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thliebig
problem running matlab examples, PlotHDF5FieldData failing
Hi, after some trouble with the Python interface I tried to run the matlab ones in octave. I added the openEMS and CSXCAD matlab paths to .octaverc and I actually got some useful output on Suse, but the script fails to complete on Suse and Ubuntu.
On the Ubuntu20 side with VTK7.1.1: I get 3 plot windows from running Rect_Waveguide, but the windows show no plots (like frozen, garbage inside).
octave:1> Rect_Waveguide
remove entire contents of tmp_mod? (yes or no) yes
args = "rect_wg.xml"
----------------------------------------------------------------------
| openEMS 64bit -- version v0.0.35
| (C) 2010-2018 Thorsten Liebig <[email protected]> GPL license
----------------------------------------------------------------------
Used external libraries:
CSXCAD -- Version: v0.6.2
hdf5 -- Version: 1.10.7
compiled against: HDF5 library version: 1.10.7
tinyxml -- compiled against: 2.6.2
fparser
boost -- compiled against: 1_74
vtk -- Version: 7.1.1
compiled against: 7.1.1
Create FDTD operator (compressed SSE + multi-threading)
FDTD simulation size: 27x12x122 --> 39528 FDTD cells
FDTD timestep is: 7.79642e-13 s; Nyquist rate: 24 timesteps @2.67217e+10 Hz
Excitation signal length is: 1225 timesteps (9.55062e-10s)
Max. number of timesteps: 10000 ( --> 8.16327 * Excitation signal length)
Create FDTD engine (compressed SSE + multi-threading)
Running FDTD engine... this may take a while... grab a cup of coffee?!?
[@ 4s] Timestep: 656 || Speed: 6.5 MC/s (6.120e-03 s/TS) || Energy: ~1.76e-22 (- 0.00dB)
[@ 8s] Timestep: 1304 || Speed: 6.4 MC/s (6.177e-03 s/TS) || Energy: ~1.19e-27 (-51.73dB)
Time for 1304 iterations with 39528.00 cells : 8.02 sec
Speed: 6.43 MCells/s
warning: legend: 'best' not yet implemented for location specifier, using 'northeast' instead
warning: legend: 'best' not yet implemented for location specifier, using 'northeast' instead
warning: function "h5readatt_octave" not found, trying to run "setup"
warning: called from
ReadHDF5Attribute at line 15 column 9
ReadHDF5FieldData_octave at line 97 column 34
ReadHDF5FieldData at line 29 column 19
PlotHDF5FieldData at line 25 column 8
Rect_Waveguide at line 121 column 1
setting up openEMS matlab/octave interface
compiling oct files
HDF5 library path found at: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so
/usr/lib/x86_64-linux-gnu/hdf5/openmpi
HDF5 include path found at: /usr/include/hdf5/serial
/usr/bin/ld: cannot open output file h5readatt_octave.oct: Permission denied
collect2: error: ld returned 1 exit status
sh: 2: /usr/lib/x86_64-linux-gnu/hdf5/openmpi: Permission denied
error: running "setup" failed...
error: called from
ReadHDF5Attribute at line 19 column 13
ReadHDF5FieldData_octave at line 97 column 34
ReadHDF5FieldData at line 29 column 19
PlotHDF5FieldData at line 25 column 8
Rect_Waveguide at line 121 column 1
octave:2>
The same thing on openSuse Tumbleweed using the binaries from the Science repo: I get 3 windows, one with Sparam, one with impedance, and #3 remains empty. The error looks similar but is not exactly the same:
...
