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 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.

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_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.