Merge remote-tracking branch 'origin/maint'

Merge branch 'barry/2019-10-20/fix-mumps-sudo/maint' into 'maint'

sudo installs did not work for MUMPS; also improved configure printing of...

See merge request petsc/petsc!2201

sudo installs did not work for MUMPS; also improved configure printing of exception tracebacks and fix for Python3 use of e.message that may not exist

Commit-type: configure, bug
Reported-by: Miguel

sudo installs did not work for MUMPS; also improved configure printing of exception tracebacks and fix for Python3 use of e.message that may not exist

Commit-type: configure, bug
Reported-by: Miguel Fosas de Pando <miguel.fosas@gmail.com>

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Merge branch 'barry/2019-08-05/features-cray-knl' into 'master'

Features for Cray KNL systems

See merge request petsc/petsc!2044

Features for Cray KNL systems

Detect Cray compilers and use them automatically, no longer need to use --with-cc=cc etc.
more installation.html information on using theta
Detect MKLROOT and use it if

Features for Cray KNL systems

Detect Cray compilers and use them automatically, no longer need to use --with-cc=cc etc.
more installation.html information on using theta
Detect MKLROOT and use it if no specific BLAS/LAPACK requested
Error if Cray environment detected but no Cray compiler modules set, prevents compiling with old sequential gnu compilers on the system
For Intel and GNU Cray environments on KNL systems allow compiling packages whose configures call executables by stripping the
KNL specific arguments from the compile libraries for the external libraries, thus --download-hdf5 etc work (note this does
not work for the Cray compilers because I could not figure out how to run the drive.cc programs that the cc compiler
lists when generating the complete compile/link list of compiler arguments, includes, and libraries)

Commit-type: ease-of-use, feature

Minor updates based on comments of the reviewers of the MR

Commit-type: style-fix
Reported-by: Satish Balay <balay@mcs.anl.gov>

Add self.installwithbatch = 0 for hypre since it attempts to run programs during configure
Note that with the PETSc automatic cross compiling on Theta hypre will configure and build successfully

Fix directory for checking default BLAS/LAPACK locations before checking MKLROOT variable

Fixed error in BlasLapack.py which resulted from bad merge and the variables were set too late, changed used of ls to Python function

Commit-type: bug-fix, style-fix
Reported-by: gitlab-ci

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Merge branch 'barry/2019-07-27/error-check-mpiexec' into 'master'

Large number of fixes, optimizations for configure, speeds up the configure

See merge request petsc/petsc!2046

Large number of fixes, optimizations for configure, speeds up the configure

1) turn off checking if MPI library is shared since that code has been broken for 3+ years

2) move pure Fortran configure

Large number of fixes, optimizations for configure, speeds up the configure

1) turn off checking if MPI library is shared since that code has been broken for 3+ years

2) move pure Fortran configure tests to compilersFortran.py

3) turned threads back on but only use them for performing timeout for *runtest() commands (since they slow everything down if used
everywhere)

4) changed parallel configure (which doesn't work anyways) to use --useParallel and not overload --useThreads

5) added runtime check of mpiexec that uses timeout (replaces previous test in MPI shared libraries)

6) removed unused tests in configure in the interest of speed

7) minor refactorization of configure for better support of parallel configure (which doesn't work)

8) added timing results in configure.log. These may be accessed with grep child configure.log | sort -k3 -g

9) add check that mpiexec given in configure test matches the MPI compilers and libraries used

Commit-type: optimization, bug-fix, portability-fix, feature
Reported-by: Carl Steefel <cisteefel@lbl.gov>

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Merge branch 'master' into this one.

Merge branch 'jed/gitlab-ci'

Add use of --package-prefix-hash for testing

Commit-type: testing

adios: fix pthread dependency

PTScotch: correctly list zlib, pthread as optional dependencies [and not hard-code the libraries her

Add use of --package-prefix-hash for testing

Commit-type: testing

adios: fix pthread dependency

PTScotch: correctly list zlib, pthread as optional dependencies [and not hard-code the libraries here]

configure hash: sort the hash of config files - this way its independent of the order of files listed by 'os.walk'

BlasLapack should use self.blaslapack.directory instead of self.libDir since this will be correct with -package-prefix-hash

Correctly handle saving hashvalue to prefix directory when --force is used

Packages that are built after PETSc configure finishes, postProcess() should never go in hash prefix location; just get rebuilt each time

Commit-type: bug-fix
Reported-by: Satish Balay <balay@mcs.anl.gov>

Need to encode hash information before passing to hash library in python3

Commit-type: portability-fix
Reported-by: gitlab CI

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Merged in barry/check-bad-urls (pull request #1685)

Barry/check bad urls

Approved-by: Patrick Sanan <patrick.sanan@gmail.com>
Approved-by: Junchao Zhang <junchao.zhang@gmail.com>

Fixed out-dated URLS using make checkbadURLS REPLACE=1

One manual fix of https://en.wikipedia.org/wiki/Buckingham_π_theorem since the automatic tool dropped the first _ for some reason
Manual fix of

Fixed out-dated URLS using make checkbadURLS REPLACE=1

One manual fix of https://en.wikipedia.org/wiki/Buckingham_π_theorem since the automatic tool dropped the first _ for some reason
Manual fix of //faq.html since the automatic tool incorrectly replaced /faq.html to //faq.html in some locations

