[FLASH-USERS] Error writing initial HDF5 checkpoint and plot files

[Adam Reyes]

Hi Deepali,

FLASH should work with hdf5 1.12.0. Which IO implementation did you set up
with (+hdftTypeIO, +parallelIO)? You could try the other one. If you could
share the log file from the run it might be helpful as well.

*************************************************************************
Adam Reyes

Code Group Leader, Flash Center for Computational Science
Research Scientist, Dept. of Physics and Astronomy
University of Rochester
River Campus: Bausch and Lomb Hall, 369
500 Wilson Blvd. PO Box 270171, Rochester, NY 14627
Email adam.reyes at rochester.edu
Web https://flash.rochester.edu
 (he / him / his)

*************************************************************************

On Mon, Dec 19, 2022 at 12:00 PM Deepali <ddeepali at hs.uni-hamburg.de> wrote:

> Hi Ryan,
>
>
> I am using FLASH4.6.2. I tried other available HDF5 versions - hdf5/intel/1.12.0,
> hdf5/intel/1.12.1 , but received different errors with 10.5 and 12.x
> (tried with -DH5_USE_16_API, -DH5_USE_110_API, -DH5_USE_112_API).
>
> I also went through the mailing lists where a patch was made available for
> FLASH4.5, but it didn't work for me.
>
> Could someone tell me which library versions are compatible with FLASH
> 4.6.2? Is there a documentation available for the compatible HDF5 library
> and FLASH versions?
>
>
> Best,
>
> Deepali
>
>
> On 15.12.22 18:40, Ryan Farber wrote:
>
> Hi Deepali,
>
> I think if you search the flash-users mailing list there were issues with
> hdf5 1.10.x a few years ago. I think those were patched but definitely
> worth trying different hdf5 versions. For reference I'm using
>
> hdf5-mpi/1.8.21
>
> but I'm still on FLASH4.2.2...which version of FLASH are you using?
>
> Best,
> --------
> Ryan
>
>
> On Thu, Dec 15, 2022 at 12:33 PM Deepali <ddeepali at hs.uni-hamburg.de>
> wrote:
>
>> Hi Ryan,
>>
>>
>> Thank you for your reply!
>>
>> I checked the space on hard drive and majority of it is available (~ 3
>> TB). So no problem there. Also I have the permission to write. Could it be
>> a problem between flash and the HLRN cluster HDF5 library version?
>>
>>
>> Best,
>>
>> Deepali
>>
>>
>>
>> On 12.12.22 18:54, Ryan Farber wrote:
>>
>> Hi Deepali,
>>
>> I haven't seen your error before:
>> flash4: io_h5create_dataset.c:29: io_h5create_dataset: Assertion
>> `diskSize[i] > 0' failed.
>>
>> But from the sound of it, that file doesn't think you have space on the
>> hard drive it's trying to write to. Maybe a permissions problem(?)
>>
>> Best,
>> --------
>> Ryan
>>
>>
>> On Mon, Dec 12, 2022 at 5:44 PM Deepali <ddeepali at hs.uni-hamburg.de>
>> wrote:
>>
>>> Dear Flash users & developers,
>>>
>>> I am trying to simulate a 3D Bonnor-Ebert sphere type setup using AMR
>>> grid on HLRN machine (https://www.hlrn.de/doc/display/PUB/Usage+Guide).
>>> I use the following compiler and hdf5 modules:
>>>
>>> intel/18.0.6
>>>
>>> impi/2018.5(default)
>>>
>>> hdf5/intel/1.10.5
>>>
>>> But I am facing a problem with the writing of initial HDF5 checkpoint
>>> and plot files. FLASH initializes all the units needed and then produces
>>> the error mentioned in the simulation log file (flash.log) attached with
>>> this email.
>>>
>>> I would appreciate any help or suggestions in order to resolve this
>>> error. Please let me know if I should share any other information.
>>>
>>> Thanks and regards,
>>>
>>> Deepali
>>> _______________________________________________
>>> flash-users mailing list
>>> flash-users at flash.rochester.edu
>>>
>>> For list info, including unsubscribe:
>>> https://flash.rochester.edu/mailman/listinfo/flash-users
>>>
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