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Running the Mesher xmeshfem3D

You are now ready to compile the mesher. In the directory with the source code, type ‘make meshfem3D’. If all paths and flags have been set correctly, the mesher should now compile and produce the executable xmeshfem3D. Note that all compiled executables are placed into the directory bin/. To run the executables, you must call them from the root directory, for example type ‘mpirun -np 64 ./bin/meshfem3D‘ to run the mesher in parallel on 64 CPUs. This will allow the executables to find the parameter file Par_file in the relative directory location ./DATA.

Input for the mesher (and the solver) is provided through the parameter file Par_file, which resides in the subdirectory DATA. Before running the mesher, a number of parameters need to be set in the Par_file. This requires a basic understanding of how the SEM is implemented, and we encourage you to read Komatitsch and Vilotte (1998; Komatitsch and Tromp 1999, 2002a, 2002b; Chaljub 2000; Komatitsch, Ritsema, and Tromp 2002; Chaljub, Capdeville, and Vilotte 2003; Capdeville et al. 2003) and Chaljub and Valette (2004). A detailed theoretical analysis of the dispersion and stability properties of the SEM is available in Cohen (2002), De Basabe and Sen (2007) and Seriani and Oliveira (2007).

In this chapter we will focus on simulations at the scale of the entire globe. Regional simulations will be addressed in Chapter [cha:Regional-Simulations]. The spectral-element mesh for a SPECFEM3D_GLOBE simulation is based upon a mapping from the cube to the sphere called the cubed sphere (Sadourny 1972; Ronchi, Ianoco, and Paolucci 1996). This cubed-sphere mapping breaks the globe into 6 chunks, each of which is further subdivided in terms of $n^{2}$ mesh slices, where $n\ge1$ is a positive integer, for a total of $6\times n^{2}$ slices (Figure [figure:mpi_slices]). Thus the minimum number of processors required for a global simulation is 6 (although it is theoretically possible to run more than one slice per processor).

Figure: image

To run the mesher for a global simulation, the following parameters need to be set in the Par_file (the list below might be slightly obsolete or incomplete; for an up-to-date version, see comments in the default Par_file located in directory DATA:

SIMULATION_TYPE
is set to 1 for forward simulations, 2 for adjoint simulations for sources (see Section [sec:Adjoint-simulation-sources]) and 3 for kernel simulations (see Section [sec:Finite-Frequency-Kernels]).

SAVE_FORWARD
is only set to .true. for a forward simulation with the last frame of the simulation saved, as part of the finite-frequency kernel calculations (see Section [sec:Finite-Frequency-Kernels]). For a regular forward simulation, leave SIMULATION_TYPE and SAVE_FORWARD at their default values.

NCHUNKS
must be set to 6 for global simulations.

ANGULAR_WIDTH_XI_IN_DEGREES
Not needed for a global simulation. (See Chapter [cha:Regional-Simulations] for regional simulations.)

ANGULAR_WIDTH_ETA_IN_DEGREES
Not needed for a global simulation. (See Chapter [cha:Regional-Simulations] for regional simulations.)

CENTER_LATITUDE_IN_DEGREES
Not needed for a global simulation. (See Chapter [cha:Regional-Simulations] for regional simulations.)

CENTER_LONGITUDE_IN_DEGREES
Not needed for a global simulation. (See Chapter [cha:Regional-Simulations] for regional simulations.)

GAMMA_ROTATION_AZIMUTH
Not needed for a global simulation. (See Chapter [cha:Regional-Simulations] for regional simulations.)

NEX_XI
The number of spectral elements along one side of a chunk in the cubed sphere (see Figure [figure:mpi_slices]); this number must be a multiple of 16 and 8 $\times$ a multiple of $\nprocxi$ defined below. We do not recommend using $\nexxi$ less than 64 because the curvature of the Earth cannot be honored if one uses too few elements, and distorted elements can lead to inaccurate and unstable simulations, i.e., smaller values of $\nexxi$ are likely to result in spectral elements with a negative Jacobian, in which case the mesher will exit with an error message. Table [table:nex] summarizes various suitable choices for $\nexxi$ and the related values of $\nprocxi$. Based upon benchmarks against semi-analytical normal-mode synthetic seismograms, Komatitsch and Tromp (2002a, 2002b) determined that a $\nexxi=256$ run is accurate to a shortest period of roughly 17 s. Therefore, since accuracy is determined by the number of grid points per shortest wavelength, for any particular value of $\nexxi$ the simulation will be accurate to a shortest period determined approximately by $$\mbox{shortest period (s)}\simeq(256/\nexxi)\times17.\label{eq:shortest_period}$$ The number of grid points in each orthogonal direction of the reference element, i.e., the number of Gauss-Lobatto-Legendre points, is determined by NGLLX in the constants.h file. In the globe we use $\mbox{\texttt{NGLLX}}=5$, for a total of $5^{3}=125$ points per elements. We suggest not to change this value.

NEX_ETA
For global simulations $\nexeta$ must be set to the same value as $\nexxi$.

NPROC_XI
The number of processors or slices along one chunk of the cubed sphere (see Figure [figure:mpi_slices]); we must have $\nexxi=8\times c\times\nprocxi$, where $c\ge1$ is a positive integer. See Table [table:nex] for various suitable choices.

NPROC_ETA
For global simulations $\nproceta$ must be set to the same value as $\nprocxi$.

MODEL
Must be set to one of the following:

1D models with real structure:
1D_isotropic_prem
Isotropic version of the spherically symmetric Preliminary Reference Earth Model (PREM) (Dziewoński and Anderson 1981).

1D_transversely_isotropic_prem
Transversely isotropic version of PREM.

1D_iasp91
Spherically symmetric isotropic IASP91 model (Kennett and Engdahl 1991).

1D_1066a
Spherically symmetric earth model 1066A (Gilbert and Dziewoński 1975). When ATTENTUATION is on, it uses an unpublished 1D attenuation model from Scripps.

