* 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.
* adding mfem variants; do not assume build defaults
* adjusting format to clarify options
* fixing some build issues
* fixing mfem+sundials
* removing mesquite variant...turns out it is obsolete
* adding examples to mfem; fixing sundials darwin installs
* adding some additional variants and setting some configure flags by fiat
* switching most check_variants logic to conflicts() directives
* adding comment about cmake config
* fixing flake8 issues; thought I had already done that
* moving func def into install method
* switch yes_no to no_yes; fix miss-spelling of miniapps
* switching make target all to lib
* changing yes_no to function as requested; fix problem with same in sundials
* fix missing import sys directive
* adding master and develop versions to amrex
* Added a package for the MDAnalysis toolkit.
* Added additional packages that Elemental depends on.
* Changed LBANN to not ask for the scalapack variant in Elemental.
* Removed variant control on scalapack
* New package: qbox
* API changes
* Use install instead of shutil for comd
* Use any BLAS library
* Fix typo
* Python2 fix
* python2 + fix backslashes
* Modified to respond to ld_flags correctly
* Modified to use ld_flags
* Add ld_flags support
* Updated Changes
* Updated AMG with required MPI
* Updated AMG with Version ' changes'
* Fixed Issues with flag's and variant checks
* Updated with MPI Alone and Changes - NO Serial Variant
* Updated with MPI Alone and Changes - NO Serial Variant
* Fixed Flake 8 line length error
* Updated Spack Issues
* 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.
* Add new OpenSpeedShop gui package based on qt4/qt5 gui toolkit.
* Fix flake8 errors.
* Fix flake8 errors.
* Update bcl2fastq2 with info for 2.19.1.403
Heads up, the download location changed (domain name AND protocol).
* Flake8 fix
What's one space between friends?
* Adding lower bound to pnetcdf conflict in Trilinos to allow for use of develop and master branch.
* Using even lower bound for pnetcdf conflict in Trilinos.
* Added a package for the MDAnalysis toolkit.
* Changed cmake_options to args to be consistent with the rest of the
file and fix a cmake error about undefined errors. Additionally,
added guards for both png and zlib to not include their cmake options
when those variants are not specified.
* slurm: added initial recipe
* Modified variants following Adam comment.
The MV variant 'features' has been turned into a set of BV variants. The
dependency on 'readline' has been made optional.
* 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
* install readme and license; fix mpi version build issues
* fix build issues for ~mpi
* pep8 compliant
* new package: amr-exp-parabolic
* removed boilerplate and added tag
* install license and readme
* fix mpi build issues
* change access to include/lib directories and pep8 compliant now
* 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.
* Add new package for the Argo Navis/Krell new graphical user support library: QtGraph.
* Revert "Add new package for the Argo Navis/Krell new graphical user support library: QtGraph."
This reverts commit f8883de446c404e46d4c33fe497ae1e9ab2f04a6.
* Add new package for the Argo Navis/Krell new graphical user support library: qtgraph.
* Fix flake8 errors.
* Fix flake8 errors.
* Fix flake8 errors.
* Fix flake8 errors.
* Fix flake8 errors.
* Add changes to support QMakePackage class instead of Package class for qtgraph.
* Update change for suggested reviewer improvements.
* Fix flake8 errors.
* Fix flake8 errors.
* new package: VPFFT
* install readme and license
* misc
* changed version name to 'develop'
* removed the misplaced package file
* updated eigen path, fixed docstring, and updated 'docs' installation method
* pep8 compliant, changed installation of docs
IceT places its CMake module in the wrong directory,
which is not included in the default CMake search paths.
This fixes it for *directly* depending packages without the
need to add
```yaml
icet:
environment:
prepend_path:
CMAKE_PREFIX_PATH: '${PREFIX}/lib'
```
to the `modules.yaml` as a workaround.
* Molcas 8.2: Adding molcas spec file
* Molcas 8.2: Putting in patch file for molcas driver not to be installed in spack stage directory
* Molcas making changes
* Making changes in ordering
* transabyss: new package and dependencies
* fixed build deps in igraph and version conflict spec in abyss
* fixed versioning stuff and package structure
* fixed dep type
* fixing dep type for real this time
Build system "usually" autodetects mpi library but this is
not the case on many platforms. Provide mpi library name/version
as part for configure args.
