[FLASH-USERS] HDF5 problem in FLASH restart

[Klaus Weide]

On Fri, 25 May 2018, Sylvain Turcotte wrote:

> Hi all,
> 
> I am moving my version of FLASH3.0 to another machine 

I would strongly recommend that you jump forward to a current version of 
FLASH 4. The general structure of the code is still the same as in FLASH 
3, so porting your applications from FLASH 3 to FLASH4 should not be too 
difficult. (That was different for FLASH2 -> FLASH3.)

> and when I try to 
> restart a run I get the following error message: "can't open dataset 
> string runtime parameters".

Does 'h5dump' or 'h5ls' show that there is a dataset "/string runtime 
parameters' in the file?

The format of HDF5 files has not changed significantly between FLASH 3 and 
4, and should still be compatible.

> I have verified the problem is in the output and not the input. Flash 
> does not write the _chk_ files correctly but I have no problems looking 
> at the data in those files with xflash3 in IDL.

> As far as I can tell the new machine has hdf5_mpi version 1.8.18 while the old machine had version 1.8.16.
> Also, to compile the code I had to change all the calls from H5Dcreate to H5Dcreate1, and similarly for H5Dopen and a few other Hdf5 calls.

With current FLASH4, such code changes are not needed if one compiles 
FLASH with -DH5_USE_16_API (see your Makefile.h). I assume (but have not 
tested) that the same should work for FLASH3 with hdf5 1.8.x.

> I am unsure how to solve this issue. Suggestions are welcome!

HTH,

Klaus