ERROR: HDF5 file "../dataset.h5" not found.

[jimbo...@gmail.com]

Hi,

I'm new to pflotran. I followed the installation instructions and got pflotran to compile, but I've hit a brick wall trying to run 2D or 3D example.in files from the verification suite.

I can run a 1D simulation and can also successfully run a regression test, but when I try and run a 2D simulation I get the error:

HDF5-DIAG: Error detected in HDF5 (1.8.18) MPI-process 0:
#000: H5F.c line 604 in H5Fopen(): unable to open file
major: File accessibilty
minor: Unable to open file
#001: H5Fint.c line 992 in H5F_open(): unable to open file: time = Fri Aug 31 12:55:55 2018
, name = '../dataset.h5', tent_flags = 0
major: File accessibilty
minor: Unable to open file
#002: H5FD.c line 993 in H5FD_open(): open failed
major: Virtual File Layer
minor: Unable to initialize object
#003: H5FDmpio.c line 1059 in H5FD_mpio_open(): MPI_File_open failed
major: Internal error (too specific to document in detail)
minor: Some MPI function failed
#004: H5FDmpio.c line 1059 in H5FD_mpio_open(): File does not exist, error stack:
ADIOI_UFS_OPEN(42): File ../dataset.h5 does not exist
major: Internal error (too specific to document in detail)
minor: MPI Error String

ERROR: HDF5 file "../dataset.h5" not found.

Stopping!
Note: The following floating-point exceptions are signalling: IEEE_DENORMAL

I suspect this issue is with the way PETSc is configured with it's HDF5 package. This is the command I used to configure petsc before compiling.

./configure --CFLAGS='-O3' --CXXFLAGS='-O3' --FFLAGS='-O3' --with-debugging=no --download-mpich=no --download-hdf5=yes --download-fblaslapack=yes --download-metis=yes --download-parmetis=yes --download-make=yes --download-cmake=yes

notes: I installed the mpich package separately, and I'm using an ubuntu 18.04 console. I get the same error on 2 separate machines, so I'm doing something consistently wrong here.

I have also tried adding the following a suggestion in this post, where a native installation of HDF5 was overriding the one used by PETSc: https://groups.google.com/forum/#!topic/pflotran-dev/YFPsvqbZkRk

so I added this line to my .bashrc file

export LD_LIBRARY_PATH=~/petsc/arch-linux2-c-opt/externalpackages/hdf5-1.8.18/src/.libs:$LD_LIBRARY_PATH

but unfortunately no dice.

Any help would be greatly appreciated as I'm looking at running 3D problems.

[Karra, Satish]

ADIOI_UFS_OPEN(42): File ../dataset.h5 does not exist

    major: Internal error (too specific to document in detail)

    minor: MPI Error String

 

ERROR: HDF5 file "../dataset.h5" not found.

 

Looks like it can’t find ../dataset.h5. Have you checked that this file is in the location where you’ve specified?

 

Thanks,

Satish

--

You received this message because you are subscribed to the Google Groups "pflotran-dev" group.

To view this discussion on the web visit https://groups.google.com/d/msgid/pflotran-dev/38ea028e-b095-42d7-b58e-eb3d0cad9573%40googlegroups.com.

 

[jimbo...@gmail.com]

Hi

Thank you for the reply, I did a quick search for the file but I couldn't find anything. Annoyingly the error doesn't return the full file path. I'll have to look the code directly and see what it's attempting to reference.

Out of curiosity what version for the HDF5 package are you using? I'm wondering if its a recent update of the package which might be causing the issue.

Thanks again,
Jimmy

[Hammond, Glenn E]

Jimmy,

Which input file are you attempting to run (full path)?

We currently build against HDF5 1.8.x. One can run with 1.10.x as long as HDF5 checkpoint/restart is not used.

Thanks,

Glenn

> --
> You received this message because you are subscribed to the Google Groups "pflotran-dev" group.

> To view this discussion on the web visit https://groups.google.com/d/msgid/pflotran-dev/7821d9e4-9d61-4678-9728-32b10982c19e%40googlegroups.com.

[jimbo...@gmail.com]

Hi Glenn,

The validation suite deck file I'm using is "2D Steady Flow (Pressure), BCs of 1st Kind, (in Richard's mode)" which can be found here:

https://www.pflotran.org/documentation/include_toctree_flow_steady.html#flow-general-steady-2d-pressure-bc-1st-kind-pflotran-input

I then use

mpirun -n 1 $PFLOTRAN_DIR/src/pflotran/pflotran -input_prefix [insert_file_name_here]

Hope that gives you what you were looking for.

I appreciate the time/effort taken to reply, good to know my version of HDF5 should be supported.

Many thanks,
Jimmy

[Karra, Satish]

Jimmy,

The specified file path is '../dataset.h5'. Did you create this file and place in this path?

Thanks,
Satish

[Karra, Satish]

You'll need to make sure that you create dataset.h5 file using the 'create_dataset.py' that is at

https://www.pflotran.org/documentation/include_toctree_flow_steady.html#flow-steady-2d-pressure-bc-1st-kind-dataset

Then make sure it's located at '../dataset.h5'.

Thanks,
Satish

--
You received this message because you are subscribed to the Google Groups "pflotran-dev" group.

To view this discussion on the web visit https://groups.google.com/d/msgid/pflotran-dev/081afe01-0cd9-48a7-b7ef-03a75eb981c7%40googlegroups.com.

[jimbo...@gmail.com]

Ah I missed this step entirely. Sorry for missing something fairly obvious.

Thank you so much (both of you). Hopefully this will help anyone else wanting to test pflotran once it has compiled.

Regards,
Jimmy