- added an explicit print, but only report profiling to the log
file from master process.
We don't wish to overwrite any profiling that was conducted during
the simulation. Besides which, we don't have a proper Time object
for handling the write nicely either.
- add note in BuildIssues about the I_MPI_CC variable, which is needed
when building with Intel-MPI and gcc/clang.
This additional setting is needed since the changes needed to solve
the issue of building scotch with Intel-MPI and icc (issue #434)
means that mpiicc is now being used as the wrapper when compiling
scotch.
- have the FOAM_MPI short name for INTELMPI start with 'impi-' instead
of just the version number.
Intel-MPI is often installed as /opt/intel/impi/4.1.3.049, which
results in 'FOAM_MPI=4.1.3.049' and the mpi flavour is lost.
Prefix these cases with 'impi-'
- suppress error messages that appear with zsh.
According to unset(1p), 'unset -f' unsets a function.
If the function was not previously defined, this is a no-op.
This is similar for zsh, but there it emits a warning if the
function was not previously defined.
- avoid 'local' in functions sources from etc/bashrc.
ksh does not support this.
- use 'command' shell builtin instead of 'type'.
Seems to be more consistent between shell flavours.
- just check WM_PROJECT_DIR instead.
- provide a fallback value when FOAM_EXT_LIBBIN might actually be needed.
Only strictly need FOAM_EXT_LIBBIN for scotch/metis decomposition, and
when these are actually supplied by ThirdParty.
All other ThirdParty dependencies are referenced by BOOST_ARCH_PATH etc.
Can therefore drop the FOAM_EXT_LIBBIN dependency for VTK-related
things, which do not use scotch/metis anyhow.
- this implies that jobControl is a user-resource for OpenFOAM.
It was previously located under $WM_PROJECT_INST_DIR/jobControl,
but few users will have write access there.
- an unset FOAM_JOB_DIR variable is treated as "~/.OpenFOAM/jobControl",
which can partially reduce environment clutter.
- provide argList::noJobInfo() to conveniently suppress job-info on an
individual basis for short-running utilities (eg, foamListTimes) to
avoid unneeded clutter.
- permit SYSTEMMPI user adjustments via
etc/config.{csh,sh}/mpi-system
This can be a convenient place for setting up SYSTEMMPI for OpenFOAM
without adjusting bashrc, prefs.sh ...
- add a USERMPI type. This represents any generic mpi implementation.
The user is responsible for supplying an appropriate
wmake/rules/General/mplibUSERMPI file and managing all settings.
This type of setup can be useful in combination with specific build
systems (SPACK, EASYBUILD, etc) or module systems for which the MPI
variant is part of the installed configuration.
- handle sourcing bashrc with a relative path (issue #383)
- handle sourcing from bash and zsh.
Still need manual intervention when sourcing dash, sh, or ksh.
- replace grep in etc/cshrc with sed only
- logical instead of physical path for WM_PROJECT_DIR (issue #431).
Doesn't seem to be possible for csh/tcsh.
* Continue using physical locations when comparing directories,
but not for the top-level FOAM_INST_DIR, WM_PROJECT_DIR.
- relocate WM_CC, WM_CXX overrides from etc/config.*/compiler
to etc/config.*/settings to ensure that they are left untouched
when etc/config.sh/compiler is sourced while making third-party
packages (eg, gcc, llvm, CGAL).
- provide fallback FOAM_TUTORIALS setting in RunFunctions
STYLE: remove "~OpenFOAM" fallback as being too rare, non-obvious
Can now use this:
_foamSourceEtc config.sh/scotch
_foamSourceEtc config.csh/scotch
instead of this:
_foamSource $($WM_PROJECT_DIR/bin/foamEtcFile config.sh/scotch)
_foamSource `$WM_PROJECT_DIR/bin/foamEtcFile config.csh/scotch`
In the bash/sh version, leave the _foamSource function for now, since
ThirdParty is still relying on it.
STYLE: elminate while-loop for _foamAddPath etc since this type of
construct isn't readily possible for csh and isn't being used anywhere.
- as per bashrc,cshrc delimit with
"# USER EDITABLE PART"
"# END OF (NORMAL) USER EDITABLE PART"
this can help simplify any patching for system-building scripts etc.
- LD_LIBRARY_PATH was not being cleaned at all when switching between
paraview versions.
- PATH was cleaned against the third-party paraview-*, although 3rd
party paraview is installed as ParaView-*.
The additional cleanup for ParaView_DIR may not catch this (if it
was unset elsewhere).
- wm32/wm64 were for changing between -m32, -m64 builds on x86_64
architectures. This is seldom enough not to warrant a special alias.
Also ambiguous if these could refer to label sizes.
- Remove wm32,wm64 aliases.
- Add wmInt32, wmInt64 aliases for switching WM_LABEL_SIZE.
STYLE: only use paraview settings when actually available
- this means executing makeParaView prior to building OpenFOAM itself,
but is consistent with the instructions given by makeParaView,
and elminates anticipating the source location from the paraview
config file, which increases the build flexibilty for ThirdParty
- support gperftools-none, gperftools-system configurations
as per other third-party packages.
STYLE: clean up more environment variables
CONFIG: testing adios rule
* boost 1_62_0 (Sept 2016)
* CGAL 4.9 (Sept 2016)
- now has headers-only mode that could be interesting
* FFTW 3.3.5 (Jul 2016)
* openmpi 1.10.4 (Sept 2016)
- the first openmpi 2.x release is also available, but too early to switch
* paraview 5.2.0 (Nov 2016)
- builds without additional patching
STYLE: removed unneeded CMake environment variables
- Now that the metisDecomp uses the metis definition for float/double,
do not need to verify the scalar sizes.
Note:
- could drop precision qualifier for metis, scotch installation
(include, lib) as being unneeded, but it is simpler to keep them
and continue to use the FOAM_EXT_LIBBIN path
(in case other ThirdParty software is compiled with different
precisions).
- Cannot test if these older reader modules actually build,
owning largely to build issues since with paraview 3.14 (Feb 2012)
and paraview 3.98 (Dec 2012) themselves.
- Follow similar pattern as per boost/CGAL with the '*-none' to disable,
and '*-system' for system installations.
Also support central non-ThirdParty installations by specifying the
version as "*-system", but also providing the fully qualified
*_ARCH_PATH too.
--
ENH: Verify label and scalar sizes used in the metis header.
- ensure they match with expected values, which can be obtained via
the OpenFOAM definitions for WM_LABEL_SIZE and WM_PRECISION_OPTION
On 64-bit systems, the system installations of boost, cgal are under
lib64/. The behaviour for a ThirdParty build is mostly lib/ but this
can also be changing.
Boost 1_62_0 and older build into 'lib/'.
CGAL-4.9 builds into 'lib64/', older versions into 'lib/'.
Future-proof things by using lib$WM_COMPILER_LIB_ARCH for boost and
cgal build rules, and forcing these as build targets in the ThirdParty
makeCGAL as well.
--
STYLE: check for boost/version.hpp, CGAL/version.h instead their directories
- In the foundation version they introduced a construct to handle
the transition from 'wmRefresh' as an alias to 'wmRefresh' as
a shell function. This transition is unnecessary for OpenFOAM+
since 1606 used wmREFRESH (not wmRefresh) as an alias.
For portability it is important to avoid this non-POSIX
"type -t". It causes issues with dash and with zsh
(mentioned in issue #277).
type -t dash -> -t: not found
type -t zsh -> zsh: bad option: -t
Note: zsh users may still noticed other problems.
For example, the POSIX 'unset -f' normally has no output, but in zsh
it reports an error and has exit code 1 if the function was not
previously defined. Whereas in POSIX (including bash, dash) it only
returns non-zero if the name(s) could not be unset.
- instead we use the CGAL settings directly since they have the
same option of (version | system | none)
- may wish to review this again in the future.
- "$FOAM_USER_APPBIN" and "$FOAM_USER_LIBBIN" have been added to
"foamOldDirs" in "etc/bashrc" and "etc/config.sh/unset"
- "$OPAL_PREFIX" is now undefined in the option "SYSTEMOPENMPI" within
"etc/config.sh/mpi", but only if the path defined in this variable
is cleaned when using "foamCleanPath".
- "$OPAL_PREFIX" is now also conditionally undefined in
"etc/config.sh/unset" when the path is picked up by "foamCleanPath".
Patch contributed by Bruno Santos
Resolved bug-report http://bugs.openfoam.org/view.php?id=2210
The change from C++0x to C++11 allows all of C++11 functionality to be
used in OpenFOAM, in particular constructor delegation which avoids code
duplication or constructor helper functions. However, this also means a
change to the minimum gcc version supported which is now 4.7 rather than
4.5.
Note that gcc-4.7 does not support the entire C++11 standard but does
support all of the functionality currently needed for further OpenFOAM
development. The minimum gcc-version which supports the entire C++11
standard is 4.8 which is now the recommended minimum gcc version.
- export/setenv WM_COMPILER_TYPE as suggested by Mattijs.
- for overall consistency, don't carp about an unset WM_COMPILER_TYPE,
since this would only be on the first instance (prior to the
export/setenv) and would be confusing about why/when this message
may occur.
- reduce clutter: only use (system|ThirdParty) for WM_COMPILER_TYPE.
Drop the old 'OpenFOAM' setting for WM_COMPILER_TYPE, which was
transitional in early 2011.
- make the error messages more meaningful
with the more general and flexible 'postProcess' utility and '-postProcess' solver option
Rationale
---------
Both the 'postProcess' utility and '-postProcess' solver option use the
same extensive set of functionObjects available for data-processing
during the run avoiding the substantial code duplication necessary for
the 'foamCalc' and 'postCalc' utilities and simplifying maintenance.
Additionally consistency is guaranteed between solver data processing
and post-processing.
The functionObjects have been substantially re-written and generalized
to simplify development and encourage contribution.
Configuration
-------------
An extensive set of simple functionObject configuration files are
provided in
OpenFOAM-dev/etc/caseDicts/postProcessing
and more will be added in the future. These can either be copied into
'<case>/system' directory and included into the 'controlDict.functions'
sub-dictionary or included directly from 'etc/caseDicts/postProcessing'
using the '#includeEtc' directive or the new and more convenient
'#includeFunc' directive which searches the
'<etc>/caseDicts/postProcessing' directories for the selected
functionObject, e.g.
functions
{
#includeFunc Q
#includeFunc Lambda2
}
'#includeFunc' first searches the '<case>/system' directory in case
there is a local configuration.
Description of #includeFunc
---------------------------
Specify a functionObject dictionary file to include, expects the
functionObject name to follow (without quotes).
Search for functionObject dictionary file in
user/group/shipped directories.
The search scheme allows for version-specific and
version-independent files using the following hierarchy:
- \b user settings:
- ~/.OpenFOAM/\<VERSION\>/caseDicts/postProcessing
- ~/.OpenFOAM/caseDicts/postProcessing
- \b group (site) settings (when $WM_PROJECT_SITE is set):
- $WM_PROJECT_SITE/\<VERSION\>/caseDicts/postProcessing
- $WM_PROJECT_SITE/caseDicts/postProcessing
- \b group (site) settings (when $WM_PROJECT_SITE is not set):
- $WM_PROJECT_INST_DIR/site/\<VERSION\>/caseDicts/postProcessing
- $WM_PROJECT_INST_DIR/site/caseDicts/postProcessing
- \b other (shipped) settings:
- $WM_PROJECT_DIR/etc/caseDicts/postProcessing
An example of the \c \#includeFunc directive:
\verbatim
#includeFunc <funcName>
\endverbatim
postProcess
-----------
The 'postProcess' utility and '-postProcess' solver option provide the
same set of controls to execute functionObjects after the run either by
reading a specified set of fields to process in the case of
'postProcess' or by reading all fields and models required to start the
run in the case of '-postProcess' for each selected time:
postProcess -help
Usage: postProcess [OPTIONS]
options:
-case <dir> specify alternate case directory, default is the cwd
-constant include the 'constant/' dir in the times list
-dict <file> read control dictionary from specified location
-field <name> specify the name of the field to be processed, e.g. U
-fields <list> specify a list of fields to be processed, e.g. '(U T p)' -
regular expressions not currently supported
-func <name> specify the name of the functionObject to execute, e.g. Q
-funcs <list> specify the names of the functionObjects to execute, e.g.
'(Q div(U))'
-latestTime select the latest time
-newTimes select the new times
-noFunctionObjects
do not execute functionObjects
-noZero exclude the '0/' dir from the times list, has precedence
over the -withZero option
-parallel run in parallel
-region <name> specify alternative mesh region
-roots <(dir1 .. dirN)>
slave root directories for distributed running
-time <ranges> comma-separated time ranges - eg, ':10,20,40:70,1000:'
-srcDoc display source code in browser
-doc display application documentation in browser
-help print the usage
pimpleFoam -postProcess -help
Usage: pimpleFoam [OPTIONS]
options:
-case <dir> specify alternate case directory, default is the cwd
-constant include the 'constant/' dir in the times list
-dict <file> read control dictionary from specified location
-field <name> specify the name of the field to be processed, e.g. U
-fields <list> specify a list of fields to be processed, e.g. '(U T p)' -
regular expressions not currently supported
-func <name> specify the name of the functionObject to execute, e.g. Q
-funcs <list> specify the names of the functionObjects to execute, e.g.
'(Q div(U))'
-latestTime select the latest time
-newTimes select the new times
-noFunctionObjects
do not execute functionObjects
-noZero exclude the '0/' dir from the times list, has precedence
over the -withZero option
-parallel run in parallel
-postProcess Execute functionObjects only
-region <name> specify alternative mesh region
-roots <(dir1 .. dirN)>
slave root directories for distributed running
-time <ranges> comma-separated time ranges - eg, ':10,20,40:70,1000:'
-srcDoc display source code in browser
-doc display application documentation in browser
-help print the usage
The functionObjects to execute may be specified on the command-line
using the '-func' option for a single functionObject or '-funcs' for a
list, e.g.
postProcess -func Q
postProcess -funcs '(div(U) div(phi))'
In the case of 'Q' the default field to process is 'U' which is
specified in and read from the configuration file but this may be
overridden thus:
postProcess -func 'Q(Ua)'
as is done in the example above to calculate the two forms of the divergence of
the velocity field. Additional fields which the functionObjects may depend on
can be specified using the '-field' or '-fields' options.
The 'postProcess' utility can only be used to execute functionObjects which
process fields present in the time directories. However, functionObjects which
depend on fields obtained from models, e.g. properties derived from turbulence
models can be executed using the '-postProcess' of the appropriate solver, e.g.
pisoFoam -postProcess -func PecletNo
or
sonicFoam -postProcess -func MachNo
In this case all required fields will have already been read so the '-field' or
'-fields' options are not be needed.
Henry G. Weller
CFD Direct Ltd.
See commit b627924a4bf104521b567d3aa3dc80c864325b1a
Allwmake: Added scripted changes for REALTYPEWIDTH and IDXTYPEWIDTH
Patch contributed by Bruno Santos
Resolves bug-report http://bugs.openfoam.org/view.php?id=2085
Patch contributed by Bruno Santos:
- "etc/config.sh/CGAL":
- Indented the contents of the recently added if block.
- Added comment about using system versions.
- Library paths are now only added if the respective version is not "boost-system" and "cgal-system".
- "src/renumber/Allwmake":
It now relies on the previous file to get the version for
Boost (the same way as in "makeCGAL"). This is so that it will also
build "SloanRenumber" if "boost_version" is set to "boost-system".
- "applications/utilities/mesh/generation/Allwmake":
It now also relies on the script "config.sh/CGAL" to get the
version for CGAL. If "cgal_version" is set to "cgal-system", it
will now also build "foamy*Mesh" utilities and respective
libraries.
Resolves report http://www.openfoam.org/mantisbt/view.php?id=1232
1. "foamCompiler" was changed to a more permanent "WM_COMPILER_TYPE"
environment variable, so that it can be used by 3rd party
installation scripts, such as "makeGcc", "makeLLVM" and so on. More
on this will be provided in issue #1215.
