Hi,
I ran the tutorial code below from the data analysis tutorial. I get an
error because the hdf5 library version mismatch. I see on the main
download page for mpb it says that:
*HDF5*: Version 1.8 of HDF5 changed the API, and programs like MPB that
compiled with the earlier versions of HDF5 no longer work. The workaround
is to pass -DH5_USE_16_API=1 in the CPPFLAGS when running the
configurescript for MPB. i.e. ./configure
CPPFLAGS="-DH5_USE_16_API=1", or ./configure CPPFLAGS="-DH5_USE_16_API=1 -I*
...include-paths...*" if you also need to pass -I flags.
How do I configure this on Mac osx running 10.6.8 in the terminal? Has
anyone had this problem and figured out how to change this?
Thanks,
-Neal
mpb> (set! num-bands 8)
mpb>
mpb> (set! geometry-lattice (make lattice (size 1 1 no-size)
... (basis1 (/ (sqrt 3) 2) 0.5)
... (basis2 (/ (sqrt 3) 2) -0.5)))
mpb> (set! geometry (list (make cylinder
... (center 0 0 0) (radius 0.2) (height infinity)
... (material (make dielectric (epsilon 12))))))
mpb>
mpb> (set! k-points (list (vector3 0 0 0) ; Gamma
... (vector3 0 0.5 0) ; M
... (vector3 (/ -3) (/ 3) 0) ; K
... (vector3 0 0 0))) ; Gamma
... (set! k-points (interpolate 4 k-points))
mpb>
mpb> (set! resolution 32)
mpb>
mpb> (run-tm (output-at-kpoint (vector3 (/ -3) (/ 3) 0)
... fix-efield-phase output-efield-z))
init-params: initializing eigensolver data
Computing 8 bands with 1.000000e-07 tolerance.
Working in 2 dimensions.
Grid size is 32 x 32 x 1.
Solving for 8 bands at a time.
Creating Maxwell data...
Allocating fields...
Mesh size is 3.
Lattice vectors:
(0.866025, 0.5, 0)
(0.866025, -0.5, 0)
(0, 0, 1)
Cell volume = 0.866025
Reciprocal lattice vectors (/ 2 pi):
(0.57735, 1, -0)
(0.57735, -1, 0)
(-0, 0, 1)
Geometric objects:
cylinder, center = (0,0,0)
radius 0.2, height 1e+20, axis (0, 0, 1)
dielectric constant epsilon = 12
Geometric object tree has depth 1 and 1 object nodes (vs. 1 actual objects)
Initializing dielectric function...
16 k-points:
(0,0,0)
(0,0.1,0)
(0,0.2,0)
(0,0.3,0)
(0,0.4,0)
(0,0.5,0)
(-0.0666667,0.466667,0)
(-0.133333,0.433333,0)
(-0.2,0.4,0)
(-0.266667,0.366667,0)
(-0.333333,0.333333,0)
(-0.266667,0.266667,0)
(-0.2,0.2,0)
(-0.133333,0.133333,0)
(-0.0666667,0.0666667,0)
(0,0,0)
Solving for band polarization: tm.
Initializing fields to random numbers...
elapsed time for initialization: 0 seconds.
epsilon: 1-12, mean 2.59342, harm. mean 1.17825, 17.2852% > 1, 14.4857%
"fill"
Outputting epsilon...
Warning! ***HDF5 library version mismatched error***
The HDF5 header files used to compile this application do not match
the version used by the HDF5 library to which this application is linked.
Data corruption or segmentation faults may occur if the application
continues.
This can happen when an application was compiled by one version of HDF5 but
linked with a different version of static or shared HDF5 library.
You should recompile the application or check your shared library related
settings such as 'LD_LIBRARY_PATH'.
You can, at your own risk, disable this warning by setting the environment
variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'.
Setting it to 2 or higher will suppress the warning messages totally.
Headers are 1.6.8, library is 1.6.10
SUMMARY OF THE HDF5 CONFIGURATION
=================================
HDF5 Version: 1.6.10
Configured on: Sun Oct 23 22:22:02 EDT 2011
Configured by: [email protected]
Configure mode: production
Host system: i686-apple-darwin10.8.0
Byte sex: little-endian
Libraries: static, shared
Parallel support: no
Installation point: /sw
Compiler: /sw/var/lib/fink/path-prefix-10.6/gcc (gcc-4.2.1)
Compiler switches: -std=c99 -Wno-long-long -O -fomit-frame-pointer
-finline-functions -UH5_DEBUG_API -DNDEBUG -I/sw/include
Extra libraries: -Wl,-dead_strip_dylibs -L/sw/lib -lsz -lz -lm -lsz
Archiver: ar
Ranlib: ranlib
Debugged Packages:
API Tracing: no
Configure Summary
Compiling Options:
Compilation Mode: Production
C Compiler: gcc
CFLAGS: -std=c99 -Wno-long-long -O
-fomit-frame-pointer -finline-functions
CPPFLAGS: -UH5_DEBUG_API -DNDEBUG -I/sw/include
LDFLAGS: -Wl,-dead_strip_dylibs -L/sw/lib
Debug Mode: None
Shared Libraries: Yes
Static Libraries: Yes
Statically Linked Executables: No
Tracing: No
Optimization Instrumentation: No
Languages:
----------
C++: Yes
C++ Compiler: g++
CXXFLAGS: -O2
Fortran: Yes
Fortran Compiler: /sw/bin/gfortran
FFLAGS: -I. -fsecond-underscore -I.
C Compiler: gcc
CFLAGS: -march=i686 -ansi -O
-fomit-frame-pointer -finline-functions
CPPFLAGS: -I/sw/include
LDFLAGS: -Wl,-dead_strip_dylibs -L/sw/lib
Features:
---------
dmalloc: No
Function Stack Tracing: Disabled
GPFS: No
Strict File Format Checks: Disabled
HDF5 v1.4 Compatibility: No
I/O filters (external): deflate,szip(encoder)
I/O filters (internal): shuffle,fletcher32
Linux Large File Support (LFS): Disabled
MPE: No
Parallel HDF5: No
Threadsafety: Disabled
High Level library: Enabled
Bye...
Abort trap
Thanks,
-Neal Pfeiffenberger
_______________________________________________
mpb-discuss mailing list
[email protected]
http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/mpb-discuss
