UCVM create new model with ucvm2mesh
From SCECpedia
Contents
goal
How to add a new model into UCVM using ucvm2mesh
background
ucvm2mesh generates mesh with upper-left corner as origin with seeking_axis in fast-Y mode going from upper left to lower-left corners. This is the same as using the ucvm web tool to generate a mesh.
The confusion part is nx is number of steps in the seeking_axis direction and so this example actually looks like
70 o
*
140 o
o
the generic model plugin code is assuming the mesh origin is at the lower-left corner and going from lower-left to upper left corner as fast-Y mode.
Although Cypershake uses upper-left corner as origin during its processing, the mesh it created to be included into UCVM has an additional translation such that it origin is at the lower-left corner
Steps:
create a mesh using ucvm2mesh translate data file import into UCVM with the generic model plugin code
generate mesh data
Select a region of interest with existing cvm models,
Generate vp/vs/rho data files using ucvm2mesh
config file for ucvm2mesh
ucvm2mesh -f southbay_sfcvm.conf > southbay_sfcvm.out
Origin is at the upper-, and going down in fast-Y axis in writing out the binary data
# List of CVMs to query ucvmlist=sfcvm # UCVM conf file ucvmconf=/var/www/html/UCVM_web_sfcvm_mei/web/model/UCVM_TARGET/conf/ucvm.conf # Gridding cell centered or vertex gridtype=CENTER # Spacing of cells spacing=20.0 # Projection proj=+proj=utm +datum=WGS84 +zone=10 rot=-39.9 x0=-121.8468 y0=37.2146 z0=0.0 # Number of cells along each dim nx=140 ny=70 nz=60 # Partitioning of grid among processors px=2 py=2 pz=2 # Vs/Vp minimum vp_min=0 vs_min=0 # Mesh and grid files, format meshfile=southbay_sfcvm gridfile=southbay_sfcvm.grid meshtype=SORD # Location of scratch dir scratch=./scratch
Output:
[0] Using config file southbay_sfcvm.conf [0] Configuration: [0] UCVM Model List: sfcvm [0] UCVM Conf file: /var/www/html/UCVM_web_sfcvm_mei/web/model/UCVM_TARGET/conf/ucvm.conf [0] Gridtype: 0 [0] Querymode: 0 [0] Spacing: 20.000000 [0] Projection: +proj=utm +datum=WGS84 +zone=10 [0] Rotation Angle: -39.900000 [0] Origin x0,y0,z0: -121.846800, 37.214600, 0.000000 [0] Dimensions: 140, 70, 60 [0] Proc Dimensions: 2, 2, 2 [0] Vp Min: 0.000000, Vs Min: 0.000000 [0] Mesh File: southbay_sfcvm.media [0] Grid File: southbay_sfcvm.grid [0] Mesh Type: 4 [0] Scratch Dir: ./scratch Setting up UCVM Generating 2D grid Converting grid to latlong Grid generation complete Allocating 9800 grid points Mesh dimensions: 140 x 70 x 60 Reading grid points Grid 4 corners: -121.846641 37.214610 (0) -121.822858 37.198302 (139) -121.836520 37.224053 (9660) -121.812736 37.207744 (9799) Extracted slice 0 (9800 pnts) in 231.25 ms, 42378.562500 pps ...
