Merge pull request #523 from geodynamics/baagaard/feature-version-3.0.2

baagaard-usgs · web-flow · commit ae1f8f19981e · 2022-08-23T15:42:30.000-06:00
Set version to 3.0.2. Updates for release.
diff --git a/CHANGES.md b/CHANGES.md
@@ -1,5 +1,36 @@
 See <https://github.com/geodynamics/pylith/commits/main> for the complete log of changes made to PyLith.
 
+## Version 3.0.2
+
+This is a bug fix release with no new features or changes to the user interface.
+
+* Add check of PyLith version against version requirements specified in metadata of parameter files.
+* Update defaults to better match most use cases.
+  * Use nonlinear solver.
+  * Basis order is 1 for solution fields.
+  * Basis order is 0 for Cauchy stress and strain.
+  * Use ML algebraic multigrid preconditioner (from Trilinos) instead of GAMG preconditioner for more robust solves. This is a temporary change until we find better GAMG settings.
+* Update PETSc to v3.17.3.
+* Remove obsolete LaTeX documentation.
+* Bug fixes
+  * Add `viz` directory missing from `examples/subduction-2d` in source distribution.
+  * Project output fields using correct PETSc routine (`DMProjectFieldLabel()`). Fixes memory access bugs in both serial and parallel.
+  * Fix build warnings.
+  * Fix reordering that causes errors when importing Gmsh files.
+* Documentation
+  * Add discussion of translating boundary value problem information to parameter settings. Add more code blocks to manual.
+  * Add discussion of `examples/troubleshooting-2d` to manual.
+
+### Binary packages
+
+* Added PyQT5 Python module for interactive plotting with matplotlib.
+* Update PyLith Parameter Viewer to v2.0.1 (fix errors in packaging).
+
+### Known issues
+
+* The default PETSc options provide a computationally expensive preconditioner when solving incompressible elasticity problems in parallel. We expect to have a more optimal preconditioner in the next release.
+* You may still encounter a few bugs when running in parallel; they appear to cases with specific partitioning of the mesh in relation to one or more faults.
+
 ## Version 3.0.1
 
 This is a bug fix release with no new features or changes to the user interface.
diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 # PyLith
 
-[![DOI](https://www.zenodo.org/badge/DOI/10.5281/zenodo.6667614.svg)](https://doi.org/10.5281/zenodo.6667614)
+[![DOI](https://www.zenodo.org/badge/DOI/10.5281/zenodo.6914592.svg)](https://doi.org/10.5281/zenodo.6914592)
 [![MIT License](https://img.shields.io/badge/license-MIT-blue.svg)](https://github.com/geodynamics/pylith/blob/main/LICENSE.md)
 [![Build Status](https://dev.azure.com/baagaard-usgs/pylith/_apis/build/status/geodynamics.pylith?branchName=main)](https://dev.azure.com/baagaard-usgs/pylith/_build/latest?definitionId=2&branchName=main)
 [![codecov](https://codecov.io/gh/geodynamics/pylith/branch/master/graph/badge.svg?token=JiwLVB64EF)](https://codecov.io/gh/geodynamics/pylith)
diff --git a/configure.ac b/configure.ac
@@ -17,7 +17,7 @@ dnl ----------------------------------------------------------------------
 dnl Process this file with autoconf to produce a configure script.
 
 AC_PREREQ(2.59)
-AC_INIT([PyLith], [3.0.1], [https://geodynamics.org/resources/pylith])
+AC_INIT([PyLith], [3.0.2], [https://geodynamics.org/resources/pylith])
 AC_CONFIG_AUX_DIR([./aux-config])
 AC_CONFIG_HEADER([portinfo])
 AC_CONFIG_MACRO_DIR([m4])
@@ -179,7 +179,7 @@ CIT_FUNCTIONSTRING
 dnl VERSION
 CIG_PKG_GIT(PYLITH)
 AC_DEFINE_UNQUOTED([PYLITH_VERSION], ["$PACKAGE_VERSION"], [Define PyLith version])
-AC_DEFINE_UNQUOTED([PYLITH_DOI], ["10.5281/zenodo.6667614"], [Define PyLith doi])
+AC_DEFINE_UNQUOTED([PYLITH_DOI], ["10.5281/zenodo.6914592"], [Define PyLith doi])
 
 dnl ENDIANNESS
 AC_C_BIGENDIAN
diff --git a/docs/conf.py b/docs/conf.py
@@ -22,7 +22,7 @@
 author = 'Brad T. Aagaard, Matthew G. Knepley, Charles A. Williams'
 