* savanna: explicitly adding variant sz to adios since it is no longer enabled by default in adios
* savanna: removing +sz from adios as sz is now enabled in adios by default
* savanna: explicitly specifying adios variants required by savanna
* adios: conform to pep8
* adios: added versions 1.11.0 and 1.12.0
* adios: added variant no_mpi to explicitly disable mpi support
* adios: add new variant mxml
adios v1.12.0 onwards contains an xml library built within.
To build with an external mxml, a new variant must be used
* adios: new variant for sz transform
* adios: flexpath and dataspaces staging variants
Two new variants for staging: flexpath and dataspaces.
New variant 'staging' that will enable both
* adios: dependency on libtool:2.4.2 since adios does not build with newer libtool 2.4.6
* adios: better description for variant no-mpi
* adios: new variant for netcdf
as requested by @mamelara from LBL
* adios: renamed variant 'no_mpi' to 'serial'
* adios: removed variant mxml
* adios: corrected implementation of the mpi dependency, along with its relation with the 'serial' variant
Added conflicts between 'serial' and other variants
* adios: added 'else' clause when variants are not added
* adios: replaced variant 'serial' with 'mpi'
* adios: Added configure option to explicitly disable variants that are not enabled.
* adios: setting default zfp to true
* adios: fixed flake8 errors
* adios: removed some old comments
* adios: setting default sz to False.
It is recommended to set default to False when dependency is on develop (sz@develop).
* adios: removing dependency on develop for sz and setting default sz to true
* adios: updated url to latest release.
Just keeping it clean
* new package:SNAP
* removed boilerplate
* Delete .nfs00000000003a8b1700001358
* install another executable in bin and install readme
* added quotes around README.md
* moved readme to prefix
* Added a package for the MDAnalysis toolkit.
* Added a patch that allows Elemental to use cuBLAS internally.
* Added support for LBANN to use the new cuBLAS extension in Elemental.
* Added a proper variant for when LBANN does not want to use cuBLAS in
elemental.
* Added a package for the cnpy project and used it in the lbann package.
* Removed unnecessary comment lines.
* Removed blank lines
* Removed debug variant
* Add support for libjpeg-turbo
* Added additional variants for OpenCV features. Fixed bug when linking
in TIFF support, where libtiff used the regular JPEG library and
OpenCV used libjpeg-turbo. Now libtiff can use libjpeg-turbo.
* Removed the variant for getting Elemental to use the cublas variant.
Updated the requirements for OpenCV to add new options.
* Fixed a flake8 error in OpenCV and added a path to find cnpy in lbann.
* Fixed line too long flake8 error.
* Added a flag to specify the datatype size in lbann and fixed a flake8 error.
* Added a debug build variant using hte new build_type
* Fixed flake8
* Fixed how the debug build is pushed to Elemental
* Fixed a bug in the Elemental package where the blas search flags were
being overridden by the blas link flags. Changed how the sequential
initialization variant is implemented in LBANN.
* Added support via a variant to explicitly use mkl or openblas. This
helps work around variant forwarding problems.
* Updated package files to address pull request comments.
* 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).
* Remove unneeded patch lines which fail for the most recent CNTK version on the head of the git repo
* Really check for NVML/GDK
* Fix some violations
* gtkplus: set XDG_DATA_DIRS
* shared-mime-info: database of common MIME types
* gtkplus: needs shared-mime-info for correct handling of stock icons
* shared-mime-info: builds with newer intltool than provided by some platforms
* atk: set XDG_DATA_DIRS at run-time
* gdk-pixbuf: set XDG_DATA_DIRS at run-time
* gtkplus: set XDG_DATA_DIRS at run-time
* pango: set XDG_DATA_DIRS at run-time
* shared-mime-info: set XDG_DATA_DIRS at run-time
* enable some of the tools
do not make zoltan default
* modify moab package
add shared, debug options to cgm, too
build some tools by default (mbsize, mbconvert)
add hdf5, netcdf dependency
add pnetcdf variant (dependency), metis, parmetis, zoltan
add shared, debug, fortran options to moab
* few kinks for moab
zoltan should be built without fortran api, otherwise moab
complains (need to fix)
also, notice that when built with cgm, shared can't find
cgm libraries for the new tools/geometry execs
install in serial for the time being (because of example makefile
duplicate?)