extract 4 corners
using ucvm2mesh, 4 latlon corners are available from the stderr output
for any other means,
UCVM's grid4corner on the grid file and dimension will return the corners
./grid4corners southbay_sfcvm.grid 140 70
returns
Grid 4 corners: -121.846641 37.214610 (0) -121.822858 37.198302 (139) -121.836520 37.224053 (9660) -121.812736 37.207744 (9799)
the location of the 4 corners are
upper-left lower-left upper-right lower-right
4 corners in utm
prepare input file
0 -121.846641 37.214610 0 -121.822858 37.198302 0 -121.836520 37.224053 0 -121.812736 37.207744
using a utm converter in cs242/src,
latlon2utm < in
and output
lon(-121.846641)lat(37.214610) => utm_e(69925.762628),utm_n(4129496.547620) lon(-121.822858)lat(37.198302) => utm_e(71945.561215),utm_n(4127577.595911) lon(-121.836520)lat(37.224053) => utm_e(70878.246875),utm_n(4130499.113105) lon(-121.812736)lat(37.207744) => utm_e(72898.029959),utm_n(4128580.270241)
can double check by extract the utm_e and utm_n out from the output, prepend with 1 and call latlon2utm and the result should match the original latlon data
setup config for the new ucvm model
# UTM Zone utm_zone = 10 # Model directory model_dir = cs242 model_data_path = https://g-c662a6.a78b8.36fe.data.globus.org/ucvm/models # Number of cells in x, y, and z. nx = 140 ny = 70 nz = 60 interpolation = on # Depth, in meters depth = 1200 depth_interval = 20 # Corners, in UTM projection. #-121.838241,37.253310,0 #-121.814448,37.237001,0 #-121.828113,37.262752,0 #-121.804320,37.246441,0 # #lon(-121.838241)lat(37.253310) => utm_e(603123.693099),utm_n(4123409.463672) #lon(-121.814448)lat(37.237001) => utm_e(605256.447077),utm_n(4121626.242860) #lon(-121.828113)lat(37.262752) => utm_e(604008.906310),utm_n(4124468.090587) #lon(-121.804320)lat(37.246441) => utm_e(606141.579119),utm_n(4122684.881493) top_left_corner_e = 603123.693099 top_left_corner_n = 4123409.463672 bottom_left_corner_e = 605256.447077 bottom_left_corner_n = 4121626.242860 top_right_corner_e = 604008.906310 top_right_corner_n = 4124468.090587 bottom_right_corner_e = 606141.579119 bottom_right_corner_n = 4122684.881493 # Data Layout Parameters seek_axis = fast-Y seek_direction = top-down
An example: using ucvm2mesh_mpi at Frontier
the Slurm script,
#!/bin/bash
#SBATCH -J norcal # Job name
#SBATCH -o norcal.oo # Name of stdout output file
#SBATCH -e norcal.ee # Name of stderr error file
#SBATCH -N 50 # Total # of nodes
#SBATCH -n 1000
#SBATCH -t 2:00:00 # Run time (hh:mm:ss)
#SBATCH --mail-user=mei@usc.edu
#SBATCH --mail-type=all
#SBATCH -p batch
#SBATCH -A geo156
#SBATCH --open-mode=truncate
source /ccs/home/mei/scratch/TARGET_UCVM_SFCVM_mei/ucvm_install/conf/ucvm_env.sh
cp ${UCVM_INSTALL_PATH}/bin/ucvm2mesh_mpi .
srun -N50 -n1000 ./ucvm2mesh_mpi -f ./norcal_mesh.conf
the mesh conf script,
# List of CVMs to query ucvmlist=sfcvm,cca,nc1d # UCVM conf file ucvmconf=/ccs/home/mei/scratch/TARGET_UCVM_SFCVM_mei/ucvm_install/conf/ucvm.conf # Gridding cell centered or vertex gridtype=CENTER # Spacing of cells spacing=100.0 # Projection proj=+proj=utm +datum=WGS84 +zone=10 rot=-53.9 x0=-121.9 y0=36.3 z0=0.0 # Number of cells along each dim (3000*1400*520=2,184,000,000) # x is mostly n-s,y is mostly e-w nx=3000 ny=1400 nz=520 # Partitioning of grid among processors (request px*py*pz processes in mpi submit) (8*8*8=512) # 3000/10 = 300 , 1400/10 = 140, 520/10 = 52 (10*10*10) # 3000/8 = 375 , 1400/8 = 175, 520/8 = 65 px=10 py=10 pz=10 # Vs/Vp minimum vp_min=0 vs_min=0 # Mesh and grid files, format meshfile=norcal_mesh gridfile=norcal_mesh.grid meshtype=SORD # Location of scratch dir scratch=./scratch
the output log,
