Re: [Meep-discuss] Precompiled package for meep 1.3
Dear Vladimir, If you decide to build the latest version of MEEP, you can find Meep and MPB installation instructions in Russian at Geektimes http://geektimes.ru/post/248514/ best wishes pavel On 01/06/15 08:49, Filip Dominec wrote: Dear Vladimir and all interested, to my knowledge there is no precompiled MEEP of the version 1.3 for Debian-based systems. Version 1.2.1 has been readily available for over a year thanks to Thorsten Alteholz. I prepared a compilation script, and planned to package the very latest MEEP and Python-meep on my own (and to publish them in my own PPA repository), but I ran into problems of incompatibility with the important HDF5 library. I observed this in the latest Debian Jessie and Ubuntu 14.10, 15.04. The first sign of problems in the compilation output is on the line with checking for H5Pcreate in -lhdf5... no, see the full output of Debian Jessie: https://github.com/FilipDominec/python-meep-install/blob/master/debian-jessie.log#L210 I think this is related to a new version of libhdf*. Until I spare enough time to resolve how to compile MEEP that would be again able to export data in the HDF5 format, I can not proceed with packaging. Any hints are appreciated from anybody. Best regards, Filip 2015-05-31 11:12 GMT+02:00, Владимир Борисович Новиков vb.novi...@physics.msu.ru: I would like install latest version of Meep using precompiled package (by means comand apt-get install meep h5utils). But only 1.2 version installs. Where I can find precompiled package for latest version 1.3? Sincerely yours ___ meep-discuss mailing list meep-discuss@ab-initio.mit.edu http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss ___ meep-discuss mailing list meep-discuss@ab-initio.mit.edu http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss
Re: [Meep-discuss] Python-Meep Investigation
, and that is when I encountered my original
problem with ./configure not finding HDF5 libraries either.
On Sun, 2015-03-22 at 22:17 +0100, Filip Dominec wrote:
Hi, I would traditionally refer you to the blue-boxed compilation
procedure at http://f.dominec.eu/meep/index.html#install
I tested it on different Ubuntu/Debian machines. Does it work on your
system?
Filip
2015-03-22 3:07 GMT+01:00, c7...@gmx.net c7...@gmx.net:
Unfortunately that didn't work, but it definitely has something to do
with
the MPI. I just compiled all packages without it and MEEP finds the
libraries.
Something is preventing meep from finding the HDF5 packages when it
is
compiled with mpi-support.
Greetings
c7420
Gesendet: Sonntag, 22. März 2015 um 00:34 Uhr
Von: Pavel Ivanov pavel.ivanov.2...@googlemail.com
An: c7...@gmx.net
Betreff: Re: [Meep-discuss] Meep can't find HDF5 libraries during
./configure
Dear C7420,
Try configuring and building all packages (not just HDF5 library) by
forcing
building scripts into using MPI versions of compilers. Here is an
example
from my notes:
CC=mpicc CXX=mpicxx F77=mpif77 ./configure --prefix=/home/el1pi/opt
--enable-parallel
make
make install
Sometimes, it helps. Hopefully, it will help this time.
best wishes
pavlo
On 21/03/15 20:35, c7...@gmx.net wrote:
Dear Meep-Users,
I am failing to compile meep with MPICH and HDF5. I successfully
build
mpich-3.1.4 and hdf5-1.8.9.tar from source on a Debian Jessie
machine.
(Yes, I tried the precompiled packages too. They throw out errors
when
trying to write to the hdf5 files in mpi-mode.)
The following problem may not have anything to do with the
repository
packages not working properly, but I tried to compile the programs
myself
anyway and all of the dependencies compile without errors. Only Meep
can't
find the HDF5 libraries in the custom location.
