.h
H5Gpublic.h H5PLextern.h H5Zpublic.h
H5Group.h H5PLpublic.h hdf5.h
H5IdComponent.h H5Ppublic.h hdf5_hl.h
H5Idevelop.h H5PredType.h libaec.h
H5IMpublic.h H5PropList.h szlib.h
H5Include.h H5PTpublic.h zconf.h
H5IntType.h H5pubconf.h
H5Ipublic.h H5public.h
H5LaccProp.h H5Rpublic.h

sherif542002 · January 22, 2023, 5:15pm

I found the problem in the following option Number 1 when I switch the CPP OPTIONS ON
I get error other wise gave no error. In this case the vasp never give vaspout.h5 as they mention in the vasp software guide. Unfortunately I got no answer when I put the question in their forum

This is essential for reading and writing HDF5 files, such as vaspout.h5. The HDF5 library is available for download on the HDF5 official website. To activate this feature set the following:

1-CPP_OPTIONS+= -DVASP_HDF5
2-HDF5_ROOT ?= /path/to/your/hdf5/installation3-
3-LLIBS += -L$(HDF5_ROOT)/lib -lhdf5_fortran
4-INCS += -I$(HDF5_ROOT)/include

My question I don’t understand what is CPP_OTIONS doing

sherif542002 · January 27, 2023, 1:39pm

Dear Experts
According to the advice of the vasp community for setting hd5
I have to make sure that
whether the directory which contains my installation for hdf5 {/home/sherifyehia/hdf5-1.8.14 } contains the libraries libhdf5_fortran and libhdf5
But this is NOT the case hdf5-1.8.14
please see locate
root@localhost hdf5-1.13.2]# locate libhdf5_fortran.a
/home/sherifyehia/.local/share/Trash/expunged/1280365874/lib/libhdf5_fortran.a
/home/sherifyehia/.local/share/Trash/expunged/3883262023/hdf5/lib/libhdf5_fortran.a
/home/sherifyehia/.local/share/Trash/expunged/3940400900/fortran/src/.libs/libhdf5_fortran.a
/home/sherifyehia/.local/share/Trash/expunged/3940400900/hdf5/lib/libhdf5_fortran.a
/opt/libhdf5_fortran.a
/opt/intel/oneapi/intelpython/python3.9/pkgs/hdf5-1.10.6-hb1b8bf9_0/lib/libhdf5_fortran.a
/opt/intel/oneapi/mkl/2023.0.0/lib/intel64/libhdf5_fortran.a
/opt/intel/oneapi/mpi/2021.8.0/lib/libhdf5_fortran.a
/opt/intel/oneapi/tensorflow/2.9.1.1/lib/libhdf5_fortran.a

Now my question is where I should just copy libhdf5.fortran.a
or according to the doc it is only on /usr/local/hdf5/lib
Please clarify that to me
Thanks for all your effort and time

sherif542002 · January 27, 2023, 1:45pm

Please this is the locate I have previous one didn’t show
/usr/local/hdf5/lib/libhdf5.a

/home/sherifyehia/.local/share/Trash/expunged/1280365874/lib/libhdf5.a
/home/sherifyehia/.local/share/Trash/expunged/3883262023/hdf5/lib/libhdf5.a
/home/sherifyehia/.local/share/Trash/expunged/3940400900/hdf5/lib/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