[cig-commits] [commit] devel, master: Updated README files for four examples, to reflect current directory structure. (ad49ff6)
cig_noreply at geodynamics.org
cig_noreply at geodynamics.org
Wed Jun 18 16:48:08 PDT 2014
Repository : https://github.com/geodynamics/specfem3d
On branches: devel,master
Link : https://github.com/geodynamics/specfem3d/compare/6026e367984905ab133865f62fa6293b343759b9...47f703851338234f96397e7da9fbff63d8178b8a
>---------------------------------------------------------------
commit ad49ff6b7ca50c3f905ba33953af97a49d052e8d
Author: Carl Tape <carltape at gi.alaska.edu>
Date: Fri Jan 28 19:56:59 2011 +0000
Updated README files for four examples, to reflect current directory structure.
>---------------------------------------------------------------
ad49ff6b7ca50c3f905ba33953af97a49d052e8d
homogeneous_halfspace/README | 4 ++--
layered_halfspace/README | 37 +++++++++++++++++++-------------
tomographic_model/README | 49 ++++++++-----------------------------------
waterlayered_halfspace/README | 19 ++++++++++-------
4 files changed, 45 insertions(+), 64 deletions(-)
diff --git a/homogeneous_halfspace/README b/homogeneous_halfspace/README
index c836252..8b59d8c 100644
--- a/homogeneous_halfspace/README
+++ b/homogeneous_halfspace/README
@@ -17,7 +17,7 @@ step-by-step tutorial:
- From the SPECFEM3D root directory SPECFEM3D/
configure the package, e.g. using intel's ifort compiler:
> cd SPECFEM3D
- > ./configure F90=ifort --with-scotch-path=/my_path_to_scotch
+ > ./configure F90=ifort --with-scotch-dir=/my_path_to_scotch
If successful, this will generate the files in src/shared/:
Makefile, constants.h, and precision.h, among others
@@ -103,7 +103,7 @@ step-by-step tutorial:
generated in in_out_files/OUTPUT_FILES/
- when the job is complete, you should have 3 sets (semd,semv,sema)
- of 672 (ls -1 *semd | wc) in the directory in_out_files/OUTPUT_FILES,
+ of 672 (ls -1 *semd | wc) file in the directory in_out_files/OUTPUT_FILES,
as well as 3 timestamp****** files
diff --git a/layered_halfspace/README b/layered_halfspace/README
index 1dbea03..ea9d368 100644
--- a/layered_halfspace/README
+++ b/layered_halfspace/README
@@ -4,11 +4,13 @@ README
This example creates a layered model, with three volumes and two different material
descriptions, using CUBIT.
-It is used for validation with a layer-cake solution from Komatitsch et al. (1999),
+It is used for validation with a layer-cake solution from Komatitsch and Tromp (1999),
using a 2-layer model as shown in their Figure 8, left.
step-by-step tutorial:
+0. run the example in the directory homogeneous_halfspace
+
1. create mesh:
- run cubit GUI:
@@ -49,9 +51,9 @@ step-by-step tutorial:
- run decomposer in directory bin/:
(example assumes 4 partitions with mesh files in OUTPUT_FILES/)
- > cd SPECFEM3D/
+ > cd SPECFEM3D
> make
- > ./bin/xdecompose_mesh_SCOTCH 4 ../examples/layered_halfspace/MESH/ ../in_out_files/DATABASES_MPI/
+ > ./bin/xdecompose_mesh_SCOTCH 4 examples/layered_halfspace/MESH/ in_out_files/DATABASES_MPI/
which creates mesh partitions "proc0000***_Database" in directory "DATABASES_MPI".
you can then specify "../in_out_files/DATABASES_MPI" in "Par_file" for your "LOCAL_PATH"
@@ -59,8 +61,10 @@ step-by-step tutorial:
3. generate databases:
- - copy Par_file, CMTSOLUTION & STATIONS files provided in this examples directory to in_data_files/ directory in
- the SPECFEM3D root directory
+ - copy Par_file, CMTSOLUTION & STATIONS files provided in this examples directory to SPECFEM3D/in_data_files/
+ > cd examples/layered_halfspace/in_data_files
+ > cp CMTSOLUTION Par_file STATIONS ../../../in_data_files/
+ > cd SPECFEM3D
- compile generate_databases:
> make xgenerate_databases
@@ -74,7 +78,7 @@ step-by-step tutorial:
4. run simulation:
- - modify constants.h:
+ - modify src/shared/constants.h:
to use a vertical force source, with a Ricker wavelet source time function,
turn flag on for parameter USE_FORCE_POINT_SOURCE:
...