This is the bash function I used to compile HDF5:
function HDF5 {
tar -xf hdf5-1.8.14.tar
cd ./hdf5-1.8.14
export CC=$BUILD_DIR/bin/mpicc
export F77=$BUILD_DIR/bin/mpif77
export CXX=$BUILD_DIR/bin/mpic++
./configure --prefix=$BUILD_DIR --enable-parallel 21 | tee
../Output/HDF5_configure.out
make 21 | tee ../Output/HDF5_make.out
make check 21 | tee ../Output/HDF5_make_check.out
make install 21 | tee ../Output/HDF5_make_install.out
cd ..
rm -r -f ./hdf5-1.8.14
export CC=gcc
export F77=f77
export CXX=g++
}
After Installing libctl, MPICH and HarmInv+OpenBLAS I tried:
export CFLAGS= -fPIC; export CXXFLAGS= -fPIC; export FFLAGS=
-fPIC
export CC=gcc; export F77=f77; export CXX=g++
export CPPFLAGS=-I$BUILD_DIR/include
export LDFLAGS=-L$BUILD_DIR/lib
export LD_RUN_PATH=-L$BUILD_DIR/lib
export PATH=$BUILD_DIR/bin:$PATH
function MEEP {
tar -xf meep-1.2.1.tar.gz
cd ./meep-1.2.1
export MPICXX=$BUILD_DIR/bin/mpic++
./configure --with-mpi --prefix=$BUILD_DIR
--with-libctl=$BUILD_DIR/share/libctl 21 | tee
../Output/MEEP_configure.out
#make 21 | tee ../Output/MEEP_make.out
#make install 21 | tee ../Output/MEEP_make_install.out
cd ..
rm -rf ./meep-1.2.1
}
BELOW is the Output of the ./configure command from the function
above.
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether make supports nested variables... (cached) yes
checking whether to enable maintainer-specific portions of
Makefiles...
no
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of g++... gcc3
checking for mpic++... /home/neutronst4r/Install/build/bin/mpic++
checking for mpi.h... yes
checking for extra flag needed to combine stdio.h and mpi.h... none
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... gcc3
checking for C++ compiler vendor... gnu
checking how to print strings... printf
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm
-B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
Re: [Meep-discuss] Slow calculation with meep parallelisation
Dear Ratnesh, Can you check outputs of your simulations when you were using two cores (-np 2)? Did meep-mpi run simulation for each time point twice? Alternatively you can save outputs into a file and email them to me. best wishes pavel On 02/12/14 08:18, Gupta, Ratnesh (GE Global Research, Consultant) wrote: Hi, I’ve configured a cluster with meep-mpi. I am able to execute the code. But the code while run with ‘-np 1’ is completely run within 368 seconds where it took 410 seconds while run with ‘-np 2’. Similarly, the time keeps increasing for increasing number of processors which is not expected. Also, I have a huge geometry which I want to simulate and is getting segmentation fault with single processor. I hoped to run it with multiple processor so that do decrease the probability of segmentation fault. Please help. Thanks and Regards, Ratnesh ___ meep-discuss mailing list meep-discuss@ab-initio.mit.edu http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss ___ meep-discuss mailing list meep-discuss@ab-initio.mit.edu http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss
[Meep-discuss] 3d eigenmode source
Dear Prof. Johnson, Dear All, As far I understand, meep eigenmode source can be defined in a plane (2d), in a line (1d) and in a volume (3d source). For a 3d source, the size of the source in all directions must be greater than zero (for example, (size sw sw sw)). Has anyone got a 3d eigenmode source working? Every time I try to add a third dimension to the source, Meep throws out an error message Newton solver not converging - need a better starting kpoint. However, this error is not shown when the source is a plane. Am I missing something? The example is attached - it is based one of Meep examples. In this example, edit line 19 to convert the source to 2d ((size 1.5 1.5 0.1) - (size 1.5 1.5 0)). It is a simplified example, more complex codes where k_point is evaluated in a more correct way experience the same problem. any help is highly appreciated. best wishes pavlo ; Example file illustrating an eigenmode source, generating a waveguide mode ; (requires recent