1D_ak135f_no_mud
Spherically symmetric isotropic AK135 model (Kennett, Engdahl, and Buland 1995) modified to use the density and Q attenuation models of (Montagner and Kennett 1995). That modified model is traditionally called AK135-F, see http://rses.anu.edu.au/seismology/ak135/ak135f.html for more details. As we do not want to use the 300 m-thick mud layer from that model nor the ocean layer, above the d120 discontinuity we switch back to the classical AK135 model of (Kennett, Engdahl, and Buland 1995), i.e., we use AK135-F below and AK135 above.

1D_ref
A 1D Earth model developed by Kustowski, Dziewoński, and Ekstrom (2006). This model is the 1D background model for the 3D models s362ani, s362wmani, s362ani_prem, and s29ea.

1D_CCREM
A 1D Earth model developed by Ma and Tkalcic (2021) called CCREM: a new reference Earth model from the global coda-correlation wavefield.

Ishii
Combines the 1D transversely isotropic PREM with the anisotropic inner core model defined by Ishii et al. (2002).

for Mars:

1D_Sohl
1D Mars model developed by Sohl and Spohn (1997). This model is model A, mostly constrained by geophysical moment of inertia.

1D_case65TAY
1D Mars reference model developed by Plesa et al. (2021). The model is the 1D reference model for case 65 with a compositional model by Taylor.

mars_1D
1D Mars model as defined in file mars_1D.dat in folder DATA/mars.

for Moon:

VPREMOON
1D Moon model developed by Garcia et al. (2011). Uses modified seismic model, starting from table 6 (left side, not geodesic model) with velocity values for outer core and solid inner core based on Weber et al. (2011)

For historical reasons and to provide benchmarks against normal-mode synthetics, the mesher accommodates versions of various 1D models with a single crustal layer with the properties of the original upper crust. These ‘one-crust’ models are:

  1D_isotropic_prem_onecrust
  1D_transversely_isotropic_prem_onecrust
  1D_iasp91_onecrust
  1D_1066a_onecrust
  1D_ak135f_no_mud_onecrust

Fully 3D models:
transversely_isotropic_prem_plus_3D_crust_2.0
This model has CRUST2.0 (Bassin, Laske, and Masters 2000) on top of a transversely isotropic PREM. We first extrapolate PREM mantle velocity up to the surface, then overwrite the model with CRUST2.0

s20rts
By default, the code uses 3D mantle model S20RTS (Ritsema, Van Heijst, and Woodhouse 1999) and 3D crustal model Crust2.0 (Bassin, Laske, and Masters 2000). Note that S20RTS uses transversely isotropic PREM as a background model, and that we use the PREM radial attenuation model when ATTENUATION is incorporated. See Chapter [cha:-Changing-the] for a discussion on how to change 3D models.

s40rts
A global 3D mantle model (Ritsema et al. 2011) succeeding S20RTS with a higher resolution. S40RTS uses transversely isotropic PREM as a backgroun model and the 3D crustal model Crust2.0 (Bassin, Laske, and Masters 2000). We use the PREM radial attenuation model when ATTENUATION is incorporated.

s362ani
A global shear-wave speed model developed by Kustowski, Dziewoński, and Ekstrom (2006). In this model, radial anisotropy is confined to the uppermost mantle. The model (and the corresponding mesh) incorporate tomography on the 650 km and 410 km discontinuities in the 1D reference model REF.

s362wmani
A version of S362ANI with anisotropy allowed throughout the mantle.

s362ani_prem
A version of S362ANI calculated using PREM as the 1D reference model.

s29ea
A global model with higher resolution in the upper mantle beneath Eurasia calculated using REF as the 1D reference model.

3D_anisotropic
See Chapter [cha:-Changing-the] for a discussion on how to specify your own 3D anisotropic model.

3D_attenuation
See Chapter [cha:-Changing-the] for a discussion on how to specify your own 3D attenuation model.

PPM
For a user-specified 3D model (Point-Profile-Model) given as ASCII-table, specifying Vs-perturbations with respect to PREM. See Chapter [cha:-Changing-the] for a discussion on how to specify your own 3D model.

full_sh
For a user-specified, transversely isotropic 3D model given in spherical harmonics. Coefficients for the crustal model (up to degree 40) are stored in files named C**.dat and MOHO.dat, coefficients for the mantle model (up to degree 20) are stored in files named M**.dat. All model files reside in directory DATA/full_sphericalharmonic_model/. Note that to use the crustal model, one has to set the crustal type value ITYPE_CRUSTAL_MODEL = ICRUST_CRUST_SH in file setup/constants.h. This crustal model can be transversely isotropic as well.

sgloberani_iso
By default, the code uses 3D isotropic mantle model SGLOBE-rani (Chang et al. 2015) and the 3D crustal model includes perturbations from Crust2.0 (Bassin, Laske, and Masters 2000) as discussed in (Chang et al. 2015). The model is parametrised horizontally in spherical harmonics up to lmax=35 and with 21 depth splines for the radial direction. Note that SGLOBE-rani uses transversely isotropic PREM as a background model, and that we use the PREM radial attenuation model when ATTENUATION is incorporated.

sgloberani_aniso
By default, the code uses 3D anisotropic mantle model SGLOBE-rani (Chang et al. 2015) and the 3D crustal model includes perturbations from Crust2.0 (Bassin, Laske, and Masters 2000) as discussed in (Chang et al. 2015). Note that SGLOBE-rani uses transversely isotropic PREM as a background model, and that we use the PREM radial attenuation model when ATTENUATION is incorporated.

SPiRaL
A multiresolution global tomography model of seismic wave speeds and radial anisotropy variations in the crust and mantle developed by Simmons et al. (2021). Please see folder DATA/spiral1.4 for further information on how to install the corresponding model files.