 # The full version, including alpha/beta/rc tags
-release = '3.0.1'
+release = '3.0.2'
 
 
 # -- General configuration ---------------------------------------------------
diff --git a/docs/intro/preface.md b/docs/intro/preface.md
@@ -17,9 +17,9 @@ The following peer-reviewed paper discussed the development of PyLith:
 
 To cite the software and manual, use:
 
-- Aagaard, B., M. Knepley, C. Williams (2022), *PyLith v3.0.1.* Davis, CA: Computational Infrastructure of Geodynamics. DOI: 10.5281/zenodo.6667614.
+- Aagaard, B., M. Knepley, C. Williams (2022), *PyLith v3.0.2.* Davis, CA: Computational Infrastructure of Geodynamics. DOI: 10.5281/zenodo.6914592.
 
-- Aagaard, B., M. Knepley, C. Williams (2022), *PyLith Manual, Version 3.0.1.* Davis, CA: Computational Infrastructure of Geodynamics. https://pylith.readthedocs.io/en/v3.0.1
+- Aagaard, B., M. Knepley, C. Williams (2022), *PyLith Manual, Version 3.0.2.* Davis, CA: Computational Infrastructure of Geodynamics. https://pylith.readthedocs.io/en/v3.0.2
 
 ## Support
 
diff --git a/docs/user/install/index.md b/docs/user/install/index.md
@@ -49,10 +49,10 @@ On macOS systems you can check the operating system version by clicking on the A
 3.  Unpack the tarball.
     ```{code-block} bash
       # Linux 64-bit
-      $ tar -xzf pylith-3.0.1-linux-x86_64.tar.gz
+      $ tar -xzf pylith-3.0.2-linux-x86_64.tar.gz
 
       # macOS
-      $ tar -xzf pylith-3.0.1-macOS-11.6.6-x86_64.tar.gz
+      $ tar -xzf pylith-3.0.2-macOS-10.15-x86_64.tar.gz
       ```
 4. Set environment variables.
 The provided `setup.sh` script only works if you are using bash shell.
@@ -66,20 +66,20 @@ Ready to run PyLith.
 To bypass macOS quarantine restrictions, simply use command line program `curl` to download the tarball from within a terminal rather than using a web browser.
 
 ```
-curl -L -O https://github.com/geodynamics/pylith/releases/download/v3.0.1/pylith-3.0.1-macOS-11.6.6-x86_64.tar.gz
+curl -L -O https://github.com/geodynamics/pylith/releases/download/v3.0.2/pylith-3.0.2-macOS-10.15-x86_64.tar.gz
 ```
 
 Alternatively, if you do download the tarball using a web browser, after you unpack the tarball you can remove the macOS quarantine flags using the following commands (requires Administrator access):
 
 ```
 # Show extended attributes
-xattr ./pylith-3.0.1-macOS-11.6.6-x86_64
+xattr ./pylith-3.0.2-macOS-10.15-x86_64
 
 # Output should be
 com.apple.quarantine
 
 # Remove quarantine attributes
-sudo xattr -r -d com.apple.quarantine ./pylith-3.0.1-macOS-11.6.6-x86_64
+sudo xattr -r -d com.apple.quarantine ./pylith-3.0.2-macOS-10.15-x86_64
 ```
 :::
 
@@ -142,7 +142,7 @@ For each package this utility downloads the source code, configures it, builds i
 ## Verifying PyLith is Installed Correctly
 