MPB version to be installed before Meep is compiled) (set! geometry-lattice (make lattice (size 2 2 2))) ; an asymmetrical dielectric waveguide: (set! geometry (list (make block (center 0 0 0) (size infinity infinity infinity) (material air)) (make block (center 0 0 0) (size 0.5 0.5 0.5) (material (make dielectric (epsilon 12)) (define-param beta 3.26) (set! k-point (vector3 0 0 beta)) ; create a transparent source that excites a right-going waveguide mode (set! sources (list (make eigenmode-source (src (make continuous-src (frequency 0.15))) (size 1.5 1.5 0.1) (center 0 0 0) (component ALL-COMPONENTS) (direction Z) (eig-kpoint k-point) (eig-parity TM) ))) ;(set! pml-layers (list (make pml (thickness 1.0 (set-param! force-complex-fields? true) ; so we can get time-average flux (set-param! resolution 50) (run-until 200 (at-beginning output-epsilon) (at-end (output-png+h5 Ez -a yarg -A $EPS -S3 -Zc dkbluered))) (print left-going flux = ; (averaged over y region of width 1.8) (/ (flux-in-box X (volume (center -6 0) (size 1.8 6 0))) -1.8) \n) (print right-going flux = ; (averaged over y region of width 1.8) (/ (flux-in-box X (volume (center +6 0) (size 1.8 6 0))) +1.8) \n) ___ meep-discuss mailing list meep-discuss@ab-initio.mit.edu http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss
Re: [Meep-discuss] Meep frequency snapshots and near to far field transform
Dear All, The code for MEEP-1.2.1 can also be found here: https://github.com/Arthur-Thijssen/MEEP-actt/tree/master/1.2.1 enjoy! pavlo On 27/03/14 16:10, Arthur Thijssen wrote: Dear Meep users, During the course of the my PhD I have added some functionality to Meep. This includes: - output of fields / field components in the frequency domain. Meep includes discrete Fourier transforms used mostly for flux plane calculations. I've written a wrapper class that uses this build in DFT to output fields to hdf5 files in the frequency domain. - Near to far field transform. Using the algorithm described in Computational Electrodynamics: The Finite-Difference Time-Domain Method by Taflove, the addition to Meep can perform near to far field transforms and output them to hdf5 files. The output is given in a spherical coordinate system, see the Matlab post processing script for more information. - Mode volumes in the frequency domain. Meep is able to calculate mode volumes, however it can only do this for one mode at a time. The addition to Meep is able to perform mode volume calculations for several modes at once in the frequency domain if the modes are excited. I have included a scheme interface with this functionality. See the control file example for details. The code is fully MPI compatible. In order to use my additions for Meep, you can download the modified source files from here: https://github.com/Arthur-Thijssen/MEEP-actt Simply replace those files with the original Meep code and compile normally. A few notes: - The near to far field transform has not been implemented using a FFT algorithm. This might be added in the future. - I prefer to use single precision floating point numbers when using Meep. This is the default setting for the code given here. - I have not gotten to optimizing hdf5 output yet and is thus not as fast as it could be. Let me know what you think and if you have any questions. Thanks, Arthur Thijssen ___ meep-discuss mailing list meep-discuss@ab-initio.mit.edu http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss ___ meep-discuss mailing list meep-discuss@ab-initio.mit.edu http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss
[Meep-discuss] eigenmode source in cylindrical coordinates
Dear Prof Johnson, MEEP developers and users, I tried Optical forces Meep Tutorial and its very useful eigenmode source. Everything went well. When I attempted using the eigenmode source in cylindrical coordinates (by setting (set! dimensions CYLINDRICAL) and updating my code accordingly) meep started throwing the error message: unsupported dimensionality in add_eigenmode_source Does eigenmode source work in cylindrical coordinates (or it works in Cartesian coordinates only)? many thanks pavel ___ meep-discuss mailing list meep-discuss@ab-initio.mit.edu http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss
Re: [Meep-discuss] Meep, MPB, Harminv on Cygwin
In my previous message I mentioned MPB, but this conclusion is valid for Meep as well. sorry about the confusion. ___ meep-discuss mailing list meep-discuss@ab-initio.mit.edu http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss
[Meep-discuss] h Re: Computer
Hi Rita, a computer with several CPU cores or two computers working as a cluster must be able to run meep and mpi version of meep. Just choose whatever suits you. pavel On 02/07/12 11:11, Rita Ribeiro wrote: Hi, i will buy a computer to program in python using the MEEP software, but i have several questions about it. Should i bought two computers to do parallel programming or just one computer with several cpu? R. ___ meep-discuss mailing list meep-discuss@ab-initio.mit.edu http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss ___ meep-discuss mailing list meep-discuss@ab-initio.mit.edu http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss
Re: [Meep-discuss] Issue using meep/meep-mpi on 64bit System
Hi Nicolai and all, did you compile MPB and Meep from sources? I have compiled meep, harminv and mpb with a MPI support last February and they worked fine on a 64bit system with 8 cores. The system was running CentOS release 6.2, kernel 2.6.32-220.13.el6.x86_64. I used GCC version 4.4.6. the main trick was to find a right compiler and compile HDF libraries with --enable-parallel key. I have had a number of C and fortran compilers installed on my computer, some of them did not work with MPI at all. hope it helps pavel On 25/06/2012 09:26, Walter, Nicolai wrote: Hi everyone, I have a weird problem using meep-mpi/meep on a 32-core,64gb RAM, 64bit system. It seems that after I started meep-mpi e.g. with 8 processes, one or sometimes two processes will leap behind in run time. When meep should be finished, all processes go to sleep except those two. They will run indefinitely and must be terminated by hand. If I check the meep output, sometimes everything looks fine (last line: elapsed run time=) but sometimes it stops right after harminv! This problem occurs just occasionally, sometimes everything works just as it should. I have experienced the same problem with meep, so i think it's not the MPI. I already checked for hardware issues and found none, i also ran the very same files on an 8-core 32bit system and they worked just fine! So maybe it's some problem with my harminv installation on 64bit? If anyone has experienced similar issues or has any hints i would be very thankful! Best regards, Nicolai ___ meep-discuss mailing list meep-discuss@ab-initio.mit.edu http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss ___ meep-discuss mailing list meep-discuss@ab-initio.mit.edu http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss
Re: [Meep-discuss] Meep, MPB, Harminv on Cygwin
Dear All
I would like to mention that editing the .bash_profile file with Windows
Notepad is not a good idea. The editing with Notepad introduces some
unwanted symbols into the file.
Thus, I am attaching the .bash_profile from my cygwin installation
(thanks to Neal Pfeiffenberger for suggesting me to do so) to make
building MPB and Meep on Cygwin simpler.
best regards
pavel
# base-files version 4.0-6
# ~/.bash_profile: executed by bash(1) for login shells.
# The latest version as installed by the Cygwin Setup program can
# always be found at /etc/defaults/etc/skel/.bash_profile
# Modifying /etc/skel/.bash_profile directly will prevent
# setup from updating it.
# The copy in your home directory (~/.bash_profile) is yours, please
# feel free to customise it to create a shell
# environment to your liking. If you feel a change
# would be benifitial to all, please feel free to send
# a patch to the cygwin mailing list.
# User dependent .bash_profile file
# source the users bashrc if it exists
if [ -f ${HOME}/.bashrc ] ; then