GLAD_bkmns
A Block Mantle & Spherical Harmonics (BKMNS) expansion model developed by Ciardelli et al. (submitted.) for global crust/mantle 3D models GLAD-M25 and GLAD-M15. Please see folder DATA/gladm25 for further information on how to install the corresponding model files.

EMC_model
Reads in an IRIS EMC model provided by the user. For more details how to compile and setup the code, please see the README info in folder DATA/IRIS_EMC/.

for Mars:

1D_Sohl_3d_crust
This model adds a 3D crust on top of the 1D Mars model developed by Sohl and Spohn (1997). The crustal model is defined by the files in folder DATA/crustmaps/marscrust*.cmap

1D_case65TAY_3d_crust
This model adds a 3D crust on top of the 1D Mars model developed by Plesa et al. (2021). The crustal model is defined by the files in folder DATA/crustmaps/marscrust*.cmap

mars_SH_model
For a user-specified 3D Mars model given in spherical harmonics and provided in folder DATA/mars/SH_model/. The model files need to be specified in file SH_model_files.dat. The spherical harmonic file format follows the Mars evolution model outputs developed by Plesa et al. (2021). SH models define both crustal and mantle depths, with an isotropic seismic model description (Vp, Vs, and density).

Note:
When a 3D mantle model is chosen in Par_file, the simulations are performed together with the associated 3D crustal model. For example, model s362ani would use by default crustal model Crust2.0. To select the higher-resolution Crust1.0 crustal model instead, one can append it as an ending to the model name, i.e., ***<3D mantle>***_crust1.0, as for example s362ani_crust1.0. In a similar way, various 3D crustal models defined such as ***_crust1.0, ***_crust2.0, ***_crustmaps, ***_epcrust, ***_eucrust, ***_crustSH, ***_sglobecrust and ***_crustSPiRaL can be combined with different mantle models. Regional higher-resolution models, such as the European crustal models EPcrust (Molinari and Morelli 2011) and EUCrust-07 (Tesauro, Kaban, and Cloetingh 2008) are embedded by default into the global crustal model Crust1.0.

It is also possible to run simulations using a 3D mantle model with a 1D crustal model on top. This can be done by setting the model in Par_file to ***<3D mantle>***_1Dcrust, e.g., s20rts_1Dcrust, s362ani_1Dcrust, etc. In this case, the 1D crustal model will be the one that is used in the 3D mantle model as a reference model (e.g., transversely isotropic PREM for s20rts, REF for s362ani, etc.).

Currently, the only anisotropic inner core model implemented is the one defined by Ishii et al. (2002). To use this anisotropic inner core model, one can append the ending ***<3D mantle>***_AIC to the mantle model name. With the above crustal ending, as an example one could use s362ani_crust1.0_AIC.

OCEANS
Set to .true. if the effect of the oceans on seismic wave propagation should be incorporated based upon the approximate treatment discussed in Komatitsch and Tromp (2002b). This feature is inexpensive from a numerical perspective, both in terms of memory requirements and CPU time. This approximation is accurate at periods of roughly 20 s and longer. At shorter periods the effect of water phases/reverberations is not taken into account, even when the flag is on.

ELLIPTICITY
Set to .true. if the mesh should make the Earth model elliptical in shape according to Clairaut’s equation (Dahlen and Tromp 1998). This feature adds no cost to the simulation. After adding ellipticity, the mesh becomes elliptical and thus geocentric and geodetic/geographic latitudes and colatitudes differ (longitudes are unchanged). From (Dahlen and Tromp 1998): "Spherically-symmetric Earth models all have the same hydrostatic surface ellipticity 1/299.8. This is 0.5 percent smaller than observed flattening of best-fitting ellipsoid 1/298.3. The discrepancy is referred to as the "excess equatorial bulge of the Earth", an early discovery of artificial satellite geodesy." From Paul Melchior, IUGG General Assembly, Vienna, Austria, August 1991 Union lecture, available at www.agu.org/books: "It turns out that the spheroidal models constructed on the basis of the spherically-symmetric models (PREM, 1066A) by using the Clairaut differential equation to calculate the flattening in function of the radius vector imply hydrostaticity. These have surface ellipticity 1/299.8 and a corresponding dynamical flattening of .0033 (PREM). The actual ellipticty of the Earth for a best-fitting ellipsoid is 1/298.3 with a corresponding dynamical flattening of .0034."

Thus, flattening f = 1/299.8 is what is used in SPECFEM3D_GLOBE, as it should. And eccentricity squared $e^2 = 1 - (1-f)^2 = 1 - (1 - 1/299.8)^2 = 0.00665998813529$, and the correction factor used in the code to convert geographic latitudes to geocentric is $1 - e^2 = (1-f)^2 = (1 - 1/299.8)^2 = 0.9933400118647$. As a comparison, the classical World Geodetic System reference ellipsoid WGS 84 (see e.g. http://en.wikipedia.org/wiki/World_Geodetic_System) has $f = 1/298.2572236$.

For Mars, a flattening factor 1/169.8 is used (based on Smith et al. 1999, Science, 284). For Moon, a flattening factor 1/901.0 is currently taken. These values can be modified in file setup/constants.h.

TOPOGRAPHY
Set to .true. if topography and bathymetry should be incorporated based upon model ETOPO4 (NOAA 1988). This feature adds no cost to the simulation. If you want to use other topographic models, please see folder DATA/topo_bathy/ for further infos and change the name of the topographic model to use in file setup/constants.h before re-compiling the code.

GRAVITY
Set to .true. if self-gravitation should be incorporated in the Cowling approximation (Komatitsch and Tromp 2002b; Dahlen and Tromp 1998). Turning this feature on is relatively inexpensive, both from the perspective of memory requirements as well as in terms of computational speed.

ROTATION
Set to .true. if the Coriolis effect should be incorporated. Turning this feature on is relatively cheap numerically.