@@ -87,16 +91,21 @@ step-by-step tutorial:
- submit job script:
> qsub go_solver_pbs.bash
+ note: simulation will take about 45 minutes and generate
+ 3 sets (semd,semv,sema) of 672 files in in_out_files/OUTPUT_FILES,
+ as well as 13 timestamp****** files
+
Optional:
- Compare the solution traces:
- 'OUTPUT_FILES/X31.HXZ.semd'
- and
- 'OUTPUT_FILES/X55.HXZ.semd'
+ Compare the solution traces in the directory
+ in_out_files/OUTPUT_FILES/:
+ X55.DB.HXZ.semd
+ X31.DB.HXZ.semd
- with the solutions of Komatitsch et al. (1999, Figure 9, bottom and top) provided in:
- 'VALIDATION_3D_SEM_SIMPLER_LAYER_SOURCE/REF_SEIS/Uz_file_Ycste_0031.txt'
- and
- 'VALIDATION_3D_SEM_SIMPLER_LAYER_SOURCE/REF_SEIS/Uz_file_Ycste_0055.txt'
+ with the reference solutions provided in the directory
+ examples/layered_halfspace/VALIDATION_3D_SEM_SIMPLER_LAYER_SOURCE_DEPTH/REF_SEIS/:
+ Uz_file_Ycste_0055.txt -- Komatitsch and Tromp (1999, Figure 9, top left)
+ Uz_file_Ycste_0031.txt -- Komatitsch and Tromp (1999, Figure 9, bottom left)
+ Note: a time shift is needed to align these given to differences in origin time convention
diff --git a/tomographic_model/README b/tomographic_model/README
index 8c1be14..366045c 100644
--- a/tomographic_model/README
+++ b/tomographic_model/README
@@ -7,9 +7,7 @@ as material property to run a forward simulation.
step-by-step tutorial:
-0. check that all software is available (or that modules are loaded):
- intel/openmpi, cubit, scotch, python, gnuplot
- and run ./configure in the SPECFEM3D package root directory
+0. run the example in the directory homogeneous_halfspace
1. create mesh:
@@ -22,19 +20,8 @@ step-by-step tutorial:
then run meshing script:
claro -> Menu "Tools" -> "Play Journal File" ... and select file: "tomoblock_mesh.py"
- if everything goes fine, this creates all the mesh files in a subdirectory MESH/:
- MESH/absorbing_surface_file_bottom
- MESH/absorbing_surface_file_xmax
- MESH/absorbing_surface_file_xmin
- MESH/absorbing_surface_file_ymax
- MESH/absorbing_surface_file_ymin
- MESH/free_surface_file
- MESH/materials_file
- MESH/mesh_file
- MESH/nodes_coords_file
- MESH/nummaterial_velocity_file
+ this creates all the mesh files in subdirectory MESH/
- the cubit graphics window should show a mesh similar to the file homogeneous.png
2. create tomography_model file:
@@ -50,20 +37,14 @@ step-by-step tutorial:
3. decompose mesh files:
- - compile decomposer in directory:
- > cd SPECFEM3D/
- > make
+ - run decomposer in directory decompose_mesh_SCOTCH/:
+ (example assumes 4 partitions with mesh files in OUTPUT_FILES/)
+ > cd SPECFEM3D
+ > make
+ > ./bin/xdecompose_mesh_SCOTCH 4 examples/tomographic_model/MESH/ in_out_files/DATABASES_MPI/
- NOTE 1: check that the two scotch libraries are properly specified in Makefile
- NOTE 2: compile with the same compiler (ifort or gfortran) used
- for the SCOTCH libraries
-
- - run decomposer in directory
- (example assumes 4 partitions with mesh files in ../examples/homogeneous_halfspace/MESH/)
- > ./bin/xdecompose_mesh_SCOTCH 4 ../examples/tomographic_model/MESH/ ../in_out_files/DATABASES_MPI/
-
- this creates mesh partitions "proc000***_Database" in directory DATABASES_MPI/.
- (you can then specify "../in_out_files/DATABASES_MPI" in "Par_file" for your "LOCAL_PATH")
+ which creates mesh partitions "proc0000***_Database" in directory "DATABASES_MPI".
+ you can then specify "../in_out_files/DATABASES_MPI" in "Par_file" for your "LOCAL_PATH"
4. generate databases:
@@ -75,12 +56,6 @@ step-by-step tutorial:
- submit job script
> qsub go_generate_databases_pbs.bash
- NOTE: this script will need to be tailored to your cluster, e.g.,
- > bsub < go_generate_databases_lsf.bash
-
- this will create binary mesh files, e.g. "proc000***_external_mesh.bin"
- in directory DATABASES_MPI/.
-
5. run simulation:
@@ -93,15 +68,9 @@ step-by-step tutorial:
- submit job script:
> qsub go_solver_pbs.bash
- NOTE 1: this script will need to be tailored to your cluster, e.g.,
- > bsub < go_solver_lsf.bash
- NOTE 2: the simulation runs on 4 cores and should take about 10 minutes,
- and you can track the progress with the timestamp files
-
- when the job is complete, you should have 3 sets (semd,semv,sema)
of 672 (ls -1 *semd | wc) in the directory in_out_files/OUTPUT_FILES,
as well as 3 timestamp****** files
-
===========================================================
diff --git a/waterlayered_halfspace/README b/waterlayered_halfspace/README
index a7c2754..eff4b43 100644
--- a/waterlayered_halfspace/README
+++ b/waterlayered_halfspace/README
@@ -9,6 +9,8 @@ It then runs a forward simulation which couples acoustic & elastic waves.
step-by-step tutorial:
+0. run the example in the directory homogeneous_halfspace
+
1. create mesh:
- run cubit GUI:
@@ -28,16 +30,18 @@ step-by-step tutorial:
(example assumes 4 partitions with mesh files in OUTPUT_FILES/)
> cd SPECFEM3D
> make
- > ./bin/xdecompose_mesh_SCOTCH 4 ../examples/waterlayered_halfspace/MESH/ ../in_out_files/DATABASES_MPI/
+ > ./bin/xdecompose_mesh_SCOTCH 4 examples/waterlayered_halfspace/MESH/ in_out_files/DATABASES_MPI/
which creates mesh partitions "proc0000***_Database" in directory "DATABASES_MPI".
- you can then specify "DATABASES_MPI" in "Par_file" for your "LOCAL_PATH"
+ you can then specify "../in_out_files/DATABASES_MPI" in "Par_file" for your "LOCAL_PATH"
3. generate databases:
- - copy Par_file, CMTSOLUTION & STATIONS files provided in this examples directory to in_data_files/ directory in
- the SPECFEM3D root directory
+ - copy Par_file, CMTSOLUTION & STATIONS files provided in this examples directory to SPECFEM3D/in_data_files/
+ > cd examples/waterlayered_halfspace/in_data_files
+ > cp CMTSOLUTION Par_file STATIONS ../../../in_data_files/
+ > cd SPECFEM3D
- compile generate_databases:
> make xgenerate_databases
@@ -57,7 +61,6 @@ step-by-step tutorial:
- submit job script:
> qsub go_solver_pbs.bash
-
-
-
-
+ note: simulation will take about 45 minutes and generate
+ 3 sets (semd,semv,sema) of 672 files in in_out_files/OUTPUT_FILES,
+ as well as 13 timestamp****** files
\ No newline at end of file
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