Skip to content

Commit

Permalink
Merge pull request #1608 from boutproject/v4.2.2-rc
Browse files Browse the repository at this point in the history
v4.2.2 Release
  • Loading branch information
ZedThree authored Mar 1, 2019
2 parents 33ff18b + 890148a commit a0cf8ee
Show file tree
Hide file tree
Showing 17 changed files with 144 additions and 74 deletions.
27 changes: 26 additions & 1 deletion CHANGELOG.md
Original file line number Diff line number Diff line change
@@ -1,4 +1,29 @@
# Changelog
# Change Log

## [v4.2.2](https://github.com/boutproject/BOUT-dev/tree/v4.2.2) (2019-02-27)

[Full Changelog](https://github.com/boutproject/BOUT-dev/compare/v4.2.1...v4.2.2)

**Merged pull requests:**

- Fix some clang-tidy warnings [\#1612](https://github.com/boutproject/BOUT-dev/pull/1612) ([ZedThree](https://github.com/ZedThree))
- Check if we need to link against libdl for dladdr [\#1611](https://github.com/boutproject/BOUT-dev/pull/1611) ([ZedThree](https://github.com/ZedThree))
- Fix unclean exit [\#1610](https://github.com/boutproject/BOUT-dev/pull/1610) ([dschwoerer](https://github.com/dschwoerer))
- Fix a couple of small(ish) bugs in FV::Div\_par\_K\_Grad\_par [\#1609](https://github.com/boutproject/BOUT-dev/pull/1609) ([bendudson](https://github.com/bendudson))
- Fix FV::Div\_a\_Laplace\_perp and FV::Div\_par\_K\_Grad\_par [\#1606](https://github.com/boutproject/BOUT-dev/pull/1606) ([bendudson](https://github.com/bendudson))
- Bugfix laplacexz [\#1605](https://github.com/boutproject/BOUT-dev/pull/1605) ([bendudson](https://github.com/bendudson))
- Initialise some mesh variables to sensible defaults [\#1604](https://github.com/boutproject/BOUT-dev/pull/1604) ([ZedThree](https://github.com/ZedThree))
- Fix prototype Div\(v2d, f2d\) in header [\#1603](https://github.com/boutproject/BOUT-dev/pull/1603) ([bendudson](https://github.com/bendudson))
- Hypnotoad version numbering [\#1595](https://github.com/boutproject/BOUT-dev/pull/1595) ([johnomotani](https://github.com/johnomotani))
- Provide formatting string [\#1588](https://github.com/boutproject/BOUT-dev/pull/1588) ([dschwoerer](https://github.com/dschwoerer))
- Fix bug in FCI: missed last point in Z for corner displacements [\#1587](https://github.com/boutproject/BOUT-dev/pull/1587) ([ZedThree](https://github.com/ZedThree))
- use MPIRUN if set [\#1585](https://github.com/boutproject/BOUT-dev/pull/1585) ([dschwoerer](https://github.com/dschwoerer))
- Prevent failures on parallel, clean build [\#1583](https://github.com/boutproject/BOUT-dev/pull/1583) ([dschwoerer](https://github.com/dschwoerer))
- More printf [\#1581](https://github.com/boutproject/BOUT-dev/pull/1581) ([dschwoerer](https://github.com/dschwoerer))
- Provide argument for printf [\#1580](https://github.com/boutproject/BOUT-dev/pull/1580) ([dschwoerer](https://github.com/dschwoerer))
- Ensure Coordinates is a complete type when trying to swap [\#1574](https://github.com/boutproject/BOUT-dev/pull/1574) ([ZedThree](https://github.com/ZedThree))
- Compile with BOUT_FLAGS [\#1573](https://github.com/boutproject/BOUT-dev/pull/1573) ([dschwoerer](https://github.com/dschwoerer))
- Swap coordinates when adding - to master [\#1549](https://github.com/boutproject/BOUT-dev/pull/1549) ([johnomotani](https://github.com/johnomotani))