ATTENUATION
Set to .true. if attenuation should be incorporated. Turning this feature on increases the memory requirements significantly (roughly by a factor of 2), and is numerically fairly expensive. Of course for realistic simulations this flag should be turned on. See Komatitsch and Tromp (1999, 2002a) for a discussion on the implementation of attenuation based upon standard linear solids.

ABSORBING_CONDITIONS
Set to .false. for global simulations. See Chapter [cha:Regional-Simulations] for regional simulations.

RECORD_LENGTH_IN_MINUTES
Choose the desired record length of the synthetic seismograms (in minutes). This controls the length of the numerical simulation, i.e., twice the record length requires twice as much CPU time. This feature is not used at the time of meshing but is required for the solver, i.e., you may change this parameter after running the mesher.

PARTIAL_PHYS_DISPERSION_ONLY or UNDO_ATTENUATION
To undo attenuation for sensitivity kernel calculations or forward runs with SAVE_FORWARD use one (and only one) of the two flags below. UNDO_ATTENUATION is much better (it is exact) and is simpler to use but it requires a significant amount of disk space for temporary storage. It has the advantage of requiring only two simulations for adjoint tomography instead of three in the case of PARTIAL_PHYS_DISPERSION_ONLY, i.e. for adjoint tomography it is globally significantly less expensive (each run is slightly more expensive, but only two runs are needed instead of three).

When using PARTIAL_PHYS_DISPERSION_ONLY, to make the approximation reasonably OK you need to take the following steps:

  1. To calculate synthetic seismograms, do a forward simulation with full attenuation for the model of interest. The goal is to get synthetics that match the data as closely as possible.

  2. Make measurements and produce adjoint sources by comparing the resulting synthetics with the data. In the simplest case of a cross-correlation traveltime measurement, use the time-reversed synthetic in the window of interest as the adjoint source.

  3. Do a second forward calculation with PARTIAL_PHYS_DISPERSION_ONLY = .true. and save the last snapshot.

  4. Do an adjoint calculation using the adjoint source calculated in 1/, the forward wavefield reconstructed based on 2b/, use PARTIAL_PHYS_DISPERSION_ONLY = .true. for the adjoint wavefield, and save the kernel.

Thus the kernel calculation uses PARTIAL_PHYS_DISPERSION_ONLY = .true. for both the forward and the adjoint wavefields. This is in the spirit of the banana-donut kernels. But the data that are assimilated are based on the full 3D synthetic with attenuation. Another, equivalent way of explaining it is:

  1. Calculate synthetics with full attenuation for the current model. Compare these to the data and measure frequency-dependent traveltime anomalies $\Delta \tau(\omega)$, e.g.. based upon multi-tapering.

  2. Calculate synthetics with PARTIAL_PHYS_DISPERSION_ONLY = .true. and construct adjoint sources by combining the seismograms from this run with the measurements from 1/. So in the expressions for the multi-taper adjoint source you use the measurements from 1/, but synthetics calculated with PARTIAL_PHYS_DISPERSION_ONLY = .true..

  3. Construct a kernel by calculating an adjoint wavefield based on the sources constructed in 2/ and convolving it with a forward wavefield with PARTIAL_PHYS_DISPERSION_ONLY = .true.. Again, both the forward and adjoint calculations use PARTIAL_PHYS_DISPERSION_ONLY = .true..

Note that if you replace multi-taper measurements with cross-correlation measurements you will measure a cross-correlation traveltime anomaly in 1/, i.e., some delay time $\Delta T$. Then you would calculate an adjoint wavefield with PARTIAL_PHYS_DISPERSION_ONLY = .true. and use the resulting time-reversed seismograms weighted by $\Delta T$ as the adjoint source. This wavefield interacts with a forward wavefield calculated with PARTIAL_PHYS_DISPERSION_ONLY = .true.. If $\Delta T=1$ one gets a banana-donut kernel, i.e., a kernel for the case in which there are no observed seismograms (no data), as explained for instance on page 5 of (Zhou, Liu, and Tromp 2011).

MOVIE_SURFACE
Set to .false., unless you want to create a movie of seismic wave propagation on the Earth’s surface. Turning this option on generates large output files. See Section [sec:Movies] for a discussion on the generation of movies. This feature is not used at the time of meshing but is relevant for the solver.

MOVIE_VOLUME
Set to .false., unless you want to create a movie of seismic wave propagation in the Earth’s interior. Turning this option on generates huge output files. See Section [sec:Movies] for a discussion on the generation of movies. This feature is not used at the time of meshing but is relevant for the solver.

NTSTEP_BETWEEN_FRAMES
Determines the number of timesteps between movie frames. Typically you want to save a snapshot every 100 timesteps. The smaller you make this number the more output will be generated! See Section [sec:Movies] for a discussion on the generation of movies. This feature is not used at the time of meshing but is relevant for the solver.

HDUR_MOVIE
determines the half duration of the source time function for the movie simulations. When this parameter is set to be 0, a default half duration that corresponds to the accuracy of the simulation is provided.

SAVE_MESH_FILES
Set this flag to .true``. to save AVS, OpenDX, or ParaView mesh files for subsequent viewing. Turning the flag on generates large (distributed) files in the LOCAL_PATH directory. See Section [sec:Meshes] for a discussion of mesh viewing features.

NUMBER_OF_RUNS
On machines with a run-time limit, for instance for a batch/queue system, a simulation may need to be completed in stages. This option allows you to select the number of stages in which the simulation will be completed (1, 2 or 3). Choose 1 for a run without restart files. This feature is not used at the time of meshing but is required for the solver. At the end of the first or second stage of a multi-stage simulation, large files are written to the file system to save the current state of the simulation. This state is read back from the file system at the beginning of the next stage of the multi-stage run. Reading and writing the states can be very time consuming depending on the nature of the network and the file system (in this case writing to the local file system, i.e., the disk on a node, is preferable).

