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installation of VASP with HDF5

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installation of VASP with HDF5

Posted: Mon Dec 11, 2023 5:40 am
by scanmat_centre
How to install VASP 6.4 with HDF?

Re: installation of VASP with HDF5

Posted: Mon Dec 11, 2023 7:55 am
by jonathan_lahnsteiner2
Dear scanmat_centre,

In principle, you just have to load your hdf5 library in addition to the other
used libraries such as mpi, lapack...
Then you copy the desired makefile.include from the arch folder in the vasp directory.
In the makefile.include you have to uncomment the following line:

Code: Select all

CPP_OPTIONS+= -DVASP_HDF5
HDF5_ROOT  ?= /path/to/your/hdf5/installation
LLIBS      += -L$(HDF5_ROOT)/lib -lhdf5_fortran
INCS       += -I$(HDF5_ROOT)/include
I hope this is of help.

All the best Jonathan

Re: installation of VASP with HDF5

Posted: Thu Dec 14, 2023 2:02 pm
by scanmat_centre
I installed VASP 6.3.2 using the steps given in the following link https://www.vasp.at/wiki/index.php/Pers ... untu_22.04
and I successfully compiled, while running calculation. I am getting following error

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0 0x7f1b08348960 in ???
#1 0x7f1b08347ac5 in ???
#0 0x7f1a3e548960 in ???
#1 0x7f1a3e547ac5 in ???
#0 0x7f8824748960 in ???
#1 0x7f8824747ac5 in ???
#0 0x7f88e1f48960 in ???
#1 0x7f88e1f47ac5 in ???
#0 0x7f1aef348960 in ???
#1 0x7f1aef347ac5 in ???
#0 0x7fbcbab48960 in ???
#1 0x7fbcbab47ac5 in ???
#2 0x7f88244f751f in ???
at ./signal/../sysdeps/unix/sysv/linux/x86_64/libc_sigaction.c:0
#3 0x7f8823cbd77c in ???
#2 0x7f88e1d3f51f in ???
at ./signal/../sysdeps/unix/sysv/linux/x86_64/libc_sigaction.c:0
#3 0x7f88e150577c in ???
#2 0x7f1aef13f51f in ???
at ./signal/../sysdeps/unix/sysv/linux/x86_64/libc_sigaction.c:0
#3 0x7f1aee90577c in ???
#2 0x7fbcba81051f in ???
at ./signal/../sysdeps/unix/sysv/linux/x86_64/libc_sigaction.c:0
#3 0x7fbcb9fd677c in ???
#2 0x7f1b0801051f in ???
at ./signal/../sysdeps/unix/sysv/linux/x86_64/libc_sigaction.c:0
#3 0x7f1b077d677c in ???
#2 0x7f1a3e1f051f in ???
at ./signal/../sysdeps/unix/sysv/linux/x86_64/libc_sigaction.c:0
#3 0x7f1a3d9b677c in ???
#4 0x7f8824ae0d4a in pmpi_comm_rank_
at ../../src/binding/fortran/mpif_h/comm_rankf.c:268
#4 0x7f88e22e0d4a in pmpi_comm_rank_
at ../../src/binding/fortran/mpif_h/comm_rankf.c:268
#5 0x5589e530e293 in ???
#6 0x5589e533b8ca in ???
#7 0x5589e5fa130c in ???
#5 0x55edacdd4293 in ???
#6 0x55edace018ca in ???
#7 0x55edada6730c in ???
#8 0x55edadaa39e3 in ???
#8 0x5589e5fdd9e3 in ???
#4 0x7f1aef6e0d4a in pmpi_comm_rank_
at ../../src/binding/fortran/mpif_h/comm_rankf.c:268
#5 0x5601e134b293 in ???
#6 0x5601e13788ca in ???
#7 0x5601e1fde30c in ???
#8 0x5601e201a9e3 in ???
#4 0x7fbcbaee0d4a in pmpi_comm_rank_
at ../../src/binding/fortran/mpif_h/comm_rankf.c:268
#5 0x556f944fd293 in ???
#6 0x556f9452a8ca in ???
#7 0x556f9519030c in ???
#8 0x556f951cc9e3 in ???
#4 0x7f1b086e0d4a in pmpi_comm_rank_
at ../../src/binding/fortran/mpif_h/comm_rankf.c:268
#5 0x55cd836eb293 in ???
#6 0x55cd837188ca in ???
#7 0x55cd8437e30c in ???
#8 0x55cd843ba9e3 in ???
#4 0x7f1a3e8e0d4a in pmpi_comm_rank_
at ../../src/binding/fortran/mpif_h/comm_rankf.c:268
#5 0x555d28359293 in ???
#6 0x555d283868ca in ???
#7 0x555d28fec30c in ???
#8 0x555d290289e3 in ???
#9 0x7f1a3e1d7d8f in __libc_start_call_main
at ../sysdeps/nptl/libc_start_call_main.h:58
#10 0x7f1a3e1d7e3f in __libc_start_main_impl
at ../csu/libc-start.c:392
#9 0x7f88244ded8f in __libc_start_call_main
at ../sysdeps/nptl/libc_start_call_main.h:58
#10 0x7f88244dee3f in __libc_start_main_impl
at ../csu/libc-start.c:392
#11 0x555d28326b24 in ???
#12 0xffffffffffffffff in ???
#11 0x55edacda1b24 in ???
#12 0xffffffffffffffff in ???
#9 0x7f88e1d26d8f in __libc_start_call_main
at ../sysdeps/nptl/libc_start_call_main.h:58
#10 0x7f88e1d26e3f in __libc_start_main_impl
at ../csu/libc-start.c:392
#11 0x5589e52dbb24 in ???
#12 0xffffffffffffffff in ???
#9 0x7f1aef126d8f in __libc_start_call_main
at ../sysdeps/nptl/libc_start_call_main.h:58
#10 0x7f1aef126e3f in __libc_start_main_impl
at ../csu/libc-start.c:392
#11 0x5601e1318b24 in ???
#12 0xffffffffffffffff in ???
#9 0x7fbcba7f7d8f in __libc_start_call_main
at ../sysdeps/nptl/libc_start_call_main.h:58
#10 0x7fbcba7f7e3f in __libc_start_main_impl
at ../csu/libc-start.c:392
#11 0x556f944cab24 in ???
#12 0xffffffffffffffff in ???
#9 0x7f1b07ff7d8f in __libc_start_call_main
at ../sysdeps/nptl/libc_start_call_main.h:58
#10 0x7f1b07ff7e3f in __libc_start_main_impl
at ../csu/libc-start.c:392
#11 0x55cd836b8b24 in ???
#12 0xffffffffffffffff in ???