for example, these builds are successful:
spack install moab+mpi+hdf5+zoltan ^mpich@3.2
spack install moab+mpi+hdf5+shared ^mpich@3.2
* force hdf5+mpi if both are specified
also, something like this works:
spack install moab+mpi+hdf5+cgm ^mpich@3.2 ^cgm+oce+mpi ^oce@0.17.2
use mpich32, and cgm built with oce 0.17.2
* forgot about irel, fbigeom, mbcoupler
* add meshkit package
simple build so far, moab and cgm deps only
also, an example of complex build for cgm
spack install moab+mpi+hdf5+cgm+irel+fbigeom ^mpich@3.2 ^cgm+oce+mpi ^oce@0.17.2
* for meshkit, moab needs to have irel, fbigeom
* forgot to self.spec
after building moab with cgm with oce 0.17.2, we can build
meshkit with something like this
spack install meshkit ^moab/tsb75zk
cgm depencency is found out from moab
moab has to be built with irel and fbigeom
* add netgen package and review
do not support yet older versions of meshkit
(which depend on lasso, etc)
add netgen package; tested with meshkit (netgen has to be built without
occ, for meshkit)
We are not enforcing that yet, we may have to test
* use conflicts where needed, suggested by review
remove release candidates
* flake8 alignment errors
* flake8
* reviews
flake8 alignment
explicit options, even for default variants
variant for netgen should be "gui", with the default ~gui (False)
FIXME: with-occ does not work right for netgen ; maybe it should be disabled?
also, with +gui, it should depend on a lot more, like tk, tcl?
* flake8 issues
whitespaces and a comment in netgen
* add more explicit options
--without-mpi needs fixing for cgm, moab and meshkit
add variable url for netgen (although we don''t know if other
versions will appear)
* flake8, trailing whitespace
* ninja-fortran: a Fortran-capable fork of ninja build tool
* Use url_for_version for clarity
* Clean ninja-fortran
* Cleanup in the original ninja package
* added py-tomopy package
* fixed dependencies and added import_modules
* edited deps for tomopy with import_modules and added py-olefile pkg
* changed module name
* changed dependency to python because it will not build with setuptools
* fixed dependency list for py-tomopy and py-dxchange
* added py-nose dependency
* fixed tests
* commented out dependency py-counter
* fixed dependency py-pybtex-docutils
* removed nose as a dependency
* fixed flake8 errors
* fixed import_modules
* fixed import_modules indent
* fixed various issues in tomopy and deps files
- paraview 5.2.1 -> 5.4.0 supports both Qt4 and Qt5, but the assumed
default version changes between versions. So explicitly define
which QT major version is being used.
* Several improvements for the openfoam packages
--
Refactor openfoam packages by adding an OpenfoamArch class
Use separate configure, build, install phases.
Provide FOAM_PROJECT_DIR dependent env for openfoam packages
- easier way to locate
Eliminate intermediate installation directories
- unneeded clutter.
- makes it less than easy to find the etc/bashrc file
Add versioning for all openfoam patches
- no certainty which parts (if any) will be needed in future versions,
especially if we strive to ensure that the upstream version builds
well with spack to begin with.
Support build of develop branches
- helps track build regressions for future openfoam releases
STYLE: use common/ and assets/ to provide additional (build) resources ...
* - adjust OpenFOAM provider
Move openfoam-com up front since this is the one being used as a base
for the others
Added line in package.py to patch using ipopt_ppc_build.patch. The patch simply adds support in config.guess and Ipopt/config.guess to build ipopt on ppc64le.
* adding H5Z-ZFP; updating zfp to use choice variant for bit stream word size
* fixing homepage url
* removed fortran error message...just build fortran if can, otherwise ignore
* Added magma package
* Incorporated Serban's change
* fftw: patch configuration file to remove search for xlc_r compiler
when compiler not gcc
FFTW assumes there are only 2 compilers: gcc and IBM XL. When
building threaded fftw, the configuration file is looking for
the threaded IBM XL's xlc_r compiler when the compiler is not gcc.
The PGI compiler is not gcc.
* Include depends_on for gperf
Sometime around 2.12.2 fontconfig acquired a build-time
dependency on `gperf` (this commit, I think:
59fd9960bbb58fd6257adb13ec0f918882149332).
This adds the dependency.
`gperf` is called in the `src/Makefile`, see line 907 of
`src/Makefile.in`.