## [v4.2.1](https://github.com/boutproject/BOUT-dev/tree/v4.2.1) (2019-01-23)

Expand Down
13 changes: 7 additions & 6 deletions CITATION.bib
Original file line number Diff line number Diff line change
@@ -1,11 +1,12 @@
@misc{BOUTv4-1-2,
@misc{BOUTv4-2-2,
author = {
Benjamin Daniel Dudson and
Peter Alec Hill and
David Dickinson and
Joseph Parker and
Adam Dempsey and
Andrew Allen and
Arka Bokshi and
Brendan Shanahan and
Brett Friedman and
Chenhao Ma and
Expand Down Expand Up @@ -42,11 +43,11 @@ @misc{BOUTv4-1-2
Xueqiao Xu and
Zhanhui Wang
},
title = {BOUT++},
month = {12},
year = {2017},
doi = {10.5281/zenodo.1423213},
url = {https://github.com/boutproject/BOUT-dev}
title = {BOUT++},
month = {3},
year = {2019},
doi = {10.5281/zenodo.2579077},
url = {https://github.com/boutproject/BOUT-dev}
}

@article{Dudson2009,
Expand Down
6 changes: 3 additions & 3 deletions CITATION.cff
Original file line number Diff line number Diff line change
Expand Up @@ -142,11 +142,11 @@ authors:

- family-names: Wang
given-names: Zhanhui
version: 4.2.1
date-released: 2019-01-23
version: 4.2.2
date-released: 2019-03-01
repository-code: https://github.com/boutproject/BOUT-dev
url: http://boutproject.github.io/
doi: 10.5281/zenodo.2530733
doi: 10.5281/zenodo.2579077
license: 'LGPL-3.0-or-later'
references:
- type: article
Expand Down
85 changes: 74 additions & 11 deletions configure
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
#! /bin/sh
# Guess values for system-dependent variables and create Makefiles.
# Generated by GNU Autoconf 2.69 for BOUT++ 4.2.1.
# Generated by GNU Autoconf 2.69 for BOUT++ 4.2.2.
#
# Report bugs to <[email protected]>.
#
Expand Down Expand Up @@ -580,8 +580,8 @@ MAKEFLAGS=
# Identity of this package.
PACKAGE_NAME='BOUT++'
PACKAGE_TARNAME='bout--'
PACKAGE_VERSION='4.2.1'
PACKAGE_STRING='BOUT++ 4.2.1'
PACKAGE_VERSION='4.2.2'
PACKAGE_STRING='BOUT++ 4.2.2'
PACKAGE_BUGREPORT='[email protected]'
PACKAGE_URL=''

Expand Down Expand Up @@ -1359,7 +1359,7 @@ if test "$ac_init_help" = "long"; then
# Omit some internal or obsolete options to make the list less imposing.
# This message is too long to be a string in the A/UX 3.1 sh.
cat <<_ACEOF
\`configure' configures BOUT++ 4.2.1 to adapt to many kinds of systems.
\`configure' configures BOUT++ 4.2.2 to adapt to many kinds of systems.
Usage: $0 [OPTION]... [VAR=VALUE]...
Expand Down Expand Up @@ -1421,7 +1421,7 @@ fi

if test -n "$ac_init_help"; then
case $ac_init_help in
short | recursive ) echo "Configuration of BOUT++ 4.2.1:";;
short | recursive ) echo "Configuration of BOUT++ 4.2.2:";;
esac
cat <<\_ACEOF
Expand Down Expand Up @@ -1550,7 +1550,7 @@ fi
test -n "$ac_init_help" && exit $ac_status
if $ac_init_version; then
cat <<\_ACEOF
BOUT++ configure 4.2.1
BOUT++ configure 4.2.2
generated by GNU Autoconf 2.69
Copyright (C) 2012 Free Software Foundation, Inc.
Expand Down Expand Up @@ -2131,7 +2131,7 @@ cat >config.log <<_ACEOF
This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.
It was created by BOUT++ $as_me 4.2.1, which was
It was created by BOUT++ $as_me 4.2.2, which was
generated by GNU Autoconf 2.69. Invocation command line was
$ $0 $@
Expand Down Expand Up @@ -6094,6 +6094,69 @@ fi
done


fi

if test $works = yes; then :

{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for library containing dladdr" >&5
$as_echo_n "checking for library containing dladdr... " >&6; }
if ${ac_cv_search_dladdr+:} false; then :
$as_echo_n "(cached) " >&6
else
ac_func_search_save_LIBS=$LIBS
cat confdefs.h - <<_ACEOF >conftest.$ac_ext
/* end confdefs.h. */
/* Override any GCC internal prototype to avoid an error.
Use char because int might match the return type of a GCC
builtin and then its argument prototype would still apply. */
#ifdef __cplusplus
extern "C"
#endif
char dladdr ();
int
main ()
{
return dladdr ();
;
return 0;
}
_ACEOF
for ac_lib in '' dl; do
if test -z "$ac_lib"; then
ac_res="none required"
else
ac_res=-l$ac_lib
LIBS="-l$ac_lib $ac_func_search_save_LIBS"
fi
if ac_fn_cxx_try_link "$LINENO"; then :
ac_cv_search_dladdr=$ac_res
fi
rm -f core conftest.err conftest.$ac_objext \
conftest$ac_exeext
if ${ac_cv_search_dladdr+:} false; then :
break
fi
done
if ${ac_cv_search_dladdr+:} false; then :

else
ac_cv_search_dladdr=no
fi
rm conftest.$ac_ext
LIBS=$ac_func_search_save_LIBS
fi
{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_search_dladdr" >&5
$as_echo "$ac_cv_search_dladdr" >&6; }
ac_res=$ac_cv_search_dladdr
if test "$ac_res" != no; then :
test "$ac_res" = "none required" || LIBS="$ac_res $LIBS"
works=yes
else
works=no; break
fi


fi

if test $works = yes; then :
Expand Down Expand Up @@ -12787,7 +12850,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
# report actual input values of CONFIG_FILES etc. instead of their
# values after options handling.
ac_log="
This file was extended by BOUT++ $as_me 4.2.1, which was
This file was extended by BOUT++ $as_me 4.2.2, which was
generated by GNU Autoconf 2.69. Invocation command line was
CONFIG_FILES = $CONFIG_FILES
Expand Down Expand Up @@ -12840,7 +12903,7 @@ _ACEOF
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
ac_cs_version="\\
BOUT++ config.status 4.2.1
BOUT++ config.status 4.2.2
configured by $0, generated by GNU Autoconf 2.69,
with options \\"\$ac_cs_config\\"
Expand Down Expand Up @@ -14015,7 +14078,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1
# report actual input values of CONFIG_FILES etc. instead of their
# values after options handling.
ac_log="
This file was extended by BOUT++ $as_me 4.2.1, which was
This file was extended by BOUT++ $as_me 4.2.2, which was
generated by GNU Autoconf 2.69. Invocation command line was
CONFIG_FILES = $CONFIG_FILES
Expand Down Expand Up @@ -14068,7 +14131,7 @@ _ACEOF
cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1
ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`"
ac_cs_version="\\
BOUT++ config.status 4.2.1
BOUT++ config.status 4.2.2
configured by $0, generated by GNU Autoconf 2.69,
with options \\"\$ac_cs_config\\"
Expand Down
6 changes: 5 additions & 1 deletion configure.ac
Original file line number Diff line number Diff line change
Expand Up @@ -32,7 +32,7 @@
#

AC_PREREQ([2.69])
AC_INIT([BOUT++],[4.2.1],[[email protected]])
AC_INIT([BOUT++],[4.2.2],[[email protected]])
AC_CONFIG_AUX_DIR([build-aux])
AC_CONFIG_MACRO_DIR([m4])

Expand Down Expand Up @@ -357,6 +357,10 @@ AS_IF([test "x$enable_backtrace" = "xyes" || test "x$enable_backtrace" = "xmaybe
AC_CHECK_HEADERS([execinfo.h dlfcn.h], [works=yes], [works=no; break])
])
AS_IF([test $works = yes], [
AC_SEARCH_LIBS([dladdr], [dl], [works=yes], [works=no; break])
])
AS_IF([test $works = yes], [
AC_MSG_NOTICE([Native backtrace enabled])
CXXFLAGS="$CXXFLAGS -DBACKTRACE"
Expand Down
33 changes: 5 additions & 28 deletions include/mask.hxx
Original file line number Diff line number Diff line change
Expand Up @@ -25,8 +25,8 @@
#include <vector>

#include "bout/mesh.hxx"
#include "boutexception.hxx"
#include "globals.hxx"
#include "msg_stack.hxx"