===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= RANK 0 PID 29471 RUNNING AT scanmat11
= KILLED BY SIGNAL: 11 (Segmentation fault)
===================================================================================

===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= RANK 1 PID 29472 RUNNING AT scanmat11
= KILLED BY SIGNAL: 11 (Segmentation fault)
===================================================================================

===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= RANK 2 PID 29473 RUNNING AT scanmat11
= KILLED BY SIGNAL: 11 (Segmentation fault)
===================================================================================

===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= RANK 3 PID 29474 RUNNING AT scanmat11
= KILLED BY SIGNAL: 11 (Segmentation fault)
===================================================================================

===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= RANK 4 PID 29475 RUNNING AT scanmat11
= KILLED BY SIGNAL: 11 (Segmentation fault)
===================================================================================

===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= RANK 5 PID 29476 RUNNING AT scanmat11
= KILLED BY SIGNAL: 11 (Segmentation fault)
===================================================================================

Re: installation of VASP with HDF5

Posted: Fri Dec 15, 2023 6:25 am
by jonathan_lahnsteiner2
Dear scanmat_centre,

Please submit the input files according to the vasp forum guidelines for which you received this output.
You can find the vasp forum guidelines in this link:
https://www.vasp.at/forum/viewtopic.php?t=17928
I would need the INCAR file, the POSCAR file, the KPOINTS file, and the POTCAR file.
Please also let me know what toolchain you were using.
What compiler version, which openmpi version, and so on.