* Only depend_on gperf if @2.12.2:
The gperf dependency *seems* to only be required when @2.12.2:.
Earlier releases do not check the arg type of the gperf lookup
function (which requires gperf) and are able to use pre-generated
files so gperf is not required at build time.
* 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.
* fixing Makefile override of PREFIX and install w/gcc-6
* oce changes for cgm
cgm can be configured with oce, but oce needs
to have X11 enabled, because some libraries
(like TKCAF in occ/oce) gets built only of X11 is NOT disabled
so introduce a variant +X11 for oce, which is needed when
configuring cgm with oce(+X11)
* follow up review
simplify by removing the patch and different url paths
use append instead of extend, when necessary
make mpi true by default
X11 dependency is still to be addressed; it pulls in some opengl
library (on laptop nvidia seem to work, on virtual linux machine
mesa was good enough)
- invoke make with the correct TARGET for aarch64
- foforce PILERDRIVER as openblas cannot correctly detect CPU on aarch64
- update url to more recent version
* Fix tpetra-related xsdk errors
Recent changes to the trilinos package broke the xsdk build.
xSDK explicitly disables tpetra, but packages depending on it
(such as ifpack2 and amesos2) are explicitly enabled by default
in the trilinos package. This commit explicitly disables them
within the xsdk package.py.
* Disabled exodus in the xsdk build
See issue #4502 for details
- Introduce an opengl variant that is enabled by default. Disabling it
allows building qt for X forwarding etc.
- Depend on fontconfig and freetype to make use of system fonts.
Otherwise qt can not find any fonts.
- libx11 is required when libxcb is used.
- Set MAKEFLAGS to parallelize qmake compilation.
* Initial version of the namd package
* Modified charm to consider compile against intel/intel-mpi
* Correction of namd to compile with intel-mkl and intel compiler
* Adding inclue64 in the prefix
* adding property for the build directory
* removing useless function build
Fixes#4488. When compiling metis as a shared library, the package
used the syntax `-rpath=`, followed by a path. This syntax is
non-portable, so replace it using Spack's compiler rpath argument
property.
* During install, remove prior unfinished installs
If a user performs an installation which fails, in some cases the
install prefix is still present, and the stage path may also be
present. With this commit, unless the user specifies
'--keep-prefix', installs are guaranteed to begin with a clean
slate. The database is used to decide whether an install finished,
since a database record is not added until the end of the install
process.
* test updates
* repair_partial uses keep_prefix and keep_stage
* use of mock stage object to ensure that stage is destroyed when it should be destroyed (and otherwise not)
* add --restage option to 'install' command; when this option is not set, the default is to reuse a stage if it is found.
* espresso: fixed compilation for 6.1 (elpa) and added support for hdf5
* espresso: addressed items in @davydden review
* espresso: fixed behavior for espresso@:5.4.0
* New Package: lanl-bml
Added LANL's BML library as Spack Package as dependency for future
packages
* Adjusted lanl-bml versions
Specified current master as develop and added v1.1.0 tagged version
* Renamed lanlbml package to bml
* First draft package for mono
Mono's vendor'ed boringssl interacts badly with openssl, so
you need to use `cmake~openssl`.
Left to its own devices, it wants to refer to things in
`/usr/share/.mono`. This doesn't work for installs that don't run as
root, etc... This package includes a variant to redirect those paths
to `prefix.share`.
* Whitespace/Flake8
* Adding Nalu package.
* Fixing flake8 stuff.
* Fixing flake8 stuff.
* Reorganizing trilinos package file a little to make it less verbose.
* Reorganizing trilinos package file for more general use as well as use as a dependency of the Nalu package. Setting fpic as default for yaml-cpp and superlu.
* Explicitly stating fpic variants in dependent packages.
* Updating nalu and trilinos package files with suggested changes.
* Fixing formatting issues. Making suggested changes.
* Fixing formatting.
* Reducing amount of explicit variants in Nalu. Adding suggested changes to Trilinos package file.
* Making suggested changes to Nalu package.
* Turning off superlu-dist variant.
* Cleaning up yaml-cpp file.
* Fixing pnetcdf requirements in trilinos.
* Handle missing defn of __NR_memfd_create
Generally SYS_foo is defined to __NR_foo (in sys/syscall.h) which is
then defined to a syscall number (in asm/unistd_64.h). Certain CentOS
systems have SYS_memfd_create defined to __NR_memfd_create but are
missing the second definition. This is a belt and suspenders solution
to the problem.
