* new package: cns-nospec
* made changes as suggested and added proxy-app tag
* updated edit()
* adjusted logic for '+debug'
* install readme and license
* install readme and license
* new package: SMC
* removed template and added proxy-app tag
* added comp variant in edit()
* edited comp variant in edit()
* move executable and input file into bin and install readme and license
Fixes#4898
Constraints that were supposed to be conditionally activated for
specified values of a single-valued variant were being activated
unconditionally in the case that the variant was associated with
an implicit dependency. For example if X->Y->Z and Y places a
conditional constraint on Z for a given single-valued variant on
Y, then it would have been applied unconditionally when
concretizing X.
Earlier versions of boost had a fixed maximum number of jobs. 1.54
was 64, it bumped once or twice afterwards and in 1.59 [this
commit][commit] it became dynamic.
I need 1.54 for as a prereq for bcl2fastq but I can't build 1.54 on my
144 core build box.
This fixes that.
[commit]: 316e26ca71
* Fix cdefs macro to be compatible with gcc 4.8.x
See the discussion in #4945 (after the merge) for additional
background.
libbsd builds with gcc@5.4.0 on CentOS 7, but not with the system's
gcc@4.8.5. Others have reported problems with gcc@4.8.3 on Fedora 19.
The problem boils down to the lack of support for the clang extension
`__has_include_next`. The immediate symptom seems to be the
pre-processor using defining macro like this
```
```
then then tripping over an expansion of it like this:
```
blah.h:13:23: error: missing binary operator before token "("
```
This patch changes the macro definition to:
```
```
which swallows the arguments with which the macro is invoked.
The end result is that libbsd builds for me on CentOS 7 using the
system compiler.
* Apply this patch for any compiler version before 5
This includes subversions of 4, like 4.8.5.
* chlorop: new package
* chlorop: moving main script to bin and moving runtime tmp location.
* chlorop: fixing flake8 error.
* chlorop: cleaning up, removing CHLOROTMP, advising user to set it.
* chlorop: removing unused import
Adds ADIOS2, the C++ Exascale HPC I/O rewrite of ORNL's ADIOS
library.
Currently, many variants (especially for data transforms such as
compression) are not yet added. It already provides Python bindings.
* Changed every 'fpic' variant to 'pic'. fixes#2463
Every variant that activates compilation of position independent code
has been changed to 'pic'. Hardcoded compiler flags in packages have
been substituted with `self.compiler.pic_flag`.
* Changed literal uses of '-fpic' to 'self.compiler.pic_flag'
* Add a QMakePackage base class
* Fix sqlite linking bug in qt-creator
* Add latest version of qt-creator
* Add latest version of qwt
* Use raw strings for regular expressions
* Increase minimum required version of qt
* Add comment about specific version of sqlite required
* Fixes for latest version of qwt and qt-creator
* Older versions of Qwt only work with older versions of Qt
* SCR CMake package
* Fix dtcmp variant description and set pdsh deptypes to build/run
* added variants for system config file location
* add variants for several scr cmake options
* Added more variants for compile time options
* Added libyogrt and made corrosponding changes to scr package.
* Cleanup yogrt package now that Ive verified it works
* Added description for libyogrt
* upper case async api names
* Make use of mv variants
* fix pdsh package for scr
* added IBM BBAPI as async option
* update pdsh and scr to use static pdsh modules
* Add package for libbsd, add variant to expat for libbsd
The recent expat release requires a high quality source of randomness.
CentOS 7 does not seem to have one, but one is available in libbsd.
This commit adds a package for libbsd and adds a variant to expat to
use it (defaults to False).
* Make libbsd default for newer, conflict for older
Make the libbsd variant default to true.
Conflict if you're asking for libbsd and an older version of expat.
This means that in order to install an older version of expat you'll
need to specify `~libbsd`.
* Rework so that 2.2.0 and 2.2.2 work by default
Get rid of the conflicts and use better constraints/tests in the
`depends_on` and the `configure_args` bits.
