UCVM Command Reference
UCVM Command Reference (v15.10.0)
Contents
UCVM Software Collection
The UCVM software is a software framework that builds on top of several existing scientific software packages, including CVM-H, CVM-S4, and the USGS Bay Area Model. The UCVM installation process involves first compiling the individual CVM programs, and then compiling and installed the UCVM framework.
The UCVM installation process involves two code directory trees, the src tree, and the bin tree. UCVM source codes and models are collected in the src directory tree. When UCVM is built, it is installed into a separate directory location, called the bin directory tree. Once UCVM is correctly built and installed, user configure their computing environment to point to the bin directory. All supported UCVM commands are contained in the UCVM bin tree.
Command Reference Conventions
We base our instructions and documentation assuming a standard open source software environment.
Default installation operating system is a 2015 or later Linux distribution with Python 2.7, multiple packages, gnu c and fortran compilers.
Default user shell is a bash shell and our documentation.
We will call the bin directory tree $UCVM_HOME_DIR in the command descriptions below:
UCVM commands are located in the bin tree, in several directories including $UCVM_HOME_DIR/bin, /tests, /utilities, /scripts
/bin
- basin_query
- ecoalesce
- ecompact
- grd2etree
- grd_query
- mesh-check
- mesh-op
- mesh-strip-ijk
- patchmodel
- run_grd.sh
- run_ucvm.sh
- ssh_generate
- ssh_merge
- ucvm2etree
- ucvm2mesh
- ucvm_query
- vs30_query
basin_query
UCVM(1) BSD General Commands Manual UCVM(1)
NAME
basin_query
SYNOPSIS
basin_query [-h] [-f config-file] [-m model] [-v vs-threshold]
[-p usermap] [-z zmin,zmax] [-d max-depth] [-i interval] < file.in
DESCRIPTION
The command basin_query allows you to retrieve the depth at which
vs-threshold is first crossed. By default, vs-threshold is set to be
1000m/s, but that can easily be changed.
Common Paramters
-f Location of the UCVM configuration file. Typically, this is
../conf/ucvm.conf.
-m Model to query. Usually model is either cvms, cvmh, cvmsi, or
cencal.
-v Vs threshold to use. By default this is 1000m/s, but other com-
mon values include 2500m/s and 3000m/s.
Less Used Parameters
-p Custom vs30 and elevation map location.
-z Custom depth range for GTL/crust interpolation.
-d Maximum depth, in meters, to search. Default is 15000m.
-i Interval, in meters, go go by when searching for the depth.
Default is 20m. So basin_query will get the Vs value at 0m, 20m, 40m, and so on.
EXAMPLE
basin_query -f ../conf/ucvm.conf -m cvms -v 2500
Input: -118 34 Ctrl-D
Output: -118.0000 34.0000 4780.000 4780.000
SEE ALSO
ucvm_query(1)
Linux December 3, 2016 Linux
ecoalesce
UCVM(1) BSD General Commands Manual UCVM(1)
NAME
ecoalesce
SYNOPSIS
ecoalesce [-h] input output
DESCRIPTION
The command ecoalesce helps compact an e-tree file that conforms either
to CMU or SCEC standards. It does this by replacing eight adjacent
octants with identical material properties at level N with a single
octant containing the same material properties at level N-1. Usually,
this command is run with ecompact as well.
Common Paramters
-h Shows the help message.
input E-tree input file. Typically, this was just extracted with the
ucvm2etree utilities.
output Compacted e-tree output.
EXAMPLE
ecoalesce chino_hills.etree compacted_chino_hills.etree
SEE ALSO
ecompact(1), ucvm2etree(1), ucvm2etree-extract-MPI(1),
ucvm2etree-merge-MPI(1), ucvm2etree-sort-MPI(1)
Linux December 3, 2016 Linux
ecompact
UCVM(1) BSD General Commands Manual UCVM(1)
NAME
ecompact
SYNOPSIS
ecompact [-h] input output
DESCRIPTION
The command ecompact helps compact an e-tree file that conforms either to
CMU or SCEC standards. It does this by removing empty space in the Etree
data structure. Usually, this command is run with ecoalesce as well.
Common Paramters
-h Shows the help message.
input E-tree input file. Typically, this was just extracted with the
ucvm2etree utilities.
output Compacted e-tree output.
EXAMPLE
ecompact chino_hills.etree compacted_chino_hills.etree
SEE ALSO
ecoalesce(1), ucvm2etree(1), ucvm2etree-extract-MPI(1),
ucvm2etree-merge-MPI(1), ucvm2etree-sort-MPI(1)
Linux December 3, 2016 Linux
grd_query
UCVM(1) BSD General Commands Manual UCVM(1)
NAME
grd_query
SYNOPSIS
grd_query [-h] [-e] [-v] -d datadir [-b bkgdir] < file.in
DESCRIPTION
The command grd_query queries data from a set of ArcGIS grid files in
GridFloat format.