 The easiest way to verify that PyLith has been installed correctly is to run one or more of the examples supplied with the binary and source code.
-In the binary distribution, the examples are located in `src/pylith-3.0.1/examples` while in the source distribution, they are located in `pylith-3.0.1/examples`.
+In the binary distribution, the examples are located in `src/pylith-3.0.2/examples` while in the source distribution, they are located in `pylith-3.0.2/examples`.
 {ref}`sec-examples` discusses how to run and visualize the results for the examples.
 To run the example discussed in Section {ref}`sec-examples-box-2d`:
 
diff --git a/examples/reverse-2d/step06_twofaults_elastic.cfg b/examples/reverse-2d/step06_twofaults_elastic.cfg
@@ -21,7 +21,7 @@ base = [pylithapp.cfg]
 description = Reverse prescribed slip on main and splay fault with zero displacement Dirichlet boundary condition.
 authors = [Charles Williams, Brad Aagaard]
 keywords = [reverse slip, prescribed slip, multiple faults]
-arguments = [step06_twofaults_elastic.cfg, solver_fault.cfg]
+arguments = [step06_twofaults_elastic.cfg]
 version = 1.0.0
 pylith_version = [>=3.0, <4.0]
 
diff --git a/examples/subduction-3d/step06_slowslip.cfg b/examples/subduction-3d/step06_slowslip.cfg
@@ -24,6 +24,7 @@ description = Slow slip on a patch in the middle of the top of the slab.
 keywords = [prescribed slip, slow slip, generate spatial database]
 arguments = [step06_slowslip.cfg, mat_elastic.cfg]
 version = 2.0.0
+pylith_version = [>3.0]
 
 features = [
     Quasi-static simulation,
diff --git a/examples/subduction-3d/step07a_leftlateral.cfg b/examples/subduction-3d/step07a_leftlateral.cfg
@@ -16,7 +16,7 @@ base = [pylithapp.cfg, greensfns.cfg, mat_elastic.cfg]
 description = "Generate static Green's functions for left-lateral slip on the subduction interface."
 arguments = [step07a_leftlateral.cfg, mat_elastic.cfg]
 version = 2.0.0
-pylith_version = [>=2.0, <3.0]
+pylith_version = [>3.0]
 
 features = [
     pylith.meshio.OutputSolnPoints,
diff --git a/examples/subduction-3d/step07b_reverse.cfg b/examples/subduction-3d/step07b_reverse.cfg
@@ -16,7 +16,7 @@ base = [pylithapp.cfg, greensfns.cfg, mat_elastic.cfg]
 description = "Generate static Green's functions for reverse slip on the subduction interface."
 arguments = [step07b_reverse.cfg, mat_elastic.cfg]
 version = 2.0.0
-pylith_version = [>=2.0, <3.0]
+pylith_version = [>3.0]
 
 features = [
     pylith.meshio.OutputSolnPoints,
diff --git a/examples/subduction-3d/step08a_gravity_refstate.cfg b/examples/subduction-3d/step08a_gravity_refstate.cfg
@@ -17,6 +17,7 @@ description = Gravitational body forces with reference state.
 keywords = [gravitational body forces, reference state]
 arguments = [step08a_gravity_refstate.cfg, mat_elastic.cfg]
 version = 2.0.0
+pylith_version = [>3.0]
 
 features = [
     Static simulation,
diff --git a/examples/subduction-3d/step08b_gravity_incompressible.cfg b/examples/subduction-3d/step08b_gravity_incompressible.cfg
@@ -14,6 +14,7 @@ description = Gravitational body forces with incompressible elasticity.
 keywords = [gravitational body forces, incompressible elasticity, field split conditioner, Schur complemenet preconditioner]
 arguments = [step08b_gravity_incompressible.cfg, mat_elastic_incompressible.cfg]
 version = 2.0.0
+pylith_version = [>3.0]
 
 features = [
     Static simulation,
diff --git a/examples/subduction-3d/step08c_gravity_viscoelastic.cfg b/examples/subduction-3d/step08c_gravity_viscoelastic.cfg
@@ -23,7 +23,7 @@ description = Gravitational body forces with viscoelasticity, reference state, a
 keywords = [gravitational body forces, reference state, small strain formulation]
 arguments = [step08c_gravity_viscoelastic.cfg, mat_viscoelastic.cfg]
 version = 1.0.0
-pylith_version = [>=2.0, <3.0]
+pylith_version = [>3.0]
 
