Sorry for a little advertisement, but this might help you. The
following compilation procedure for MEEP (and Python-meep, both
supporting HDF and OpenMPI) works also for Debian 8.5:
https://github.com/FilipDominec/python-meep-install
I tested it today again in a virtual machine, and MEEP passed all its
19 tests. Note that the Python-meep scripts presented on my github
page facilitate much of the "housekeeping", including graphical
export.
Filip
2017-01-08 6:05 GMT+01:00, Robin Whittle <r...@firstpr.com.au>:
> Thanks Steven and colleagues for Meep!
>
> I wrote a message to the list on 2015-04-20 about compiling Meep 1.3 on
> a Debian 8 (testing) system. Here is a revised version for Debian 8.5.
> Again, I built HDF5 from sources, which are now up to version
> 1.10.0-patch1. This also documents how I tested Meep with the first
> three tutorial examples.
>
> As before, I was able to compile the single threaded version ("serial",
> I didn't try MPI) of Meep with two problems:
>
> 1 - "make check" failed for near2far. I will email the
> log file to m...@ab-initio.mit.edu as requested.
>
> 2 - Meep's configure script did not find the HDF5 libraries. I fixed
> this by compiling HDF5 from source, with a configure option
> suggested in a recent list message by Pavel Ivanov.
>
> This description is detailed in the hope that it will help people who
> are stuck somewhere. There are many decisions to make about compiling
> and/or installing from packages the various things Meep itself relies
> on, and other tools required to use Meep.
>
> - Robin
>
>
>
> This is a dual hex-core Xeon X5670 machine with Debian 8.5 which I
> installed some months ago.
>
> Low-key preliminaries:
>
> The system has X Windows and I am sshing to it from a Windows
> machine and using Xming for the Windows display of X windows
> programs. To run Synaptic (package manager) like this without
> any fuss, I needed to (from non-root account and then "su -")
> add "PermitRootLogin yes" to /etc/ssh/sshd_config and restart
> the sshd server with: "/etc/init.d/ssh restart". Then I could
> use PuTTY to log into the machine as root, and the command
> "synaptic" would bring up the GUI package manager. (PuTTY:
> Connection > SSH > X11 > Enable X11 forwarding.)
>
> Apart from running Synaptic, which I did as root, I did all the
> following, including untargzipping the tarballs, as a mortal user, with
> sudo to run "make install" commands as root. I have not attempted to to
> compile for MPI -so this is a single-threaded Meep. This is based on
> the instructions at:
>
> http://ab-initio.mit.edu/wiki/index.php/Meep_Installation
>
> which was last updated on 2016-11-27, and which has only very slight
> changes since I referred to it last time, with latest updates on 2015-02-13.
>
> I used Synaptic Reload and "Mark All Upgrades" to update the system.
>
> (Note for newbies and myself since I tend to forget this: If
> the Installing Software dialog box seems to be stuck forever,
> click the little right-pointing arrow to the left of "Details".
> This will probably reveal some script which is waiting for the
> user to press Enter, 'q' etc.)
>
> I had already installed the build-essential 11.7 package, which sets up
> the GCC compiler and lots of other things for compiling programs in C
> and C++. (BTW, Synaptic makes Meep 1.2.1-2+b1 available.)
>
> Since harminv's use of BLAS and LAPACK requires a Fortran compiler, I
> installed (with Synaptic):
>
> gfortran-4.9 4.9.2-10
> libgfortran-4.9-dev 4.9.2-10
>
>
> Here are some packages which were already installed, or which I
> installed now:
>
> gcc
>
> Some gcc packages were already installed, not counting some 4.8
> packages:
>
> gcc 4:4.9.2-2
>
> gcc-4.9 4.9.2-10
> gcc-4.9-base 4.9.2-10
>
>
>
> BLAS
> libblas-common 1.2.20110419-10 was already installed.
> libblas3 1.2.20110419-10 was already installed.
> libblas.dev 1.2.20110419-10 I installed.
>
>
> LAPACK (search Synaptic for "liblapack".)
> liblapack3 3.5.0-4 was already installed.
> liblapack-dev 3.5.0-4 I installed.
>
>
> Harminv
>
> Via Synaptic I could have installed 1.3.1-10, but since 1.4 is
> needed, I compiled it. (It requires BLAS and LAPACK).
>
> http://ab-initio.mit.edu/wiki/index.php/Harminv_installation
>
> (The last change to this page was in 2005.)
