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Erman Engin | 3 Mar 2010 21:28
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mpb & mpb-mpi installation problem


Hi,

We have mpb-mpi installed on a multi core computer following the 
installation instructions.  I still get the following error lines in my 
.out file.  You get this error not only when you invoke the parallel mpb 
but it occurs also in the non-parallel one.

Has anyone encountered this before and have an idea how to fix it?

thanks
erman

mpb:577 terminated with signal 11 at PC=3f96471f65 SP=7fff700e21d0. 
Backtrace:
/lib64/libc.so.6[0x3f96471f65]
/lib64/libc.so.6(__libc_malloc+0x7a)[0x3f9647402a]
/lib64/libc.so.6(realloc+0x20c)[0x3f96475c6c]
/usr/lib64/libguile.so.17(scm_realloc+0x42)[0x3a3ea58a02]
/usr/lib64/libguile.so.17(scm_gc_malloc+0x1e)[0x3a3ea58bfe]
/usr/local/apps/mpb-mpi/bin/mpb(create_sqmatrix+0x2b)[0x42da6b]
/usr/local/apps/mpb-mpi/bin/mpb(eigensolver+0x24c)[0x427a5c]
/usr/local/apps/mpb-mpi/bin/mpb(solve_kpoint+0xcc6)[0x40f5a6]
/usr/local/apps/mpb-mpi/bin/mpb(solve_kpoint_aux+0x3b)[0x40a70b]
/usr/lib64/libguile.so.17[0x3a3ea52883]
/usr/lib64/libguile.so.17[0x3a3ea51b90]
/usr/lib64/libguile.so.17[0x3a3ea50714]
/usr/lib64/libguile.so.17(scm_eval_body+0x84)[0x3a3ea52bc4]
/usr/lib64/libguile.so.17(scm_map+0x2c3)[0x3a3ea53763]
/usr/lib64/libguile.so.17[0x3a3ea5161d]
(Continue reading)

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Erman Engin | 3 Mar 2010 21:34
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mpb & mpb-mpi installation problem

Hi,

We have installed mpb and mpb-mpi to a multi core machine.  When I run 
my ctl file (which works ok in another machine) the .out file has the 
error lines below.

Anyone encountered before or have any ideas how to solve it?

thanks
erman

mpb:577 terminated with signal 11 at PC=3f96471f65 SP=7fff700e21d0. 
Backtrace:
/lib64/libc.so.6[0x3f96471f65]
/lib64/libc.so.6(__libc_malloc+0x7a)[0x3f9647402a]
/lib64/libc.so.6(realloc+0x20c)[0x3f96475c6c]
/usr/lib64/libguile.so.17(scm_realloc+0x42)[0x3a3ea58a02]
/usr/lib64/libguile.so.17(scm_gc_malloc+0x1e)[0x3a3ea58bfe]
/usr/local/apps/mpb-mpi/bin/mpb(create_sqmatrix+0x2b)[0x42da6b]
/usr/local/apps/mpb-mpi/bin/mpb(eigensolver+0x24c)[0x427a5c]
/usr/local/apps/mpb-mpi/bin/mpb(solve_kpoint+0xcc6)[0x40f5a6]
/usr/local/apps/mpb-mpi/bin/mpb(solve_kpoint_aux+0x3b)[0x40a70b]
/usr/lib64/libguile.so.17[0x3a3ea52883]
/usr/lib64/libguile.so.17[0x3a3ea51b90]
/usr/lib64/libguile.so.17[0x3a3ea50714]
/usr/lib64/libguile.so.17(scm_eval_body+0x84)[0x3a3ea52bc4]
/usr/lib64/libguile.so.17(scm_map+0x2c3)[0x3a3ea53763]
/usr/lib64/libguile.so.17[0x3a3ea5161d]
/usr/lib64/libguile.so.17[0x3a3ea50714]
/usr/lib64/libguile.so.17[0x3a3ea50714]
(Continue reading)

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Kadir Ustun | 27 Mar 2010 21:02
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Re: MPB

I could not observe the higher order modes in mpb.
Best Wishes,
Kadir

2010/3/27 Lukáš Ondič <luki.ondic <at> gmail.com>
Hello,
I`ve read yours post on MPB discuss forum about the planar waveguide.
Did you manage to count it? I am trying to do it but I cant.
Would you please send me your source if it works? Thanks.
Regards,
Lukas.

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barry stevensson | 25 Mar 2010 21:44

installation problem (HDF5-DIAG: Error detected in HDF5 library version: 1.6.6)

Dear MPB users,

I just installed MPB package on Debian Lenny. No error message during instalation. Then, I tried to run tri-rods.ctl file as written in manual. No error message until i wrote :

h5topng -C epsilon.h5:data-new -c bluered -Z -d z.r-new e.k11.b*.z.th.h5
then i got this message:

HDF5-DIAG: Error detected in HDF5 library version: 1.6.6 thread 3083253424.
Back trace follows.