NUMBER_OF_THIS_RUN
If you choose to perform the run in stages, you need to tell the solver what stage run to perform. This feature is not used at the time of meshing but is required for the solver.

LOCAL_PATH
Directory in which the databases generated by the mesher will be written. Generally one uses a directory on the local disk of the compute nodes, although on some machines these databases are written on a parallel (global) file system (see also the earlier discussion of the LOCAL_PATH_IS_ALSO_GLOBAL flag in Chapter [cha:Getting-Started]). The mesher generates the necessary databases in parallel, one set for each of the $6\times\nprocxi^{2}$ slices that constitutes the mesh (see Figure [figure:mpi_slices]). After the mesher finishes, you can log in to one of the compute nodes and view the contents of the LOCAL_PATH directory to see the (many) files generated by the mesher.

NTSTEP_BETWEEN_OUTPUT_INFO
This parameter specifies the interval at which basic information about a run is written to the file system (timestamp``* files in the OUTPUT_FILES directory). If you have access to a fast machine, set NTSTEP_BETWEEN_OUTPUT_INFO to a relatively high value (e.g., at least 100, or even 1000 or more) to avoid writing output text files too often. This feature is not used at the time of meshing. One can set this parameter to a larger value than the number of time steps to avoid writing output during the run.

NTSTEP_BETWEEN_OUTPUT_SEISMOS
This parameter specifies the interval at which synthetic seismograms are written in the LOCAL_PATH directory. The seismograms can be created in three different formats by setting the parameters OUTPUT_SEISMOS_ASCII_TEXT, OUTPUT_SEISMOS_SAC_ALPHANUM and OUTPUT_SEISMOS_SAC_BINARY. One can choose any combination of these parameters (details on the formats follow in the description of each parameter). SAC is a signal-processing software package. If a run crashes, you may still find usable (but shorter than requested) seismograms in this directory. On a fast machine set NTSTEP_BETWEEN_OUTPUT_SEISMOS to a relatively high value to avoid writing to the seismograms too often. This feature is not used at the time of meshing.

NTSTEP_BETWEEN_READ_ADJSRC
The number of adjoint sources read in each time for an adjoint simulation.

USE_FORCE_POINT_SOURCE
Turn this flag on to use a (tilted) FORCESOLUTION force point source instead of a CMTSOLUTION moment-tensor source. When the force source does not fall exactly at a grid point, the solver interpolates the force between grid points using Lagrange interpolants. This option can be useful for vertical force, normal force, tilted force, impact force, etc. Note that in the FORCESOLUTION file, you will need to edit the East, North and vertical components of an arbitrary (not necessarily unitary, the code will normalize it automatically) direction vector of the force vector; thus refer to Appendix [cha:Reference-Frame-Convention] for the orientation of the reference frame. This vector is made unitary internally in the solver and thus only its direction matters here; its norm is ignored and the norm of the force used is the factor force source times the source-time function.

OUTPUT_SEISMOS_ASCII_TEXT
Set this flag to .true. if you want to have the synthetic seismograms written in two-column ASCII format (the first column contains time in seconds and the second column the displacement in meters of the recorded signal, no header information). Files will be named with extension .ascii, e.g., NT.STA.?X?.sem.ascii where NT and STA are the network and station codes given in STATIONS file, and ?X? is the channel code (see Appendix [cha:channel-codes]).

OUTPUT_SEISMOS_SAC_ALPHANUM
Set this flag to .true. if you want to have the synthetic seismograms written in alphanumeric (human readable) SAC format, which includes header information on the source and receiver parameters (e.g., source/receiver coordinates, station name, etc., see Appendix [cha:SAC-headers]). For details on the format, please check the SAC webpage. Files will be named with extension .sacan.

OUTPUT_SEISMOS_SAC_BINARY
Set this flag to .true. if you want to have the synthetic seismograms written in binary SAC format. The header information included is the same as for the alphanumeric SAC format (see Appendix [cha:SAC-headers]). Using this format requires the least disk space, which may be particulary important if you have a large number of stations. For details on the binary format please also check the SAC webpage and Appendix [cha:SAC-headers]. Files will be named with extension .sac.

ROTATE_SEISMOGRAMS_RT
Set this flag to .true. if you want to have radial (R) and transverse (T) horizontal components of the synthetic seismograms (default is .false. $\rightarrow$ East (E) and North (N) components).

WRITE_SEISMOGRAMS_BY_MAIN
Set this flag to .true. if you want to have all the seismograms written by the main process (no need to collect them on the nodes after the run).

SAVE_ALL_SEISMOS_IN_ONE_FILE
Set this flag to .true. if you want to have all the seismograms saved in one large combined file instead of one file per seismogram to avoid overloading shared non-local file systems such as GPFS for instance.

USE_BINARY_FOR_LARGE_FILE
Set this flag to .true. if you want to use binary instead of ASCII for that large file (not used if SAVE_ALL_SEISMOS_IN _ONE_FILE = .false.)

RECEIVERS_CAN_BE_BURIED
This flag accommodates stations with instruments that are buried, i.e., the solver will calculate seismograms at the burial depth specified in the STATIONS file. This feature is not used at the time of meshing.

PRINT_SOURCE_TIME_FUNCTION
Turn this flag on to print information about the source-time function in the file OUTPUT_FILES/plot_source_time_function.txt. This feature is not used at the time of meshing.

NUMBER_OF_SIMULTANEOUS_RUNS
adds the ability to run several calculations (several earthquakes) in an embarrassingly-parallel fashion from within the same run; this can be useful when using a very large supercomputer to compute many earthquakes in a catalog, in which case it can be better from a batch job submission point of view to start fewer and much larger jobs, each of them computing several earthquakes in parallel.