>
> From the link at:
>
> http://ab-initio.mit.edu/wiki/index.php/Harminv
>
> (The last change to this page was in 2015-03-31.)
>
> I downloaded:
>
> http://ab-initio.mit.edu/harminv/harminv-1.4.tar.gz
>
> and untargzipped it to:
>
> /xx/meep-build/harminv/harminv-1.4/
>
> From there:
>
> ./configure
>
> seemed to run OK to the point of an error:
>
> cannot compile a simple Fortran program
>
> By right clicking the gfortran-4.9 item in Synaptic and selecting
> Properties > Installed files, I ascertained that the compiler was:
>
> /usr/bin/gfortran-4.9
>
> Following the instructions on the Harminv installation page, I gave
> this command instead:
>
> ./configure F77=/usr/bin/gfortran-4.9
>
> This produced the Makefile and no errors. Then I could give the next
> command:
>
> make
>
> Next, for the installation command to run as root I want to be able
> to give this command from a non-root shell:
>
> sudo make install
>
> (See my 2015-04-20 email for how I has set up my mortal account
> a sudoer.)
>
>
> GNU Guile
>
> Searching Synaptic for "guile" indicated that no packages with names
> including "guile" had been installed. The minimum version for Meep
> is 1.6. I installed:
>
> guile-2.0 2.0.11+1-9
> guile-2.0-libs 2.0.11+1-9
> guile-2.0-dev 2.0.11+1-9 (This brought in many other packages.)
>
>
> libctl
>
> I installed these packages.
>
> libctl-dev 3.2.2-2
> libctl-doc 3.2.2-2
> libctl5 3.2.2-2
>
>
>
> HDF5 (This is where the trouble begins . . . I did this next set of
> installations, but I suggest that you don't. See my notes below
> starting at AAA for how to compile HDF5 for uniprocessor AKA "serial"
> systems, that is not MPI meep.)
>
> I installed:
>
> h5utils 1.12.1-2.1+b2
>
> which brought in:
>
> hdf5-tools 1.8.13+docs-15+deb8ul
> libhdf5-8 1.8.13+docs-15+deb8ul
>
> Since we want the -dev packages too, I installed:
>
> libhdf5-dev 1.8.13+docs-15+deb8ul
>
> which brought in:
>
> hdf5-helpers 1.8.13+docs-15+deb8ul
> libhdf5-cpp-8 1.8.13+docs-15+deb8ul
> libjpeg-dev 1:1.3.1-12
> libjpeg62-turbo-dev 1:1.3.1-12
>
> I have no real idea what these packages are, other than that the
> H5utils are vital for using Meep:
>
> http://ab-initio.mit.edu/wiki/index.php/H5utils
>
> I later recognized that Meep uses a shared library for the many
> HDF5 functions it typically has, and which most people want.
> This set of packages turned out to be incompatible with the Meep
> configure system. I discuss this, and the fix for it, below.
>
>
> From http://ab-initio.mit.edu/wiki/index.php/Meep_download I downloaded
> meep-1.3.tar.gz and untargzipped it to:
>
> /xx/meep-build/meep-1.3/
>
>
> and from there:
>
> ./configure F77=/usr/bin/gfortran-4.9
>
> There were no errors. Then:
>
> make
> sudo make install
>
> This all went without errors, which is quite remarkable considering how
> many packages are required. Then I ran the self-tests:
>
> make check
>
> The known_results test took less than 3 minutes. (7 minutes last time,
> but the machine's memory system was running slower then.) One test -
> near2far - failed. This concerns the new feature added in 1.3: "New
> near-to-far-field functionality: given a bounding surface, automatically
> computes the Fourier-transformed field in any desired grid of
> 'far-field' points arbitrarily far away." As instructed, I am about
> to email the test results to m...@ab-initio.mit.edu. I will send the
> file meep-1.3/tests/near2far.log.
>
> I also dumped the help material in Meep's configure file:
>
> ./configure --help > configure-help.txt
>
>
> However, all was not well . . . I should be able to run the interactive
> commands at the start of the tutorial:
>
> http://ab-initio.mit.edu/wiki/index.php/Meep_Tutorial
>
> - - - -
>
> (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! sources (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))
>
> - - - -
>
> (Control D to exit Meep.)
>
> and have it produce a .h5 file. However, now, it generated a message:
>
> creating output file "./eps-000000.00.h5"...
