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. There are many examples in the ./pbs directory. The generate 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
• Check mesh for correctness

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

• 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.