internal error in: vhdf5.F

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md_ashraf_ali
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HDF5 call in vhdf5.F:84 produced error: -1

#1 Post by md_ashraf_ali » Tue Nov 28, 2023 6:17 am

Hi,
I am facing this bug while running a test calculation after installing vasp 6.4.2.
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Re: HDF5 call in vhdf5.F:84 produced error: -1

#2 Post by fabien_tran1 » Tue Nov 28, 2023 8:34 am

Hi,

At the beginning of your screenshot, the line "running 1 mpi-ranks, with 36 threads/rank ..." is printed twice instead of only once as it should. This indicates that there is an inconsistency in your usage of MPI. For instance, this can occur if you attempt to run the calculation with e.g., OpenMPI, while VASP was compiled with the intel MPI library. Are you using the same MPI library for compilation and executing the calculation?

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Re: HDF5 call in vhdf5.F:84 produced error: -1

#3 Post by md_ashraf_ali » Thu Nov 30, 2023 5:57 am

yes I am using the same libarary for compilation.I have followed the attached procedure for compilation.

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Re: HDF5 call in vhdf5.F:84 produced error: -1

#4 Post by fabien_tran1 » Thu Nov 30, 2023 8:02 am

You forgot the attachment.

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internal error in: vhdf5.F

#5 Post by md_ashraf_ali » Thu Dec 07, 2023 5:44 am

Hi,
I am facing the following problem after installing my vasp while running a test atom.
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Re: internal error in: vhdf5.F

#6 Post by jonathan_lahnsteiner2 » Thu Dec 07, 2023 8:54 am

Dear md_ashraf_ali,

Please supply the input files of your test calculation as stated in the vasp forum guidelines https://www.vasp.at/forum/viewtopic.php?t=17630.
I would need the INCAR, POSCAR, KPOINTS, and POTCAR file.
Could you tell me what compilers, mpi, and hdf5 library you were using? Then I can try to reproduce your problem.
Without this information, I am not able to help you.

All the best Jonathan

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Re: internal error in: vhdf5.F

#7 Post by md_ashraf_ali » Mon Dec 11, 2023 6:42 am

I have attached the zip file containing the necessary files and a screenshot of my compilation information.
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Re: internal error in: vhdf5.F

#8 Post by jonathan_lahnsteiner2 » Tue Dec 12, 2023 7:16 am

Dear md_ashraf_ali,

I am not able to reproduce your problem with the supplied test case and using a similar environment as you.
In the first picture you supply you start the code with mpirun -np 2 vasp and get the output

Code: Select all

running 1 mpi-ranks
twice. And in the second picture, you supply, you get the output

Code: Select all

running 1 mpi-ranks.
But what you should get is

Code: Select all

running 2 mpi-ranks,
so this means that there are issues with the mpi. Are you sure that you are compiling and running vasp with the same mpi version.
You can verify this by using the ldd command.
First use

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ldd /path_to_vasp_bin/vasp_std | grep mpi
to check with which mpi version vasp was compiled. Then check with

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mpirun --version
the mpi version with which you execute vasp. Those version numbers should match.
The next step is to check to which hdf5 library vasp is linked. This can be obtained with

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ldd /path_to_vasp_bin/vasp_std | grep hdf5
Now you know the absolute path to your hdf5 library and the names of the library files. Now check which mpi version was used to compile the hdf5 library.
Therefore type

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ldd /absoulte_path_to_hdf5_from_previous_command/libhdf5_fortran.so
The filename libhdf5_fortran.so might be slightly different in your case. But you will figure the file name out from the ldd /path_to_vasp_bin/vasp_std | grep hdf5 command.
Now you have to compare all the mpi versions if they are the same. Please try doing this and post the output of all the
terminal commands here.

I hope this is of help

All the best Jonathan

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Re: internal error in: vhdf5.F

#9 Post by md_ashraf_ali » Thu Dec 14, 2023 6:17 am

here is the output
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Re: internal error in: vhdf5.F

#10 Post by jonathan_lahnsteiner2 » Thu Dec 14, 2023 6:57 am

Dear md_ashraf_ali,

Thank you for submitting the output. Here the linked libraries look okay.
Could you please also supply the output of

Code: Select all

which mpirun
All the best Jonathan

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Re: internal error in: vhdf5.F

#11 Post by md_ashraf_ali » Thu Dec 14, 2023 7:14 am

which mpirun output
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Re: internal error in: vhdf5.F

#12 Post by jonathan_lahnsteiner2 » Thu Dec 14, 2023 7:32 am

Dear md_ashraf_ali,

Thank you for posting the output.
So the problem with your calculation is the following:
You are compiling vasp properly, also with the hdf5. For this
compilation, you are using an mpi which is located in a folder /lib/x86_64-linux-gnu/

But for executing the code with mpirun you are using a different mpi.
You can see this because the output of which mpirun does not match the library path against you link
vasp. So all you have to do is use the mpirun belonging to the mpi with which you compile vasp.

All the best Jonathan

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Re: internal error in: vhdf5.F

#13 Post by md_ashraf_ali » Thu Dec 14, 2023 10:32 am

Could you please tell me how can I use the exact mpi which is linked with vasp?

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Re: internal error in: vhdf5.F

#14 Post by jonathan_lahnsteiner2 » Thu Dec 14, 2023 11:04 am

Dear md_ashraf_ali,

I would first try to deactivate the conda environment, because the mpi that you are using for execution is the anaconda mpi.

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conda deactivate
The (base) in your command prompt should vanish. Then try to execute vasp.
You can also check again what mpirun version you are using with

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which mpirun
Please try this and post again the output in case vasp execution does not work.

All the best Jonathan

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Re: internal error in: vhdf5.F

#15 Post by md_ashraf_ali » Thu Dec 14, 2023 4:56 pm

vasp calculation is running successfully without any bug error.But my vaspout.h5 is not opening.
More, I am facing the following problem in py4vasp.How can I fix the LORBIT setting issue?
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Last edited by md_ashraf_ali on Thu Dec 14, 2023 6:23 pm, edited 2 times in total.

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