See [this post][syscall] for a nice general description of how these
parts fit together.
[syscall]: https://www.uninformativ.de/blog/postings/2017-02-11/0/POSTING-en.html
* Avoid flake8 warning
* postgresql: Fix build with threadsafe and add variant.
* postgresql: Convert Package to AutotoolsPackage.
Also add explicit enable flag for +threadsafe variant.
* Add add'l output formats for graphviz
Add support for additional output formats to graphviz, including gif,
jpg, pdf, and png.
Graphviz calls its pango+cairo option *pangocairo* so I followed suit.
Libgd was missing jpeg/jpg support. None of the other supported
formats are conditionalized and there is no --with/--without support,
so I followed suit.
* Fix ghostscript plugin
When I installed thusly:
spack install graphviz+pangocairo+libgd^cairo+X^pango+X
the ghostscript plugin tripped over some variable names that had
changes in `gs@9.18:`. This fixes them.
* Remove wayward import of tty
* Need to help Makefile.PL find the expat bits
We need to provide Makefile.PL with a clue about where our
expat bits live. We had the dependency, but I suspect
that the lib was actually linking against a system version.
* Use prefix.lib instead of building path myself
Ditto with .include
I've had non-repeatable failures in my CI runs on all three clusters
at the bamutil's step. In each case there are .o or .so files that
are corrupt or truncated.
I suspect that the homebrewed bamutil Makefile scheme doesn't actually
support parallel builds.
* Tighten up graphviz package
The fun started when configure discovered a broken/partial
installation of `swig` in `/usr/local`, then auto-discovered my
system's python and ruby packages.
- SpackException doesn't seem to exist. Convert it to a SpackError
and call `.format(...)` on the error string to fill in the
placeholder.
- Pull swig out of the list of languages. It's something that can be
asked for explicitly and that is needed if *any* of the langagues
are enabled. It's disabled by default.
- Explicitly disable the languages that are in "untested_bindings"
list lest the configure script pick up things from the system.
* Touch up variant description string
* Clean up conditional statement
* Use InstallError, not SpackError
* Drop the swig variant
Get rid of the swig variant and drive that bit based on whether any
languages are enabled.
* Move perl to the untested list
That's not strictly accurate. I tested it and it doesn't work.
There's a missing depends_on(). When you add that you'll discover
that the language binding bit can't find Perl's 'EXTERN.h'. Then
you'll discover that graphviz's `configure` script doesn't have a good
way to include the paths to Perl's bits (looks like I'll have to
gather them for each language and then use them to build `CFLAGS` and
`CXXFLAGS` and `LDFLAGS`). While pondering that, you'll discover that
EXTERN.h is buried down here:
```
opt/spack/linux-centos7-x86_64/gcc-4.8.5/perl-5.24.1-35ejv4426dmzreum4ekdibu3ddmhquvi/lib/5.24.1/x86_64-linux/CORE/EXTERN.h
```
and decide that you wish you had never thought to actually test
`graphviz+perl`.
I could find that directory with a snippet like so:
```
perl -MConfig -e 'print "$Config{archlib}\n"'
```
but at this point I'm much, much further down this rabbit hole then I
ever wanted to go.
* Convince python that tested_bindings is a list
When I removed `+perl` and made `tested_bindings` a list of one
thing, I ended up with this:
```
==> Error: cannot concatenate 'str' and 'tuple' objects
```
* Flake8 cleanup
* Don't convert a string to a string
* rm unused () and clarify variable name
Feedback from @adamjstewart
- Get rid of some unnecessary parens.
- Clearer variable name and use.
* Further cleanup of language enabling loop
Now we don't need that pesky temporary variable.
* Add package for cctools
Add a package for cctools.
Requires the recently submitted "useshrplib" support in Perl (or some
other mechanism to enable -fPIC for perl).
* Delete extraneous import
* Perl's shared variant changed, adapt...
The name of the variant that perl uses to build a shared lib changed and
it now defaults to True. Use the new name and continue to be insistent
about using the shared variant.
* Flake8 cleanup
* Added magma package
* Incorporated Serban's change
* boost-pgi: Add support for PGI compiler
There are two patches required:
(1) general fixes required by PGI
(2) workaround for a bug in PGI 17.4
Conflicts:
var/spack/repos/builtin/packages/boost/package.py
* Add variant to build shared Perl lib
Add a variant that enables Perl's "useshrplib" feature, which builds a
shared perl library.
