Merge pull request #1258 from danielpeter/devel

updates tests and scripts; updates source arrays; adds additional source time functions; adds additional mesh outputs for visualization

Author: danielpeter

.azure-pipelines.yml

@@ -84,7 +84,7 @@ jobs:
     displayName: 'Run checks'
 
 - job: compilation_default
-  # ubuntu-latest: ubuntu-22.04 w/ GCC 11
+  # ubuntu-latest: ubuntu-24.04 w/ GCC 13.3
   displayName: 'Compilation Default GCC'
   steps:
   - template: .azure-pipelines/install-template.yml
@@ -96,14 +96,14 @@ jobs:
       CUDA: false
       BUILD: true
 
-- job: compilation_default_gcc9
-  displayName: 'Compilation Default GCC 9'
+- job: compilation_default_gcc10
+  displayName: 'Compilation Default GCC 10'
   pool:
-    vmImage: 'ubuntu-20.04'
+    vmImage: 'ubuntu-22.04'
   variables:
-    CC: gcc-9
-    CXX: g++-9
-    FC: gfortran-9
+    CC: gcc-10
+    CXX: g++-10
+    FC: gfortran-10
   steps:
   - template: .azure-pipelines/install-template.yml
     parameters:
@@ -114,14 +114,14 @@ jobs:
       CUDA: false
       BUILD: true
 
-- job: compilation_default_gcc10
-  displayName: 'Compilation Default GCC 10'
+- job: compilation_default_gcc11
+  displayName: 'Compilation Default GCC 11'
   pool:
-    vmImage: 'ubuntu-20.04'
+    vmImage: 'ubuntu-22.04'
   variables:
-    CC: gcc-10
-    CXX: g++-10
-    FC: gfortran-10
+    CC: gcc-11
+    CXX: g++-11
+    FC: gfortran-11
   steps:
   - template: .azure-pipelines/install-template.yml
     parameters:
@@ -132,52 +132,52 @@ jobs:
       CUDA: false
       BUILD: true
 
-- job: compilation_CUDA11_gcc9
-  displayName: 'Compilation CUDA 11 GCC 9'
+- job: compilation_CUDA11_gcc10
+  displayName: 'Compilation CUDA 11 GCC 10'
   pool:
-    vmImage: 'ubuntu-20.04'
+    vmImage: 'ubuntu-22.04'
   variables:
-    CC: gcc-9
-    CXX: g++-9
-    FC: gfortran-9
+    CC: gcc-10
+    CXX: g++-10
+    FC: gfortran-10
   steps:
   - template: .azure-pipelines/install-template.yml
     parameters:
       CUDA: true
-      CUDA_V: '11.4'
+      CUDA_V: '11.7'
   - template: .azure-pipelines/configure-template.yml
     parameters:
-      TESTFLAGS: '--with-mpi --with-cuda=cuda10'
+      TESTFLAGS: '--with-mpi --with-cuda=cuda11'
       CUDA: true
       BUILD: true
 
-- job: compilation_CUDA11_gcc10
-  displayName: 'Compilation CUDA 11 GCC 10'
+- job: compilation_CUDA11_gcc11
+  displayName: 'Compilation CUDA 11 GCC 11'
   pool:
-    vmImage: 'ubuntu-20.04'
+    vmImage: 'ubuntu-22.04'
   variables:
-    CC: gcc-10
-    CXX: g++-10
-    FC: gfortran-10
+    CC: gcc-11
+    CXX: g++-11
+    FC: gfortran-11
   steps:
   - template: .azure-pipelines/install-template.yml
     parameters:
       CUDA: true
-      CUDA_V: '11.4'
+      CUDA_V: '11.7'
   - template: .azure-pipelines/configure-template.yml
     parameters:
-      TESTFLAGS: '--with-mpi --with-cuda=cuda11'
+      TESTFLAGS: '--with-mpi --with-cuda=cuda10'
       CUDA: true
       BUILD: true
 
 - job: compilation_CUDA12
-  displayName: 'Compilation CUDA 12 GCC 10'
+  displayName: 'Compilation CUDA 12 GCC 12'
   pool:
-    vmImage: 'ubuntu-20.04'
+    vmImage: 'ubuntu-22.04'
   variables:
-    CC: gcc-10
-    CXX: g++-10
-    FC: gfortran-10
+    CC: gcc-12
+    CXX: g++-12
+    FC: gfortran-12
   steps:
   - template: .azure-pipelines/install-template.yml
     parameters:
@@ -195,7 +195,7 @@ jobs:
   - template: .azure-pipelines/install-template.yml
     parameters:
       CUDA: true
-      CUDA_V: '12.1'
+      CUDA_V: '12.9'
   - template: .azure-pipelines/configure-template.yml
     parameters:
       TESTFLAGS: '--with-mpi --with-cuda=cuda12'