To turn that option on, set parameter NUMBER_OF_SIMULTANEOUS_RUNS to a value greater than 1. To implement that, we create NUMBER_OF_SIMULTANEOUS_RUNS MPI sub-communicators, each of them being labeled "my_local_mpi_comm_world", and we use them in all the routines in "src/shared/parallel.f90", except in MPI_ABORT() because in that case we need to kill the entire run.

When that option is on, of course the number of processor cores used to start the code in the batch system must be a multiple of NUMBER_OF_SIMULTANEOUS_RUNS, all the individual runs must use the same number of processor cores, which as usual is NPROC in the Par_file, and thus the total number of processor cores to request from the batch system should be NUMBER_OF_SIMULTANEOUS_RUNS * NPROC. All the runs to perform must be placed in directories called run0001, run0002, run0003 and so on (with exactly four digits).

Imagine you have 10 independent calculations to do, each of them on 100 cores; you have three options:

1/ submit 10 jobs to the batch system

2/ submit a single job on 1000 cores to the batch, and in that script create a sub-array of jobs to start 10 jobs, each running on 100 cores (see e.g. http://www.schedmd.com/slurmdocs/job_array.html )

3/ submit a single job on 1000 cores to the batch, start SPECFEM3D on 1000 cores, create 10 sub-communicators, cd into one of 10 subdirectories (called e.g. run0001, run0002,... run0010) depending on the sub-communicator your MPI rank belongs to, and run normally on 100 cores using that sub-communicator.

The option NUMBER_OF_SIMULTANEOUS_RUNS implements 3/.

BROADCAST_SAME_MESH_AND_MODEL
: if we perform simultaneous runs in parallel, if only the source and receivers vary between these runs but not the mesh nor the model (velocity and density) then we can also read the mesh and model files from a single run in the beginning and broadcast them to all the others; for a large number of simultaneous runs for instance when solving inverse problems iteratively this can DRASTICALLY reduce I/Os to disk in the solver (by a factor equal to NUMBER_OF_SIMULTANEOUS_RUNS), and reducing I/Os is crucial in the case of huge runs. Thus, always set this option to .true. if the mesh and the model are the same for all simultaneous runs. In that case there is no need to duplicate the mesh and model file database (the content of the DATABASES_MPI directories) in each of the run0001, run0002,... directories, it is sufficient to have one in run0001 and the code will broadcast it to the others).

USE_FAILSAFE_MECHANISM
: if one or a few of these simultaneous runs fail, kill all the runs or let the others finish using a fail-safe mechanism (in most cases, should be set to true).

TODO / future work to do: currently the BROADCAST_SAME_MESH_AND_MODEL option assumes to have the (main) mesh files in run0001/DATABASES_MPI or run0001/OUTPUT_FILES/DATABASES_MPI. However, for adjoint runs you still need a DATABASES_MPI folder in each of the sub-runs directories, e.g. run0002/DATABASES_MPI, etc. to store the forward wavefields, kernels etc. of each sub-run. This would not be needed for forward simulations.

TODO / future work to do: the sensitivity kernel summing and smoothing tools in directory src/tomography are currently not ported to this new option to do many runs simultaneously, only the solver (src/specfem3d) is. Thus these tools should work, but in their current version will need to be run for each simulation result independently. More precisely, the current kernel summing and smoothing routines work fine, with the exception that you need to move out the mesh files (and also the parameters). This works because these routines consider multiple runs by design. You simply have to provide them the directories where the kernels are.