These are largely updates of http to https but have a variety of other website location changes

Once this branch is in master individual developers can run make checkbadURLS and fix URLs related to their projects manually

Commit-type: bug-fix, documentation

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Merge branch 'master' into m.diehl/fortran-tests

Merge branch 'balay/fix-configure-non-english-text-handling/maint' into maint [PR #1587]

* balay/fix-configure-non-english-text-handling/maint:
configure: correctly convert non-english chars to utf-

Merge branch 'balay/fix-configure-non-english-text-handling/maint' into maint [PR #1587]

* balay/fix-configure-non-english-text-handling/maint:
configure: correctly convert non-english chars to utf-8 in python3

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Merge branch 'balay/fix-configure-non-english-text-handling/maint' [PR #1587]

* balay/fix-configure-non-english-text-handling/maint:
configure: correctly convert non-english chars to utf-8 in python3

configure: correctly convert non-english chars to utf-8 in python3

This issue came up on a windows machine with MS compilers with French language

Reported-by: Clausen Pascal <pascal.clausen@epfl.ch>

Merge branch 'maint'

Merged in barry/rm-log-preprocessor/maint (pull request #1516)

Remove logging in configure.log the output generated by running the preprocessor, i.e. the copies of all the include files

Approved-by

Merged in barry/rm-log-preprocessor/maint (pull request #1516)

Remove logging in configure.log the output generated by running the preprocessor, i.e. the copies of all the include files

Approved-by: Jed Brown <jed@59a2.org>

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Remove logging in configure.log the output generated by running the preprocessor,
i.e. the copies of all the include files

On my Mac this eliminated over 80% of the log file size

Note: if at some p

Remove logging in configure.log the output generated by running the preprocessor,
i.e. the copies of all the include files

On my Mac this eliminated over 80% of the log file size

Note: if at some point a user has a problem that requires access to the include file
details to debug we can add a ./configure flag to retain the information

Commit-type: feature
Reported-by: Jed Brown <jed@jedbrown.org>

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Merged petsc/petsc into master

Merge branch 'master' into jpusztay/feature-swarm-symplectic-example

Merge branch 'master' into jpustay/feature-swarm-example

Merged petsc/petsc into master

Merge branch 'master' into arcowie-rem/feature-error-logging

* master: (393 commits)
Bib: Update reference
Mat: Doc fix
Bib: Updated ref
PetscDS: Doc fixes
PC+LU: Do not try to refactor an

Merge branch 'master' into arcowie-rem/feature-error-logging

* master: (393 commits)
Bib: Update reference
Mat: Doc fix
Bib: Updated ref
PetscDS: Doc fixes
PC+LU: Do not try to refactor an already factored matrix
Mat: Small fix for checking and docs
Mat: Added MatSetFactorType() - Needed it when making a shell matrix look factored
PetscDS: Added PetscDSUpdateBoundary() - Lets the user change the boundary condition
single precision produces different convergence history
p4est: has a dependency on zlib - so handle it correctly
Add -mat_mffd_complex to use the Lyness complex number trick to compute J_u * v instead of differencing.
Replace VecWAXPY by VecAXPY if needed
Revert "Replace VecWAXPY by VecAXPY if needed"
Replace VecWAXPY by VecAXPY if needed
MatHermitianTransposeGetMat and MatCreateVecs
ex19: Updated test filter to avoid false positives.
DM: Improved Global-To-Natural docs Suggested-by: Josh L <ysjosh.lo@gmail.com>
Do not build shared openblas when doing static build
Upgrade OpenBLAS to 0.3.3
test: add alt output file for changes in OSX-10.14 and Xcode-10.0 [perhaps related to ML]
...

Conflicts:
src/vec/is/utils/vsectionis.c

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Merge branch 'jed/python3-futurize' [PR #1122]

Merge announces support for Python 3.4+ in changes/dev.html.

* jed/python3-futurize: (44 commits)
gmakegentest: avoid prefix matching in regex
dm

Merge branch 'jed/python3-futurize' [PR #1122]

Merge announces support for Python 3.4+ in changes/dev.html.

* jed/python3-futurize: (44 commits)
gmakegentest: avoid prefix matching in regex
dm tests ex23.c: fix test args: -one -two -three
gmakegentest: more fixes
gmakegentest: fix processing of arguments containing number followed by "-"
gmakegentest: always loop over nsize; Python-3 fixes
python3: add in a python-3.4 test
python: fix build on osx/opensolaris - where 'RANLIB=ranlib -c' i.e with a space..
python3: fix --download-ptscotch error
configure: glob() gets executed early - whereas we need to get file list later [after 'make all' or equivalent] so revert back to using shell to get file-list
python3: map() requires a list modifier for this usage.
python: replace ModuleNotFoundError a python3.6+ feature with ImportError
config: call setup to ensure that debugLevel is set
nightlies: switch linux-pkg-dbg-ftn-interfaces to python3
config: enable Python-3
config: urllib/urlparse updates for Python-3 compatibility
config fblaslapack: use isIBM instead of manual test
python: replace commands with subprocess
Fix LOCDIR paths
generateetags.py: switch from commands to subprocess; unicode fix
python: don't import commands when it isn't used
...

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