[0] /lustre/orion/geo156/scratch/mei/test_sfcvm_mesh/./ucvm2mesh_mpi Version: 22.7.0 [0] Running on 1000 cores [0] Using config file ./norcal_mesh.conf [0] Configuration: [0] UCVM Model List: sfcvm,cca,nc1d [0] UCVM Conf file: /ccs/home/mei/scratch/TARGET_UCVM_SFCVM_mei/ucvm_install/conf/ucvm.conf [0] Gridtype: 0 [0] Querymode: 0 [0] Spacing: 100.000000 [0] Projection: +proj=utm +datum=WGS84 +zone=10 [0] Rotation Angle: -53.900000 [0] Origin x0,y0,z0: -121.900000, 36.300000, 0.000000 [0] Dimensions: 3000, 1400, 520 [0] Proc Dimensions: 10, 10, 10 [0] Vp Min: 0.000000, Vs Min: 0.000000 [0] Mesh File: norcal_mesh [0] Grid File: norcal_mesh.grid [0] Mesh Type: 4 [0] Scratch Dir: ./scratch [0] Initialization complete [0] Converting grid to latlong [0] Grid generation complete [0] Configuring UCVM [740] Allocating 42000 grid points [740] Partition dimensions: 300 x 140 x 52 [740] I,J,K start: 0, 560, 364 [740] I,J,K end: 300, 700, 416 ... [800] Extracted 2184000 points [860] Extracted 2184000 points [820] Extracted 2184000 points [0] Max Vp: 8451.263672 at [0] i,j,k : 1636, 739, 475 [0] Max Vs: 5028.872559 at [0] i,j,k : 2528, 1134, 305 [0] Max Rho: 3456.249756 at [0] i,j,k : 2528, 1134, 305 [0] Min Vp: 718.195862 at [0] i,j,k : 0, 433, 0 [0] Min Vs: 84.268837 at [0] i,j,k : 0, 433, 0 [0] Min Rho: 1600.008789 at [0] i,j,k : 0, 429, 0 [0] Min Ratio: 1.460094 at [0] i,j,k : 2987, 610, 0
Next: process for 4 corners
in $UCVM_SRC_PATH/src/ucvm2mesh
make grid4corners
run,
grid4corners norcal_mesh.grid 3000 1400
output,
Grid 4 corners: -121.899223 36.299894 (0) -120.013908 34.083659 (2999) -120.618201 37.024137 (4197000) -118.753975 34.789165 (4199999)
convert to 4 corners to umm, code is in cs242/src/latlon2utm using
snprintf(_projstr, 64, "+proj=utm +zone=%d +datum=NAD27 +units=m +no_defs", 10);
if (!(_geo2utm = proj_create_crs_to_crs(PJ_DEFAULT_CTX, "EPSG:4326", _projstr, NULL))) {
fprintf(stderr,"%s\n",(char *)proj_context_errno_string(PJ_DEFAULT_CTX, proj_context_errno(PJ_DEFAULT_CTX)));
return (1);
}
input format :
0, lon, lat 1, utm_e, utm_n
0 -121.899223 36.299894 0 -120.013908 34.083659 0 -120.618201 37.024137 0 -118.753975 34.789165
lon(-121.899223)lat(36.299894) => utm_e(598928.315878),utm_n(4017582.107443) lon(-120.013908)lat(34.083659) => utm_e(775627.918078),utm_n(3775266.509192) lon(-120.618201)lat(37.024137) => utm_e(711965.823647),utm_n(4100010.510239) lon(-118.753975)lat(34.789165) => utm_e(888665.421967),utm_n(3857694.945671)
Compose model data/config,
# # Phil's norcal_ucvm2mesh # # UTM Zone -- sfcvm,cca,nc1d utm_zone = 10 # Model directory, for 6 iterations model_dir = cs242 model_data_path = https://g-c662a6.a78b8.36fe.data.globus.org/ucvm/models #proj=+proj=utm +datum=WGS84 +zone=10 #rot=-53.9 #x0=-121.9 #y0=36.3 #z0=0.0 # Number of cells in x, y, and z. # tr # tl # # br # bl # # x is from top-left to bottom-left nx = 3000 ny = 1400 nz = 520 interpolation = on # Depth, in meters depth = 52000 depth_interval = 100 #Grid 4 corners: # -121.899223 36.299894 (0) # -120.013908 34.083659 (2999) # -120.618201 37.024137 (4197000) # -118.753975 34.789165 (4199999) # #lon(-121.899223)lat(36.299894) => utm_e(598928.315878),utm_n(4017582.107443) #lon(-120.013908)lat(34.083659) => utm_e(775627.918078),utm_n(3775266.509192) #lon(-120.618201)lat(37.024137) => utm_e(711965.823647),utm_n(4100010.510239) #lon(-118.753975)lat(34.789165) => utm_e(888665.421967),utm_n(3857694.945671) top_left_corner_e = 598928.315878 top_left_corner_n = 4017582.107443 bottom_left_corner_e = 775627.918078 bottom_left_corner_n = 3775266.509192 top_right_corner_e = 711965.823647 top_right_corner_n = 4100010.510239 bottom_right_corner_e = 888665.421967 bottom_right_corner_n = 3857694.94567 # Data Layout Parameters seek_axis = fast-Y seek_direction = top-down
Pack up a model tar ball,