* Add package for canu
There's a top-level perl script, which is touched up to use a
spack-built perl instead of `#!/usr/bin/env perl`. It's
self-contained, it uses `FindBin` to locate it's libaries.
* Add dependency on gnuplot
I noticed a hidden mention of the use of gnuplot in the docs.
This adds the dependency.
* Tighten dependencies, flake8 cleanup
gnuplot is a run dependency.
jdk is a run dependency.
perl is a run dependency.
Make flake8 happy.
* Protobuf: CMake
This rebuilds protobuf to be build with CMake,
so cmake config packages are created and installed, too.
Unfurtunately, this drops support for protobuf < 3.
* Protobuf CMake: Add .pc files
* libprotobuf.a: -fPIC
* Protobuf: Minor Updates
Updates from upstream review and planned patch inclusion.
* Fix xsdk build broken by petsc and trilinos
See #4891 for details
* Fix version conflict in trilinos package
Trilinos version 11 may conflict with superlu-dist.
The version "xsdk-0.2.0" was conflicting with superlu-dist,
even though it shouldn't. I added a lower bound to the
comparison to fix this problem.
Thanks for the help @davydden!
For packages which contain a mix of versions with formats X.Y and
X.Y.Z, if the user entered an X.Y version as a preference in
packages.yaml, Spack would get confused and favor any version A.B.Z
where X=A and Y=B. In the case where there is a mix of these version
types, this commit updates preferences so Spack will favor an exact
match.
Adds the cppzmq library, adding a C++ API to ZeroMQ (libzmq). In order to find the autotools-build libzmq, this requires the upcoming cppzmq release (or development branch).
zsh's configure script fails if there's it tries to test for terminal
functionality if there's not a terminal (e.g. in a Jenkins build).
The configure script has a switch that asserts that tcsetpgrp works
and thereby avoids running that test.
This commit adds a variant that invokes that switch, defaulting to
True.
Adds a the latest version of gBenchmark, release 1.2.0.
This is the first gBenchmark version with proper
[CMake config package installs](https://github.com/google/benchmark/issues/363).
This is important for dependencies building against it, such as gRPC.
* Initial Spackage for qmd-progress library
PROGRESS is a library is focused on the development of general solvers
that are commonly used in quantum chemistry packages.
* Removed LA-CC from description to fix formatting
* Added Additional Formatting Requests
Added requested formatting changes and also ensured that graphlib and
mpi are disabled if not enabled
* New Pacakge: lcals
* added logic for arch detection and compiler choice.
* fixes for comments.
* addressed comments.
* removed LCALS_ARCH and added flags though spack.
* addressed comments.
* flake 8 fix.
* reerted the changes along with comments.
* Update the krell institute products to use the latest features of spack for building on cluster platforms.
* Address travis error messages and resubmit the pull request.
* Update the contents of openspeedshop package.py so it passes the flake8 tests.
* Fix flake8 error-whitespack issue in mrnet package.py file.
* Add updates based on spack reviewer feedback.
* More fixes based on comments from reviewers. Switch using extend to using append, remove additional setting of PATH and LD_LIBRARY_PATH that should not be required due to RPATH.
* More review related changes. Update MPIOption.append lines and take out xercesc references.
* Create a base options function for common openspeedshop base cmake options to reduce redundencies.
* Add libxml2+python depends on to get around issues with the libxml2 package file.
* Using boost over 1.60.0 causes compile errors. This is a known boost bug. Also, dyninst-9.2.0 is set to be the vesrion of dyninst to use with OSS, as of now. The newer version fails to build.
* Fix bad syntax in specifying the boost version range.
* Update the version numbers for the krell institute components and tools: cbtf and openspeedshop.
* Do not build glib for qt3, it is not needed and causes build problems at this time anyway.
* A fix was added for setting LD_LIBRARY_PATH in the qt3 build, but if LD_LIBRARY_PATH is not set the qt build fails. So so check and set LD_LIBRARY_PATH if not set, update if it is set.