... all ok up to here
Speed: 26.20 MCells/s
warning: legend: 'best' not yet implemented for location specifier, using 'northeast' instead
warning: legend: 'best' not yet implemented for location specifier, using 'northeast' instead
warning: function "h5readatt_octave" not found, trying to run "setup"
warning: called from
ReadHDF5Attribute at line 15 column 9
ReadHDF5FieldData>ReadHDF5FieldData_octave at line 97 column 34
ReadHDF5FieldData at line 29 column 19
PlotHDF5FieldData at line 25 column 8
Rect_Waveguide at line 121 column 1
setting up openEMS matlab/octave interface
compiling oct files
HDF5 library path found at: /usr/lib/hpc/gnu14/mvapich2/hdf5/1.12.3/lib64/libhdf5.so
/usr/lib/hpc/gnu14/hdf5/1.12.3/lib64/libhdf5.so
/usr/lib/hpc/gnu14/openmpi4/hdf5/1.12.3/lib64/libhdf5.so
/usr/lib/hpc/gnu14/mpich/hdf5/1.12.3/lib64/libhdf5.so
/usr/lib/hpc/gnu13/mvapich2/hdf5/1.12.2/lib/libhdf5.so
/usr/lib/hpc/gnu13/hdf5/1.12.2/lib/libhdf5.so
/usr/lib/hpc/gnu13/openmpi4/hdf5/1.12.2/lib/libhdf5.so
/usr/lib/hpc/gnu13/mpich/hdf5/1.12.2/lib
HDF5 include path found at: /usr/include
/usr/lib64/gcc/x86_64-suse-linux/14/../../../../x86_64-suse-linux/bin/ld: /usr/lib64/gcc/x86_64-suse-linux/14/../../../../lib64/crt1.o: in function `_start':
/home/abuild/rpmbuild/BUILD/glibc-2.40/csu/../sysdeps/x86_64/start.S:103:(.text+0x1b): undefined reference to `main'
collect2: error: ld returned 1 exit status
sh: line 8: /usr/lib/hpc/gnu13/mpich/hdf5/1.12.2/lib: Is a directory
error: running "setup" failed...
error: called from
ReadHDF5Attribute at line 19 column 13
ReadHDF5FieldData>ReadHDF5FieldData_octave at line 97 column 34
ReadHDF5FieldData at line 29 column 19
PlotHDF5FieldData at line 25 column 8
Rect_Waveguide at line 121 column 1
octave:2>
I don't understand what's happening at this point. What is doing a setup and why? The errors are apparently triggered by the command PlotHDF5FieldData(dump_file, PlotArgs).
Both systems created output files including a h5 in the tmp_mod, but on Suse the Et.h5 is twice as large (may explain why I get plots only there), I didn't figure out the reason yet
On Ubuntu this looks like
h5stat tmp_mod/Et.h5
Filename: tmp_mod/Et.h5
File information
# of unique groups: 4
# of unique datasets: 330
# of unique named datatypes: 0
# of unique links: 0
# of unique other: 0
Max. # of links to object: 1
Max. # of objects in group: 327
File space information for file metadata (in bytes):
Superblock: 96
Superblock extension: 0
User block: 0
Object headers: (total/unused)
Groups: 280/0
Datasets(exclude compact data): 89760/384
Datatypes: 0/0
Groups:
B-tree/List: 31360
Heap: 6024
Attributes:
B-tree/List: 0
Heap: 0
Chunked datasets:
Index: 0
Datasets:
Heap: 0
Shared Messages:
Header: 0
B-tree/List: 0
Heap: 0
Free-space managers:
Header: 0
Amount of free space: 0
Small groups (with 0 to 9 links):
# of groups with 1 link(s): 1
# of groups with 2 link(s): 1
# of groups with 3 link(s): 1
Total # of small groups: 3
Group bins:
# of groups with 1 - 9 links: 3
# of groups with 100 - 999 links: 1
Total # of groups: 4
Dataset dimension information:
Max. rank of datasets: 4
Dataset ranks:
# of dataset with rank 1: 3
# of dataset with rank 4: 327
1-D Dataset information:
Max. dimension size of 1-D datasets: 61
Small 1-D datasets (with dimension sizes 0 to 9):
# of datasets with dimension sizes 6: 1
Total # of small datasets: 1
1-D Dataset dimension bins:
# of datasets with dimension size 1 - 9: 1
# of datasets with dimension size 10 - 99: 2
Total # of datasets: 3
Dataset storage information:
Total raw data size: 20106900
Total external raw data size: 0
Dataset layout information:
Dataset layout counts[COMPACT]: 0
Dataset layout counts[CONTIG]: 330
Dataset layout counts[CHUNKED]: 0
Dataset layout counts[VIRTUAL]: 0
Number of external files : 0
Dataset filters information:
Number of datasets with:
NO filter: 330
GZIP filter: 0
SHUFFLE filter: 0
FLETCHER32 filter: 0
SZIP filter: 0
NBIT filter: 0
SCALEOFFSET filter: 0
USER-DEFINED filter: 0
Dataset datatype information:
# of unique datatypes used by datasets: 1
Dataset datatype #0:
Count (total/named) = (330/0)
Size (desc./elmt) = (22/4)
Total dataset datatype count: 330
Small # of attributes (objects with 1 to 10 attributes):
# of objects with 1 attributes: 328
Total # of objects with small # of attributes: 328
Attribute bins:
# of objects with 1 - 9 attributes: 328
Total # of objects with attributes: 328
Max. # of attributes to objects: 1
Free-space persist: FALSE
Free-space section threshold: 1 bytes
Small size free-space sections (< 10 bytes):
Total # of small size sections: 0
Free-space section bins:
Total # of sections: 0
File space management strategy: H5F_FSPACE_STRATEGY_FSM_AGGR
File space page size: 4096 bytes
Summary of file space information:
File metadata: 127520 bytes
Raw data: 20106900 bytes
Amount/Percent of tracked free space: 0 bytes/0.0%
Unaccounted space: 553772 bytes
Total space: 20788192 bytes
I don't know what permission it is looking for. The path is a directory with read access, inside are symlinks to libraries, the libraries have read access (no executable), that should be ok?