source ${HOME}/.bashrc
fi
# Set PATH so it includes user's private bin if it exists
# if [ -d ${HOME}/bin ] ; then
# PATH=${HOME}/bin:${PATH}
# fi
# Set MANPATH so it includes users' private man if it exists
# if [ -d ${HOME}/man ]; then
# MANPATH=${HOME}/man:${MANPATH}
# fi
# Set INFOPATH so it includes users' private info if it exists
# if [ -d ${HOME}/info ]; then
# INFOPATH=${HOME}/info:${INFOPATH}
# fi
LDFLAGS=-L/usr/local/lib export LDFLAGS
CPPFLAGS=-I/usr/local/include export CPPFLAGS
PATH=/usr/local/bin:$PATH export PATH
LD_LIBRARY_PATH=/usr/local/lib export LD_LIBRARY_PATH
CC=gcc-3 export CC
F77=g77 export F77
CXX=c++-3 export CXX___
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Re: [Meep-discuss] Meep, MPB, Harminv on Cygwin
Recently, Wesley Wand has drawn my attention to issues with compiling MPB and Meep on cygwin of latest version. He noticed that the above recipe does not longer work. The latest Setup.exe version is 2.761 and the latest Cygwin version is 1.7.9-1. To make things simpler, you can install the following cygwin packages as shown below: Accessibility: Default Admin: Default Archive: Install hdf5: HDF5 Hierarchal Data Format /version 1.8.8-1/, libhfd5-devel: HDF5 Hierarchal Data Format (development) /version 1.8.8-1/, libhfd5_7: HDF5 Hierarchal Data Format (runtime) /version 1.8.8-1/ Audio: Default Base: Default Database: Default Devel: Install all Doc: Default Editors: Default Games: Default Gnome: Default Graphics: Default Interpreters: Install guile: the GNU extension language and Scheme interpreter -- executables /version 1.8.7-2/ KDE: Default Libs: Install all Mail: Default Math: Install: lapack: Comprehensive FORTRAN library for linear algebra operations /version 3.2.2-2/, liblapack-devel: Development libs for LAPACK /version 3.2.2-2/, liblapack0: Comprehensive FORTRAN library for linear algebra operations /version 3.2.2-2/ Net: Default Perl: Default Publishing: Default Python: Default Security: Default Shells: Default System: Default Text: Default Utils: Default Web: Default X11: Default I. If you want to compile Meep, MPB and Harminv. The actual Cygwin version includes GNU compiler versions 3.4.4 and 4.5.3. To compile MEEP, MPB and Harminv, we need to use the GCC version 3.4.4. Add the following lines at the end of you .bash_profile file to choose GCC version 3.4.4 and fortan compiler version 3.4.4. LDFLAGS=-L/usr/local/lib export LDFLAGS CPPFLAGS=-I/usr/local/include export CPPFLAGS PATH=/usr/local/bin:$PATH export PATH LD_LIBRARY_PATH=/usr/local/lib export LD_LIBRARY_PATH CC=gcc-3 export CC F77=g77 export F77 CXX=c++-3 export CXX 1. Build and install FFTW 1.1 download http://www.fftw.org/fftw-2.1.5.tar.gz 1.2 gzip -d fftw-2.1.5.tar.gz 1.3 tar -xvf fftw-2.1.5.tar 1.4 cd fftw-2.1.5 1.5 ./configure --prefix=/usr/local 1.6 make 1.7 make install 2. libctl 2.1 Download it from http://ab-initio.mit.edu/libctl/libctl-3.1.tar.gz 2.2 gzip -d libctl-3.1.tar.gz 2.3 tar -xvf libctl-3.1.tar 2.4 cd libctl-3.1 2.5 ./configure --prefix=/usr/local 2.6 make 2.7 make install 3. MPB 3.1 download it from http://ab-initio.mit.edu/mpb/mpb-1.4.2.tar.gz 3.2 gzip -d mpb-1.4.2.tar.gz 3.3 tar -xvf mpb-1.4.2.tar 3.4 cd mpb-1.4.2 3.5 ./configure --prefix=/usr/local CPPFLAGS=-DH5_USE_16_API=1 3.6 make 3.7 make install 4. Harminv 4.1 download it from http://ab-initio.mit.edu/harminv/harminv-1.3.1.tar.gz 4.2 gzip -d harminv-1.3.1.tar.gz 4.3 tar -xvf harminv-1.3.1.tar 4.4 cd harminv-1.3.1 4.5 ./configure --prefix=/usr/local 4.6 make 4.7 make install Run following commands in the cygwin terminal ln -s /usr/lib/gcc/i686-pc-cygwin/3.4.4/libg2c.la /usr/lib/gcc/i686-pc-cygwin/libg2c.la ln -s /usr/lib/gcc/i686-pc-cygwin/3.4.4/libg2c.a /usr/lib/gcc/i686-pc-cygwin/libg2c.a 5. MEEP 5.1 download it from http://ab-initio.mit.edu/meep/meep-1.1.1.tar.gz 5.2 gzip -d meep-1.1.1.tar.gz 5.3 tar -xvf meep-1.1.1.tar 5.4 cd meep-1.1.1 5.5 ./configure --prefix=/usr/local F77=gfortran 5.6 make 5.7 make install 6. Build and install h5utils (optional, you need them if you want to convert .h5 files created