* Update the fix for qt3 build by setting LD_LIBRARY_PATH instead of checking for whether it is set or not per Adams comment that spack clears LD_LIBRARY_PATH.
* A fix was added for setting LD_LIBRARY_PATH in the qt3 build, but if LD_LIBRARY_PATH is not set the qt build fails. So so check and set LD_LIBRARY_PATH if not set, update if it is set.
* Trim comments to fit more concisely.
* Fix tabs versus spaces and swap if and else clause check from a negative to a positive check.
* Fix issues with the cbtf-argonavis build, update to use dyninst-9.3.2, fixes to openspeedshop package build.
* Fix issues with the cbtf-argonavis package.py files related to comments.
* Add changes for changing the krell packages from Package to CMakePackage.
* Add better changes for changing the krell packages from Package to CMakePackage.
* Add more modifications for changing the krell packages from Package to CMakePackage.
* Add additional modifications for changing the krell packages from Package to CMakePackage and fixing Travis erros
* Fix new travis errors.
* Fix new travis errors.
* Add more changes for PR 4765.
* Add more refinements to the conversion from Package to CMakePackage.
* Fix new travis errors.
* Add dependencies for MPI to be passed to cbtf-krell, so it can build the MPI collectors requested by the builder of openspeedshop.
* Remove extra unnecessary routine to adjust build arguments. Fix if-else clause issue.
* Fix more flake issues caused by last changes.
* Fix a bug where openspeedshop will not build when no mpi variants are specified. Also switch to a multiple level variant for building the gui(s). Use none, qt3, and qt4 as the variants with qt3 being the default.
* Add fix for spack issue #4843, where LTDL include files were not found.
* Add the build_type variant back into the openspeedshop package file.
* removed the tags as per comment in PR# 4749
* addressed above comments
* changed fortran compiler.
* added proxy application tags.
* added tags by removing them from description.
* addressed comments
* used join_path instead of path concat.
* removed the tags as per comment in PR# 4749
* addressed above comments
* changed fortran compiler.
* added proxy application tags.
* added tags by removing them from description.
* addressed comments
* used join_path instead of path concat.
* added tags.
* changes to use MPI as depedency.
* removed MPI as variant.
* changed pointer to filtered makenek file.
* flake 8 fix.
* Add universal build_type variant to CMakePackage
* Override build_type in some packages with different possible values
* Remove reference to no longer existent debug variant
* Update CBTF packages with new build_type variant
* Keep note on build size of LLVM
* fixes#967
* Version bump to 0.9.1
- Bugfixes for spack find
- 0.9.1 can read specs from current develop.
* Don't assume spack is in the path when building docs.
* Remove PKG_CONFIG_PATH from tmux configure
* Change tmux to AutotoolsPackage
* Correct link to libtinfo in tmux
* Change version.up_to() to return Version() object
* Add unit tests for Version.up_to()
* Fix packages that expected up_to() to return a string
* Ensure that up_to() preserves separator characters
* Use version indexing instead of up_to
* Make all Version formatting properties return Version objects
* Update docs
* Tests need to test string representation
* perl: prepend default perl @INC path to support package activation
* perl: remove stray comma from list of configure arguments
* perl: final comma in configure arguments makes adding arguments safer
This reverts commit fdc10cd611f525ebc31ca1953e048095b1c75350.
* perl: add comment about modified @INC (thanks to George Hartzell)
* perl: use self.prefix.lib and self.prefix.bin for clarity
* perl: convert tabs added by editor to spaces for flake8
* perl: use new path syntax: prefix.lib.perl5
* perl: avoid line break before binary operator
* perl: use compact spack syntax for perl executable
* gBenchmark: Development Package
Add the development version (master branch) of `gBenchmark`
* gBenchmark: Remove Duplicate
Remove duplicate `gbenchmark` library
and keep its patch to remove the shipped
-Werror
Adds SpackCommand class allowing Spack commands to be easily in Python
Example usage:
from spack.main import SpackCommand
info = SpackCommand('info')
out, err = info('mpich')
print(info.returncode)
This allows easier testing of Spack commands.
Also:
* Simplify command tests
* Simplify mocking in command tests.
* Simplify module command test
* Simplify python command test
* Simplify uninstall command test
* Simplify url command test
* SpackCommand uses more compatible output redirection
Installing the stable version 0.5 through the checksummed tar.gz does not fetch the git submodule in the package.
The submodule appears as an empty directory.
Thus, clone the commit tagged as v0.5 using git to get around this issue
* savanna: modified adios dependency spec
* Replaced adios+staging with adios+flexpath+dataspaces
* savanna: Enabling fortran support in adios by default
* savanna: reverting to variant 'staging' for enabling all staging transports
- +swrender variant lets you compile an off-screen only version for
software rendering on clusters.
- +swrender+llvm for using llvm for the software pipe
- added newer versions (17.1 and 13.0) and corrected the url location
to use the canonical location.
* gtkorvo-atl: atl library from gtkorvo
* gtkorvo-dill: dill library from gtkorvo
* gtkorvo-cercs-env: cercs_env library from gtkorvo
* gtkorvo-enet: Enet networking library from gtkorvo
* libffs: FFS middleware communication library from GTKorvo
* libevpath: EVPath high performance communication library from GTKorvo
* gtkorvo-cercs-env: Added homepage and removed function configure_args
* gtkorvo-cercs-env: Re-add of accidental removal of cmake_args function in previous commit
* gtkorvo-enet: Removed configure_args since unused
* removed the tags as per comment in PR# 4749
* addressed above comments
* changed fortran compiler.
* added proxy application tags.
* added tags by removing them from description.
* addressed comments
* used join_path instead of path concat.
* addressed comments
* removed string formatting for LDFLAGS.
* Update the krell institute products to use the latest features of spack for building on cluster platforms.
* Address travis error messages and resubmit the pull request.
* Update the contents of openspeedshop package.py so it passes the flake8 tests.
* Fix flake8 error-whitespack issue in mrnet package.py file.
* Add updates based on spack reviewer feedback.
* More fixes based on comments from reviewers. Switch using extend to using append, remove additional setting of PATH and LD_LIBRARY_PATH that should not be required due to RPATH.
* More review related changes. Update MPIOption.append lines and take out xercesc references.
* Create a base options function for common openspeedshop base cmake options to reduce redundencies.
* Add libxml2+python depends on to get around issues with the libxml2 package file.
* Using boost over 1.60.0 causes compile errors. This is a known boost bug. Also, dyninst-9.2.0 is set to be the vesrion of dyninst to use with OSS, as of now. The newer version fails to build.
* Fix bad syntax in specifying the boost version range.
* Update the version numbers for the krell institute components and tools: cbtf and openspeedshop.
* Do not build glib for qt3, it is not needed and causes build problems at this time anyway.
* A fix was added for setting LD_LIBRARY_PATH in the qt3 build, but if LD_LIBRARY_PATH is not set the qt build fails. So so check and set LD_LIBRARY_PATH if not set, update if it is set.
* Update the fix for qt3 build by setting LD_LIBRARY_PATH instead of checking for whether it is set or not per Adams comment that spack clears LD_LIBRARY_PATH.
* A fix was added for setting LD_LIBRARY_PATH in the qt3 build, but if LD_LIBRARY_PATH is not set the qt build fails. So so check and set LD_LIBRARY_PATH if not set, update if it is set.
* Trim comments to fit more concisely.
* Fix tabs versus spaces and swap if and else clause check from a negative to a positive check.
* Fix issues with the cbtf-argonavis build, update to use dyninst-9.3.2, fixes to openspeedshop package build.
* Fix issues with the cbtf-argonavis package.py files related to comments.
* Add changes for changing the krell packages from Package to CMakePackage.
* Add better changes for changing the krell packages from Package to CMakePackage.
* Add more modifications for changing the krell packages from Package to CMakePackage.
* Add additional modifications for changing the krell packages from Package to CMakePackage and fixing Travis erros
* Fix new travis errors.
* Fix new travis errors.
* Add more changes for PR 4765.
* Add more refinements to the conversion from Package to CMakePackage.
* Fix new travis errors.
* Add dependencies for MPI to be passed to cbtf-krell, so it can build the MPI collectors requested by the builder of openspeedshop.
* Remove extra unnecessary routine to adjust build arguments. Fix if-else clause issue.
* Fix more flake issues caused by last changes.
* Initial work on flag trapping using functions called <flag>_handler and default_flag_handler
* Update packages so they do not obliterate flags
* Added append to EnvironmentModifications class
* changed EnvironmentModifications to have append_flags method
* changed flag_val to be a tuple
* Increased test coverage
* added documentation of flag handling
* removed the tags as per comment in PR# 4749
* addressed above comments
* changed fortran compiler.
* added proxy application tags.
* added tags by removing them from description.
* addressed comments
* used join_path instead of path concat.
* added tags and other minor changes.
* removed tags from description.
* new package: CLAMR
* changed from bool variants to single value variants and corresponding logic in build_type and cmake_args
* lowercase variant values
* updated conditionals for variants
* adjusted url and docstring
* new package to be added: NuT
* removed cmake_args() and made other changes as suggested
* Added setup_environment()
* PEP8 compliant
* edited version name, build_targets, and files/directories to install
* corrected executable directory
* compiler dependencies based on version
* Change path to CMakeLists.txt to be relative to root, not pwd
* Changes requested during code review
* Revert back to old naming of root_cmakelists_dir
* Make relative directory more clear in docs
* Revert change causing build_type AttributeError
* Fix forgotten abs_path var
* Update CLHEP with new relative path
* Update more packages with new root_cmakelists_dir syntax
somatic-sniper installs its own copy of samtools, which needs curses.
I'm not sure why I didn't stumble on this in my dev environment, but I
just stumbled over it in a standalone build.
The 4.X branches are now on the homepage, so we take the GitHub release
artifact (careful: take their upload, not the automatic tarball).
Adds a development version of ZeroMQ.
Requires a autogen run, as for all their unreleased versions,
and the pkg-config fix in #4736
Always sets the `pkg-config` environment hint for
autotools.
Required dependency for `autoreconf` of ZeroMQ when
build from source (e.g. v4.2.2) via autotools in `autogen.sh`
step for `autoreconf`.
* Add package for r-ada, update r-rpart version
Adds a package for r-ada.
Update the version for r-rpart because the previous version is
no longer at that URL. The previous version *is* in the Archive,
but list_url does not seem to be able to find it.
* Clean up FIXMEs (blush)
* savanna: Runtime framework for online workflow management from the ECP CODAR project
* savanna: added version 0.5
* savanna: Copying the package contents to prefix as part of installation
* savanna: Doing submodules=true for git checkout of develop version
* savanna: removed dependency on adios@develop. depends on adios
* Savanna: Converted package to MakefilePackage
* New Package: Pathfinder
* Added index for String format
* Changed to make Makefile edit more specific
* Make Flake8 Happy
* Removed unneeded conversion
* Add package for Sniffles
* Wire up a manual install step
The cmake infra doesn't install anything, so do it by hand.
The binaries land in a location that embeds the version...
* hybpiper: new package and spades dependency
* hybpiper: making flkae8 happy
* hybpiper: fixing dependency errors
* fixing python dep type
* removing cmake from spade dependencies
* libwebsockets: new versions
both new versions fix a nasty bug leading to a hanging
connection on connect.
* ISAAC Server: Fix libwebsockets
ISAAC server did hang in docker containers due to a bug
in libwebsockets.
* Add two python packages for editing mach-O headers. Much faster than calling otool and install_name_tool directly
* remove non-overriding function
* autopep8
* Adding OpenMP variant to Trilinos. Also building NetCDF with PNetCDF in Trilinos when necessary.
* Adding runtime error for PNetCDF variant in Trilinos when necessary. Omitting unnecessary openmp variant for Trilinos in Nalu.
* Changing variant checks to conflicts statements.
* Adding comments to Trilinos package.
Adds the `gearshifft` package, a benchmark suite for heterogeneous implementations of FFTs.
Adds clFFT, a software library containing FFT functions written in OpenCL.
see: https://github.com/clMathLibraries/clFFT
The vcftools package was installing its Perl libraries into a
directory in the staging directory named 'lib', instead of installing
them into `prefix.lib` where they should have been because the value
passed to the configure script was wrong.
The result was that any attempt to run one of the scripts in the
package failed with something like:
> Can't locate VcfStats.pm in @INC (you may need to install the
> VcfStats module) [...]
This fix provides the correct information in `configure_args`.
Tested lightly on CentOS 7.
* Dataspaces spack package, hard-wired for ubuntu VM
* Initial commit of dataspaces spack package
* Made changes and additions necessary to install on Cori and Titan
* Added temp 1.6.2.1 for testing
* Updated tar file for 1.6.2
* Fixed formatting
* Set the type of build dependencies
* Changed the way autogen.sh is called for compatibility
* Use append instead of extend to add configure flags
* Various syntax fixes
* Switched string checking to method for compatibility
Now using the six library for Python 3 compatibility. Thanks @adamjstewart
* Made MPI variant default
- renamed develop version from 'plus' to 'develop'
- patches now prefixed by corresponding OpenFOAM version number.
This makes it easier to sort and see what old/junk exists.
- remove MPI_BUFFER_SIZEk env variable (for all openfoam variants).
The OpenFOAM shell setup addresses this and there is no reason
to pollute the module environment at this stage.
* sabre initial commit, works but test does not
* removing test until I have time to fix it
* sabre: fixing flake8 errors
* sabre: changing to MakefilePackage
* mpifileutils: update to v0.7
* mpifileutils: disable --enable-experimental in v0.6 and earlier
* mpifileutils: list newest version first, avoid experimental switch unless at v0.7 or later
* * add mpii* wrappers for use with intel compilers
* in mumps package, scotch is compiled without metis option when
ptscotch variant is selected. This removes confusion over which
metis.h to use
* for intel mkl, add SPACK_COMPILER_EXTRA_RPATHS ending in 'intel64'
* scotch lib requires libz when compression is turned on. This
caused a link issue on some Ubuntu distributions (not
redhat). Change Scotch package to add -lz when needed
* * intel-mkl append to SPACK_COMPILER_EXTRA_RPATHS rather than setting
* use more concise method to obtain libz libraries for scotch
* remove changes to intel mpi
* remove commented out depends_on
* fix flake8 errors
* Add package for primer3
Built and mildly tested on CentOS 7.
* Convert to MakefilePackage
I always forget about this...
* Set build_directory the easy way
Life's not always complicated. Don't go out of my way
to make it so....
* Fix Flake8 issue
* added perl-star-fusion and perl-intervaltree
* added perl-star-fusion and all dependencies
* changes
* made changes as requested to perl-star-fusion dependencies
* changed perl-intervaltree dependency
* changes to star fusion
* now using perl properly
- Thanks to pointer from @adamjstewart - can avoid this either by
avoiding an external mxml dependency, or by making certain that they
both use consistent code generation.
The adios package uses '-fPIC' for python linkage and this seems to
require the same for mxml too. If the adios-internal version of mxml
is used, it has the same flags for both.
- The buggy flex-2.6.2 was blacklisted in the corresponding flex
package, but now also removed the md5sum to avoid suggesting that
this version should be revived.
The 2.6.3 has similar problems (at least for scotch), but 2.6.4
seems to work.
- Rejig flex restriction for scotch to exclude 2.6.2-2.6.3 only. Since
flex-2.6.4 appears to be okay again, we can remove the flex version
restriction that trickled through into the openfoam packages as a
consequent of an spack spec bug.
- Make flex a build dependency for the openfoam packages
(seems to have been an earlier oversight).
