[visit-users] FLASH database reader

Andrew Szymkowiak andrew.szymkowiak at yale.edu
Tue Apr 7 10:55:09 EDT 2009


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.



More information about the visit-users mailing list