[cig-commits] [commit] devel, master: updated README files for examples. also added go_decomposer_pbs.bash to remind user not to run huge partition jobs on the head node, but rather on a (high-memory) compute node (7fbec60)
cig_noreply at geodynamics.org
cig_noreply at geodynamics.org
Wed Jun 18 16:48:14 PDT 2014
Repository : https://github.com/geodynamics/specfem3d
On branches: devel,master
Link : https://github.com/geodynamics/specfem3d/compare/6026e367984905ab133865f62fa6293b343759b9...47f703851338234f96397e7da9fbff63d8178b8a
>---------------------------------------------------------------
commit 7fbec602590ccacd6a5ca4adc82eb6ce08de6886
Author: Carl Tape <carltape at gi.alaska.edu>
Date: Tue Feb 1 07:00:23 2011 +0000
updated README files for examples. also added go_decomposer_pbs.bash to remind user not to run huge partition jobs on the head node, but rather on a (high-memory) compute node
>---------------------------------------------------------------
7fbec602590ccacd6a5ca4adc82eb6ce08de6886
homogeneous_halfspace/README | 18 ++++++++------
layered_halfspace/README | 56 ++++++++++++++++++++++++++++++++------------
tomographic_model/README | 3 +++
3 files changed, 55 insertions(+), 22 deletions(-)
diff --git a/homogeneous_halfspace/README b/homogeneous_halfspace/README
index 7da7664..329452a 100644
--- a/homogeneous_halfspace/README
+++ b/homogeneous_halfspace/README
@@ -22,7 +22,7 @@ step-by-step tutorial:
If successful, this will generate the files in src/shared/:
Makefile, constants.h, and precision.h, among others
- NOTE: the same compiler used for SCOTCH must be used for SPECFEM3D (ifort or gfortran)
+ note: the same compiler used for SCOTCH must be used for SPECFEM3D (ifort or gfortran)
- copy two run scripts from utils/Cluster/ into SPECFEM3D/, e.g.,
pbs/go_generate_databases_pbs.bash
@@ -40,7 +40,7 @@ step-by-step tutorial:
then run meshing script:
claro -> Menu "Tools" -> "Play Journal File" ... and select file: "block_mesh.py"
- if everything goes fine, this creates all the mesh files in a subdirectory MESH/:
+ if everything goes fine, this creates the ten mesh files in subdirectory MESH/:
MESH/absorbing_surface_file_bottom
MESH/absorbing_surface_file_xmax
MESH/absorbing_surface_file_xmin
@@ -71,18 +71,22 @@ step-by-step tutorial:
(for your convenience, these resulting database files are also provided in the example's
DATABASES-default/ directory for comparison.)
+ note 1: the program xdecompose_mesh_SCOTCH is a serial program (runs on 1 core)
+ note 2: alternatively, run decomposer on a compute node using
+ utils/Cluster/pbs/go_partition_pbs.bash
+
4. generate databases:
- - compile generate_databases from SPECFEM3D/ :
- > cd SPECFEM3D
+ - compile generate_databases in directory SPECFEM3D/ :
> make xgenerate_databases
- submit job script
> qsub go_generate_databases_pbs.bash
- NOTE: this script will need to be tailored to your cluster, e.g.,
+ note 1: this script will need to be tailored to your cluster, e.g.,
> bsub < go_generate_databases_lsf.bash
+ note 2: you may want to explicity specify the desired queue
this will create binary mesh files, e.g. "proc000***_external_mesh.bin"
in directory in_out_files/DATABASES_MPI/.