NPROC_XI processors NEX_XI
1 6 64 80 96 112 128 144 160 176 192 208
2 24 64 80 96 112 128 144 160 176 192 208
3 54 96 144 192 240 288 336 384 432 480 528
4 96 64 96 128 160 192 224 256 288 320 352
5 150 80 160 240 320 400 480 560 640 720 800
6 216 96 144 192 240 288 336 384 432 480 528
7 294 112 224 336 448 560 672 784 896 1008 1120
8 384 64 128 192 256 320 384 448 512 576 640
9 486 144 288 432 576 720 864 1008 1152 1296 1440
10 600 80 160 240 320 400 480 560 640 720 800
11 726 176 352 528 704 880 1056 1232 1408 1584 1760
12 864 96 192 288 384 480 576 672 768 864 960
13 1014 208 416 624 832 1040 1248 1456 1664 1872 2080
14 1176 112 224 336 448 560 672 784 896 1008 1120
15 1350 240 480 720 960 1200 1440 1680 1920 2160 2400
16 1536 128 256 384 512 640 768 896 1024 1152 1280
17 1734 272 544 816 1088 1360 1632 1904 2176 2448 2720
18 1944 144 288 432 576 720 864 1008 1152 1296 1440
19 2166 304 608 912 1216 1520 1824 2128 2432 2736 3040
20 2400 160 320 480 640 800 960 1120 1280 1440 1600
21 2646 336 672 1008 1344 1680 2016 2352 2688 3024 3360
22 2904 176 352 528 704 880 1056 1232 1408 1584 1760
23 3174 368 736 1104 1472 1840 2208 2576 2944 3312 3680
24 3456 192 384 576 768 960 1152 1344 1536 1728 1920
25 3750 400 800 1200 1600 2000 2400 2800 3200 3600 4000
26 4056 208 416 624 832 1040 1248 1456 1664 1872 2080
27 4374 432 864 1296 1728 2160 2592 3024 3456 3888 4320
28 4704 224 448 672 896 1120 1344 1568 1792 2016 2240
29 5046 464 928 1392 1856 2320 2784 3248 3712 4176 4640
30 5400 240 480 720 960 1200 1440 1680 1920 2160 2400
31 5766 496 992 1488 1984 2480 2976 3472 3968 4464 4960
32 6144 256 512 768 1024 1280 1536 1792 2048 2304 2560
33 6534 528 1056 1584 2112 2640 3168 3696 4224 4752 5280
34 6936 272 544 816 1088 1360 1632 1904 2176 2448 2720
35 7350 560 1120 1680 2240 2800 3360 3920 4480 5040 5600
36 7776 288 576 864 1152 1440 1728 2016 2304 2592 2880
37 8214 592 1184 1776 2368 2960 3552 4144 4736 5328 5920
38 8664 304 608 912 1216 1520 1824 2128 2432 2736 3040
39 9126 624 1248 1872 2496 3120 3744 4368 4992 5616 6240
40 9600 320 640 960 1280 1600 1920 2240 2560 2880 3200
41 10086 656 1312 1968 2624 3280 3936 4592 5248 5904 6560
42 10584 336 672 1008 1344 1680 2016 2352 2688 3024 3360
43 11094 688 1376 2064 2752 3440 4128 4816 5504 6192 6880
44 11616 352 704 1056 1408 1760 2112 2464 2816 3168 3520
45 12150 720 1440 2160 2880 3600 4320 5040 5760 6480 7200
46 12696 368 736 1104 1472 1840 2208 2576 2944 3312 3680
47 13254 752 1504 2256 3008 3760 4512 5264 6016 6768 7520
48 13824 384 768 1152 1536 1920 2304 2688 3072 3456 3840
49 14406 784 1568 2352 3136 3920 4704 5488 6272 7056 7840
50 15000 400 800 1200 1600 2000 2400 2800 3200 3600 4000
51 15606 816 1632 2448 3264 4080 4896 5712 6528 7344 8160
52 16224 416 832 1248 1664 2080 2496 2912 3328 3744 4160
53 16854 848 1696 2544 3392 4240 5088 5936 6784 7632 8480
54 17496 432 864 1296 1728 2160 2592 3024 3456 3888 4320
55 18150 880 1760 2640 3520 4400 5280 6160 7040 7920 8800
56 18816 448 896 1344 1792 2240 2688 3136 3584 4032 4480
57 19494 912 1824 2736 3648 4560 5472 6384 7296 8208 9120
58 20184 464 928 1392 1856 2320 2784 3248 3712 4176 4640
59 20886 944 1888 2832 3776 4720 5664 6608 7552 8496 9440
60 21600 480 960 1440 1920 2400 2880 3360 3840 4320 4800
61 22326 976 1952 2928 3904 4880 5856 6832 7808 8784 9760
62 23064 496 992 1488 1984 2480 2976 3472 3968 4464 4960
63 23814 1008 2016 3024 4032 5040 6048 7056 8064 9072 10080
64 24576 512 1024 1536 2048 2560 3072 3584 4096 4608 5120
65 25350 1040 2080 3120 4160 5200 6240 7280 8320 9360 10400
66 26136 528 1056 1584 2112 2640 3168 3696 4224 4752 5280
67 26934 1072 2144 3216 4288 5360 6432 7504 8576 9648 10720
68 27744 544 1088 1632 2176 2720 3264 3808 4352 4896 5440
69 28566 1104 2208 3312 4416 5520 6624 7728 8832 9936 11040
70 29400 560 1120 1680 2240 2800 3360 3920 4480 5040 5600
71 30246 1136 2272 3408 4544 5680 6816 7952 9088 10224 11360
72 31104 576 1152 1728 2304 2880 3456 4032 4608 5184 5760
73 31974 1168 2336 3504 4672 5840 7008 8176 9344 10512 11680
74 32856 592 1184 1776 2368 2960 3552 4144 4736 5328 5920
75 33750 1200 2400 3600 4800 6000 7200 8400 9600 10800 12000
76 34656 608 1216 1824 2432 3040 3648 4256 4864 5472 6080
77 35574 1232 2464 3696 4928 6160 7392 8624 9856 11088 12320
78 36504 624 1248 1872 2496 3120 3744 4368 4992 5616 6240
79 37446 1264 2528 3792 5056 6320 7584 8848 10112 11376 12640
80 38400 640 1280 1920 2560 3200 3840 4480 5120 5760 6400
81 39366 1296 2592 3888 5184 6480 7776 9072 10368 11664 12960
82 40344 656 1312 1968 2624 3280 3936 4592 5248 5904 6560
83 41334 1328 2656 3984 5312 6640 7968 9296 10624 11952 13280
84 42336 672 1344 2016 2688 3360 4032 4704 5376 6048 6720
85 43350 1360 2720 4080 5440 6800 8160 9520 10880 12240 13600
86 44376 688 1376 2064 2752 3440 4128 4816 5504 6192 6880
87 45414 1392 2784 4176 5568 6960 8352 9744 11136 12528 13920
88 46464 704 1408 2112 2816 3520 4224 4928 5632 6336 7040
89 47526 1424 2848 4272 5696 7120 8544 9968 11392 12816 14240
90 48600 720 1440 2160 2880 3600 4320 5040 5760 6480 7200
91 49686 1456 2912 4368 5824 7280 8736 10192 11648 13104 14560
92 50784 736 1472 2208 2944 3680 4416 5152 5888 6624 7360
93 51894 1488 2976 4464 5952 7440 8928 10416 11904 13392 14880
94 53016 752 1504 2256 3008 3760 4512 5264 6016 6768 7520
95 54150 1520 3040 4560 6080 7600 9120 10640 12160 13680 15200
96 55296 768 1536 2304 3072 3840 4608 5376 6144 6912 7680
97 56454 1552 3104 4656 6208 7760 9312 10864 12416 13968 15520
98 57624 784 1568 2352 3136 3920 4704 5488 6272 7056 7840
99 58806 1584 3168 4752 6336 7920 9504 11088 12672 14256 15840
100 60000 800 1600 2400 3200 4000 4800 5600 6400 7200 8000
101 61206 1616 3232 4848 6464 8080 9696 11312 12928 14544 16160
102 62424 816 1632 2448 3264 4080 4896 5712 6528 7344 8160
103 63654 1648 3296 4944 6592 8240 9888 11536 13184 14832 16480
104 64896 832 1664 2496 3328 4160 4992 5824 6656 7488 8320
105 66150 1680 3360 5040 6720 8400 10080 11760 13440 15120 16800
106 67416 848 1696 2544 3392 4240 5088 5936 6784 7632 8480
107 68694 1712 3424 5136 6848 8560 10272 11984 13696 15408 17120
108 69984 864 1728 2592 3456 4320 5184 6048 6912 7776 8640
109 71286 1744 3488 5232 6976 8720 10464 12208 13952 15696 17440
110 72600 880 1760 2640 3520 4400 5280 6160 7040 7920 8800
111 73926 1776 3552 5328 7104 8880 10656 12432 14208 15984 17760
112 75264 896 1792 2688 3584 4480 5376 6272 7168 8064 8960
113 76614 1808 3616 5424 7232 9040 10848 12656 14464 16272 18080
114 77976 912 1824 2736 3648 4560 5472 6384 7296 8208 9120
115 79350 1840 3680 5520 7360 9200 11040 12880 14720 16560 18400
116 80736 928 1856 2784 3712 4640 5568 6496 7424 8352 9280
117 82134 1872 3744 5616 7488 9360 11232 13104 14976 16848 18720
118 83544 944 1888 2832 3776 4720 5664 6608 7552 8496 9440
119 84966 1904 3808 5712 7616 9520 11424 13328 15232 17136 19040
120 86400 960 1920 2880 3840 4800 5760 6720 7680 8640 9600
121 87846 1936 3872 5808 7744 9680 11616 13552 15488 17424 19360
122 89304 976 1952 2928 3904 4880 5856 6832 7808 8784 9760
123 90774 1968 3936 5904 7872 9840 11808 13776 15744 17712 19680
124 92256 992 1984 2976 3968 4960 5952 6944 7936 8928 9920
125 93750 2000 4000 6000 8000 10000 12000 14000 16000 18000 20000
126 95256 1008 2016 3024 4032 5040 6048 7056 8064 9072 10080
127 96774 2032 4064 6096 8128 10160 12192 14224 16256 18288 20320
128 98304 1024 2048 3072 4096 5120 6144 7168 8192 9216 10240
129 99846 2064 4128 6192 8256 10320 12384 14448 16512 18576 20640