.azure-pipelines/install-template.yml

@@ -6,9 +6,9 @@
 # https://github.com/actions/virtual-environments/blob/main/images/linux/Ubuntu1804-README.md
 # ubuntu-20.04:
 # https://github.com/actions/virtual-environments/blob/main/images/linux/Ubuntu2004-README.md
-# ubuntu-22.04 "ubuntu-latest":
+# ubuntu-22.04:
 # https://github.com/actions/runner-images/blob/main/images/linux/Ubuntu2204-Readme.md
-#
+# ubuntu-24.04: "ubuntu-latest"
 parameters:
 - name: CUDA
   type: boolean
@@ -118,35 +118,38 @@ steps:
       #UBUNTU_VERSION=ubuntu2004
       ## distribution jammy: from ubuntu 22.04
       #UBUNTU_VERSION=ubuntu2204
+      ## distribution noble: from ubuntu 24.04
+      #UBUNTU_VERSION=ubuntu2204
 
       # default
-      UBUNTU_VERSION=ubuntu2004
+      UBUNTU_VERSION=ubuntu2204
 
       # CUDA_VERSION - specifies CUDA toolkit version
       echo "CUDA version: $CUDA_V"
       # http://developer.download.nvidia.com/compute/cuda/repos/
       if [ "$CUDA_V" == "6.5" ]; then
-        ## trusty
         CUDA_VERSION=6.5-14
       elif [ "$CUDA_V" == "9.2" ]; then
-        ## xenial
         CUDA_VERSION=9.2.148-1
       elif [ "$CUDA_V" == "10.2" ]; then
-        ## bionic
         CUDA_VERSION=10.2.89-1
       elif [ "$CUDA_V" == "11.4" ]; then
-        ## focal
         CUDA_VERSION=11.4.0-1
+      elif [ "$CUDA_V" == "11.7" ]; then
+        CUDA_VERSION=11.7.0-1
       elif [ "$CUDA_V" == "12.1" ]; then
-        ## focal
         CUDA_VERSION=12.1.1-1
+      elif [ "$CUDA_V" == "12.9" ]; then
+        CUDA_VERSION=12.9.0-1
       else
         # note: - on azure VM nodes with ubuntu 18.04, default gcc version is 9.3;
         #       needs at least CUDA version 10.x
         #       - on azure VM nodes with ubuntu 20.04, default gcc version is 10.3;
         #       needs at least CUDA version 11.x
-        #       - on azure VM nodes with ubuntu-latest (22.04), default gcc version is 11.3;
+        #       - on azure VM nodes with ubuntu 22.04, default gcc version is 11.3;
         #       needs at least CUDA version 11.7
+        #       - on azure VM nodes with ubuntu 24.04 (ubuntu-latest), default gcc version is 13.3;
+        #       needs at least CUDA version ?
         CUDA_VERSION=12.1.1-1
       fi
       echo

.azure-pipelines/test-template.yml

@@ -40,7 +40,7 @@ steps:
     echo "workdir: $WORKDIR"
     echo "current dir: `pwd`"
     echo
-    ln -s $WORKDIR/utils/compare_seismogram_correlations.py
+    ln -s $WORKDIR/utils/scripts/compare_seismogram_correlations.py
     ./compare_seismogram_correlations.py REF_SEIS/ OUTPUT_FILES/
     if [[ $? -ne 0 ]]; then exit 1; fi
     ./compare_seismogram_correlations.py REF_SEIS/ OUTPUT_FILES/ | grep min/max | cut -d \| -f 3 | awk '{print "correlation:",$1; if ($1 < 0.999 ){print $1,"failed"; exit 1;}else{ print $1,"good"; exit 0;}}'

.travis/run_tests.sh

@@ -31,9 +31,9 @@ case "$TESTDIR" in
 10) dir=EXAMPLES/applications/Rayleigh_wave_no_crack/ ;;
 11) dir=EXAMPLES/applications/Rayleigh_wave_with_crack/ ;;
 12) dir=EXAMPLES/reproducible_study/Tape2007/ ;;
-13) dir=EXAMPLES/check_absolute_amplitude_of_pressure_source_seismograms_acoustic/ ;;
-14) dir=EXAMPLES/check_absolute_amplitude_of_force_source_seismograms_elastic/ ;;
-15) dir=EXAMPLES/check_absolute_amplitude_of_force_source_seismograms_viscoelastic/ ;;
+13) dir=EXAMPLES/benchmarks/check_absolute_amplitude_of_pressure_source_seismograms_acoustic/ ;;
+14) dir=EXAMPLES/benchmarks/check_absolute_amplitude_of_force_source_seismograms_elastic/ ;;
+15) dir=EXAMPLES/benchmarks/check_absolute_amplitude_of_force_source_seismograms_viscoelastic/ ;;
 16) dir=EXAMPLES/reproducible_study/Komatitsch2000_fluid_solid/fluid_solid_external_mesh/ ;;
 17) dir=EXAMPLES/reproducible_study/Morency2008_poroelastic_semi_infinite_homogeneous/ ;;
 18) dir=EXAMPLES/applications/initial_mode_LDDRK/ ;;

