Error in vaspout.h5
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Error in vaspout.h5
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
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
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- Newbie
- Posts: 28
- Joined: Wed Aug 24, 2022 5:36 pm
Error In Hdf5 Installation
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 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
-
- Global Moderator
- Posts: 542
- Joined: Fri Nov 08, 2019 7:18 am
Re: Error in vaspout.h5
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.
Code: Select all
ldd bin/vasp_std
Code: Select all
libhdf5.so => not found
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.
Martin Schlipf
VASP developer
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- Newbie
- Posts: 28
- Joined: Wed Aug 24, 2022 5:36 pm
Re: Error in vaspout.h5
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
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
-
- Global Moderator
- Posts: 542
- Joined: Fri Nov 08, 2019 7:18 am
Re: Error in vaspout.h5
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.
Martin Schlipf
VASP developer
-
- Newbie
- Posts: 28
- Joined: Wed Aug 24, 2022 5:36 pm
Re: Error in vaspout.h5
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
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
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Re: Error in vaspout.h5
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.
Martin Schlipf
VASP developer
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Re: Error in vaspout.h5
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
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
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Re: Error in vaspout.h5
Please disregard my previous attachment for error
The right one is here
Sorry for the inconvenience
Thanks again
The right one is here
Sorry for the inconvenience
Thanks again
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Re: Error in vaspout.h5
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.
Code: Select all
ls /usr/local/hdf5/lib
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.
Martin Schlipf
VASP developer
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- Newbie
- Posts: 28
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Re: Error in vaspout.h5
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
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
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Re: Error in vaspout.h5
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.
Code: Select all
nm /home/sherifyehia/hdf5-1.13.2/lib/libhdf5_fortran.so
Code: Select all
grep h5f_mp_h5fopen
For the record, here is a script that I used many times to install HDF5 with the Intel compiler
Code: Select all
source /opt/intel/oneapi/setvars.sh intel64
export HDF5_VERSION=1.12.2
export STRIP_PATCH=$(echo $HDF5_VERSION | awk -F. '{ print $1"."$2 }')
export CC=icx
export CXX=icpx
export FC=ifort
export CFLAGS='-O3 -xHost -ip'
export CXXFLAGS='-O3 -xHost -ip'
export FCFLAGS='-O3 -xHost -ip'
wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-$STRIP_PATCH/hdf5-$HDF5_VERSION/src/hdf5-$HDF5_VERSION.tar.gz
tar -zxvf hdf5-$HDF5_VERSION.tar.gz
cd hdf5-$HDF5_VERSION
./configure --prefix=/usr/local/hdf5-$HDF5_VERSION --enable-fortran --enable-cxx
make
make check
sudo bash
source /opt/intel/oneapi/setvars.sh intel64
make install
exit
Code: Select all
cp arch/makefile.include.intel makefile.include
cat << EOF >> makefile.include
CPP_OPTIONS += -DVASP_HDF5
LLIBS += -L/usr/local/hdf5-$HDF5_VERSION/lib -lhdf5_fortran
INCS += -I/usr/local/hdf5-$HDF5_VERSION/include
EOF
make
Martin Schlipf
VASP developer
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Re: Error in vaspout.h5
Thanks for sending those great codes 1&2
Here is what happened when I run the first one I got the following error
configure: error: cannot run C compiled programs.
If you meant to cross compile, use `--host'.
See `config.log' for more details
make: *** [Makefile:32: _config] Error 1
I put in the 3 lines of the first code as you recomend before
export CFLAGS='-march=core-avx2'
export CXXFLAGS='-march=core-avx2'
export FCFLAGS='-march=core-avx2'
Instead
export CFLAGS='-O3 -xHost -ip'
export CXXFLAGS='-O3 -xHost -ip'
export FCFLAGS='-O3 -xHost -ip'
It workks fine but in the installation part names became hdf5-1.12.2 NOT hdf5
(base) [sherifyehia@192 ~]$ 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
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
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Re: Error in vaspout.h5
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
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
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Re: Error in vaspout.h5
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.
Martin Schlipf
VASP developer