Fixes#12007.
The Cray cc wrappers don't handle the -s flag (strip) cleanly, It's
not essential to strip the binary, so just remove the flag on Cray.
Note: the default build on Cray is for the back end and the unzip
binary won't run on the front end. To build for FE, use something
like arch=cray-fe-x86_64.
* Add +shared variant, which builds shared library in addition to the
static library.
* Install libraries even when specifying the header-only option
(header-only is just about installing an additional folder).
* An additional make call is not required to build generator
executables (they are built by default).
* Streamlined help-line of each variant.
* Fix Mac platform check for dependency in py-ipython package: 'when'
constraints in Spack directives must be Specs (either a Spec
object or a Spec in string format)
* Fix Mac version check in py-numpy: platform.mac_ver() returns a
3-part string as its first tuple item so the check as written would
never pass; use Spack Version object to simplify check.
* Fix Mac version check in qt package (the check was incorrectly
comparing ints and strings) and use Spack version object to
simplify check.
* Add versions 4.3.0, 4.3.1, and 4.3.2
* The URL format changed after 4.1.4, so this adds a url_for_version
function to choose the URL format based on the version
With this PR, a user can designate older versions of OpenGL as an
external Spack package, and dependents can use that installation
as long as they do not have version requirements.
MacOS currently comes with OpenGL 2.1; there is currently no
'provides' directive in the OpenGL Spack package which specifies a
gl version provided for versions earlier than OpenGL 3.3, so earlier
versions of OpenGL are not considered to provide any version of gl.
This PR records that any version of OpenGL provides 'gl' (which is
sufficient for any package that does not require a specific version
of gl).
* Version 1.3.0 requires python 3.5 or later (no Python 2 support)
* Remove test of scipy.weave import (not available since 1.0)
* Add more-sensitive py-numpy constraints based on py-scipy version
* Replace py-nose dependency with py-pytest
* Add adamjstewart as maintainer
* Rename py-pytorch to py-torch
* Add versions 1.1.0 and 1.0.1
* Define modules to test import of after installation (import_modules)
* py-typing dependency is only needed for older versions of Python
(3.4 or before)
* Newer versions of py-torch depend on newer versions of CUDA
* Add adamjstewart as maintainer
* Remove libuuid dependency for python on Darwin
Python 2.7 includes Carbon, which requires a proprietary typedef defined in
the system `/usr/include/uuid/uuid.h`:
```
In file included from /rnsdhpc/code/spack/var/spack/stage/python-2.7.16-chgwvgls4ezgujsknn27vlmkhwbzpqik/Python-2.7.16/Python/mactoolboxglue.c:27:
In file included from /rnsdhpc/code/spack/var/spack/stage/python-2.7.16-chgwvgls4ezgujsknn27vlmkhwbzpqik/Python-2.7.16/Include/pymactoolbox.h:10:
In file included from /System/Library/Frameworks/Carbon.framework/Headers/Carbon.h:20:
In file included from /System/Library/Frameworks/CoreServices.framework/Headers/CoreServices.h:23:
In file included from /System/Library/Frameworks/CoreServices.framework/Frameworks/AE.framework/Headers/AE.h:20:
In file included from /System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/CarbonCore.h:208:
In file included from /System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/HFSVolumes.h:25:
/usr/include/hfs/hfs_format.h:794:2: error: unknown type name 'uuid_string_t'; did you mean 'io_string_t'?
```
Similarly, even with Python 3, having Spack's libuuid in the toolchain
causes matplotlib to fail to build downstream because its `osx` backend
links against Carbon:
```
building 'matplotlib.backends._macosx' extension
/rnsdhpc/code/spack/lib/spack/env/clang/clang -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -fPIC -I/usr/local/include -I/usr/X11/include -I/opt/X11/include -I. -I/rnsdhpc/code/spack/opt/spack/darwin-mojave-x86_64/clang-10.0.1-apple/python-3.7.2-bipx24oyxqxowqc75o5vfih7dljiaohz/include/python3.7m -c src/_macosx.m -o build/temp.macosx-10.14.5-x86_64-3.7/src/_macosx.o
In file included from src/_macosx.m:1:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Cocoa.framework/Headers/Cocoa.h:12:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Foundation.framework/Headers/Foundation.h:87:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Foundation.framework/Headers/NSURLError.h:15:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/CoreServices.framework/Headers/CoreServices.h:24:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/CoreServices.framework/Frameworks/AE.framework/Headers/AE.h:20:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/CarbonCore.h:208:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/HFSVolumes.h:25:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include/hfs/hfs_format.h:794:2: error: unknown type name 'uuid_string_t'; did you mean 'io_string_t'?
uuid_string_t ext_jnl_uuid;
^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include/device/device_types.h:89:33: note: 'io_string_t' declared here
typedef char io_string_t[512];
```
MacOS version 10.14.5
Xcode 10.2.1
Apple LLVM version 10.0.1 (clang-1001.0.46.4)
* Mark libuuid as conflicting with Darwin due to framework
If Spack's libuuid is included by any other package that tests for or
requires the Cocoa or Carbon frameworks, the build will *fail* becuse it
appears that Apple's libraries require a special version of libuuid and
uuid.h.