-h Shows the help message.
-e Employ GRD bathymetry heuristic.
-v Employ GRD vs30 heuristic.
-d Main ArcGIS Gridfloat data directory. Default is ./ned.
-b Background/Bathymetry data directory. Default is ./bath.
EXAMPLE
Input format is:
lon lat
Output format is:
lon lat val valid
SEE ALSO
grd2etree(1)
Linux December 3, 2016 Linux
grd2etree
UCVM(1) BSD General Commands Manual UCVM(1)
NAME
grd2etree
SYNOPSIS
grd2etree [-h] -f config
DESCRIPTION
The command grd2etree extracts a SCEC-formatted Etree map from a set of
DEM and Vs30 grid files in ArcGIS Gridfloat format.
Common Paramters
-h Shows the help message.
-f Specifies the location of the configuration file to use.
EXAMPLE
grd2etree -f ./grd2float_sample.conf
Where grd2float_sample.conf looks like:
# grd2etree UCM Map config file
# Domain corners coordinates (degrees): proj=+proj=aeqd +lat_0=36.0
+lon_0=-120.0 +x_0=0.0 +y_0=0.0 lon_0=-129.75 lat_0=40.75 rot=55.0
# Domain dimensions (meters): x-size=1800000.0 y-size=900000.0
# Spacing spacing=250.0
# Etree parameters and info title=UCVM_Elev_Vs30_Map_Wills_Wald
author=P_Small date=05/2011 outputfile=../../model/ucvm/ucvm.e
# Grid data directories elev_hr_dir=/home/scec-00/USER/opt/ned
elev_lr_dir=/home/scec-00/USER/opt/bath
vs30_hr_dir=/home/scec-00/USER/opt/vs30/wills_gridfloat
vs30_lr_dir=/home/scec-00/USER/opt/vs30/wald_gridfloat
SEE ALSO
grd_query(1)
Linux December 3, 2016 Linux
mesh-check
UCVM(1) BSD General Commands Manual UCVM(1)
NAME
mesh-check
SYNOPSIS
mesh-check input format
DESCRIPTION
The command mesh-check does a basic quality assurance check of a mesh
file. It checks to make sure that each record in the file is of the cor-
rect size. Furthermore, it checks to make sure that each value is not
NaN, infinity, or negative.
input The input mesh to check.
format The mesh format. Can be either IJK-12, IJK-20, or IJK-32
EXAMPLE
mesh-check new_mesh.mesh IJK-12
SEE ALSO
mesh-op(1), mesh-strip-ijk(1)
Linux December 3, 2016 Linux
mesh-op
UCVM(1) BSD General Commands Manual UCVM(1)
NAME
mesh-op
SYNOPSIS
mesh-op op inmesh1 inmesh2 format outmesh
DESCRIPTION
The command mesh-op subtracts inmesh2 from inmesh1 and outputs the dif-
ference to outmesh.
op The operation. Currently the only supported operation is "diff".
inmesh1 The first mesh to read.
inmesh2 The second mesh to read.
format Supported formats include IJK-12, IJK-20, and IJK-32.
outmesh The mesh that represents inmesh1 - inmesh2.
EXAMPLE
mesh-op diff ./inmesh1 ./inmesh2 IJK-12 ./outmesh
SEE ALSO
mesh-check(1), mesh-strip-ijk(1)
Linux December 3, 2016 Linux
mesh-strip-ijk
UCVM(1) BSD General Commands Manual UCVM(1)
NAME
mesh-strip-ijk
SYNOPSIS
mesh-strip-ijk inmesh format outmesh
DESCRIPTION
The command mesh-strip-ijk converts an IJK-20 or IJK-32 mesh, inmesh, to
an IJK-12 formatted mesh, outmesh.
inmesh The input mesh in IJK-20 or IJK-32 format.
format The format of the input mesh (IJK-20 or IJK-32).
outmesh The resulting IJK-12 mesh.
EXAMPLE
mesh-strip-ijk ijk20_mesh IJK-20 output_mesh
SEE ALSO
mesh-check(1), mesh-op(1)
Linux December 3, 2016 Linux
ucvm2etree-extract-MPI.txt
UCVM(1) BSD General Commands Manual UCVM(1)
NAME
ucvm2etree-extract-MPI
SYNOPSIS
ucvm2etree-extract-MPI [-h] -f config
DESCRIPTION
Notice: This command is intended to be run as a MPI job (e.g. mpirun
./ucvm-extract-MPI). Please do not attempt to run it as a regular
process.
The command ucvm2etree-extract-MPI extracts components of an e-tree from
the specifications in a given configuration file, config.
Specifically, it divides the etree region into C columns for extraction.