with Meep and MPB) 6.1 Download http://ab-initio.mit.edu/h5utils/h5utils-1.12.1.tar.gz 6.2 gzip -d h5utils-1.12.1.tar.gz 6.3 tar -xvf h5utils-1.12.1.tar 6.4 cd h5utils-1.12.1 6.5 ./configure --prefix=/usr/local 6.6 make 6.7 make install II. If you want to install MPB only You can add the following lines at the end of your .bash_profile file to choose GCC version 4.5.3 and fortran compiler version 4.5.3. LDFLAGS=-L/usr/local/lib export LDFLAGS CPPFLAGS=-I/usr/local/include export CPPFLAGS PATH=/usr/local/bin:$PATH export PATH LD_LIBRARY_PATH=/usr/local/lib export LD_LIBRARY_PATH CC=gcc-4 export CC F77=gfortran export F77 CXX=c++-4 export CXX Then build and install all packages as described above. P.S. Moreover, if you need MPB only, then you can add the following lines into your bash_profile file LDFLAGS=-L/usr/local/lib export LDFLAGS CPPFLAGS=-I/usr/local/include export CPPFLAGS PATH=/usr/local/bin:$PATH export PATH LD_LIBRARY_PATH=/usr/local/lib export LD_LIBRARY_PATH Configure Harminv as ./configure --prefix=/usr/local F77=gfortran Configure MPB as ./configure --prefix=/usr/local CPPFLAGS=-DH5_USE_16_API=1 F77=gfortran Best regards ___ meep-discuss mailing list meep-discuss@ab-initio.mit.edu http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss
Re: [Meep-discuss] Problem: h5math doesn't work
Hi Steffen, it is good to hear from you again. Do you have libmatheval installed on your computer? If not, did you try to download, build and install it? http://www.gnu.org/software/libmatheval/ If h5math does not work you can use matlab (as Judson has already suggested) or octave (a free clone of matlab). I have checked and it seems that Octave can read h5 files. h5read command is responsible for this. best wishes pavel On 08/09/10 09:48, ixnayonthehombre-...@gmx.de wrote: Dear Meep-User, it's not possible to use h5math, because h5utils cannot find libmatheval: Warning: can't find libmatheval: won't be able to compile h5math I need h5math to average the h5-files. Is there a solution for this problem? thanks steffen ___ meep-discuss mailing list meep-discuss@ab-initio.mit.edu http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss
[Meep-discuss] Meep, MPB, Harminv on Cygwin
Dear Meep users, Recently, we have interacted with Michel Devel (CC:) and Steffen (CC:) on compiling of Harminv, Meep and MPB on Cygwin (Windows XP, Vista and Windows 7). It seems that we found the recipe that works for many of us. Finally Cygwin allows these packages to be installed and worked well. Here is the list of steps for installing Meep, Harminv and MPB on Cygwin for these of you who wants to install them on Cygwin. Download and install Cygwin from http://www.cygwin.com/ What to install: Accessibility - Default Admin - Default Archive - all install Audio - default Base - default Database - default Devel - Install all Docs - default Editors - default (but I install mc because I like it) Games - default Gnome - default Graphics - install all Interpreters - default KDE - default Libs - install all Mail - default Math - add liblapack and can remove fftw3 and libfftw3 from the list Mingw - default net - default perl - default publishing - default python - default security - default shells - default System - install all Text - default Utils - default Web - default X11 - install all I know that many non-required packages will be installed this way, but I do not spend much time on optimizing the Cygwin installation. The Cygwin already contains compiled BLAS and Lapack libraries, so there is no need to build them. After installing Cygwin, test cygwin and xwindows: 1. start cygwin bash shell 2. start xwindows - run startxwin.exe in the Cygwin shell 3. if cygwin and xterminal are able to be started then they are installed well. Stop Xwindows and exit cygwin. 