This addresses problems like so:
```
/usr/bin/ld: /blah/blah/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/perl-5.24.1-y43dp3p5w66v7qh5xkwgufxohyuodyew/lib/5.24.1/x86_64-linux/CORE/libperl.a(op.o): relocation R_X86_64_32S against `PL_opargs' can not be used when making a shared object; recompile with -fPIC
/blah/blah/spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/perl-5.24.1-y43dp3p5w66v7qh5xkwgufxohyuodyew/lib/5.24.1/x86_64-linux/CORE/libperl.a: could not read symbols: Bad value
```
It should also address the Intel compiler issue discussed in #3081
while respecting Perl's configuration machinery.
* Rename shared variant and default to True
* Use correct variant to add configure arg
* Restore bits that set ccflags for intel compilers
After some experimentation we've established that setting
the flag to build a shared perl library is tightly tied to
the use of -fPIC.
This commit restores the code that sets ccflags for
intel compilers.
* Flake8 cleanup
See the discussion about installing jar files in #4386.
Also installs a wrapper script that has explicit references to the
prerequisite java exe and to the jar file in it's final resting place.
* Add packages for clustalw and clustalo (and argtable)
Add packages for the classic multiple alignment package, `clustalw`
and its younger sibling, `clustalo`.
`clustalo` needed the `argtable` package (command line arg parsing).
Lightly tested on CentOS 7.
* Remove FIXME (sigh...)
* Add mpi support to R
* Add multiple precision math routines to R
* Updated the URL to match the version
* Remove duplicate packages
* Add packages for r-ergm and it's dependents
* Fixed depends-on types
* Correct flake8 errors
* Correct Build type
* r-factoextra and dependents
* Revert "r-factoextra and dependents"
This reverts commit afbf477fd66e565fd187262c386bcc08c98a4d7e.
* Add only r-factoextra files
* Add a package for Trimmomatic
See the discussion about installing jar files in #4386.
Also installs a wrapper script that has explicit references to the prerequisite java exe and to the jar file in it's final resting place.
* Fix bad format statement
Apparently something like this "blah{}".format(...) works (it's missing
something inside the curly braces) but fails the travis test.
The two given versions of mariadb are not fetchable under the given
URL, probably because older versions are purged and only kept in
an archive.
Add two working, latest revisions of each release line.
Somehow the path to `CMakeLists.txt` via the class property
`root_cmakelists_dir` was relative but is now actually relative
to `spack-build/`.
Close 4324 by providing a path relative to the source repo
of the stage via a method instead of a member variable
* Add package for vcftools@0.1.14
The package munges the various perl scripts so that their sbang lines
point to the depended upon perl (perhaps with Spack sbanger in the
dance) instead of relying on `/usr/bin/env perl`.
As it stands it installs its Perl libraries into `prefix/lib` and then
depends on `setup_environment` to prepend that dir onto PERL5LIB.
See my [vcftools issue
80](https://github.com/vcftools/vcftools/issues/80) for a discussion
about fixing its non-functional attempt at isolating itself from
PERL5LIB shenanigans.
* perl dependency should be build/run
* Ensure Config.pm has correct setting for cc
Run a filter after install so that Config.pm records the compiler that
Spack built the package with. If this isn't done, $Config{cc} will be
set to Spack's cc wrapper script.
* Also patch compilers Config_heavy.pl
This patch sets ld=gcc, which appears to work. I'm not sure if
there's a good way to get at the ld that Spack uses.
* Clean up quoting
* Fix pattern for Config.pm
Does not start at beginning of line...
What the user wants, the user etc....
Add info for STAR@2.4.2a. It's URL looks different, so added a URL for
it. This broke the URL for the current version, so added a URL for it
also (known bug).
*Minimally* tested on CentOS 7.
* python: ensure that distutils sets valid compiler options for RPATH on cray
* python: add cray-rpath patches for python@2.3:3.0.1 and python@3.1:
* python: in patch(..., when="@a:b platform=c"), limit b must be specified
* python: assume that python@4 will break the cray patches
* Fix mummerplot when ^perl@5.20:
Calling defined() on a hash has been deprecated for ages. It became
an error in perl@5.20. If we're building with a perl where it's
illegal, we should fix it.
