[visit-users] FLASH database reader

Randy Hudson hudson at mcs.anl.gov
Tue Apr 7 12:32:58 EDT 2009


Andrew,

If it isn't too big, I'd like to have a copy of the file, too.

Thanks.


On Apr 7, 2009, at 9:55 AM, Andrew Szymkowiak wrote:

> I am also having problems with VisIt reading HDF5 files from FLASH,  
> and thought that I would add some symptoms to help with the diagnosis.
>
> On version 1.11.2, on intel-x86_64, the mdserver vlog ends with  
> (with -debug 5)
>
> Read the Metadata for /home2/as543/FLASH3.1.1a/aesgrav1-1/ 
> aesgrav1-11_hdf5_chk_0036, timeState=0,  
> forceReadAllCyclesAndTimes=0, forcedFileType=FLASH_1.0,  
> treatAllDBsAsTimeVarying = 0, createMeshQualityExpressions = 1,  
> createTimeDerivativeExpressions = 1,  
> createVectorMagnitudeExpressions = 1
> MDServerConnection::GetDatabase: Need to get a new database. file=/ 
> home2/as543/FLASH3.1.1a/aesgrav1-1/aesgrav1-11_hdf5_chk_0036,  
> timeState=0, forceReadAllCyclesAndTimes=0, forcedFileType=FLASH_1.0,  
> treatAllDBsAsTimeVarying = 0
> avtDatabaseFactory: specifically told to use FLASH_1.0
> Trying to open the file with the FLASH file format.
> Initializing HDF5 Library
> Determining FLASH file format version.
> File format version not found in global attributes.  Looking for sim  
> info.
> sim info found; reading it to get file format version.
> signalhandler_core: SIGSEGV!
>
> If I gdb the corefile, I get:
>
> (gdb) where
> #0  0x0000003321c30215 in raise () from /lib64/libc.so.6
> #1  0x0000003321c31cc0 in abort () from /lib64/libc.so.6
> #2  0x00002aaaac93e9bf in ?? ()
>  from /home2/as543/VISIT/1.11.2/linux-x86_64/lib/libmisc.so
> #3  <signal handler called>
> #4  0x00002aaab0152328 in H5T_sort_value ()
>  from /home2/as543/VISIT/1.11.2/linux-x86_64/plugins/databases/../../ 
> lib/libsiloh5.so
> #5  0x00002aaab0148c6e in ?? ()
>  from /home2/as543/VISIT/1.11.2/linux-x86_64/plugins/databases/../../ 
> lib/libsiloh5.so
> #6  0x00002aaab0149157 in H5T_conv_struct_opt ()
>  from /home2/as543/VISIT/1.11.2/linux-x86_64/plugins/databases/../../ 
> lib/libsiloh5.so
> #7  0x00002aaab00cd4c5 in H5T_path_find ()
>  from /home2/as543/VISIT/1.11.2/linux-x86_64/plugins/databases/../../ 
> lib/libsiloh5.so
> #8  0x00002aaab052b4fe in ?? ()
>  from /home2/as543/VISIT/1.11.2/linux-x86_64/plugins/databases/../../ 
> lib/libhdf5.so.5
> #9  0x00002aaab052cabb in H5Dread ()
>  from /home2/as543/VISIT/1.11.2/linux-x86_64/plugins/databases/../../ 
> lib/libhdf5.so.5
> ---Type <return> to continue, or q <return> to quit---
> #10 0x00002aaab27dff85 in avtFLASHFileFormat::ReadVersionInfo ()
>  from /home2/as543/VISIT/1.11.2/linux-x86_64/plugins/databases/ 
> libMFLASHDatabase.so
> #11 0x00002aaab27e79a1 in avtFLASHFileFormat::ReadAllMetaData ()
>  from /home2/as543/VISIT/1.11.2/linux-x86_64/plugins/databases/ 
> libMFLASHDatabase.so
> #12 0x00002aaab27e9afe in  
> avtFLASHFileFormat::PopulateDatabaseMetaData ()
>  from /home2/as543/VISIT/1.11.2/linux-x86_64/plugins/databases/ 
> libMFLASHDatabase.so
> #13 0x00002aaaab9ab4f8 in  
> avtSTMDFileFormatInterface::SetDatabaseMetaData ()
>  from /home2/as543/VISIT/1.11.2/linux-x86_64/lib/libdatabase_ser.so
> #14 0x00002aaaab9483fc in avtGenericDatabase::SetDatabaseMetaData ()
>  from /home2/as543/VISIT/1.11.2/linux-x86_64/lib/libdatabase_ser.so
> #15 0x00002aaaab9345f7 in avtDatabase::GetNewMetaData ()
>  from /home2/as543/VISIT/1.11.2/linux-x86_64/lib/libdatabase_ser.so
> #16 0x00002aaaab934ba3 in avtDatabase::GetMetaData ()
>  from /home2/as543/VISIT/1.11.2/linux-x86_64/lib/libdatabase_ser.so
> #17 0x00002aaaab93c539 in avtDatabaseFactory::SetupDatabase ()
>  from /home2/as543/VISIT/1.11.2/linux-x86_64/lib/libdatabase_ser.so
> #18 0x00002aaaab93cd46 in avtDatabaseFactory::FileList ()
>  from /home2/as543/VISIT/1.11.2/linux-x86_64/lib/libdatabase_ser.so
> #19 0x0000000000416393 in ?? ()
> #20 0x00000000004170f5 in ?? ()
> ---Type <return> to continue, or q <return> to quit---
> #21 0x00000000004093b6 in ?? ()
> #22 0x00002aaaac47b42d in Subject::Notify ()
>  from /home2/as543/VISIT/1.11.2/linux-x86_64/lib/libstate.so
> #23 0x00002aaaac3996ed in AttributeSubject::Notify ()
>  from /home2/as543/VISIT/1.11.2/linux-x86_64/lib/libstate.so
> #24 0x00002aaaac49fd26 in Xfer::Process ()
>  from /home2/as543/VISIT/1.11.2/linux-x86_64/lib/libstate.so
> #25 0x000000000040bfa3 in ?? ()
> #26 0x000000000040b1ff in ?? ()
> #27 0x000000000041d495 in ?? ()
> #28 0x0000003321c1d974 in __libc_start_main () from /lib64/libc.so.6
> #29 0x0000000000407869 in __gxx_personality_v0 ()
> #30 0x00007fff04ae9968 in ?? ()
> #31 0x0000000000000000 in ?? ()
> (gdb)
>
> The same file is opened okay with VisIt 1.11.1 under linux-intel  
> (i.e. moved to a 32-bit machine) so it may not be problem with the  
> file.
> For various reasons, I suspect that there may be some difficulties  
> with libhdf5 versions (I am aware of the 1.6 vs 1.8 API differences).
> I've also noticed, that on the 32-bit machine, after opening several  
> FLASH files, further opens will fail, reporting problems with the  
> SILO format reader, even though I've explicitly specified FLASH in  
> the open dialog.  When I shutdown VisIt, and re-start, the same  
> files open fine (for a while)...
>
> I can make the file available, if anyone thinks that would help...
>
> Thanks,
>   Andy S.
>
> --
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>


Randy.



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