You're welcome! :-) BTW, for now you could also try this:
bsub -o meepout.out -eo meeperr.err -n 2 pam -mpi mpirun -np 2 env PATH=<specify path> meep-mpi ctlfile.ctl the 'env' command wraps around your meep-mpi command and runs it in a modified environment, in the process letting you define additional environment variables as NAME=VALUE pairs before the command+args to be executed. cheers! Manoj Li, Jingjing wrote: > Hi Manoj, > > Thanks for your reply. I'm consulting our system admin. Let me see what he > says about it. > > Jingjing > > ---------- > 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 > > >> -----Original Message----- >> From: Manoj Rajagopalan [mailto:[EMAIL PROTECTED] >> Sent: Monday, January 28, 2008 8:29 AM >> To: Li, Jingjing; '[email protected]' >> Subject: Re: [Meep-discuss] Output-png problem >> >> 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
