Re: [Meep-discuss] time-averaged magnetic field amplitude
Steven G. Johnson wrote: On Jun 19, 2008, at 1:40 PM, matt wrote: I discovered that this approach is incompatible with meep-mpi as-is. The h5math and file deletion needs to be run serially. I just output the files I need and use h5math from the command line, but that would require either a long h5math expression "d1*d1 + d2*d2 + ...", or a bash script which operates on two h5 files at a time. I tried putting a (= 0 (meep-my-rank)) in the step function to serialize this, but then meep-mpi deadlocked as warned in the documentation. Hi Matt, Checking for (zero? (meep-my-rank)) should work, but you have to put it in the right place. I suspect that you based your convert-complex-h5 function on the convert-h5 in an old version of Meep. If you look at convert-h5 in the latest version (0.10.1), you'll find that it looks like: (define (convert-h5 rm? convert-cmd . step-funcs) (define (convert fname) (if (zero? (meep-my-rank)) (if (and (zero? (system (string-append convert-cmd " \"" fname "\""))) rm?) .) where the check of meep-my-rank was inserted in Meep 0.10.1 precisely to serialize any conversion commands done on the output files. Steven ___ meep-discuss mailing list meep-discuss@ab-initio.mit.edu http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss Hi, everyone I think, this file-based solution consumes lots of CPU time which is not suitable for some particular tasks such as far-field calculations, although manipulating fields in certain areas in meep-C++ is relatively easy and fast. Zheng 2008-6-20 ___ meep-discuss mailing list meep-discuss@ab-initio.mit.edu http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss
Re: [Meep-discuss] time-averaged magnetic field amplitude
On Jun 19, 2008, at 1:40 PM, matt wrote: > I discovered that this approach is incompatible with meep-mpi as-is. > The h5math and file deletion needs to be run serially. I just > output the files I need and use h5math from the command line, but > that would require either a long h5math expression "d1*d1 + d2*d2 > + ...", or a bash script which operates on two h5 files at a time. > > I tried putting a (= 0 (meep-my-rank)) in the step function to > serialize this, but then meep-mpi deadlocked as warned in the > documentation. Hi Matt, Checking for (zero? (meep-my-rank)) should work, but you have to put it in the right place. I suspect that you based your convert-complex-h5 function on the convert-h5 in an old version of Meep. If you look at convert-h5 in the latest version (0.10.1), you'll find that it looks like: (define (convert-h5 rm? convert-cmd . step-funcs) (define (convert fname) (if (zero? (meep-my-rank)) (if (and (zero? (system (string-append convert-cmd " \"" fname "\""))) rm?) .) where the check of meep-my-rank was inserted in Meep 0.10.1 precisely to serialize any conversion commands done on the output files. Steven ___ meep-discuss mailing list meep-discuss@ab-initio.mit.edu http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss
[Meep-discuss] Question on h5tovtk
Dear Alex,
You can decide which dataset extract with the command 'h5tovtk' using the
modifier "-d" followed by the name of the dataset.
By default extracts the first dataset that in your case is 'ex' (look at the
man page)
To extract 'Ey' dataset for instance:
>> h5tovtk -t 150 -o test.vtk -d ey test-e.h5
Best,
J.D.Domenech
Alex wrote :
>
> Dear Steven and meep community,
> I created a hdf5-file with all E-field components using
> ...
> (to-appended "e" (at-every 0.5 output-efield))
> ...
>
> this seems to work, since h5ls gives:
>
> h5ls test-e.h5
> ex Dataset {50, 50, 50, 200/Inf}
> ey Dataset {50, 50, 50, 200/Inf}
> ez Dataset {50, 50, 50, 200/Inf}
>
> Now I want to convert this hdf5-file into the vtk format, a vector vtk
> file for mayavi (to get a vector plot with arrows), using
>
> h5tovtk -t 150 -o test.vtk test-e.h5
>
> .
>
> .
>
> What am I doing wrong?
> Thank you very much for your help in advance!
