Hello,
I have problems trying to visualize in visit the h5 files created with the new HDF and zlib thorns. The errors are:
$ visit -debug-5 Running: gui2.2.0 -debug-5 Running: viewer2.2.0 -host 127.0.0.1 -port 5600 -debug-5 -geometry 1558x1150+362+25 -borders 24,5,5,5 -shift 5,25 -preshift 0,-1 -defer Running: mdserver2.2.0 -host 127.0.0.1 -port 5601 -debug-5 HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0: #000: H5L.c line 1184 in H5Literate(): link iteration failed major: Symbol table minor: Iteration failed #001: H5G.c line 1532 in H5G_iterate(): error iterating over links major: Symbol table minor: Iteration failed #002: H5Gobj.c line 599 in H5G_obj_iterate(): can't iterate over symbol table major: Symbol table minor: Iteration failed #003: H5Gstab.c line 506 in H5G_stab_iterate(): unable to protect symbol table heap major: Symbol table minor: Protected metadata error #004: H5HL.c line 360 in H5HL_protect(): unable to load heap major: Heap minor: Unable to load metadata into cache #005: H5AC.c line 1831 in H5AC_protect(): H5C_protect() failed. major: Object cache minor: Unable to protect metadata #006: H5C.c line 6160 in H5C_protect(): can't load entry major: Object cache minor: Unable to load metadata into cache #007: H5C.c line 10990 in H5C_load_entry(): unable to load entry major: Object cache minor: Unable to load metadata into cache #008: H5HLcache.c line 259 in H5HL_load(): bad heap free list major: Heap minor: Unable to load metadata into cache
Hi Maria,
1) did you explicitly selected the visit plugin to load the data? Sometimes the Pixie format tries to load the data first.
2) Are you able to do an h5ls on the h5-files?
3) What version of Visit are you using - I guess v2.2.0?
4) What version of the plugin are you using?
cheers, Christian
On Thursday, February 03, 2011 07:09:42 am Babiuc-Hamilton, Maria wrote:
Hello,
I have problems trying to visualize in visit the h5 files created with the new HDF and zlib thorns. The errors are:
$ visit -debug-5 Running: gui2.2.0 -debug-5 Running: viewer2.2.0 -host 127.0.0.1 -port 5600 -debug-5 -geometry 1558x1150+362+25 -borders 24,5,5,5 -shift 5,25 -preshift 0,-1 -defer Running: mdserver2.2.0 -host 127.0.0.1 -port 5601 -debug-5 HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0: #000: H5L.c line 1184 in H5Literate(): link iteration failed major: Symbol table minor: Iteration failed #001: H5G.c line 1532 in H5G_iterate(): error iterating over links major: Symbol table minor: Iteration failed #002: H5Gobj.c line 599 in H5G_obj_iterate(): can't iterate over symbol table major: Symbol table minor: Iteration failed #003: H5Gstab.c line 506 in H5G_stab_iterate(): unable to protect symbol table heap major: Symbol table minor: Protected metadata error #004: H5HL.c line 360 in H5HL_protect(): unable to load heap major: Heap minor: Unable to load metadata into cache #005: H5AC.c line 1831 in H5AC_protect(): H5C_protect() failed. major: Object cache minor: Unable to protect metadata #006: H5C.c line 6160 in H5C_protect(): can't load entry major: Object cache minor: Unable to load metadata into cache #007: H5C.c line 10990 in H5C_load_entry(): unable to load entry major: Object cache minor: Unable to load metadata into cache #008: H5HLcache.c line 259 in H5HL_load(): bad heap free list major: Heap minor: Unable to load metadata into cache
Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users
Maria
These errors look severs. Were there other errors or warnings, e.g. during startup? Is there e.g. a version mismatch between different HDF5 libraries, or was there an error while writing this file? Can you h5ls or h5dump this file?