```
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Cocoa.framework/Headers/Cocoa.h:12:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Foundation.framework/Headers/Foundation.h:87:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/Foundation.framework/Headers/NSURLError.h:15:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/CoreServices.framework/Headers/CoreServices.h:24:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/CoreServices.framework/Frameworks/AE.framework/Headers/AE.h:20:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/CarbonCore.h:208:
In file included from /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/CoreServices.framework/Frameworks/CarbonCore.framework/Headers/HFSVolumes.h:25:
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include/hfs/hfs_format.h:794:2: error: unknown type name 'uuid_string_t'; did you mean 'io_string_t'?
uuid_string_t ext_jnl_uuid;
^
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include/device/device_types.h:89:33: note: 'io_string_t' declared here
typedef char io_string_t[512];
```
* Revert "Mark libuuid as conflicting with Darwin due to framework"
This reverts commit 9a68b75202005fc265abe2033e4ad36312a9a34d.
* Document libuuid exception in python package
* update to kim-api-2.1.1 and openkim-models-2019-07-25
* openkim-models provide needed dependency constraints and settings
* add maintainers and fixup flake8 errors
* font-util: Remove duplicated dependencies.
* font-util: Fix path handling for font resources.
The "join_path" call made no sense but still managed to work somehow most of the times.
If +pthreads is specified, googletest actually gets build without
pthreads support and vice versa.
If pthreads is not available, googletest should detect it itself which
is why "enabling" pthreads in case of ~pthreads does not seem to cause
any error.
Change-Id: I29de8c4a23dc3901124b27a1ead3354949b7e65b
* xsdk: phist has a conflict with gcc version <= gcc-4.9.1 - so add a variant to disable it on older compiler builds
This is triggered by #11677
* fix typo
* Added a new package for LAME and a variant in sox for it.
* Fixed download url for LAME
* libmad: Added new package libmad for mp3 decoding. Changed sox variant from lame to mp3.
* libmad: Added m4 as a requirement
* libmad: Added comment on patch origins
* libmad: Added a list_url for alternate download location
* libmad: Fixing libmad download url
- We don't currently make enough use of the maintainers field on
packages, though we could use it to assign reviews.
- add a command that allows maintainers to be queried
- can ask who is maintaining a package or packages
- can ask what packages users are maintaining
- can list all maintained or unmaintained packages
- add tests for the command
* Add QMCPACK v. 3.8.0
* Remove QE variant conflict for serial QMCPACK installations.
* Add support for QE 6.4.1 converter.
* FindLibxml2QMC patch function only needed prior to QMCPACK 3.8.0
* ioapi: add version 3.2
* ioapi: unwrap version checksum; it's exempt from line length QA
* ioapi: drop overridden build(); it's the same as the default
* cmake: Move cxx11 flags for fujitsu into the flag_handler method
* cmake: sanitization and error checking in flag_handler
* cmake: Fix fujitsu flag check from 'fc' to 'fj'
* openjdk
* Removing preferred from latest and adding a few lines for readability.
* Remove bad whitesapce
* removing formatting changes
* stable url for openjdk 1.8
* remove extra blank line
* actual binary
Add version for 'gpu' and variant for 'cuda'. These are currently available from the 'master-gpu' branch.
* hpctoolkit: add version gpu and variant cuda
* The gcc >= 4.8.x requirement only applies for dyninst >= 10.x.
ibm-java: fix the URL to only use a machine type that ibm-java
supports so that 'spack info' doesn't report a non-existent URL on
platforms that it doesn't support.
* Fix scikit-learn build with Apple clang
* Update compiler unit tests
* Fix unit tests
* Fix OpenMP dep
* recursive=True no longer necessary
* Add myself as a maintainer
* Specify which versions require OpenMP
* Typo fixes
* LLVM-OpenMP is the correct dependency, no OMPT
* Flake8 fix
* Undo Apple Clang OpenMP flag change, split into a separate PR
Later versions of libjpeg-turbo build with CMake; to build with
user-specified cflags, the user must supply these to CMake as
-DCMAKE_C_FLAGS (Spack's typical approach of injecting these flags
into the compiler wrapper invocation is insufficient in this case).
Currently libjpeg-turbo cannot be implemented as a CMakePackage
(and thereby take advantage of the flag_handler implementation it
provides) because not all versions of libjpeg-turbo use CMake, so
this adds a custom implementation of flag_handler and
flags_to_build_system_args to libjpeg-turbo.
* cmake: change c++ spec when building with Fujitsu compiler.
* cmake: define cxxflags using a Fujitsu compiler's method.
* cmake: Add condition of whether to add cxx11 option.
It seems that GitHub's output changed slightly for this patch (one more
letter for both short hashes on the index line), probably due to the
number of objects in the repository.