 features = [
     Quasi-static simulation,
diff --git a/examples/troubleshooting-2d/step06_twofaults.cfg b/examples/troubleshooting-2d/step06_twofaults.cfg
@@ -21,7 +21,7 @@ base = [pylithapp.cfg]
 description = Reverse prescribed slip on main and splay fault with zero displacement Dirichlet boundary condition.
 authors = [Charles Williams]
 keywords = [reverse slip, prescribed slip, multiple faults]
-arguments = [step06_twofaults.cfg, solver_fault.cfg]
+arguments = [step06_twofaults.cfg]
 version = 1.0.0
 pylith_version = [>=3.0, <4.0]
 
diff --git a/release-notes/Makefile.am b/release-notes/Makefile.am
@@ -46,7 +46,8 @@ EXTRA_DIST = \
 	announce_v2.2.0.txt \
 	announce_v2.2.1.txt \
 	announce_v3.0.0.txt \
-	announce_v3.0.1.txt
+	announce_v3.0.1.txt \
+	announce_v3.0.2.txt
 
 
 # End of file 
diff --git a/release-notes/announce_v3.0.2.txt b/release-notes/announce_v3.0.2.txt
@@ -0,0 +1,46 @@
+# PyLith v3.0.2 now available
+
+I am pleased to announce the release of PyLith 3.0.2, a finite-element code designed to solve dynamic elastic problems and quasistatic viscoelastic problems in tectonic deformation.
+
+You can download the source code and binaries from
+  <https://geodynamics.org/resources/pylith>
+
+Documentation
+  <https://pylith.readthedocs.org/en/v3.0.2>
+
+## Release Notes
+
+This is a bug fix release with no new features or changes to the user interface.
+
+* Add check of PyLith version against version requirements specified in metadata of parameter files.
+* Update defaults to better match most use cases.
+  * Use nonlinear solver.
+  * Basis order is 1 for solution fields.
+  * Basis order is 0 for Cauchy stress and strain.
+  * Use ML algebraic multigrid preconditioner (from Trilinos) instead of GAMG preconditioner for more robust solves. This is a temporary change until we find better GAMG settings.
+* Update PETSc to v3.17.3.
+* Remove obsolete LaTeX documentation.
+* Bug fixes
+  * Add `viz` directory missing from `examples/subduction-2d` in source distribution.
+  * Project output fields using correct PETSc routine (`DMProjectFieldLabel()`). Fixes memory access bugs in both serial and parallel.
+  * Fix build warnings.
+  * Fix reordering that causes errors when importing Gmsh files.
+* Documentation
+  * Add discussion of translating boundary value problem information to parameter settings. Add more code blocks to manual.
+  * Add discussion of `examples/troubleshooting-2d` to manual.
+
+### Binary packages
+
+* Added PyQT5 Python module for interactive plotting with matplotlib.
+* Update PyLith Parameter Viewer to v2.0.1 (fix errors in packaging).
+
+### Known issues
+
+* The default PETSc options provide a computationally expensive preconditioner when solving incompressible elasticity problems in parallel. We expect to have a more optimal preconditioner in the next release.
+* You may still encounter a few bugs when running in parallel; they appear to cases with specific partitioning of the mesh in relation to one or more faults.
+
+## Contributors
+
+* Brad Aagaard
+* Matthew Knepley
+* Charles Williams
diff --git a/release-notes/checklist.txt b/release-notes/checklist.txt
@@ -73,9 +73,9 @@ TAG
 
 RELEASE
 
-  * Create release from tag on GitHub.
+  * Reserve DOI at zenodo and update DOI in README.md, configure.ac, and preface.md.
 
-  * Get DOI at zenodo and update DOI in README.md, configure.ac, and userguide.tex.
+  * Create release from tag on GitHub.
 
   * Upload source tarballs to GitHub. 
 
diff --git a/setup.cfg b/setup.cfg
@@ -4,7 +4,7 @@ tag_date = 0
 
 [metadata]
 name = pylith
-version = 3.0.1
+version = 3.0.2
 author = Brad Aagaard, Matthew Knepley, Charles Williams
 author_email = baagaard@usgs.gov, knepley@buffalo.edu, c.williams@gns.cri.nz
 description = Finite-element software for modeling crustal deformation with an emphasis on earthquake faulting.