-erik
On Thu, Feb 3, 2011 at 10:09 AM, Babiuc-Hamilton, Maria babiuc@marshall.edu wrote:
Hello,
I have problems trying to visualize in visit the h5 files created with the new HDF and zlib thorns. The errors are:
$ visit -debug-5 Running: gui2.2.0 -debug-5 Running: viewer2.2.0 -host 127.0.0.1 -port 5600 -debug-5 -geometry 1558x1150+362+25 -borders 24,5,5,5 -shift 5,25 -preshift 0,-1 -defer Running: mdserver2.2.0 -host 127.0.0.1 -port 5601 -debug-5 HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0: #000: H5L.c line 1184 in H5Literate(): link iteration failed major: Symbol table minor: Iteration failed #001: H5G.c line 1532 in H5G_iterate(): error iterating over links major: Symbol table minor: Iteration failed #002: H5Gobj.c line 599 in H5G_obj_iterate(): can't iterate over symbol table major: Symbol table minor: Iteration failed #003: H5Gstab.c line 506 in H5G_stab_iterate(): unable to protect symbol table heap major: Symbol table minor: Protected metadata error #004: H5HL.c line 360 in H5HL_protect(): unable to load heap major: Heap minor: Unable to load metadata into cache #005: H5AC.c line 1831 in H5AC_protect(): H5C_protect() failed. major: Object cache minor: Unable to protect metadata #006: H5C.c line 6160 in H5C_protect(): can't load entry major: Object cache minor: Unable to load metadata into cache #007: H5C.c line 10990 in H5C_load_entry(): unable to load entry major: Object cache minor: Unable to load metadata into cache #008: H5HLcache.c line 259 in H5HL_load(): bad heap free list major: Heap minor: Unable to load metadata into cache
Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users
Hello,
When I am using PUGHIOHDF5 to output h5 files I see this error. Things seem OK with CarpetIOHDF5. Can I use PUGH, or I need to use Carpet? The output for h5ls is:Cactus\ Parameters Group Global\ Attributes Group WAVETOY::phi\ timelevel\ 0\ at\ iteration\ 0 Dataset {20, 20, 20} etc...
The h5 data written by CarpetIoHdf5 looks chunked. Is there a way to combine it? Or I need to ask support from VisIt to do this?
One more thing: when hdf5 is build on the fly with the HDF5 thorn I see a lot of warnings like: H5*.c:*: warning:etc..... I don't see this when I use an externally installed hdf5 library.
Maria
________________________________________ From: Erik Schnetter [schnetter@cct.lsu.edu] Sent: Thursday, February 03, 2011 10:40 AM To: Babiuc-Hamilton, Maria Cc: users@einsteintoolkit.org Subject: Re: [Users] VisIt could not read from the file
Maria
These errors look severs. Were there other errors or warnings, e.g. during startup? Is there e.g. a version mismatch between different HDF5 libraries, or was there an error while writing this file? Can you h5ls or h5dump this file?
-erik
On Thu, Feb 3, 2011 at 10:09 AM, Babiuc-Hamilton, Maria babiuc@marshall.edu wrote:
Hello,
I have problems trying to visualize in visit the h5 files created with the new HDF and zlib thorns. The errors are:
$ visit -debug-5 Running: gui2.2.0 -debug-5 Running: viewer2.2.0 -host 127.0.0.1 -port 5600 -debug-5 -geometry 1558x1150+362+25 -borders 24,5,5,5 -shift 5,25 -preshift 0,-1 -defer Running: mdserver2.2.0 -host 127.0.0.1 -port 5601 -debug-5 HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0: #000: H5L.c line 1184 in H5Literate(): link iteration failed major: Symbol table minor: Iteration failed #001: H5G.c line 1532 in H5G_iterate(): error iterating over links major: Symbol table minor: Iteration failed #002: H5Gobj.c line 599 in H5G_obj_iterate(): can't iterate over symbol table major: Symbol table minor: Iteration failed #003: H5Gstab.c line 506 in H5G_stab_iterate(): unable to protect symbol table heap major: Symbol table minor: Protected metadata error #004: H5HL.c line 360 in H5HL_protect(): unable to load heap major: Heap minor: Unable to load metadata into cache #005: H5AC.c line 1831 in H5AC_protect(): H5C_protect() failed. major: Object cache minor: Unable to protect metadata #006: H5C.c line 6160 in H5C_protect(): can't load entry major: Object cache minor: Unable to load metadata into cache #007: H5C.c line 10990 in H5C_load_entry(): unable to load entry major: Object cache minor: Unable to load metadata into cache #008: H5HLcache.c line 259 in H5HL_load(): bad heap free list major: Heap minor: Unable to load metadata into cache
Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users
-- Erik Schnetter schnetter@cct.lsu.edu http://www.cct.lsu.edu/~eschnett/
Hi Maria,
When I am using PUGHIOHDF5 to output h5 files I see this error. Things seem OK with CarpetIOHDF5. Can I use PUGH, or I need to use Carpet? The output for h5ls is:Cactus\ Parameters Group Global\ Attributes Group WAVETOY::phi\ timelevel\ 0\ at\ iteration\ 0 Dataset {20, 20, 20} etc...
