Looks like the actual node that is running meep in your cluster isn't seeing your PATH variable. Ask your sysadmin on which file you must set your path to so that the definition is propagaged.
For now you could try to "man" your bsub command to see if it accepts env variable arguments. Try, PATH=$PATH:<path-to-h5utils> bsub -o meepout.out .... Note that the way you specify paths will change depending on the shell. cheers! Manoj Li, Jingjing wrote: > Hi all, > > I was trying to use the "Output-png" function, similar to that in the online > meep tutorial. However, I did not get the .png file as expected. Rather, > the program output a long list of the same error as this: > > "sh: h5topng: command not found". > > And the program outputs a lot of h5 file, rather than the .png file. I can > still generate the .png file correctly from these .h5 file by using the > h5topng command mannualy. > > The path of the h5utils is correctly set, as checked by "echo $PATH". And > actually I can use h5topng command to generate figures from the h5 files > manually thus the path should not be a problem. The system is a HP-XC > cluster, and the job is submitted using the PAM feature of the LSF > applications as this: > > "bsub -o meepout.out -eo meeperr.err -n 2 pam -mpi mpirun -np 2 meep-mpi > ctlfile.ctl" > > The structure is actually very simple, a 2D waveguide bounded in the +/- y > direction by PEC, with three dielectric slabs inside. The source code is > attached below. > > Thank you for any suggestions. > > The code: > ----------------- > > (define-param thick1 5); Thickness of the left slab layer > (define-param thick2 5); Thickness of the right slab layer > (define-param thick_diel 50); Thickness of the sandwitched dielectrics > (define-param thick_pml 200); Thickness of the PML > (define-param thick_stack 200); Thickness of the stack between the PML and > ; the dielectric slab > > (define-param sx (+ thick_pml > (+ thick_stack > (+ thick1 > (+ thick_diel > (+ thick2 > (+ thick_stack thick_pml) > ))))) > ); The size along x-direction. Include the PML, the distance between the > ; the PML and the layer, etc. > > (define-param sy (* thick1 5)); > > (set! geometry-lattice (make lattice (size sx sy no-size))); > > (set! geometry (list (make block > (center (- (- 0 (/ thick_diel 2)) (/ thick1 2)) 0 > 0) > (size thick1 sy infinity) > (material (make dielectric (epsilon 3)))) > (make block > (center 0 0 0) > (size thick_diel sy infinity) > (material (make dielectric (epsilon 1.0)))) > (make block > (center (+ (/ thick2 2) (/ thick_diel 2)) 0 0) > (size thick2 sy infinity) > (material (make dielectric (epsilon 3)))) > )); > > (set! sources (list (make source > (src (make gaussian-src (frequency 0.01) (fwidth > 0.002))) > (component Ey) > (center (+ 100 (- 0 (+ (+ (/ thick_diel 2) (/ > thick1 2)) thick_stack))) 0 0) > (size 0 sy infinity) > ))); > > (set! pml-layers (list (make pml (thickness thick_pml) (direction X)))); > (set! resolution 1); > > (init-fields); > (meep-fields-set-boundary fields High Y Metallic); > (meep-fields-set-boundary fields Low Y Metallic); > > (run-sources+ > (stop-when-fields-decayed 200 Ey > (vector3 (- (* 0.5 sx) thick_pml 10) 0 0) > 1e-6)); > > > ---------- > Jingjing Li, Ph.D > Postdoc, Quantumn Science Research > Hewlett-Packard Laboratories > 1501 Page Mill Road, MS 1l23 > Palo Alto, CA 94304 > Phone: 650 857 5454 > > _______________________________________________ > meep-discuss mailing list > [email protected] > http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss > > _______________________________________________ meep-discuss mailing list [email protected] http://ab-initio.mit.edu/cgi-bin/mailman/listinfo/meep-discuss
