* First draft of amrvis package file.
* More additions to amrvis.
* Formatting.
* Forcing compiler environment variables to point to spack mpi compilers when using mpi.
* Disabling intel compiler for amrvis.
* Comments.
* Refining amrvis package file.
* Moving library and include locations variables to be inserted at the first lines of the makefile.
* Globbing amrvis binary instead of constructing its name.
* Making env variable setting consistent and fixing globbing of executable.
* Using iglob instead of glob.
* Turning MPI on by default for Amrvis.
* ENH: Building OpenFOAM sub-packages (issue #8579)
* Some support for packages building with OpenFOAM
- Adjust the wrappers calling the OpenFOAM Allwmake script. Have them
look for a Allwmake-spack file first, which is assumed to contain
special adjustments for compiling with spack.
This file could be delivered as part of a tarball (which is unlikely)
or generated on the fly by the spack sub-package as part of its
patch or configure stage.
CONFIG: change the default paraview variant for openfoam to be False
- the different combinations of paraview backends, off-screen etc
make it difficult to suggest that building with paraview as
a standard dependency makes much sense.
Additionally, building paraview with qt can become quite an issue.
So it makes much more sense to only enable that upon request.
ENH: add a +vtk variant.
- for VTK with off-screen rendering to be used by the runTimePostProcessing
function object, which is a fairly simple framework for generating images of
some OpenFOAM derived objects (eg, sampling planes).
SPACK spec problem:
- reflect the flex restriction impose by the scotch dependency within
the openfoam spec as well, as partial workaround for buggy or annoying
spec resolution.
OTHER:
- updated the backstop foamEtcFile file to include args handling
as per the OpenFOAM-v1806 updates.
* new version: OpenFOAM-v1806
- https://www.openfoam.com/releases/openfoam-v1806/
Functional updates:
- `python` now creates a copy of the `python` binaries when it is added
to a view
- Python extensions (packages which subclass `PythonPackage`) rewrite
their shebang lines to refer to python in the view
- Python packages in the same namespace will not generate conflicts if
both have `...lib/site-packages/namespace-example/__init__.py`
- These `__init__` files will also remain when removing any package in
the namespace until the last package in the namespace is removed
Generally (Updated 2/16):
- Any package can define `add_files_to_view` to customize how it is added
to a view (and at the moment custom definitions are included for
`python` and `PythonPackage`)
- Likewise any package can define `remove_files_from_view` to customize
which files are removed (e.g. you don't always want to remove the
namespace `__init__`)
- Any package can define `view_file_conflicts` to customize what it
considers a merge conflict
- Global activations are handled like views (where the view root is the
spec prefix of the extendee)
- Benefit: filesystem-management aspects of activating extensions are
now placed in views (e.g. now one can hardlink a global activation)
- Benefit: overriding `Package.activate` is more straightforward (see
`Python.activate`)
- Complication: extension packages which have special-purpose logic
*only* when activated outside of the extendee prefix must check for
this in their `add_files_to_view` method (see `PythonPackage`)
- `LinkTree` is refactored to have separate methods for copying a
directory structure and for copying files (since it was found that
generally packages may want to alter how files are copied but still
wanted to copy directories in the same way)
TODOs (updated 2/20):
- [x] additional testing (there is some unit testing added at this point
but more would be useful)
- [x] refactor or reorganize `LinkTree` methods: currently there is a
separate set of methods for replicating just the directory structure
without the files, and a set for replicating everything
- [x] Right now external views (i.e. those not used for global
activations) call `view.add_extension`, but global activations do not
to avoid some extra work that goes into maintaining external views. I'm
not sure if addressing that needs to be done here but I'd like to
clarify it in the comments (UPDATE: for now I have added a TODO and in
my opinion this can be merged now and the refactor handled later)
- [x] Several method descriptions (e.g. for `Package.activate`) are out
of date and reference a distinction between global activations and
views, they need to be updated
- [x] Update aspell package activations
* Add specific version to package verilator
Change-Id: If7645410ec192f92a5eed83ee9b317b569576b4a
* fix dependency types
Change-Id: Ib36c72257c1fa6678c8553225ca21a010d7ae6d1
- Spack was assuming that a group with gid == current uid would always exist.
- This was breaking the travis build for macos.
- also fix issue with the DB tarball test finding coverage filesx
* A new package: perl-compress-raw-zlib.
* A new package: perl-compress-raw-bzip2.
* A new perl package: perl-io-compress.
* flake8.
* Add zlib and bzip2 dependency.
* petsc: remove dependency on boost - its required only as a dependency on trilinos
Also set COPTFLAGS='' etc - this way CFLAGS is the primary way optimization flags are set by spack
* petsc: update pkgs with petsc~boost dependency
* fix flake8
* boost is optional for trilinos - so adjust petsc dependency on boost [via trilinos] accordingly
* do not add boost dependency on petsc [due to trilinos requirement]. Trilinos adds this dependency anyway.
plasma@develop has another flag 'DHAVE_MKL' that needs to be disabled [for non-mkl build]
add dependency on gcc-6.0
add in new dependency on readline
plasma: requires both LIBS in make.inc and command line?
If cmd line is missing -some internal values from plasma makefile gets used - causing link errors [on Mac]
tools/lua-5.3.4/src/Makefile: $(MAKE) $(ALL) SYSCFLAGS="-DLUA_USE_LINUX" SYSLIBS="-Wl,-E -lreadline"
if make.inc is missing - I get:
/usr/bin/ld: cannot find -lmkl_intel_lp64
/usr/bin/ld: cannot find -lmkl_sequential
/usr/bin/ld: cannot find -lmkl_core
collect2: error: ld returned 1 exit status
Also add a new dependency -ldl
m4 exited immediately (causing the nettle build to fail).
```
(alice)[11:09:46]spack>>/Users/hartzell/tmp/spack-mac/spack/opt/spack/darwin-highsierra-x86_64/clang-9.1.0-apple/m4-1.4.18-caxsf7l5yd7qbq2bown6bzi5el3ltfwf/bin/m4
Abort trap: 6
(alice)[11:10:18]spack>>fg
```
Tracked down a fix via the Homebrew recipe. I'll send a note to the
`bug-m4@gnu.org` list to ensure that upstream knows about it.
* Fix gcc@5.5.0 on OS X 10.13.5
gcc@5.5.0 failed to build on my OS X 10.13.5 box.
I found/modified a patch in the MacPorts world that traced back to
Homebrewy, https://trac.macports.org/ticket/56502#no1
The issue has also been reported to gcc,
https://gcc.gnu.org/bugzilla/show_bug.cgi?id=83531
I eventually discovered a nearly identical version of the patch at
Homebrew.
https://github.com/Homebrew/formula-patches/blob/master/gcc%405/10.13_headers.patch
gcc builds with this and I can compile many things, but e.g. curl and
cmake both fail. As @davydden and others observed in #1847, it seems
to be an apple thing.
* Fix mistaken change to patch when clause (added :)
I mistakenly deleted a colon from the
'darwin/gcc-7.1.0-headerpad.patch'.
cd /tmp/balay/spack-stage/spack-stage-joxtpr/omega_h-9.13.4/spack-build/src && /home/balay/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/openmpi-3.1.0-7ws4tgx4z3o
ru5g5skjrxs5sobpeiyef/bin/mpic++ -Domega_h_EXPORTS -I/home/balay/spack/var/spack/stage/omega-h-9.13.4-th4b67fz5es6cbgcar742jxamjt3tqjb/omega_h-9.13.4/src -I/tmp/bala
y/spack-stage/spack-stage-joxtpr/omega_h-9.13.4/spack-build/src -I/home/balay/spack/var/spack/stage/omega-h-9.13.4-th4b67fz5es6cbgcar742jxamjt3tqjb/omega_h-9.13.4/tpl
-I/home/balay/spack/opt/spack/linux-ubuntu16.04-x86_64/gcc-5.4.0/zlib-1.2.11-5nus6knzumx4ik2yl44jxtgtsl7d54xb/include -O2 -g -DNDEBUG -fPIC -o CMakeFiles/omega_h.di
r/Omega_h_map.cpp.o -c /home/balay/spack/var/spack/stage/omega-h-9.13.4-th4b67fz5es6cbgcar742jxamjt3tqjb/omega_h-9.13.4/src/Omega_h_map.cpp
In file included from /usr/include/c++/5/chrono:35:0,
from /home/balay/spack/var/spack/stage/omega-h-9.13.4-th4b67fz5es6cbgcar742jxamjt3tqjb/omega_h-9.13.4/src/Omega_h_timer.hpp:4,
from /home/balay/spack/var/spack/stage/omega-h-9.13.4-th4b67fz5es6cbgcar742jxamjt3tqjb/omega_h-9.13.4/src/Omega_h_timer.cpp:1:
/usr/include/c++/5/bits/c++0x_warning.h:32:2: error: #error This file requires compiler and library support for the ISO C++ 2011 standard. This support must be enabled with the -std=c++11 or -std=gnu++11 compiler options.
#error This file requires compiler and library support \
^
* Added minuit package
* Removed default method and template
* Different URLs for old versions
* Patches for versions down to 1.5.0
* Reverted ROOT package changes
* Removed print statement
* Added checksums for older versions
* Consistent version names