the CarpetHDF5 plugin for VisIt only works for Carpet. PUGH organizes the dataset structure and attributes in the HDF5 file differently. You need to use Carpet for HDF5 output.
The h5 data written by CarpetIoHdf5 looks chunked. Is there a way to combine it? Or I need to ask support from VisIt to do this?
the CarpetHDF5 plugin will internally combine dataset chunks that belong to a larger decomposed array or 3D gridfunction.
cheers, Christian
One more thing: when hdf5 is build on the fly with the HDF5 thorn I see a lot of warnings like: H5*.c:*: warning:etc..... I don't see this when I use an externally installed hdf5 library.
Maria
From: Erik Schnetter [schnetter@cct.lsu.edu] Sent: Thursday, February 03, 2011 10:40 AM To: Babiuc-Hamilton, Maria Cc: users@einsteintoolkit.org Subject: Re: [Users] VisIt could not read from the file
Maria
These errors look severs. Were there other errors or warnings, e.g. during startup? Is there e.g. a version mismatch between different HDF5 libraries, or was there an error while writing this file? Can you h5ls or h5dump this file?
-erik
On Thu, Feb 3, 2011 at 10:09 AM, Babiuc-Hamilton, Maria
babiuc@marshall.edu wrote:
Hello,
I have problems trying to visualize in visit the h5 files created with the new HDF and zlib thorns. The errors are:
$ visit -debug-5 Running: gui2.2.0 -debug-5 Running: viewer2.2.0 -host 127.0.0.1 -port 5600 -debug-5 -geometry 1558x1150+362+25 -borders 24,5,5,5 -shift 5,25 -preshift 0,-1 -defer Running: mdserver2.2.0 -host 127.0.0.1 -port 5601 -debug-5
HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0: #000: H5L.c line 1184 in H5Literate(): link iteration failed
major: Symbol table minor: Iteration failed
#001: H5G.c line 1532 in H5G_iterate(): error iterating over links
major: Symbol table minor: Iteration failed
#002: H5Gobj.c line 599 in H5G_obj_iterate(): can't iterate over symbol table
major: Symbol table minor: Iteration failed
#003: H5Gstab.c line 506 in H5G_stab_iterate(): unable to protect symbol table heap
major: Symbol table minor: Protected metadata error
#004: H5HL.c line 360 in H5HL_protect(): unable to load heap
major: Heap minor: Unable to load metadata into cache
#005: H5AC.c line 1831 in H5AC_protect(): H5C_protect() failed.
major: Object cache minor: Unable to protect metadata
#006: H5C.c line 6160 in H5C_protect(): can't load entry
major: Object cache minor: Unable to load metadata into cache
#007: H5C.c line 10990 in H5C_load_entry(): unable to load entry
major: Object cache minor: Unable to load metadata into cache
#008: H5HLcache.c line 259 in H5HL_load(): bad heap free list
major: Heap minor: Unable to load metadata into cache
Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users
-- Erik Schnetter schnetter@cct.lsu.edu http://www.cct.lsu.edu/~eschnett/ _______________________________________________ Users mailing list Users@einsteintoolkit.org http://lists.einsteintoolkit.org/mailman/listinfo/users
users@lists.einsteintoolkit.org
-
Babiuc-Hamilton, Maria -
Christian Reisswig -
Erik Schnetter