[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
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] 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
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
