Improvements to artifacts

Following the gitlab ref page on artifacts, this is an attempt to
upload the test log files and the gcov tarbal from `make gcov`
Includes update of gcov.py to use optparse

Improvements to artifacts

Following the gitlab ref page on artifacts, this is an attempt to
upload the test log files and the gcov tarbal from `make gcov`
Includes update of gcov.py to use optparse and eliminate os.environ for
getting petsc_dir and petcs_arch.
Also include {configure,make}.log to artifacts.

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build: fix usage of preprocessor flags across languages
- consistently set flags CPP_FLAGS, FPP_FLAGS, CXXPP_FLAGS, PCPP_FLAGS
- add PPPFLAGS, PFLAGS to map user-make-flags CFLAGS/CXXFLAGS or CPPFL

build: fix usage of preprocessor flags across languages
- consistently set flags CPP_FLAGS, FPP_FLAGS, CXXPP_FLAGS, PCPP_FLAGS
- add PPPFLAGS, PFLAGS to map user-make-flags CFLAGS/CXXFLAGS or CPPFLAGS/CXXPPFLAGS correctly to the PCC compile targets
- use PCPP_FLAGS with PCC targets and CXXPP_FLAGS with CXX targets

Notes
- CFLAGS/CPPFLAGS [API] for makefile does not override the the same variables specified to configure.
[CFLAGS/CPPFAGS to configure are saved in CC_FLAGS, CPP_FLAGS]
- For some reason CPPFLAGS gets added to both CC_FLAGS [via self.setCompilers.getCompilerFlags()] and CPP_FLAGS. Its not clear if one can be remoted
- We do not have a clean C compile target like we have for Cxx - due to --with-clanguage [hence PCC etc intertwined with PETSC_COMPILE..]

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Add .f90 to Fortran compile rule
Reported-by: Randall Mackie <rlmackie862@gmail.com>

awk-5: fix warning

make: [/home/balay/tmp/petsc/lib/petsc/conf/rules:551: html] Error 2 (ignored)
awk: cmd. line:1: warning: regexp escape sequence `\"' is not a known regexp operator

Only mv files if they differ

makefile: add back .F.o compile target

Fixes pflotran build

release: set v3.12 strings

update exclude files for release tarball

Merge branch 'jed/pcbddc-lumped' into 'master'

Jed/pcbddc lumped

See merge request petsc/petsc!1390

petscdiff: update to ignore diff of type

< 0.816052 + 0.i
< 0.882676 + 0.i
---
> 0.814213 + 6.39015e-18i
> 0.862679 - 2.57658e-17i

added layout type to bfort-petsc.txt

Merge branch 'scott/test-improve' into 'master'

Various improvements to test harness

See merge request petsc/petsc!2024

Merge branch 'master' into 'barry/2019-08-22/fix-fblaslapack-for-nag'

# Conflicts:
# lib/petsc/conf/test

Various improvements

1. Test logging now separates tap output and just the error output.
What is streamed is now controlled with the -o flag to the shell
scripts which now has two options curr

Various improvements

1. Test logging now separates tap output and just the error output.
What is streamed is now controlled with the -o flag to the shell
scripts which now has two options currently: 'interactive' and
'err_only'. The V=0 flag and OUTPUT=1 flags to gmakefile.test
turn on the err_only option
The OUTPUT=1 is default for gitlab

2. gmakegentest.py has a (-c,--check-output) option which does nothing
but check if the output files specified by tests are in the output
directories, and return a non-zero error code if they are not there
check_output target is in outer makefile and add `make check_output` to
stage zero tests to prevent running stage 2 and 3 with missing output
files

3. report_tests.py was not giving the correct command to invoke just the
files that failed. This is because it was coded assuming a
particular naming scheme for the tests: an assumption that was both
incorrect, and led to an ill-posed problem for fixing: If a test
label has underscores, it was not easy to fix. The solution was to
change to telling users to globsearch. In fixing, globsearch had to
be generalized to allow for multiple patterns: e.g.,
make -f gmakefile test globsearch='dm_impls_plex_tutorials-ex5_* ts_tutorials-ex11_*'

4. Bug fix for subtests with loop variables
(Reported Jakub Kruzik <jakub.kruzik@vsb.cz> on 6/26/19)

5. This does a minor fix in this utility script which prints out datafiles.

Commit-type: testing-fix, feature

Out check_output rule to outer makefile

Commit-type: feature
Reported-by: gitlab-ci

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Merge branch 'barry/2019-08-21/updates-pardiso' into 'master'

Add some additional error checking for MKL_Pardiso and MKL_CPardiso and turn...

See merge request petsc/petsc!2013

Remove unneeded variable, allow users to provide initial LDLIBS value

CI: always check for latest datafiles

Remove stray space from library name, remove filtering from test makefile for LDFLAGS since it cannot handle blanks in directory names (Windows)

Commit-type: bug-fix, portability-fix
Reported-by: Mo

Remove stray space from library name, remove filtering from test makefile for LDFLAGS since it cannot handle blanks in directory names (Windows)

Commit-type: bug-fix, portability-fix
Reported-by: Mohammad Asghar <mohammad.asghar@lusas.com>

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Merge branch 'barry/2019-08-21/add-matfdcoloringsetvalues' into 'master'

Added MatFDColoringSetValues() takes matrix in compressed color form (as often...

See merge request petsc/petsc!1999

Fix spelling of ID to Id so that bfort generates correct code

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

Many fixes to get PETSc and --download-fblaslapack working with nagfor compiler

Works with --download-fblaslapack, --download-scalapack, --download-mpich (does not work with --download-mumps)

Uses

Many fixes to get PETSc and --download-fblaslapack working with nagfor compiler

Works with --download-fblaslapack, --download-scalapack, --download-mpich (does not work with --download-mumps)

Uses lib/petsc/bin/petscnagfor as wrapper compiler since nagfor cannot work natively with the PETSc/standard Unix build environment

Required fixes/modernizations for BLAS/LAPACK source code (updated in the branch used by this branch, need to make it a tag when done)

Found a couple of portability issues with PETSc mpif.h

When package build fails they will no longer dump all the (huge amount) build output to the screeen

Commit-type: portability-fix

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tests: create check-test-errors allgtests-tap [which ignores timeout errors] for gitlab-ci.

Also pass PETSC_ARCH/PETSC_DIR to gmakefile for allgtest, allgtest-tap, cleantest

fix allgtests-tap - as

tests: create check-test-errors allgtests-tap [which ignores timeout errors] for gitlab-ci.

Also pass PETSC_ARCH/PETSC_DIR to gmakefile for allgtest, allgtest-tap, cleantest

fix allgtests-tap - as it was not stopping on error

do not flag failure on test timeout

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Fixes for testing

added p4est to valgrind supression file
add missing error checking in xxt and xyt
mark as TODO system examples for error checking that produce inconsistent output
single precision

Fixes for testing

added p4est to valgrind supression file
add missing error checking in xxt and xyt
mark as TODO system examples for error checking that produce inconsistent output
single precision alt files
filters for yaml test

Commit-type: portability-fix, testing-fix

Commit-type: bug-fix

Commit-type: testing-fix
Reported-by: gitlab ci

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website: update bitbucket -> gitlab

Extract comments from .c[xx] and .h.