Difference between revisions of "CVM-T User Guide"

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Note: Options -d and -v are mutually exclusive. Specifying neither option instructs vx_lite to interpret the z coordinate as elevation offset from free surface.
 
Note: Options -d and -v are mutually exclusive. Specifying neither option instructs vx_lite to interpret the z coordinate as elevation offset from free surface.
  
−
The query data is printed to stdout, and this may be redirected to a file. The six sample point test shown below:
+
The query data is printed to stdout, and this may be redirected to a file. For the sample test points (./bin/test_data/test.dat) shown below:
  
−
  % ./vx_lite -s -v < ./test_data/test.data
+
  -125 35 -7777
 +
-118.56 32.55 -2450
 +
360061 3750229 -1400
 +
-118.52 34.12 -1400
 +
-116.40 32.34 -1000
 +
376592 3773379 -1770
 +
376592 3773379 -17700
 +
408669 3766189 -3000
  
−
Will generate this annotated output:
+
These may be submitted to vx_lite with this command:
 +
 
 +
% ./vx_lite -s -v < ./test_data/test.dat
 +
 
 +
The following annotated output will be produced:
  
 
       X              Y            Z      utmX        utmY      elevX      elevY      topo      mtop      base      moho  hr/lr/cm cellX    cellY    cellZ      tag        vp        vs      rho
 
       X              Y            Z      utmX        utmY      elevX      elevY      topo      mtop      base      moho  hr/lr/cm cellX    cellY    cellZ      tag        vp        vs      rho

Revision as of 20:10, 1 November 2010

CVM-H

Requirements

None.


Installation

  • The package is built by executing the following make command from the root directory:
% make clean;make all


Utilities

The following executable utilities are provided:

vx
Original interface to Harvard's model. Accepts lon/lat/elev points from stdin and prints material properties to stdout. The original user guide can be found here (TBD).
vx_lite
Updated interface to Harvard's model that supports optional 1D background, Vs30 derived GTL, and querying by depth. Accepts lon/lat/z points from stdin and prints material properties to stdout.
vx_slice
Visualization utility for extracting a 2D horizontal slice of Vp, Vs, or Rho (density) from the model, suitable for plotting with a graphics package.


Querying for SoCal Material Properties

The command line format for vx_lite is as follows: 

% vx_lite [-s] [-d] [-v] [< input_coords]

where the options:

-s
Instructs use of SCEC 1D background model
-d
Interpret z coordinate as depth from free surface
-v
Interpret z coordinate as elevation
input_coords
3D point specified as either (lon, lat, z (meters)) or (easting, northing, z (meters)), space delimited. Input coordinates can be specified interactively or redirected to stdin from a file.

Note: Options -d and -v are mutually exclusive. Specifying neither option instructs vx_lite to interpret the z coordinate as elevation offset from free surface.

The query data is printed to stdout, and this may be redirected to a file. For the sample test points (./bin/test_data/test.dat) shown below: 

-125 35 -7777
-118.56 32.55 -2450
360061 3750229 -1400
-118.52 34.12 -1400
-116.40 32.34 -1000
376592 3773379 -1770
376592 3773379 -17700
408669 3766189 -3000

These may be submitted to vx_lite with this command: 

% ./vx_lite -s -v < ./test_data/test.dat

The following annotated output will be produced: 

     X               Y             Z       utmX        utmY      elevX       elevY      topo      mtop      base      moho  hr/lr/cm cellX     cellY     cellZ       tag        vp        vs       rho
  -125.000000       35.000000  -7777.00 -230844.88  3902223.73  -99999.00   -99999.00      0.00      0.00 -99999.00 -99999.00 bk  -99999.00   -99999.00 -99999.00     14.00   6300.00   3637.31   2859.77
  -118.560000       32.550000  -2450.00  353525.18  3602285.14  353625.00  3602375.00  -1114.91  -1150.00  -1327.54 -21571.67 lr  354000.00  3602000.00  -2400.00      2.00   5575.15   3132.10   2631.81
360061.000000  3750229.000000  -1400.00  360061.00  3750229.00  360125.00  3750125.00    -56.93    -50.00  -1404.07 -24868.83 lr  360000.00  3750000.00  -1400.00      2.00   4554.52   2313.56   2469.78
  -118.520000       34.120000  -1400.00  359819.67  3776309.78  359875.00  3776375.00    491.46    450.00     38.42 -28061.40 lr  360000.00  3776000.00  -1400.00      2.00   5066.61   2916.30   2545.10
  -116.400000       32.340000  -1000.00  556464.74  3578092.46  556375.00  3578125.00    780.43    750.00    616.39 -31413.62 lr  556000.00  3578000.00  -1000.00      2.00   5372.79   3024.30   2595.55
376592.000000  3773379.000000  -1770.00  376592.00  3773379.00  376625.00  3773375.00     99.38    100.00  -2374.53 -28165.35 hr  376552.25  3773500.00  -1800.00      3.00   4181.37   2432.22   2418.45
376592.000000  3773379.000000 -17700.00  376592.00  3773379.00  376625.00  3773375.00     99.38    100.00  -2374.53 -28165.35 cm  380000.00  3770000.00 -18000.00      2.00   6533.31   3776.40   2841.47
408669.000000  3766189.000000  -3000.00  408669.00  3766189.00  408625.00  3766125.00     93.89     50.00  -2820.45 -29799.86 hr  408552.25  3766250.00  -3000.00      2.00   4997.06   2889.03   2534.30


Known Issues

None.


cvm2mesh

Requirements

integer, parameter :: ibig = 10000000

# CVM-4 Makefile
all: cvm4_txt cvm4_bin cvm4_mpi
cvm4_txt: cvm4.f iotxt.f
       gfortran -Wall -O3 cvm4.f iotxt.f -o cvm4_txt
cvm4_bin: cvm4.f iobin.f
       gfortran -Wall -O3 cvm4.f iobin.f -o cvm4_bin
cvm4_mpi: cvm4.f iompi.f
       gfortran -Wall -O3 cvm4.f iobin.f -o cvm4_mpi
clean:
       rm *.o *~ cvm4_txt cvm4_bin cvm4_mpi


Installation

  • If you wish to extract meshes from CVM-4, it must be installed (see requirements).
  • Update ./src/Makefile with paths to the CVM-H library libvxapi.a and system compilers. Execute 'make' to build all meshing executables.


Generating a Mesh

Prepatory steps

  • Determine meshing region, projection to use (CMU or UTM), and desired dimensions.
  • Determine if CVM can be pre-staged before the job executes. One copy of each CVM (model, extraction binary) is required per core in the MPI extraction job. Some computing resources (jaguar, kraken, ranger) have a permanent scratch space where these CVMs may be staged before the job executes, while others (USC HPCC) have sratch space that exists only while the job is in progress.
    • If CVM pre-staging is possible and desired, copy N copies of the CVM to your scratch space. Example pbs scripts which perform this task can be found in ./pbs.


Create extraction configuration file

Create extraction configuration file that defines the following properties:

cvmtype
CVM4 or CVMH
cvmdir
Root directory containing pre-staged CVM if using that option, or CVM install directory that mesh-create-MPI will use to stage the data itself
spacing
grid spacing in meters
proj
UTM or CMU
rot
rotation angle in degrees, only used in UTM mode
lon
longitude of SW corner of mesh box
lat
latitude of SW corner of mesh box
dep
starting depth in km from free surface
x-size
length along x-axis in km
y-size
length along y-axis in km
z-size
length along z-axis in km. NOTE: Ensure (z-size/spacing) is equally divisible by your anticipated number of cores
vp_min
vp to assign when model vs < vs_min in m/s
vs_min
vs to assign when model vs < vs_min in m/s
outputfile
Name of final mesh file
format
Output format, IJK-12, IJK-20, IJK-32, SORD

The following is an example configuration file: 

# Example cvm2mesh config file for IJK12 CVM4 extraction
cvmtype=CVM4
cvmdir=/lustre/widow1/scratch/spatrick/tmp/cvm4
spacing=80
proj=UTM
rot=-45.42589966
lon=-122.500798753
lat=35.796092162
dep=0
x_size=810
y_size=400
z_size=84.8
vp_min=0
vs_min=0
outputfile=/lustre/widow1/proj/geo008/yfcui/w2w1hz40m_SN_cvmH/input/mesh_m8_cvm4_ijk12_1hz
meshtype=IJK-12


Create PBS job submission script

There are many examples in the ./pbs directory. The general command-line format for mesh-create-MPI is as follows: 

./mesh-create-MPI [-i input_cvm_dir] [-o output_mesh_file] -f mesh_params.conf

where the options -i and -o are used for optional staging in of the CVM and stage out of the final mesh:

-i
Option instructing mesh-create-MPI to stage in NUM_CORES copies of the CVM from the directory specified in the option argument into the scratch directory specified by the cvmdir keyword in the configuration file. Each copy will be placed in cvmdir/# where # is the rank number (0 to NUM_CORES-1). Useful on systems with temporary scratch space.
-o
Option instructing mesh-create-MPI to stage out the mesh file from scratch space to a permanent directory. The scratch space mesh file name is specified by the outputfile keyword in the configuration file, an the final stage out mesh file is specified by the option argument. Useful on systems that employ temporary scratch space.


Submit Extraction Job to Job Scheduler

System dependent, but generally accomplished with the qsub command: 

% qsub example_extract_mesh.pbs


Check Mesh for Correctness

  • Check for correct size of the mesh file (for IJK-12, x-size/spacing * y-size/spacing * z-size/spacing * 4 bytes/float * 3 floats)
  • Perform octal dump on file to sanity check values:
% od -f mesh_file | more
  • Visualize slices with viz-cvm


Known Issues

None.


cvmtest

Requirements


Installation

TBD

Running the Existing Chino Hills scenario with CVM-H

TBD

Known Issues

None.


viz-cvm

The viz-cvm package contains scripts for plotting slices and profiles from either CVM-H, CVM-4, or 3D meshes.


Requirements

integer, parameter :: ibig = 10000000

# CVM-4 Makefile
all: cvm4_txt cvm4_bin cvm4_mpi
cvm4_txt: cvm4.f iotxt.f
       gfortran -Wall -O3 cvm4.f iotxt.f -o cvm4_txt
cvm4_bin: cvm4.f iobin.f
       gfortran -Wall -O3 cvm4.f iobin.f -o cvm4_bin
cvm4_mpi: cvm4.f iompi.f
       gfortran -Wall -O3 cvm4.f iobin.f -o cvm4_mpi
clean:
       rm *.o *~ cvm4_txt cvm4_bin cvm4_mpi


Installation

  • If you wish to plot slices from CVM-H/CVM-4, the CVMs must be installed (see requirements).
  • Within your CVM-4 installation directory, install the following shell script, run_cvm4_gely.sh:
#!/bin/bash
# CVM-4 helper script that abstracts stdin, stdout redirection
IN_FILE=$1
OUT_FILE=$2
CVMBIN=cvm_txt
./${CVMBIN} < ${IN_FILE} > ${OUT_FILE}
if [ $? -ne 0 ]; then
    exit 1
fi
exit 0

An equivalent script for CVM-H is already present in the official CVM-H distribution.

  • Update CVM-H/CVM-4 installation paths in Slice.py
# CVM Constants
cvmh_dir = '/home/rcf-104/patrices/cvmh/trunk/bin'
cvmh_bin = './run_vx_lite.sh'
cvm4_dir = '/home/rcf-104/patrices/utils/cvm4_gely'
cvm4_bin = 'run_cvm4_gely.sh'


Plotting from a CVM

Supported plot types include horizontal slices from either CVM, horizontal difference (CVM-H - CVM-4) slice, and profile slices from either CVM or both. 

./Slice.py <map_type> <outfile> <map_params>

where:

map_type
hor/prof/hordiff
outfile
Name of PNG plot
map_params
with hor map_type: depth, value_type, source (CVM-H, CVM-4, Both)
with hordiff map_type: depth, value_type
with prof map_type: lon1, lat1, lon2, lat2, value_type, source (CVM-H, CVM-4, Both)
value_type
Vp, Vs, Rho, Topo, Vs30, Z2500


Plotting from a mesh

Supported plot types include horizontal slices and profile slices from either SORD or AWP formatted meshes. 

./PlotGrid.py <map_type> <mesh_file> <outfile> <title> <map_params>

where:

map_type
hor, prof
mesh_file
Name of the SORD or AWP formatted mesh.
outfile
Name of PNG plot
title
Title for the plot
map_params
with hor map_type: k_offset, imax, jmax, kmax, decimation, source, value_type
with prof map_type: imax, jmax, kmax, p1_x, p1_y, p2_x, p2_y, depth, decimation, source, value_type
value_type
Vp, Vs, Rho
source
IJK-32, IJK-20, IJK-12, SORD


Known Issues

Small scale slices or highly decimated slices may take on a pixellated look. This is due to a low pixel density in the plots. The work-around is to reduce the decimation factor or increase the size of the slice.

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