On Suse this looks like
h5stat tmp_mod/Et.h5
Filename: tmp_mod/Et.h5
File information
# of unique groups: 4
# of unique datasets: 667
# of unique named datatypes: 0
# of unique links: 0
# of unique other: 0
Max. # of links to object: 1
Max. # of objects in group: 664
File space information for file metadata (in bytes):
Superblock: 96
Superblock extension: 0
User block: 0
Object headers: (total/unused)
Groups: 280/0
Datasets(exclude compact data): 181424/384
Datatypes: 0/0
Groups:
B-tree/List: 60544
Heap: 11656
Attributes:
B-tree/List: 0
Heap: 0
Chunked datasets:
Index: 0
Datasets:
Heap: 0
Shared Messages:
Header: 0
B-tree/List: 0
Heap: 0
Free-space managers:
Header: 0
Amount of free space: 0
Small groups (with 0 to 9 links):
# of groups with 1 link(s): 1
# of groups with 2 link(s): 1
# of groups with 3 link(s): 1
Total # of small groups: 3
Group bins:
# of groups with 1 - 9 links: 3
# of groups with 100 - 999 links: 1
Total # of groups: 4
Dataset dimension information:
Max. rank of datasets: 4
Dataset ranks:
# of dataset with rank 1: 3
# of dataset with rank 4: 664
1-D Dataset information:
Max. dimension size of 1-D datasets: 61
Small 1-D datasets (with dimension sizes 0 to 9):
# of datasets with dimension sizes 6: 1
Total # of small datasets: 1
1-D Dataset dimension bins:
# of datasets with dimension size 1 - 9: 1
# of datasets with dimension size 10 - 99: 2
Total # of datasets: 3
Dataset storage information:
Total raw data size: 40828356
Total external raw data size: 0
Dataset layout information:
Dataset layout counts[COMPACT]: 0
Dataset layout counts[CONTIG]: 667
Dataset layout counts[CHUNKED]: 0
Dataset layout counts[VIRTUAL]: 0
Number of external files : 0
Dataset filters information:
Number of datasets with:
NO filter: 667
GZIP filter: 0
SHUFFLE filter: 0
FLETCHER32 filter: 0
SZIP filter: 0
NBIT filter: 0
SCALEOFFSET filter: 0
USER-DEFINED filter: 0
Dataset datatype information:
# of unique datatypes used by datasets: 1
Dataset datatype #0:
Count (total/named) = (667/0)
Size (desc./elmt) = (22/4)
Total dataset datatype count: 667
Small # of attributes (objects with 1 to 10 attributes):
# of objects with 1 attributes: 665
Total # of objects with small # of attributes: 665
Attribute bins:
# of objects with 1 - 9 attributes: 665
Total # of objects with attributes: 665
Max. # of attributes to objects: 1
Free-space persist: FALSE
Free-space section threshold: 1 bytes
Small size free-space sections (< 10 bytes):
Total # of small size sections: 0
Free-space section bins:
Total # of sections: 0
File space management strategy: H5F_FSPACE_STRATEGY_FSM_AGGR
File space page size: 4096 bytes
Summary of file space information:
File metadata: 254000 bytes
Raw data: 40828356 bytes
Amount/Percent of tracked free space: 0 bytes/0.0%
Unaccounted space: 1126956 bytes
Total space: 42209312 bytes
Plotting on Ubuntu fails even after commenting out PlotHDF5FieldData, so I have more trouble there. On Suse that looks fine. Any ideas how to debug the PlotHDF5FieldData?