2. The script functions such as "_foamSource()" and "_foamAddPath()"
were moved to a new file "etc/config.sh/functions". It has the
ability to set or unset, depending on whether "WM_BASH_FUNCTIONS" is
defined or not. This allows for these functions to be reused by
other scripts, such as "makeGcc".
3. The script "etc/config.sh/CGAL" relies on whether a local
environment variable "SOURCE_CGAL_VERSIONS_ONLY" is defined or not,
so that it will load only the version settings if it's defined. This
is to make it easier to call this script from "makeCGAL". Although
it still feels a bit of a clunky hack, but I didn't manage to deduce
any other way we could do this :( I didn't add indentation within
the if-block, to make it easier to read the changes. In addition,
the local variable "common_path" is used to shorten the length of
the lines and use slightly less repeated code.
4. Added another new script "etc/config.sh/compiler", which has only
the version numbers for the compilers taken out from the "settings"
file. It currently depends on "WM_COMPILER_TYPE" for setting the
variables, the same way it did with "foamCompiler". This script is
now always sourced from the "settings" file, for the following
reasons:
- "makeGCC" and "makeLLVM" can now take advantage of this script file.
- The example "compiler" script (detailed next) can rely on this
script file and then override parameters on-demand, as well as
allowing for system compilers to have dedicated settings, such as
setting "WM_CC". This is similar to how the example environment
script for "paraview" works.
5. To the script "etc/config.sh/example/compiler" were added a few more examples:
- It now starts with a block where it first loads the default "compiler" script.
- Has a "WM_COMPILER=Gcc48u" case example for when we try to use GCC
4.8 in Ubuntu 15.10. This is just to give the idea that in a
particular system, we might have several system-wide compiler
versions. For example, in Ubuntu 15.10, there is GCC 4.7, 4.8 and
5.2, which could be used for testing performances or compatibility
with some other 3rd party library.
- Has the "WM_COMPILER=Icc" case example, related to the original bug
report, where "WM_CC=icc" and "WM_CXX=icpc", so that the user then
simply copies this file to their own local preferences folder.
6. Small bug fix in "etc/config.sh/mpi", where unsetting "minBufferSize" was missing at the end of the script.
7. Small change in "etc/config.sh/paraview", where "CMAKE_ROOT" is set
along with "CMAKE_HOME". This is due to a rare issue that occurs on
people's systems where they have a custom system-wide CMake version
installed and which is used by having "CMAKE_ROOT" set on that
environment. This can mess up OpenFOAM's custom ParaView builds,
given that conflicting CMake versions can lead to not building
ParaView at all.
- For more details about "CMAKE_ROOT":
https://cmake.org/Wiki/CMake_Useful_Variables [^]
8. The scripts "_foamAddPath _foamAddLib _foamAddMan" were not being
unset at the end of "settings". They are now unset at the end of
"bashrc", through a call to the new double-use "functions" script.
Additionally all references to "foamCompiler" have been changed to
"WM_COMPILER_TYPE".
See also http://www.openfoam.org/mantisbt/view.php?id=1232
- move unset mpi buffer size from config.csh/settings -> config.csh/mpi
- wmUNSET now also unalias wmREFRESH
Note: unsetenv WM_COMPILER_TYPE in csh variant?
- drop reference to paraview-3 in config files.
Cannot say anything definite about support for versions
this old (2012)
- replace with an alternative workaround.
Unset the _foamAddLib function prior to sourcing config.sh/CGAL:
- LD_LIBRARY_PATH will not be adjusted.
- cgal_version/boost_version variables will be retained.
Note: for ThirdParty builds, it is important that the boost and CGAL
paths are added into LD_LIBRARY_PATH even if before they are created.
This ensures that the OpenFOAM environment is functional after the
build.
The '*-none' and '*-system' specifications can still be used to avoid
setting them at all.
- not previously possible to configure a third-party gcc
with system gmp/mpfr/mpc.
This makes it easier to switch between compilers for testing.
- use system libraries by default
etc/config.sh and etc/config.csh
This structure is more convenient to add support for other shells, e.g. zsh, fish etc.
Resolves feature request to simplify support for other shells in
http://www.openfoam.org/mantisbt/view.php?id=1232
