[FLASH-USERS] Error writing initial HDF5 checkpoint and plot files
Deepali
ddeepali at hs.uni-hamburg.de
Wed Dec 21 11:35:58 EST 2022
Hi Adam & Aaron,
Thank you for your time and help!
I am using serial HDF5 for AMR grid. I cleaned my Makefile further and
tried running FLASH 4.6.2 again with HDF5 1.10.5 and 1.12.0 (both
usingintel/19.0.5 and impi/2019.5.281). I am getting the following error:
Gravity initialized
Initial dt verified
Particles_sinkAccelSinksOnGasAndSinksOnGas:: sink_softening_type_gas =
linear
HDF5-DIAG: Error detected in HDF5 (1.10.5) thread 46912496411200:
#000: H5Ddeprec.c line 126 in H5Dcreate1(): not a location ID
major: Invalid arguments to routine
minor: Inappropriate type
#001: H5Gloc.c line 246 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
Driver_abortC called
Error: H5Dcreate particle names, io_h5write_particles
Calling MPI_Abort for immediate shutdown
Abort(1) on node 0 (rank 0 in comm 0): application called
MPI_Abort(MPI_COMM_WORLD, 1) - process 0
Please find attached the log (flash*.log) and output files (op*.log) for
each hdf5 version for more details and the Makefile used. I checked that
this query has been addressed before
https://flash.rochester.edu/pipermail/flash-users/2019-September/003039.html
but I do not quite understand how to proceed further.
Best regards,
Deepali
On 19.12.22 19:05, Adam Reyes wrote:
> 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
> Emailadam.reyes at rochester.edu <mailto:adam.reyes at rochester.edu>
> Webhttps://flash.rochester.edu <https://flash.rochester.edu/>
> (he / him / his)
>
> *************************************************************************
>
> On Mon, Dec 19, 2022 at 12:00 PM Deepali <ddeepali at hs.uni-hamburg.de
> <mailto: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 <mailto: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
>>> <mailto: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
>>> <mailto:flash-users at flash.rochester.edu>
>>>
>>> For list info, including unsubscribe:
>>> https://flash.rochester.edu/mailman/listinfo/flash-users
>>>
> _______________________________________________
> flash-users mailing list
> flash-users at flash.rochester.edu
> <mailto:flash-users at flash.rochester.edu>
>
> For list info, including unsubscribe:
> https://flash.rochester.edu/mailman/listinfo/flash-users
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://flash.rochester.edu/pipermail/flash-users/attachments/20221221/97b07df4/attachment.htm>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: op_hdf1_12.log
Type: text/x-log
Size: 2214 bytes
Desc: not available
URL: <http://flash.rochester.edu/pipermail/flash-users/attachments/20221221/97b07df4/attachment.bin>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: op_hdf1_10.log
Type: text/x-log
Size: 2123 bytes
Desc: not available
URL: <http://flash.rochester.edu/pipermail/flash-users/attachments/20221221/97b07df4/attachment-0001.bin>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Makefile.h
Type: text/x-chdr
Size: 7443 bytes
Desc: not available
URL: <http://flash.rochester.edu/pipermail/flash-users/attachments/20221221/97b07df4/attachment-0002.bin>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: flash_hdf1_12.log
Type: text/x-log
Size: 33843 bytes
Desc: not available
URL: <http://flash.rochester.edu/pipermail/flash-users/attachments/20221221/97b07df4/attachment-0003.bin>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: flash_hdf1_10.log
Type: text/x-log
Size: 33843 bytes
Desc: not available
URL: <http://flash.rochester.edu/pipermail/flash-users/attachments/20221221/97b07df4/attachment-0004.bin>
More information about the flash-users
mailing list