Dear MEEP Helper:
Recently I have been trying to install MEEP and related interfaces into a
Linux(Fedora 7). I followed the instructions in web pages and I think
everything was installed. Summary of my MEEP installation procedure is listed
at the end of this mail. However, when I tested the first example in the MEEP
tutorial page (http://ab-initio.mit.edu/wiki/index.php/Meep_Tutorial ). I do
not get the right output. I wrote the input, outputs, and error messages below.
Can somebody tell me what is wrong?
Input file (ex1.ctl);
(reset-meep)
(set! geometry-lattice (make lattice (size 16 8 no-size)))
(set! geometry (list
(make block (center 0 0) (size infinity 1 infinity)
(material (make dielectric (epsilon 12))))))
(set! source (list
(make source
(src (make continuous-src (frequency 0.15)))
(component Ez)
(center -7 0))))
(set! pml-layers (list (make pml (thickness 1.0))))
(set! resolution 10)
(run-until 200
(at-beginning output-epsilon)
(at-end output-efield-z))
Output message:
-----------
Initializing structure...
Working in 2D dimensions.
block, center = (0,0,0)
size (1e+20,1,1e+20)
axes (1,0,0), (0,1,0), (0,0,1)
dielectric constant epsilon = 12
time for set_epsilon = 0.0223849 s
-----------
creating output file "./ex1-eps-000000.00.h5"...
creating output file "./ex1-ez-000200.00.h5"...
run 0 finished at t = 200.0 (4000 timesteps)
Elapsed run time = 0.191832 s
Deprecated error message:
SCM_STRINGP is deprecated. Use scm_is_string instead.
SCM_STRING_LENGTH is deprecated. Use scm_c_string_length instead.
scm_must_malloc is deprecated. Use scm_gc_malloc and scm_gc_free instead.
SCM_STRING_CHARS is deprecated. See the manual for alternatives.
scm_must_free is deprecated. Use scm_gc_malloc and scm_gc_free instead.
Outputs:
ex1-eps-000000.00.h5 looks O.K.
ex1-ez-000200.00.h5 shows all 0's (when converted using "h5totxt")
Thanks in advance.
Jiha
Summary of MEEP installation (Jan. 8 – Jan. 12, 2007)
For the functions of the programs to be installed, please read the MEEP
installation page.
(http://ab-initio.mit.edu/wiki/index.php/Meep_Installation )
1. Installing guile (This installation is not difficult)
In any root directories,
% yum list | grep guile
% yum install guile-devel.x86.64
% guile --version → It shows guile 1.8.1 is installed
2. Installing libctl (This installation is not difficult.)
Downloaded “libctl-3.0.2.tar.tar” into /root/Download.
In /root/Download,
% tar –xvf libctl-3.0.2
% mv libctl-3.0.2 ..
% cd /root/libctl-3.0.2
% ./configure
(If there comes error messages “Permission denied”,
then “configure” file should be made executable;
% chmod 744 configure
% chmod 744 install-sh )
% make
% make install
This produced “gen-ctl-io” in /usr/local/bin,
“libctl.a”, “libctlgeom.a”, “libctlgeom.1a”, libctl.la” in
/usr/local/lib
“ctlgeom.h”, “ctl-geom-types.h”, “ctl.h” in /usr/local/include
“gen-ctl-io.1” in /usr/local/man/man1
many files in /usr/local/share/libctl/base and
/usr/local/share/libctl/utils
3. Installing hdf5 (This installation needs care.)
I followed the instructions of SCI institute web page
(http://software.sci.utah.edu/doc/Installation/Guide/osx/sec.sr_hdf5_build.html
).
There are also instructions in CBLFS web pages
(http://cblfs.cross-lfs.org/index.php/HDF5 and
http://cblfs.cross-lfs.org/index.php/H5utils).
% Downloaded “hdf5-1.6.6.tar.gz” into /root/Download
In the /root/Download directory,
% gunzip < hdf5-1.6.6.tat.gz | tar xf
% cd /root/hdf5-1.6.6
% CC=gcc
% CXX=g++
% export CC CXX
% ./configure --enable-threadsafe --with-pthread=/usr --prefix=/usr/local
% make all
% make install
This produced files in /usr/local/bin, /usr/local/lib, /usr/local/doc.
Finally, the followings are needed; check if there is a line /usr/local/lib in
/etc/ld.so.conf and run /sbin/ldconfig.
4. Installing libpng and libpng-devel
This is needed to install “h5toping” in h5utils package. “libpng” is usually
installed in Linux systems, but the header files need to be installed through
“libpng-devel”.
% yum list | grep libpng
(“libpng.x86_64” was already installed.)
% yum install libpng-devel.x86_64
5. Installing h5utils (Once the installations of 3 and 4 are done correctly,
this is simple.)
Downloaded “h5utils-1.10.1.tar.tar” into /root/Downloaded
In the directory,
% tar –xvf h5utils-1.10.1.tar.tar
% mv h5utils-1.10.1 ..
% cd /root/h5utils-1.10.1
% ./configure
% make
% make install
This installed “h5toping”, “h5totxt”, “h5fromtxt”, “h5tovtk” in /usr/local/bin.
and many other files in /usr/local/share/h5utils.
6. Installing BLAS and LAPACK
Downloaded “blas.gz” into /root/Download.
In the directory, the file name is changed to “blas.tgz”.
% gunzip blas.tgz
% tar xf blas.tar
% cd BLAS
% g77 –c –O3 *.f
% ar rv libblas.a *.o
% cp libblas.a /usr/local/lib
Downloaded “lapack.gz” into /root/Download.
In the directory, the file name is changed to “lapack.tgz”.
% gunzip lapack.tgz
% tar xf lapack.tar
% cd lapack-3.1.1
% cp INSTALL/make.inc.LINUX make.inc
Edit “make.inc” for BLASLIB
(BLASLIB = /usr/local/lib/libblas.a)
% make
% cp lapack_LINUX.a /usr/local/lib /liblapack.a
7. Installing Harmiv
Since this is not critical to run MEEP, I did not install it this time. It can
be installed later. Then, the MEEP has to be complied again.
8. Installing MEEP.
(Once all the required interfaces are installed, installing it is simple.)
Downloaded “meep-0.10.1.tar.tar into /root/Download-xvf
In the directory,
% tar –xvf meep-0.10.1.tar.tar
% mv meep-0.10.1 ..
% cd /root/ meep-0.10.1
% ./configure
% make
% make install
This produced “meep” in /usr/local/bin, and some files
in /usr/local/include/meep and in /usr/local/share/meep.
This should be ready to run test files in MEEP tutorial
(http://ab-initio.mit.edu/wiki/index.php/Meep_Tutorial ).
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