1. Environment variables Using you favourite text editor, add the following lines at the end of your ./bash_profile file LDFLAGS=-L/usr/local/lib export LDFLAGS CPPFLAGS=-I/usr/local/include export CPPFLAGS PATH=/usr/local/bin:$PATH export PATH LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH export LD_LIBRARY_PATH 2. Build and install h5utils (optional, you need them if you want to convert .h5 files created with Meep and MPB) 2.1 Download http://ab-initio.mit.edu/h5utils/h5utils-1.12.1.tar.gz 2.2 gzip -d h5utils-1.12.1.tar.gz 2.3 tar -xvf h5utils-1.12.1.tar 2.4 cd h5utils-1.12.1 2.5 ./configure --prefix=/usr/local 2.6 make 2.7 make install 3. Build and install FFTW 3.1 download http://www.fftw.org/fftw-2.1.5.tar.gz 3.2 gzip -d fftw-2.1.5.tar.gz 3.3 tar -xvf fftw-2.1.5.tar 3.4 cd fftw-2.1.5 3.5 ./configure --prefix=/usr/local 3.6 make 3.7 make install 4. libctl 4.1 Download it from http://ab-initio.mit.edu/libctl/libctl-3.1.tar.gz 4.2 gzip -d libctl-3.1.tar.gz 4.3 tar -xvf libctl-3.1.tar 4.4 cd libctl-3.1 4.5 ./configure --prefix=/usr/local 4.6 make 4.7 make install o. Build and install HDF5 (optional) o.1 Download hdf5-1.6.10.tar.gz from http://www.hdfgroup.org/ftp/HDF5/prev-releases/hdf5-1.6.9/src/hdf5-1.6.9.tar.gz o.2 gzip -d hdf5-1.6.9.tar.gz o.3 tar -xvf hdf5-1.6.9.tar o.4 cd hdf5-1.6.9 o.5 ./configure --prefix=/usr/local o.6 make o.7 make install 5. MPB 5.1 download it from http://ab-initio.mit.edu/mpb/mpb-1.4.2.tar.gz 5.2 gzip -d mpb-1.4.2.tar.gz 5.3 tar -xvf mpb-1.4.2.tar 5.4 cd mpb-1.4.2 5.5 ./configure --prefix=/usr/local 5.6 make 5.7 make install 6. Harminv 6.1 download it from http://ab-initio.mit.edu/harminv/harminv-1.3.1.tar.gz 6.2 gzip -d harminv-1.3.1.tar.gz 6.3 tar -xvf harminv-1.3.1.tar 6.4 cd harminv-1.3.1 6.5 ./configure --prefix=/usr/local F77=gfortran 6.6 make 6.7 make install 7. MEEP 7.1 download it from http://ab-initio.mit.edu/meep/meep-1.1.1.tar.gz 7.2 gzip -d meep-1.1.1.tar.gz 7.3 tar -xvf meep-1.1.1.tar 7.4 cd meep-1.1.1 7.5 ./configure --prefix=/usr/local F77=gfortran 7.6 make 7.7 make install All examples of MPB work well after the installation. Meep examples work well, except of bend-flux.ctl. If HDF5 is not installed, MEEP cannot run bend-flux.ctl and interrupts with the following error message: #001: /pub/cygports/hdf5/hdf5-1.6.9-2/src/hdf5-1.6.9/src/H5F.c line 1749 in H5 F_open(): unable to open file major(04): File interface minor(17): Unable to open file #002: /pub/cygports/hdf5/hdf5-1.6.9-2/src/hdf5-1.6.9/src/H5FD.c line 1033 in H 5FD_open(): open failed major(22): Virtual File Layer minor(29): Unable to initialize object #003: /pub/cygports/hdf5/hdf5-1.6.9-2/src/hdf5-1.6.9/src/H5FDsec2.c line 367 i n H5FD_sec2_open(): unable to open file major(04): File interface minor(17): Unable to open file #004: /pub/cygports/hdf5/hdf5-1.6.9-2/src/hdf5-1.6.9/src/H5FDsec2.c line 367 i n H5FD_sec2_open(): No such file or directory major(03): Internal HDF5 error minor(87): System error message meep: error on line 252 of h5file.cpp: error opening HDF5 input file If HDF5 is installed and both meep and harminv are compiled after installing the HDF5 libraries, then MEEP cannot run bend-flux.ctl and interrupts with the different error message: #000: H5F.c line 2072 in H5Fopen(): unable to open file major(04): File interface minor(17): Unable to open file #001:
Re: [Meep-discuss] Strange error when installing meep
Hello Colleague, Are you using a Linux or Windows/Cygwin to build and run meep? I believe I had similar problem with compiling mpb under Cygwin/Windows. pavel 李志强 wrote: Hi all! When I try to compile meep for the second time on my computer where I compiled meep successfully before. I came across the error: Linking to guile failed. guile-config is broken after configure. Everything needed has been intalled including libctl-3.1. There was never similar mistake before. I tried both the guile-1.6 and guile-1.8, the problem cannot be solved. I searched the archive of meep-discuss, someone asked the same question before, but nobody answered him. Can anyone help? Thank you! -- 李志强 北京大学物理学院光学所 ___ meep-discuss mailing list meep-discuss@ab-initio.mit.edu http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss ___ meep-discuss mailing list meep-discuss@ab-initio.mit.edu http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss
