CVM-T User Guide

cvm2mesh

Requirements

• SCEC CVM-H https://source.usc.edu/svn/cvmh
• SCEC CVM-4 [Optional] http://earth.usc.edu/~gely/coseis/www/index.html Set ibig var in newin.h to 9,000,000+ and recompile using the following Makefile.

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 scratch 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, 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

# 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
• Submit extraction job to job scheduler
• Check mesh for correctness

viz-cvm

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

Requirements

• Python 2.6+, with numpy, matplotlib, and basemap modules
• SCEC CVM-4 [Optional] http://earth.usc.edu/~gely/coseis/www/index.html Set ibig var in newin.h to 9,000,000+ and recompile using the following Makefile.

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

• SCEC CVM-H [Optional] https://source.usc.edu/svn/cvmh

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_parameters>

where:

• map_type: hor/prof/hordiff
• outfile: Name of PNG plot
• hor map_parameters: depth, value_type, source (CVM-H, CVM-4, Both)
• hordiff map_parameters: depth, value_type
• prof map_parameters: 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
• hor map_parameters: k_offset, imax, jmax, kmax, decimation, source, value_type
• prof map_parameters: 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.