> meep: not compiled with HDF5, required for HDF5 output
>
> This is the same as what happened in April 2015. My solution to it then
> was to compile HDF5 from source. I did this again, because it worked
> for me, and because my attempt to understand what Filip Dominec did to
> fix the same problem in his context (automating compilation of
> everything MPI and with a Python front-end for Meep) got me nowhere.
>
>
> With Synaptic I uninstalled (complete removal) the following packages
> listed above as the ones you probably shouldn't install:
>
> h5utils 1.12.1-2.1+b2
> hdf5-tools 1.8.13+docs-15+deb8ul
> libhdf5-8 1.8.13+docs-15+deb8ul
> libhdf5-dev 1.8.13+docs-15+deb8ul
> hdf5-helpers 1.8.13+docs-15+deb8ul
> libhdf5-cpp-8 1.8.13+docs-15+deb8ul
> libjpeg-dev 1:1.3.1-12
> libjpeg62-turbo-dev 1:1.3.1-12
>
> AAA
>
> The source is at:
>
> http://www.hdfgroup.org/HDF5/release/obtainsrc.html
>
> for HDF5-1.10.0-patch1:
>
>
> https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.0-patch1/src/hdf5-1.10.0-patch1.tar.gz
>
> This is much later than the version I compiled in April 2015:
> HDF5-1.8.14. I untargzipped this to:
>
> /astro/meep-build/HDF5/hdf5-1.10.0-patch1/
>
> and from there dumped the help material in HDF5's configure file:
>
> ./configure --help > configure-help.txt
>
> The only other guidance I could find on using the configure file was:
>
>
> https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.0-patch1/src/unpacked/release_docs/INSTALL
>
> but I didn't need any extra guidance.
>
>
> From the just-mentioned directory, I gave these commands to compile
> HDF5. (This is based on what I did in April 2015):
>
> ./configure --prefix=/usr/local > configure-output-HDF5.txt
> make
> sudo make install > install-HDF5.txt
>
> (Compilation generated hundreds of warnings.)
>
> Now the HDF5 shared libraries and a settings file are in /usr/local/lib
> as reported in install-HDF5.txt.
>
>
> I have not yet tried compiling h5utils from source - maybe it will be
> good enough to install the package via Synaptic again. For now, I tried
> the Meep configure command again to see if it was happy about HDF5:
>
> ./configure F77=/usr/bin/gfortran-4.9 > configure-output-3.txt
>
> It only produced the first three warnings mentioned above - the warning:
> "Couldn't find the HDF5 library!!" did not appear.
>
> I compiled, installed and tested Meep:
>
> make
> sudo make install
>
> Now, as explained in my April 2015 message to the list, what should be
> done at this point is this next command:
>
> sudo ldconfig
>
> Then continue with the tests:
>
> make check
>
> This runs OK, with the same near2far failure as listed previously.
>
> The interactive commands from the first part of the tutorial (for the
> straight waveguide, as previously listed) produced two .h5 files as
> expected. The final lines from meep were:
>
> creating output file "./eps-000000.00.h5"...
> creating output file "./ez-000200.00.h5"...
> run 0 finished at t = 200.0 (4000 timesteps)
>
> The next step in the tutorial involves programs from H5utils.
>
> Rather than compile h5utils, I tried re-installing with Synaptic:
>
> h5utils 1.12.1-2.1+b2
>
> which requires:
>
> hdf5-tools 1.8.13+docs-15+deb8ul
> libhdf5-8 1.8.13+docs-15+deb8ul
>
> I was wary about potentially interdependent programs being a mix of
> installed packages and compilations from source. There were no obvious
> problems.
>
> After exiting Meep with control-D, I was able to complete the next two
> steps of the tutorial:
>
> h5topng -S3 eps-000000.00.h5
> h5topng -S3 -Zc dkbluered -a yarg -A eps-000000.00.h5 ez-000200.00.h5
>
> ez-000200.00.png looked a little different to the image in the tutorial:
>
> http://ab-initio.mit.edu/wiki/index.php/Image:Tutorial-wvg-straight-ez-000200.00.png
>
> It looks the same in principle, but as if the snapshot was taken when
> the source was at a different phase of its sinewave cycle. It is binary
> identical to the ez-000200.00.png I produced in April 2015, about which
> I wrote: "identical to a file I produced with an earlier version of Meep
> in 2011." This is pretty good going, considering that the versions of
> Meep, HDF5 and I guess h5utils have all changed since 2011, and that
> this version of Meep predates by more than a year the version of HDF5 I
> am using.
