UCVM 13.9.0 User Guide

Overview

Released on September 8th, 2013, UCVM 13.9.0 represents the second major release of the Unified Community Velocity Model (UCVM) framework. UCVM is a collection of software utilities that are designed to make querying velocity models, building meshes, and visualizing velocity models easier to do through a uniform software interface. UCVM has been used extensively to generate meshes and e-trees that are then used for 3D wave propagation simulations within California.

The full feature list is as follows:

• Seamlessly combine two or more models into a composite model for querying
• Optionally include a California statewide geotechnical layer and interpolate it with the crustal velocity models
• Extract a 3D mesh or CVM Etree (octree) of material properties from any combination of models
• Standard California statewide elevation and Vs30 data map is provided
• Miscellaneous tools are provided for creating 2D etree maps, and optimizing etrees
• Numerically smooth discontinuities at the interfaces between different regional models
• Add support for future velocity models with the extendable interface

Currently, we support CVM-S4, CVM-H 11.9.1, CVM-S4.23, CenCal 0.8.0, and the Hadley-Kanamori as part of our automated installation package. Other models, such as SCEC CVM-NCI, Magistrale WFCVM, Graves Cape Mendocino, Lin-Thurber Statewide, and Tape SoCal are supported, however they will require a manual installation. We have also tested and include support for three major high-performance computing resources: NICS Kraken, TACC Stampede, and NCSA Blue Waters. It should work with other HPC machines as well.

The API itself is written entirely in C. We will show how to query UCVM through both C and Fortran in this user guide.

Finally, UCVM requires either Linux or OS X, GCC 4.3+, Python 2.5+, and an active internet connection to download and retrieve the models. For parallel mesh or e-tree extraction, the MPI libraries are also required. If you are installing UCVM on OS X, you must have the OS X Developer Tools (Xcode and Command Line Tools) and you must also have gfortran installed.

Installation Instructions

Easy Method

If you are installing UCVM on Linux or OS X and only need CVM-S4, CVM-H 11.9.1, CVM-S4.23, and/or CenCal, we strongly recommend following the easy installation method. Simply download UCVM 13.9.0 and run the following commands:

tar zxvf ucvm-13.9.0.tar.gz
cd ./UCVM
./ucvm_setup.py


You will then be asked a series of questions:

It looks like you are installing UCVM for the first time.
Where would you like UCVM to be installed?
(Default: /your/home/dir)>
Enter path or blank to use default:


Hit enter to use the default path or type your own. On high-performance computing resources you must change this path to be in the scratch or work directory so that UCVM can be seen by the compute nodes.

You will then be asked which models you'd like to download, such as:

Would you like to download and install CVM-S4?
Enter yes or no:


Enter "yes" (without quotation marks) or "no" if you would like to download this model or not.

After answering a few of these questions, UCVM will then begin the process of downloading and building the models you have requested. When the process is completed, you will be advised on how to test to verify that your installation is working and also any modifications that may be needed to your ~/.bash_profile.

Custom Method

Please see this page on how to install UCVM with models other than CVM-S4, CVM-H, CVM-S4.23, and CenCal.

Troubleshooting

Shared Library Paths

If you see an error similar to the following while running either the tests or the UCVM programs:

error while loading shared libraries: libsomelib.so: cannot open shared object file: No such file or directory

This indicates that UCVM was linked against one or more shared libraries and the dynamic library loader cannot find the actual .so library at run-time. The solution is to update your LD_LIBRARY_PATH to include the directory containing the library mentioned in the error message. For example, the following command adds a new search directory to LD_LIBRARY_PATH in a csh shell:

$ setenv LD_LIBRARY_PATH /home/USER/opt/somepkg/lib:${LD_LIBRARY_PATH}

By default, the ucvm_setup.py script uses static libraries. UCVM is only compiled dynamically if you pass ucvm_setup.py the "-d" option or if your system does not support static linking.

Proj. 4 Error: major axis or radius = 0 or not given

On systems with home filesystems that are not viewable to compute nodes (such as NICS Kraken), you may encounter errors with Proj.4 when trying to run any component of UCVM on compute nodes. This is due to the fact that Proj.4 actually relies on a file called proj_defs.dat which is located in the ${MAKE_INSTALL_LOCATION}/share/proj directory. So for example, suppose you had configured Proj.4 with ./configure --prefix=/not_viewable_to_compute_nodes/proj-4.7.0, Proj. 4 would then search for proj_defs.dat in /not_viewable_to_compute_nodes/proj-4.7.0/share/proj/proj_defs.dat. This will cause UCVM to throw the error "Proj.4 Error: major axis or radius = 0 or not given" and your job will fail.