All the best Jonathan

Re: installation of VASP with HDF5

Posted: Fri Dec 15, 2023 10:38 am
by scanmat_centre
I installed VASP 6.3.2 using the steps given in the following link https://www.vasp.at/wiki/index.php/Pers ... untu_22.04
with g++ (4:11.2.0-1ubuntu1),
gfortran (4:11.2.0-1ubuntu1),
libfftw3-dev (3.3.8-2ubuntu8),
make (4.3-4.1build1),
libhdf5-openmpi-dev (1.10.7+repack-4ubuntu2),
libopenblas-dev (0.3.20+ds-1),
libopenmpi-dev (4.1.2-2ubuntu1),
libscalapack-openmpi-dev (2.1.0-4)

and I successfully compiled, while running calculation. I am getting Error given in output_error file

Re: installation of VASP with HDF5

Posted: Fri Dec 15, 2023 11:46 am
by jonathan_lahnsteiner2
Dear scanmat_centre,

I tried your job and it is working as expected.
When considering your error output I recognized the following line:

Code: Select all

../../src/binding/fortran/mpif_h/comm_rankf.c:268
It could be that you are using different MPI versions for compilation and execution.
Could you check with

Code: Select all

ldd /path_to_vasp/vasp_std | grep mpi
to what openmpi vasp is linked. Then compare this output with the output of

Code: Select all

which mpirun
and check if the path to the library matches.

All the best Jonathan

Re: installation of VASP with HDF5

Posted: Sun Dec 17, 2023 5:38 am
by scanmat_centre
Dear Jonathan,
I think I'm using different MPI versions for compilation and execution. For your reference I gave the output of the codes given by you. Can you help me to compile with same MPI version

(base) scanmat11@scanmat11:~/VASP6/vasp.6.3.2$ ldd /home/scanmat11/VASP6/vasp.6.3.2/bin/vasp_std | grep mpi
libscalapack-openmpi.so.2.1 => /usr/lib/x86_64-linux-gnu/libscalapack-openmpi.so.2.1 (0x00007f8ab4818000)
libhdf5_openmpi_fortran.so.102 => /usr/lib/x86_64-linux-gnu/libhdf5_openmpi_fortran.so.102 (0x00007f8ab2144000)
libmpifort.so.12 => /home/scanmat11/intel/oneapi/mpi/2021.6.0//lib/libmpifort.so.12 (0x00007f8ab1c00000)
libmpi.so.40 => /usr/lib/x86_64-linux-gnu/libmpi.so.40 (0x00007f8ab0e57000)
libhdf5_openmpi.so.103 => /usr/lib/x86_64-linux-gnu/libhdf5_openmpi.so.103 (0x00007f8ab0aa2000)
libmpi.so.12 => /home/scanmat11/intel/oneapi/mpi/2021.6.0//lib/release/libmpi.so.12 (0x00007f8aaf200000)

(base) scanmat11@scanmat11:~/VASP6/vasp.6.3.2$ which mpirun
/home/scanmat11/intel/oneapi/mpi/2021.6.0//bin/mpirun

Re: installation of VASP with HDF5

Posted: Mon Dec 18, 2023 7:02 am
by jonathan_lahnsteiner2
Dear scanmat_centre,

Yes, you are using a mixed setup. You compiled vasp with openmpi and for execution,
you are using intel mpi. You can see this because the mpirun executable is located in
the intel oneapi. So before executing vasp you should not load the intel oneapi. Execute
the vasp binary with the openmpi mpirun.

Another possibility would be to install the intel-oneapi-base kit (which you already have) and the intel-oneapi-hpc-kit.
You can find these on that homepage for download
https://www.intel.com/content/www/us/en ... l#base-kit
And then recompile vasp with the makefile.include.intel.

All the best Jonathan
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