>
>
> NOTE! There is no file for this in the examples directory of the
> Meep source code, and the file there "bend-flux.ctl", which
> is commented as being for the "transmission around a 90-degree
> waveguide bend in 2d" actually matches the third example,
> which has the title: "Transmission spectrum around a waveguide
> bend".
>
> I copied the text from the tutorial page for the second example "A 90°
> bend" and saved this as "90-degree-bend.ctl":
>
> - - - - -
>
> (set! geometry-lattice (make lattice (size 16 16 no-size)))
> (set! geometry (list
> (make block (center -2 -3.5) (size 12 1 infinity)
> (material (make dielectric (epsilon 12))))
> (make block (center 3.5 2) (size 1 12 infinity)
> (material (make dielectric (epsilon 12))))))
> (set! pml-layers (list (make pml (thickness 1.0))))
> (set! resolution 10)
> (set! sources (list
> (make source
> (src (make continuous-src
> (wavelength (* 2 (sqrt 12))) (width 20)))
> (component Ez)
> (center -7 -3.5) (size 0 1))))
> (run-until 200
> (at-beginning output-epsilon)
> (to-appended "ez" (at-every 0.6 output-efield-z)))
>
> - - - - -
>
> I ran this:
>
> meep 90-degree-bend.ctl
>
> and then gave the rest of the command lines listed in the tutorial, with
> the name of the .ctl file added to the file names, since I generated
> them from a .ctl file while in the tutorial they are generated from an
> interactive session:
>
> h5ls 90-degree-bend-ez.h5
>
> The tutorial page indicates that this should respond with:
>
> ez Dataset {161, 161, 330/Inf}
>
> but I got:
>
> ez Dataset {160, 160, 333/Inf}
>
> Adapting the next line of the tutorial:
>
> h5topng -t 0:329 -R -Zc dkbluered -a yarg -A eps-000000.00.h5 ez.h5
>
> to the different number of images, now 333 for some reason:
>
> h5topng -t 0:332 -R -Zc dkbluered -a yarg -A \
> 90-degree-bend-eps-000000.00.h5 \
> 90-degree-bend-ez.h5
>
> This produced 333 .png files. The final line of the tutorial uses a
> program from the package imagemagick, which was already installed.
> Again, adapting the tutorial line to my own filenames:
>
> 90-degree-bend-ez.tnnn.png
>
> I gave the command:
>
> convert 90-degree-bend-ez.t*.png 90-degree-bend-ez.gif
>
> This produced a .gif (read only for everyone except the owner) file
> which resembles that of the tutorial:
>
> http://ab-initio.mit.edu/wiki/images/7/7a/Tutorial-wvg-ez.gif
>
> except that instead of the bend pointing downwards, it points upwards.
> This is the same as my April 2015 experience.
>
> After installing ffmpeg I was also able to create a .mp4 video file
> (better quality than .mpg):
>
> convert 90-degree-bend-ez.t*.png 90-degree-bend-ez.mp4
>
> This was read write the owner and not even readable by others. Once I
> fixed this I could play it with VLC Player on my Windows machine, and
> slow it down with the '-' key or Playback > Speed.
>
> Everything seems to be working, so far.
>
>
> I ran the file which matches the 90 degree bend section of the tutorial
> meep-1.3/examples/bend-flux.ctl :
>
> meep bend-flux.ctl
>
> This generated errors similar to those from HDF5 (1.8.11) reported to
> this list by Léna Soun on 2016-06-01. My errors start with:
>
> - - - - -
>
> HDF5-DIAG: Error detected in HDF5 (1.10.0-patch1) thread 0:
> #000: H5F.c line 579 in H5Fopen(): unable to open file
> major: File accessibilty
> minor: Unable to open file
>
> - - - - -
>
> This is because this .ctl file is not meant to be run like this
> initially. From the tutorial, the first run is:
>
> meep no-bend?=true bend-flux.ctl | tee bend0.out
>
> and the second is:
>
> meep bend-flux.ctl | tee bend.out
>
> These produced the desired text files, but I don't know enough about
> Octave to try to reproduce the graph from them. However, the numbers in
> the second column of the .dat files seemed, when divided as described,
> to match the "transmission" curve.
>
>
>
>
>
> _______________________________________________
> meep-discuss mailing list
> meep-discuss@ab-initio.mit.edu
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