The only way it seems to solve this issue is to actually make sure your --prefix directory is actually visible to the compute nodes and do a make install there. Documentation suggests that you can set the PROJ_LIB environment variable, however this seems to not work correctly without modifications to the Proj.4 source code.

API Examples

Fortran

Calling UCVM using Fortran is a relatively trivial procedure. After you have installed UCVM as per this user guide, you must include the UCVM library, the Proj.4 library, the e-tree library, as well as any velocity model libraries that you have compiled into UCVM. For CVM-H, please note that there are actually two libraries required: lvxapi and lgeo. Because the default convention for calling C programs from Fortran automatically appends an underscore to the end of the function name, you must turn that off via a flag called "fno-underscoring". This will make the Fortran compiler try and find foo() instead of foo_().
As an example, suppose we have a Fortran file, example.f, that calls UCVM. We have compiled UCVM with CVM-S and CVM-H. The code to compile example.f would be as follows:

gfortran example.f -o ./example -L/path/to/ucvm-13.9.0/lib -L./path/to/ucvm-13.9.0/model/cvms4/lib -L/path/to/ucvm-13.9.0/model/cvmh1191/lib -L/path/to/ucvm-13.9.0/lib/proj-4/lib -L/path/to/ucvm-13.9.0/lib/euclid3/libsrc -lucvm -lcvms -lvxapi -lgeo -lproj -letree -fno-underscoring

The basic structure of how to call UCVM within Fortran is outlined in the example below.

Example.f

                program example
         
        c       UCVM Configuration Location
                CHARACTER(LEN=80) ucvmconf
        c       Model Name
                CHARACTER(LEN=4) model 
        c       Number of points we're passing to ucvm_query
                INTEGER pts      
         
        c       The UCVM point data structure. 
        c       coord(1) is longitude
        c       coord(2) is latitutde
        c       coord(3) is depth
                TYPE :: ucvm_point_t
                       REAL*8 coord(3)
                END TYPE ucvm_point_t
         
        c       Generic property structure
        c       Source is where it comes from
        c       vp is P-wave velocity in m/s
        c       vs is S-wave velocity in m/s
        c       rho is density in kg/m^3
                TYPE :: ucvm_prop_t
                        INTEGER source
                        REAL*8 vp
                        REAL*8 vs
                        REAL*8 rho
                END TYPE ucvm_prop_t
         
        c       Returned data structure
                TYPE :: ucvm_data_t
                        REAL*8 surf
                        REAL*8 vs30
                        REAL*8 depth
                        INTEGER domain
                        REAL*8 shift_cr
                        REAL*8 shift_gtl
                        type(ucvm_prop_t) crust
                        type(ucvm_prop_t) gtl
                        type(ucvm_prop_t) cmb
                END TYPE ucvm_data_t
         
        c       For our example we'll query five points
                type(ucvm_point_t) point(5)
        c       And we'll get back five sets of material properties
                type(ucvm_data_t) returnData(5)
         
        c       Number of points is 5.
                pts = 5
         
        c       We'll start at -118, 34 at 0 depth and go down by 1000m
        c       each step
                do 10 i = 1, 5
                        point(i)%coord(1) = -118
                        point(i)%coord(2) = 34
                        point(i)%coord(3) = (i - 1) * 1000
        10      continue
         
        c       Where is our configuration file?
                ucvmconf = "/home/scec-01/davidgil/ucvm.conf" // CHAR(0)
         
        c       What model are we querying?
                model = "cvms"
         
        c       Initialize UCVM
                call ucvm_init(ucvmconf)
         
        c       Add the model to UCVM
                call ucvm_add_model(model)
         
        c       Query the model. Note that the number of points is passed
        c       by value, not reference.
                call ucvm_query(%VAL(pts), point, returnData)
         
                print *, model, " results for lon -118, lat 34"
         
        c       Print out the results.
                do 20 i = 1, 5
                        print *, "Depth ", (i - 1) * 1000
                        print *, "Vs ", returnData(i)%crust%vs 
                        print *, "Vp ", returnData(i)%crust%vp 
                        print *, "Rho ", returnData(i)%crust%rho
        20      continue
         
        c       Close UCVM now that we've queried the points 
                call ucvm_finalize()
         
                end

GCC Fortran 4.3+ is required for this example to work.