This PR adds the ability to specify the auto-dispatch targets that can
be used by the Intel compilers. The `-ax` flag will be written to the
respective compiler configuration files. This ability is very handy when
wanting to build optimized builds for various architectures. This PR
does not set any optimization flags, however.
The default library search for a package checks the lib/ and lib64/
directories for libraries before the root prefix, in order to save
time when searching for libraries provided by externals (which e.g.
may have '/usr/' as their root).
This moves that logic into the "find_libraries" utility method so
packages implementing their own custom library search logic can
benefit from it.
This also updates packages which appear to be replicating this logic
exactly, replacing it with a single call to "find_libraries".
This PR has several modifications for the r package.
- The tk package is always depended on but this pulls in X11, making the
'X' variant non-functional. This PR sets a dependency of tk on '+X'.
- There is a missing dependency on libxmu when '+X' is set.
- The libraries for R wind up in a non-standard location and are thus
left out of the RPATH settings. This PR adds that directory to RPATH.
- The MKL integer interface for gfortran is not in the BLAS libs. This
PR replaces the intel interface with the gfortran interface if needed.
- Use the `LibraryList` `ld_flags` method for blas as that is more in
line with th R Installation and Administration manual.
Note that this PR depends on PR #11956. This PR closes#8642.
TK can be built with support for libXft and X Screensaver. Both of these
are turned on in the Tk configure script. That means the system
libraries will get picked up if they are on the system and nothing is
specified in the package. Since the default for both of them is 'True' I
set the default value for the variants to 'True'.
* bowtie2: Add version 2.5.3.1 and fix to build on ARM
1. Add version 2.5.3.1.
2. Add simde for ARM.
3. Disable -fopenmp-simd when gcc 4.8.X or before for ARM.
4. Add Makefile option POPCNT_CAPABILITY=0 for ARM.
* flake8.
Fixes#11781
* Rename build log to spack-build-log.txt
* Rename environment variables file to spack-build-env.txt
* The name of the log and env files is now the same during the build
and after the build completes
* Update packages which referred to the build log/env files
* For packages installed before this commit using older names for the
build and env files, search for the older names
* ferret: use libx11 from spack
* ferret: use mpi library with or without fortran support
* ferret: add version 7.2
* ferret: no need to specify ~mpi
* ferret: creating symlinks may fail for external packages; set include/lib paths instead
* use autoreconf to regenerate configure script and config.guess for
newer architectures
* Add perl build dependency for older versions. The required perl
version is constrained because the perl script uses syntax that
is deprecated in older versions
Declare a conflict for TAU versions older than 2.28.1, that they
can't depend on libelf or libdwarf. The user can still install it
by specifying tau@2.24~libelf~libdwarf.
* py-antlr4-python3-runtime: new package
* py-antlr4-python3-runtime: fix for flake8
* py-antlr4-python3-runtime: indent docstring
* py-antlr4-python3-runtime: clarify role of this package vs ANTLR in docstring
* py-antlr4-python3-runtime: remove whitespace at end of line
The py-reportlab package includes binaries for easy_install and pip.
That blocks activation if py-setuptools and/or py-pip are installed.
This PR block the binaries from py-reportlab as easy_install and pip
should be installed with their respective packages.
* py-cf-units: new package
* py-cf-units: download from pypi.io
* py-cf-units: include py-pytest-runner as build dep
* py-cf-units: remove empty build_args function
* py-cf-units: fix for flake8
* py-cf-units: indent docstring
* py-cf-units: remove excess spaces
* py-cf-units: list master branch ahead of numeric versions
* py-cf-units: remove extension keyword from version
If R is provided by the system with a module (i.e. registered in
packages.yaml with a "module" entry) and has no discernible prefix,
this allows turbine to still make use of R.
This PR corrects a problem with the opa-psm2 package. It was
installing headers into <prefix>/usr/include and libraries into
<prefix>/usr/lib instead of <prefix>/include and <prefix>/lib.
The extra level of usr/ subdirectories causes dependent packages
like libfabric to fail to build.
The original packaging, with openfoam as a virtual and with
openfoam-com, openfoam-org and openfoam-extend as
providers, adds an obfuscation layer without any benefit.
- Rename `openfoam-com` to `openfoam`, and remove the
`openfoam` virtual package.
- `parse_anonymous_spec()` is a vestige of the days when Spack didn't
support nameless specs. We don't need it anymore because now we can
write Spec() for a spec that will match anything, and satisfies()
semantics work properly for anonymous specs.
- Delete `parse_anonymous_spec()` and replace its uses with simple calls
to the Spec() constructor.
- make then handling of when='...' specs in directives more consistent.
- clean up Spec.__contains__()
- refactor directives and tests slightly to accommodate the change.
Added a wrapperrpath variant to mpich that defaults to `True`.
Users can set this to `False` (e.g., spack install mpich~wrapperrpath) to
disable the wrapper RPATHs. This makes it easier to replacing an MPICH
installation in a container with an MPICH for the host system,
e.g., Cray MPICH with Shifter on Cori, Intel MPI, MVAPICH2, etc.
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
