Question about get ascii file.

Dear Dr. Steven G. Johnson
I want to know the way to convert h5 file to ascil file, if it is possible.
Thank you,
Young-Ki Ha.

Re: Question about get ascii file.

On Sun, 5 Mar 2000, GO?51b wrote:
> I want to know the way to convert h5 file to ascil file, if it is possible.

See: http://ab-initio.mit.edu/mpb/hdf.html

In particular, the h5utils package that I wrote includes a program called
h5totxt that should do what you need.

Steven

Problem compiling mpb

Hi,
I am trying to install MPB on a intel PII as a user (what a pain, I need
to be root to feel comfortable!) and I can't get MPB to compile.  I
installed it on my Thinkpad (yeah!) and it works fine but when I try to
compile it on the departmental server, it does work.  All the other
libraries that I had to compile first installed properly.  The error I
get when "making" MPB is (only the last couple of lines):

matrices/matrices.a ../src/util/util.a  -lctl -lguile -ldl -lhdf5 -lz
-llapack -latlas -lblas -lrfftw -lfftw -lm   -lg2c -lm
-L/usr/lib/gcc-lib/i386-redhat-linux/egcs-2.91.66
-L/usr/i386-redhat-linux/lib -lm -o blastest
../src/matrices/matrices.a(blasglue.o): In function `lapackglue_potri':
blasglue.o(.text+0x309): undefined reference to `zpotri_'
../src/matrices/matrices.a(blasglue.o): In function `lapackglue_heev':
blasglue.o(.text+0x38e): undefined reference to `zheev_'
/home/ntetreau/install/lib/liblapack.a(ATL_zpotrfL.o): In function
`ATL_zpotrfL':
ATL_zpotrfL.o(.text+0xa2): undefined reference to `cblas_ztrsm'
ATL_zpotrfL.o(.text+0xc7): undefined reference to `cblas_zherk'
/home/ntetreau/install/lib/liblapack.a(ATL_zpotrfU.o): In function
`ATL_zpotrfU':
ATL_zpotrfU.o(.text+0xa4): undefined reference to `cblas_ztrsm'
ATL_zpotrfU.o(.text+0xc9): undefined reference to `cblas_zherk'
collect2: ld returned 1 exit status
make[1]: *** [blastest] Error 1
make[1]: Leaving directory `/home/ntetreau/pbg/mpb-0.11/tests'
make: *** [all-recursive] Error 1

I would appreciate any help (actually I already appreciate that you took

Re: Problem compiling mpb

On Sun, 5 Mar 2000, Nicolas Tetreault wrote:
> ATL_zpotrfU.o(.text+0xc9): undefined reference to `cblas_zherk'

It looks like you are using the ATLAS 3.0 library, which requires that you
link with -lcblas -lf77blas (included with ATLAS).  Be sure that you are
using MPB 0.11, which automatically looks for these extra libraries, and
also be sure that you have installed all of the libraries that came with
ATLAS.

Steven

compiling problem

Hello,

We have installed the full MPB package on an Ultra Sparc1 working 
with Solaris 2.7. The last version of BLAS, LAPACK and other 
softwares have been installed. When running the program it crashes 
for the calculation of the eigenvalue of the structure. The test 
program for the eigenvalue calculations provided by the LAPACK 
package did not work either. I attach you below the listing of the 
different operations.
What should we do or install to solve this problem?

Many thanks,

Bertrand P. Boussert

guile> (set! num-bands 8)

guile> (set! k-points (list (vector3 0 0 0)     ; Gamma
                      (vector3 0.5 0 0)   ; X
                      (vector3 0.5 0.5 0) ; M
                      (vector3 0 0 0)))   ; Gamma

guile> (set! k-points (interpolate 4 k-points))

guile> (set! geometry (list (make cylinder
                        (center 0 0 0) (radius 0.2) (height infinity)
                        (material (make dielectric (epsilon 12))))))

guile> (set! grid-size (vector3 32 32 1))

Re: compiling problem

>We have installed the full MPB package on an Ultra Sparc1 working
>with Solaris 2.7. The last version of BLAS, LAPACK and other
>softwares have been installed. When running the program it crashes
>for the calculation of the eigenvalue of the structure. The test
>program for the eigenvalue calculations provided by the LAPACK
>package did not work either. I attach you below the listing of the
>different operations.
>[...]
>ERROR: Bad memory access (Segmentation violation)
>ABORT: (signal)

Okay, so the LAPACK test program didn't work either?  That means it's not
an MPB problem, and that you either:

1) Have a bug in your compiler.  You could try downloading and installing
gcc, which does a pretty decent job these days on the SPARC I'm told.

2) Have a buggy BLAS implementation.  Are you using some vendor-optimized
BLAS that came with your machine?  (MPB tries to look for one by default in
the configure script.  The configure output would say something like
"checking for dgemm_ in -lsunperf... (cached) no".  You can disable the use
of the accelerated BLAS by using configure --without-fastblas in MPB.)

(2) would be my first guess.  I have run into several bugs in optimized
BLAS implementations in the course of MPB's development.  The generic BLAS
from www.netlib.org/blas works fine, although it is slow; ATLAS 3.0 is a
good accelerated BLAS (self-optimizing for any machine).

Steven

MAKE question

MAKE

ATLAS and LAPACK question

	ATLAS creates several BLAS libraries, but if I have read the
documentation correctly, none of them are a complete BLAS library.  My
question is should I use the library compiled from the standard BLAS
distribution or should I use one of the ATLAS libraries to install LAPACK?
I'm referring specifically to the definition near the end of the LAPACK
make.inc file:

BLASLIB = ../..blas($PLAT).a ---> ?

Thanks.

Grady

Re: ATLAS and LAPACK question

>	ATLAS creates several BLAS libraries, but if I have read the
>documentation correctly, none of them are a complete BLAS library.  My
>question is should I use the library compiled from the standard BLAS
>distribution or should I use one of the ATLAS libraries to install LAPACK?
>I'm referring specifically to the definition near the end of the LAPACK
>make.inc file:

ATLAS 3.0 contains a complete BLAS implementation.  In any case, it doesn't
matter as far as compiling LAPACK is concerned--the BLAS is not included in
the LAPACK library.  (You only specify it in the LAPACK makefile for the
LAPACK test programs, I think.)

Steven