This is an embarrassingly parallel operation. A dispatcher (rank 0) farms
out each column to a worker in a pool of N cores for extraction. Each
worker queries UCVM for the points in its column and writes a flat-file
formatted etree. After program execution, there are N sub-etree files,
each locally unsorted. The extractor must be run on 2^Y + 1 cores where
Y>0 and (2^Y) < C. The output flat file format is a list of octants(24
byte addr, 16 byte key, 12 byte payload) in arbitrary Z-order.
Since the number of points in a column depends on the minimum Vs values
within that column, some columns will have high octant counts and others
will have very low octant counts. Having sub-etrees that vary greatly in
size is not optimal for the sorting operations that follow, so
ucvm2etree-extract-MPI implements a simple octant balancing mechanism.
When a worker has extracted more than X octants (the default 16M
octants), it reports to the dispatcher that it cannot extract any more
columns and terminates. This strategy approximately balances the sub-
etrees so that they may be loaded into memory by ucvm2etree-sort-MPI. In
the case of very large extractions where the dispatcher reports that all
workers have reported they are full yet columns remain to be extracted,
increase the job size by a factor of 2 until there is room for all the
columns.
You would typically run this command, followed by ucvm2etree-sort-MPI and
ucvm2etree-merge-MPI.
-h Displays the help message.
-f Uses configuration file, config.
EXAMPLE
mpirun -np 768 ucvm2etree-extract-MPI -f ./ucvm2etree_example.conf
Where ucvm2etree_example.conf is:
# Domain corners coordinates (clockwise, degrees):
proj=geo-bilinear
lon_0=-119.288842
lat_0=34.120549
lon_1=-118.354016
lat_1=35.061096
lon_2=-116.846030
lat_2=34.025873
lon_3=-117.780976
lat_3=33.096503
# Domain dimensions (meters):
x-size=180000.0000
y-size=135000.0000
z-size=61875.0000
# Blocks partition parameters:
nx=32
ny=24
# Max freq, points per wavelength, Vs min
max_freq=0.5
ppwl=4.0
vs_min=200.0
# Max allowed size of octants in meters
max_octsize=10000.0
# Etree parameters and info
title=ChinoHills_0.5Hz_200ms
author=D_Gill
date=05/2011
outputfile=./cmu_cvmh_chino_0.5hz_200ms.e
format=etree
# UCVM parameters
ucvmstr=cvms
ucvm_interp_zrange=0.0,350.0
ucvmconf=../../conf/kraken/ucvm.conf
# Scratch
scratch=/lustre/scratch/scecdave/scratch
#
# Buffering parameters used by MPI version only
#
# Etree buffer size in MB
buf_etree_cache=128
# Max octants to buffer for flat file during extraction
buf_extract_mem_max_oct=4194304
# Max octants to save in flat file before reporting full during extrac-
tion
buf_extract_ffile_max_oct=16000000
# Max octants to read from input flat file during sorting
buf_sort_ffile_max_oct=20000000
# Minimum number of octants between reports during merging
buf_merge_report_min_oct=10000000
# MPI send/recv octant buffer size during merging
buf_merge_sendrecv_buf_oct=4096
# Etree read/write octant buffer size during merging
buf_merge_io_buf_oct=4194304
SEE ALSO
ucvm2etree-sort-MPI(1), ucvm2etree-merge-MPI(1), ucvm2etree(1)
Linux December 3, 2016 Linux
ucvm_query
UCVM(1) BSD General Commands Manual UCVM(1)
NAME
ucvm_query
SYNOPSIS
ucvm_query [-h] [-f config] [-m model] [-c coordtype] [-p map] [-v]
[-z zmin,zmax]
DESCRIPTION
The command ucvm_query queries an installed velocity model to retreive
its material properties at a particular latitude and longitude.
Any set of crustal and GTL velocity models may be selected and queried in
order of preference. Points may be queried by (lon,lat,dep) or
(lon,lat,elev) and the coordinate conversions for a particular model are
handled transparently.
Common Paramters
-h Displays the help message.
-f Location of the configuration file, config, that tells the pro-
gram which velocity models are installed.
-m A comma-separated list of models to query.
Less Used Parameters
-c Z-coordinate mode. Geo-depth (default) is "gd", but queries can
also be done by elevation as specified by "ge".
-p User-defined map of vs30 and elevation data.
-v Display model version information only.
-z Specifies depth range for gtl/crust interpolation.
EXAMPLE
ucvm_query -f ../conf/ucvm.conf -m cvms
Input format is:
lon lat Z
Output format is:
lon lat Z surf vs30 crustal cr_vp cr_vs cr_rho gtl gtl_vp gtl_vs
gtl_rho cmb_algo cmb_vp cmb_vs cmb_rho
If running in interactive mode, please use Ctrl-D to end the input.
SEE ALSO
basin_query(1)
Linux December 3, 2016 Linux