#000: ../../../src/H5F.c line 2049 in H5Fopen(): unable to open file
major(04): File interface
minor(17): Unable to open file
#001: ../../../src/H5F.c line 1726 in H5F_open(): unable to open file
major(04): File interface
minor(17): Unable to open file
#002: ../../../src/H5FD.c line 1045 in H5FD_open(): open failed
major(22): Virtual File Layer
minor(29): Unable to initialize object
#003: ../../../src/H5FDsec2.c line 367 in H5FD_sec2_open(): unable to open file
major(04): File interface
minor(17): Unable to open file
#004: ../../../src/H5FDsec2.c line 367 in H5FD_sec2_open(): No such file or directory
major(03): Internal HDF5 error
minor(87): System error message
h5topng error: error opening HD5 file

Please help me to know how to fix this problem.

Many thanks,

Barry
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Yanfeng Li | 30 Mar 2010 10:21
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help on reproducing paper figure

Dear Dr. Johnson and all MPB users,

Thanks for the great software!

I am using MPB to reproduce some figures in the following paper:

M. Perrin, Y. Quiquempois, G. Bouwmans and M. Douay, 
Coexistence of total internal reflexion and bandgap modes
in solid core photonic bandgap fibre with intersticial air holes, 
Optics Express, 15(21):13783-13795, 2007            
http://www.opticsinfobase.org/abstract.cfm?id=142928

To reproduce the upper panel in Fig.3, I used the following commands

mpb pbg_tri2.ctl >& pbg_tri2.txt
h5topng -S 5 epsilon.h5
mpb-data -r -m 5 -n 32 epsilon.h5
h5topng epsilon.h5:data-new
mpb-data -r -m 5 -n 32 dpwr.k*.h5
h5topng -C epsilon.h5:data-new -c bluered -Z -d data-new dpwr.k*.h5

and the pbg_tri2.ctl file 

(define-param tz 3) 
(define-param r 0.3625)
(set! num-bands 1)
(set! default-material (make dielectric (epsilon 2.1025)))
;silica index 1.45
(set! geometry-lattice (make lattice (size 1 1 no-size)
	(basis1 (/ (sqrt 3) 2) 0.5 0)
	(basis2 (/ (sqrt 3) 2) -0.5 0)))
(set! geometry (list (make cylinder 
	(center 0 0 0) (radius r) (height infinity)
	(material (make dielectric (epsilon 2.196))))))
;high-index rod index=1.45+0.032, simple index profile
(set! k-points (list (vector3 0 0 tz) ; Gamma 
		(vector3 (/ -3) (/ 3) tz))) ;K
(set! resolution 32) 
(run output-dpwr))
; or should I output something else?

It seems that the figures generated appear similar,
but I want them to look more like those in the paper.
The related question is if I ouput the Ex field using
(run fix-efield-phase output-efield-x)),
how can I handle both the real and imaginary parts
(i.e.,to put them into two files, like the lower panel in 
figure 3)?

My difficulty seems to be due to the unfamiliarity with 
the plotting functions.
Any tips or help will be appreciated.

Best regards

Yanfeng Li

----------------------------------------------------------------
Associate Professor, Ph.D
Ultrafast Laser Laboratory,
College of Precision Instrument and Optoelectronics Engineering,
Tianjin University, Tianjin 300072, China
Tel & Fax: +86-22-27404204
http://ull.tju.edu.cn 
Email: yanfengli <at> tju.edu.cn
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barry stevensson | 30 Mar 2010 10:34

installation problem (HDF5-DIAG: Error detected in HDF5 library version: 1.6.6)

Dear MPB users,

I just installed MPB package on Debian Lenny. No error message during instalation. Then, I tried to run tri-rods.ctl file as written in manual. No error message until i wrote :
h5topng -C epsilon.h5:data-new -c bluered -Z -d z.r-new e.k11.b*.z.th.h5
then i got this message:

HDF5-DIAG: Error detected in HDF5 library version: 1.6.6 thread 3083253424.
Back trace follows.

#000: ../../../src/H5F.c line 2049 in H5Fopen(): unable to open file
major(04): File interface
minor(17): Unable to open file
#001: ../../../src/H5F.c line 1726 in H5F_open(): unable to open file
major(04): File interface
minor(17): Unable to open file
#002: ../../../src/H5FD.c line 1045 in H5FD_open(): open failed
major(22): Virtual File Layer
minor(29): Unable to initialize object
#003: ../../../src/H5FDsec2.c line 367 in H5FD_sec2_open(): unable to open file
major(04): File interface
minor(17): Unable to open file
#004: ../../../src/H5FDsec2.c line 367 in H5FD_sec2_open(): No such file or directory
major(03): Internal HDF5 error
minor(87): System error message
h5topng error: error opening HD5 file

Please help me to know how to fix this problem.

Many thanks,

Barry
_______________________________________________
mpb-discuss mailing list
mpb-discuss <at> ab-initio.mit.edu
http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/mpb-discuss
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Gmane