/**
* 3D array of bools to mask Field3Ds
Expand All @@ -46,15 +46,10 @@
* }
*/
class BoutMask {
// Dimensions of mask
int nx;
int ny;
int nz;
// Internal data
Tensor<bool> mask;
public:
BoutMask(int nx, int ny, int nz, bool value=false) :
nx(nx), ny(ny), nz(nz),
mask(nx, ny, nz) {
mask = value;
}
Expand All @@ -69,32 +64,14 @@ public:
return *this;
}

inline bool& operator()(int jx,int jy,int jz) {
#if CHECK > 2
// Perform bounds checking
if((jx < 0) || (jx >= nx) ||
(jy < 0) || (jy >= ny) ||
(jz < 0) || (jz >= nz))
throw BoutException("BoutMask: (%d, %d, %d) operator out of bounds (%d, %d, %d)",
jx, jy, jz, nx, ny, nz);
#endif
inline bool& operator()(int jx, int jy, int jz) {
TRACE("BoutMask::operator()(%d, %d, %d)", jx, jy, jz);
return mask(jx, jy, jz);
}
inline const bool& operator()(int jx,int jy,int jz) const {
#if CHECK > 2
// Perform bounds checking
if((jx < 0) || (jx >= nx) ||
(jy < 0) || (jy >= ny) ||
(jz < 0) || (jz >= nz))
throw BoutException("BoutMask: (%d, %d, %d) operator out of bounds (%d, %d, %d)",
jx, jy, jz, nx, ny, nz);
#endif
inline const bool& operator()(int jx, int jy, int jz) const {
TRACE("BoutMask::operator()(%d, %d, %d)", jx, jy, jz);
return mask(jx, jy, jz);
}

};




#endif //__MASK_H__
4 changes: 2 additions & 2 deletions include/output.hxx
Original file line number Diff line number Diff line change
Expand Up @@ -65,15 +65,15 @@ public:
Output() : multioutbuf_init(), std::basic_ostream<char, _Tr>(multioutbuf_init::buf()) {
buffer_len = BUFFER_LEN;
buffer = new char[buffer_len];
enable();
Output::enable();
}

/// Specify a log file to open
Output(const char *fname)
: multioutbuf_init(), std::basic_ostream<char, _Tr>(multioutbuf_init::buf()) {
buffer_len = BUFFER_LEN;
buffer = new char[buffer_len];
enable();
Output::enable();
open("%s",fname);
}
~Output() override {
Expand Down
2 changes: 1 addition & 1 deletion manual/doxygen/Doxyfile
Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,7 @@ PROJECT_NAME = BOUT++
# could be handy for archiving the generated documentation or if some version
# control system is used.

PROJECT_NUMBER = 4.2.1
PROJECT_NUMBER = 4.2.2

# Using the PROJECT_BRIEF tag one can provide an optional one line description
# for a project that appears at the top of each page and should give viewer a
Expand Down
2 changes: 1 addition & 1 deletion manual/doxygen/Doxyfile_readthedocs
Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,7 @@ PROJECT_NAME = BOUT++
# could be handy for archiving the generated documentation or if some version
# control system is used.

PROJECT_NUMBER = 4.2.1
PROJECT_NUMBER = 4.2.2

# Using the PROJECT_BRIEF tag one can provide an optional one line description
# for a project that appears at the top of each page and should give viewer a
Expand Down
2 changes: 1 addition & 1 deletion manual/sphinx/conf.py
Original file line number Diff line number Diff line change
Expand Up @@ -133,7 +133,7 @@ def __getattr__(cls, name):
# The short X.Y version.
version = '4.2'
# The full version, including alpha/beta/rc tags.
release = '4.2.1'
release = '4.2.2'

# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
Expand Down
11 changes: 5 additions & 6 deletions src/bout++.cxx
Original file line number Diff line number Diff line change
Expand Up @@ -633,11 +633,10 @@ int BoutMonitor::call(Solver *solver, BoutReal t, int iter, int NOUT) {
// Check if enough time left

BoutReal t_remain = mpi_start_time + wall_limit - MPI_Wtime();
if (t_remain < wtime) {
// Less than 1 time-step left
output_warn.write("Only %e seconds left. Quitting\n", t_remain);

return 1; // Return an error code to quit
if (t_remain < wtime*2) {
// Less than 2 time-steps left
output_warn.write("Only %e seconds (%.2f steps) left. Quitting\n", t_remain,t_remain/wtime);
user_requested_exit=true;
} else {
output_progress.print(" Wall %s", (time_to_hms(t_remain)).c_str());
}
Expand All @@ -649,7 +648,7 @@ int BoutMonitor::call(Solver *solver, BoutReal t, int iter, int NOUT) {
if (f.good()) {
output << "\n" << "File " << stopCheckName
<< " exists -- triggering exit." << endl;
return 1;
user_requested_exit=true;
}
}

Expand Down
Loading

0 comments on commit a0cf8ee

Please sign in to comment.