Finally, you need to provide a file that tells MPI what compute nodes to use for the simulations. The file must have a number of entries (one entry per line) at least equal to the number of processors needed for the run. A sample file is provided in the file mymachines. This file is not used by the mesher or solver, but is required by the go_mesher and go_solver default job submission scripts. See Chapter [cha:Running-Scheduler] for information about running the code on a system with a scheduler, e.g., LSF.

Now that you have set the appropriate parameters in the Par_file and have compiled the mesher, you are ready to launch it! This is most easily accomplished based upon the go_mesher script. When you run on a PC cluster, the script assumes that the nodes are named n001, n002, etc. If this is not the case, change the tr -d ‘n’ line in the script. You may also need to edit the last command at the end of the script that invokes the mpirun command.

Mesher output is provided in the OUTPUT_FILES directory in output_mesher.txt; this file provides lots of details about the mesh that was generated. Alternatively, output can be directed to the screen instead by uncommenting a line in constants.h:

! uncomment this to write messages to the screen
! integer, parameter :: IMAIN = ISTANDARD_OUTPUT

Note that on very fast machines, writing to the screen may slow down the code.

Another file generated by the mesher is the header file OUTPUT_FILES/values_from_mesher.h. This file specifies a number of constants and flags needed by the solver. These values are passed statically to the solver for reasons of speed. Some useful statistics about the mesh are also provided in this file.

For a given model, set of nodes, and set of parameters in Par_file, one only needs to run the mesher once and for all, even if one wants to run several simulations with different sources and/or receivers (the source and receiver information is used in the solver only).

Please note that it is difficult to correctly sample S waves in the inner core of the Earth because S-wave velocity is very small there. Therefore, correctly sampling S waves in the inner core would require a very dense mesh, which in turn would drastically reduce the time step of the explicit time scheme because the P wave velocity is very high in the inner core (Poisson’s ratio is roughly equal to 0.44). Because shear wave attenuation is very high in the inner core ($Q_{\mu}$ is approximately equal to 85), we have therefore decided to design the inner core mesh such that P waves are very well sampled but S waves are right at the sampling limit or even slightly below. This works fine because spurious numerical oscillations due to S-wave subsampling are almost completely suppressed by attenuation. However, this implies that one should not use SPECFEM3D_GLOBE with the regular mesh and period estimates of Table [table:nex] to study the PKJKP phase very precisely. If one is interested in that phase, one should use typically 1.5 times to twice the number of elements NEX indicated in the table.

Regarding fluid/solid coupling at the CMB and ICB, in SPECFEM3D_GLOBE we do not use the fluid-solid formulation of Komatitsch and Tromp (2002a) and Komatitsch and Tromp (2002b) anymore, we now use a displacement potential in the fluid (rather than a velocity potential as in Komatitsch and Tromp (2002a) and Komatitsch and Tromp (2002b)). This leads to the simpler fluid-solid matching condition introduced by Chaljub and Valette (2004) with no numerical iterations at the CMB and ICB.

For accuracy reasons, in the mesher the coordinates of the mesh points (arrays xstore, ystore and zstore) are always created in double precision. If the solver is compiled in single precision mode, the mesh coordinates are converted to single precision before being saved in the local mesh files.

Memory requirements

The SPECFEM3D_GLOBE memory requirements can be estimated before or after running the mesher using the small serial program ./bin/xcreate_header_file, which reads the input file DATA/Par_file and displays the total amount of memory that will be needed by the mesher and the solver to run it. This way, users can easily modify the parameters and check that their simulation will fit in memory on their machine. The file created by xcreate_header_file is called OUTPUT_FILES/values_from_mesher.h and contains even more details about the future simulation.

Please note that running these codes is optional because no information needed by the solver is generated.

References

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