EXAMPLES/notebooks/specfem2d-colab-example.ipynb

@@ -3,7 +3,7 @@
 #### Script to create the axisymmetric 2.5d mesh necessary to reproduce
 #### Jensen et al. 2007.
 #### This script can be played as a journal file in
-#### Trelis/Cubit (http://www.csimsoft.com/trelis) directly or through the script:
+#### Trelis/Cubit (https://coreform.com) directly or through the script:
 #### make_mesh.sh.
 #### It first run cubit commands and then export the mesh under specfem2d format
 #### using utils/cubit2specfem2d/cubit2specfem2d.py

EXAMPLES/reproducible_study/Bottero2016_axisymmetry_example/JensenMesh.py

@@ -26,7 +26,7 @@ http://scitation.aip.org/content/asa/journal/jasa/140/5/10.1121/1.4965964?aemail
 By default: lx = 15000.0m, lz = 3000.0m, d1 = 600.0m, d2 = 100.0m, l1 = 2000.0m, l2 = 6000.0m
 
 It uses of AXISYM option with an external mesh whose files under specfem2d format are already available in MESH_SMALL.
-This mesh has been created with Cubit/Trelis (http://www.csimsoft.com/trelis) with the script JensenMesh.py which is called by
+This mesh has been created with Cubit/Trelis (https://coreform.com) with the script JensenMesh.py which is called by
 make_mesh.sh. Have a look to the comments in these files if you want to recreate the mesh or just to learn how it is done.
 
 In this example the domain studied is a water layer lying above a viscoelastic seabed with a slope.

EXAMPLES/reproducible_study/Bottero2016_axisymmetry_example/README

@@ -1,6 +1,6 @@
 #!/bin/bash
 #
-# Run Cubit/Trelis (http://www.csimsoft.com/trelis) and cubit2specfem2d to create the mesh in a new directory called MESH by default
+# Run Cubit/Trelis (https://coreform.com) and cubit2specfem2d to create the mesh in a new directory called MESH by default
 # This is how it looks:
 #  ________________________________v__________________________________
 # |   ^         ___________________|______________________________|   | ^

EXAMPLES/reproducible_study/Bottero2016_axisymmetry_example/make_mesh.sh

@@ -6,7 +6,7 @@ \chapter{Getting Started}\label{cha:Getting-Started}
 
 To download the SPECFEM2D software package, type this:
 \begin{verbatim}
-git clone --recursive --branch devel https://github.com/SPECFEM/specfem2d.git
+  git clone --recursive --branch devel https://github.com/SPECFEM/specfem2d.git
 \end{verbatim}
 
 
@@ -18,13 +18,13 @@ \chapter{Getting Started}\label{cha:Getting-Started}
 or your .cshrc file):
 %
 \begin{verbatim}
-    ./configure FC=gfortran CC=gcc
+  ./configure FC=gfortran CC=gcc
 \end{verbatim}
 %
 If you want to run in parallel, i.e., using more than one processor core, then you would type
 %
 \begin{verbatim}
-    ./configure FC=gfortran CC=gcc MPIFC=mpif90 --with-mpi
+  ./configure FC=gfortran CC=gcc MPIFC=mpif90 --with-mpi
 \end{verbatim}
 
 You can replace the GNU compilers above (gfortran and gcc) with other compilers if you want to; for instance for Intel ifort and icc use FC=ifort CC=icc instead.
@@ -53,13 +53,13 @@ \chapter{Getting Started}\label{cha:Getting-Started}
 Just as an example:
 %
 \begin{verbatim}
-    ./configure FC=ifort MPIFC=mpif90 --with-mpi --with-scotch-dir=/opt/scotch
+  ./configure FC=ifort MPIFC=mpif90 --with-mpi --with-scotch-dir=/opt/scotch
 \end{verbatim}
 %
 If you use the Intel ifort compiler to compile the code, we recommend that you use the Intel icc C compiler to compile Scotch, i.e., use:
 %
 \begin{verbatim}
-    ./configure CC=icc FC=ifort MPIFC=mpif90
+  ./configure CC=icc FC=ifort MPIFC=mpif90
 \end{verbatim}
 %
 For further details about the installation of SCOTCH,
@@ -85,7 +85,7 @@ \chapter{Getting Started}\label{cha:Getting-Started}
 After these steps, go back to the main directory of SPECFEM2D/ and type
 %
 \begin{verbatim}
-    make
+  make
 \end{verbatim}
 %
 to create all executables which will be placed into the folder \texttt{./bin/}.\newline
@@ -158,7 +158,7 @@ \section{Adding OpenMP support in addition to MPI}
 \noindent
 To enable OpenMP, add the flag \texttt{-{}-enable-openmp} to the configuration:
 \begin{verbatim}
-./configure --enable-openmp ..
+  ./configure --enable-openmp ..
 \end{verbatim}
 This will add the corresponding OpenMP flag for the chosen Fortran compiler.
 Please note that only the elastic domain solver has OpenMP support for now.\newline