@@ -96,9 +100,9 @@ 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.,
+ 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 5 minutes,
+ note 2: the simulation runs on 4 cores and should take about 5 minutes,
and you can track the progress with the timestamp files
generated in in_out_files/OUTPUT_FILES/
diff --git a/layered_halfspace/README b/layered_halfspace/README
index ba8817f..6a08efb 100644
--- a/layered_halfspace/README
+++ b/layered_halfspace/README
@@ -20,32 +20,54 @@ step-by-step tutorial:
claro -> Menu "Tools" -> "Play Journal File" ... and select file: "2lay_mesh_boundary_fig8.py"
(or select: "2lay_mesh_boundary_fig8-nodoubling.py" for regular mesh without doubling layer)
-
+open read_cubit_
this creates all the mesh files in subdirectory MESH/
- - optional:
- if you want to check mesh quality (element skewdness, stability criteria)
- using check_mesh_quality_CUBIT_Abaqus/check_mesh_quality_CUBIT_Abaqus.f90,
- then Export to Abacus (*.inp) file:
- claro -> Menu "File" -> "Export..." and select Abaqus (*.inp)
+ - optional: check mesh quality using check_mesh_quality_CUBIT_Abaqus.f90
+
+ using the CUBIT GUI:
+ claro -> Menu "File" -> "Export...", select Abaqus (*.inp)
e.g. export as "layered_halfspace_mesh.inp"
- note: only output blocks for volumes, i.e. block ids 1,2,3 for this example here,
- not for faces
+ note 1: only output blocks for volumes, i.e. block ids 1,2,3 for this example here
+ note 2: do NOT select "Export Using Cubit IDs"
+
+ alternatively, using the CUBIT command line:
+ > export Abaqus "layered_halfspace_mesh.inp" Block 1,2,3 overwrite cubitids
+
+ change directory
+ > cd ../..//src/check_mesh_quality_CUBIT_Abaqus/
- save number of nodes and number of elements and edit in header of
- check_mesh_quality_CUBIT_Abaqus.f90:
+ save number of nodes and number of elements and edit in header of
+ check_mesh_quality_CUBIT_Abaqus.f90:
character(len=100), parameter :: cubit_mesh_file = 'layered_halfspace_mesh.inp'
- integer, parameter :: NPOIN = 44436 ! number of nodes
- integer, parameter :: NSPEC = 40500 ! number of elements (only volumes, i.e. block ids 1,2,3 )
- integer, parameter :: NGNOD = 8 ! hexahedral elements
+ integer, parameter :: NPOIN = 76819 ! number of nodes
+ integer, parameter :: NSPEC = 70200 ! number of elements (only volumes, i.e. block ids 1,2,3 )
+ integer, parameter :: NGNOD = 8 ! hexahedral elements
logical, parameter :: IGNORE_OTHER_HEADERS = .false.
double precision, parameter :: delta_t = 0.005 ! arbitrary, initial guess
double precision, parameter :: VP_MAX = 7500.d0 ! maximum vp in volume block id 3
+ link Abaqus file
+ > ln -s ../../examples/layered_halfspace/layered_halfspace_mesh.inp .
+
+ compile programs
+ > make
+
+ run program
+ > ../../bin/xcheck_mesh_quality_CUBIT_Abaqus
+ at prompts, enter, for example, 1, then 0.6 to list elements with high skewness
+
+ plot skewness histogram as ps file
+ > gnuplot
+ > load "plot_mesh_quality_histogram.gnu"
+ > set term postscript color solid
+ > set output 'hist_skewness.ps'
+ > replot
+ > quit
2. decompose mesh files:
@@ -61,7 +83,7 @@ step-by-step tutorial:
3. generate databases:
- - copy Par_file, CMTSOLUTION & STATIONS files provided in this examples directory to SPECFEM3D/in_data_files/
+ - copy example files Par_file, CMTSOLUTION & STATIONS to SPECFEM3D/in_data_files/
> cd examples/layered_halfspace/in_data_files
> cp CMTSOLUTION Par_file STATIONS ../../../in_data_files/
> cd SPECFEM3D
@@ -72,9 +94,13 @@ step-by-step tutorial:
- submit job script:
> qsub go_generate_databases_pbs.bash
- (note: if execution fails due to memory shortage - most likely fails when calling routine to
+ this will create binary mesh files, e.g. "proc000***_external_mesh.bin"
+ in directory in_out_files/DATABASES_MPI/.
+ (note: if execution fails due to memory shortage - most likely fails when calling routine to
create regional mesh - then try to increase process memory stack size: ulimit -s 2000000 (2GB) )
+ optional: load a set of .vtk files into paraview to view model, mesh, and partitioning
+ (note: must have Par_file option SAVE_MESH_FILES = .true.)
4. run simulation:
diff --git a/tomographic_model/README b/tomographic_model/README
index 1bf492b..0ab7dd7 100644
--- a/tomographic_model/README
+++ b/tomographic_model/README
@@ -34,6 +34,9 @@ step-by-step tutorial:
- copy this file into directory SPECFEM3D/in_data_files/
> cp tomography_model.xyz ../../in_data_files/
+ note: this file is read in by subroutine read_model_tomography in
+ SPECFEM3D/src/generate_databases/model_tomography.f90,
+ which is called by get_model.f90
- copy Par_file, CMTSOLUTION & STATIONS files provided in this examples directory to SPECFEM3D/in_data_files/
> cd in_data_files/
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