>
> Regards
> Alex
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Re: [Meep-discuss] time-averaged magnetic field amplitude
I discovered that this approach is incompatible with meep-mpi as-is. The h5math and file deletion needs to be run serially. I just output the files I need and use h5math from the command line, but that would require either a long h5math expression "d1*d1 + d2*d2 + ...", or a bash script which operates on two h5 files at a time. I tried putting a (= 0 (meep-my-rank)) in the step function to serialize this, but then meep-mpi deadlocked as warned in the documentation. On Wed, 18 Jun 2008, matt wrote: > > > > > Neat, thanks! > > For the time average amplitude of a complex field, I changed the > convert-h5 function as shown below. It's very hokey because the field > component is hard-coded into the function, but it works. Also, it's not > really an average but rather a sum, which is okay if you just want a > pretty picture. > > > (define (convert-complex-h5 rm? convert-cmd . step-funcs) > (define (convert fname) > (if (and rm? (zero? (system (string-append convert-cmd " \"" fname > ":hz.i\" \"" fname ":hz.r\"" > (system (string-append "rm \"" fname "\"" > (lambda (to-do) > (let ((hooksave output-h5-hook)) > (set! output-h5-hook convert) > (map (lambda (f) (eval-step-func f to-do)) step-funcs) > (set! output-h5-hook hooksave > > > (define (complex-time-avg fname step-func) > (let ((first-step? true)) > (lambda (to-do) > (if first-step? > (begin ; just copy the output file to fname > (set! first-step? false) > ((convert-complex-h5 true > (string-append "h5math -e \"sqrt(d1*d1 + > d2*d2)\" " fname "") > step-func) to-do)) > ;; otherwise, add the output file to fname > ((convert-complex-h5 true > (string-append "h5math -e \"d1 + sqrt(d2*d2 + > d3*d3)\" " fname " " fname "") > step-func) to-do) > > > > > On Tue, 17 Jun 2008, Steven G. Johnson wrote: > >> On Jun 17, 2008, at 5:37 AM, matt wrote: >>> I want meep to output the amplitude of the complex time-average >>> magnetic >>> field over the computation domain, as an h5 file. >> >> >> See e.g. >> >> http://thread.gmane.org/gmane.comp.science.electromagnetism.meep.general/1456 >> >>> but I'm not looking for for the instantaneous magnetic field. I'm >>> also >>> not interested in the time-average flux or energy, which I could with >>> flux-in-box or field-energy-in-box. >> >> Those two only give you time averages if you have time-harmonic >> complex fields (i.e. a CW source, with force-complex-fields?=true, and >> have waited for transients to disappear). >> >> But in the case of a time-harmonic source, the time-average field is >> simply zero. >> >> Steven >> >> ___ >> 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 mailing list meep-discuss@ab-initio.mit.edu http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss
[Meep-discuss] p4_error: interrupt SIGx: 15
Dear meep users, I have installed meep on a large cluster consisting of some 100 nodes of which I can use some from Torque/MIPCH. Meep installs fine and can be started on as many processors as I like, but after a while the process dies sporadic with the error p23_602: p4_error: interrupt SIGx: 15 p24_11906: (441.871094) net_send: could not write to fd=5, errno = 32 Googleing this tells me that some process can't write to some disc (https://wiki.mst.edu/numerical/nic/faq) but I have no idea of how to remedy the problem or where to start looking? Anyone have seen this problem and can give me a hint where to start? Meep is compiled with hdf5 parallelised and my PBS-script looks as # Arguments to qsub can be submitted via the script as well by starting # the line with #PBS # Set your mail address #PBS -M [EMAIL PROTECTED] # # Mail on abort #PBS -m a # # Specify time for job #PBS -l walltime=00:02:00 # # Request 1 processor (node) #PBS -l nodes=2:ppn=4 # #PBS -q ada # #PBS -N bend_0406 # #PBS -v GUILE_WARN_DEPRECATED=no # #PBS -A Physics # # End of arguments to qsub #Preparation work cd ~/job/bended_pc_x_guided_new common="N=10 mtrl=0 r=0.025 a=0.5 fcen=1.5 df=2 res=192 save_field=0 save_eps=0 comp=Ey fiber_res=0.05 air_frame1=10" # Go! mpiexec -verbose /c3se/users/e9ravn/opt/bin/meep-mpi dx=0.00 with_pc=0 $common main.ctl #End of script (make sure line before this gets run) Regards, Robert -- Robert Rehammar PhD-Student Applied Physics, Chalmers University of Technology Department of Physics, Göteborg University SE-421 96 Göteborg Sweden Tel +46 (0)31 772 3156 Fax +46 (0)31 416 984 Cel +46 (0)738 328834 Web fy.chalmers.se/~e9ravn ___ meep-discuss mailing list meep-discuss@ab-initio.mit.edu http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss
