visit: Cannot read openPMD file

I want to open an ADIOS-based openPMD file. I am using VisIt 3.1.4 on macOS 11.4, downloaded as a binary.

I have written the file with our application (the Einstein Toolkit), and I can read it there as well. Both bpls and openpmd-ls display the information in the file correctly, and they don’t indicate any errors.

There are two issues:

(1) I cannot get VisIt to even open the file. The file selection box only lets me open files, but ADIOS bp file are stored as a directory. I tried pointing VisIt to one of the files in the directory, but this didn’t work either, not even when I explicitly choose OpenPMD as file format.

(2) I created a *.visit file that points to the openPMD file (i.e. directory). I cannot open this file either; VisIt reports the error

VisIt could not read from the file "/Users/eschnett/simulations/brill-lindquist-write/output-0000/brill-lindquist-write/brill-lindquist-write.openpmd.visit".

The generated error message was:

There was an error opening /Users/eschnett/simulations/brill-lindquist-write/output-0000/brill-lindquist-write/brill-lindquist-write.openpmd.visit. It may be an invalid file.  VisIt tried using the following file format readers to open the file: OpenPMD

The following error(s) may be helpful in identifying the problem:
The selected database type was not correct for the given file.  The message from the database was Not an openPMD file: Error opening the file

I again explicitly chose OpenPMD as file format.

About this issue

Original URL
State: open
Created 3 years ago
Reactions: 2
Comments: 45 (39 by maintainers)

Most upvoted comments

@biagas I cannot open the *.bp directory directly. However, I can point a *.visit file to it, and I can then explicitly open it as ADIOS2 file. This recognizes the metadata correctly. Since openPMD uses a particular way to lay out datasets in the file, a lot of internals are exposed that shouldn’t be, but I was able to find a dataset to display.

Drawing that dataset crashed the engine. This is using VisIt 3.1.4, both the viewer and the engine running locally on macOS.

I am happy to provide the file. I reduced the size to 1.3 MByte; is that sufficiently small, or should it be even smaller?

eschnett on Jun 12, 2021

Hello. We will discuss this at the next team meeting and see if we will be able to get it in 3.4.1 or 3.4.2. 3.4.1 is probably coming pretty soon to fix some issues with 3.4.0.

JustinPrivitera on Dec 11, 2023

It sounds like what you are looking for, however, is an upgrade to our openPMD reader, so that it depends on ADIOS, which depends on c-blosc. Is that correct?

Based on @ax3l’s comment above I believe an upgrade to our openPMD reader is indeed needed, perhaps utilizing the openPMD-api as suggested.

biagas on May 4, 2022

success

JustinPrivitera on Apr 29, 2022

Here is the sample file: brill-lindquist-write.it00000000.bp.tar.gz

eschnett on Jun 17, 2021

Our OpenPMD reader has no dependencies on ADIOS, only HDF5. Not sure if that is important, I am not familiar with that reader’s internals at this moment. Did you try opening as ADIOS (or ADIOS2) instead of OpenPMD?

Would you be willing to provide a minimal set of data for testing purposes?

biagas on Jun 10, 2021

I just ran into a similar issue with ParaView, which had better error messages. There, the problem was that the binary’s ADIOS library was built without support for Blosc. Could there be a similar issue here?

eschnett on Jun 10, 2021

@ax3l Would you have any insight on this issue?

biagas on Jun 10, 2021