* Simplify call to filter_file
Treat the first arg to filter_file as a string rather than
a regex, so that we don't have to figure out the escapes.
* Patch mummerplot for *any* perl version.
* Fix bwa url's
Work around varying github URLs.
See #4365 for details.
* Restore main url entry
@adamjstewart pointed out that the package still needs a main url
so that `spack versions` works.
- Add a `spack gpg` subcommand in anticipation of signed binaries.
- GPG keys are stored in var/spack/gpg, and the spack gpg command manages them.
- Docs are included on the command.
* Add info for jdk@7u80 (not downloadable)
Add version info for jdk@7u80. Oracle does't seem to be
distributing it any longer so there's no reasonable URL to
provide, but for those of us who already have the tarball
this is useful.
* Flake8 cleanup
* Add mpi support to R
* Add multiple precision math routines to R
* Updated the URL to match the version
* Remove duplicate packages
* Add packages for r-ergm and it's dependents
* Fixed depends-on types
* Correct flake8 errors
* Correct Build type
* r-adegenet and dependent packages
* fix parser
* Removed xfails
* cleaned up debug print statements
* make use of these changes in gcc
* Added comment explaining unreachable line, line left for added protection
* cairo: ensure that X support is disabled for variant "~X"
* cairo: explicitly enable X support for +X variant
* cairo: prefer "variant in spec" over spec.satisfies(variant)
* Trailing whitespace cleanup
* Handcraft an install process for mummer (grumble)
Mummer punts on an installation step, they just build in and run from
the same directory.
Mummer also has various hardcoded paths built into it that allow it to
find other executables that it needs as well as its Perl library.
This updates the package to deal with this approach.
It patches the Makefile and scripts/Makefile so that the correct info
is fed to sed when it munges the perl scripts.
The install step is now finer grained and puts things where mummer
relatively wants to find them.
* Add perl dependency
* perl should be build/run dependency
* Fix whitespace
* Delete stray u at top of file
Two changes:
- It seems that Illumina version numbers are dotted and that the
dashed version in the 2.18... filename is an anomaly (based on the
names for 2.17.1.14 and 2.19.0). `url_for_version` does the right
thing for 2.18. It will need to be fixed when support for 2.19 is
added. 2.17 is no longer generally available so it gets a pass.
- Add version and hash for 2.17.1.14.
2.17.1.14 is no longer distributed. If you have a copy of the
source tarball, you can drop it into a local mirror w/ the name
mirror/bcl2fastq2/bcl2fastq2-2.17.1.14.zip and go from there.
* Add mpi support to R
* Add multiple precision math routines to R
* Add packages for r-ergm and it's dependents
* Fixed depends-on types
* Correct flake8 errors
* flex: create variant +lex that creates symlinks for lex and libl.{a,so}
* flex: enable variant +lex by default
* flex: use dso_suffix for portability; replace repetitive code with a loop
I need boost@1.54.0 for bcl2fastq2. I tested bcl2fastq2 using the
system compiler (gcc@4.8.5). My full build uses a spack-build
gcc@5.4.0.
boost@1.54.0 won't build. I found the answer
[here](https://github.com/hashdist/hashstack/issues/802) with the
details in [this upstream/boost
ticket](https://svn.boost.org/trac/boost/ticket/10125).
I've confirmed that these combo's build:
boost version| compiler
------------ | ------------------
boost@1.54.0 | gcc@4.8.5 (system)
boost@1.54.0 | gcc@5.4.0 (Spack)
boost@1.64.0 | gcc@5.5.0 (system)
* added openmpi support to meme
* openmpi is a link dependency which leverages r_path
* openmpi support now the default - meme does not have configure argument for mpi - if it's found then it's used
* added serial option and set mpi to not be default
* modified meme
* Add the gnupg package and missing dependencies. Update versions of existing dependencies.
* this ended up in the wrong repo
* put versions back, remove uneeded function
* OK ;)
* autopep8
* typo on npth line
* whitespace
* Add a new package for Open Babel
* Add post-installation tests, stolen from the fine folks at Homebrew
* Add patch to fix Python 3.6 support
* Add a more complete patch to get Python 3.6 support working
* Add patch to convert tabs to spaces in test script
testpdbformat.py contains mixed tabs and spaces
causing the unit tests to fail. With this patch,
all tests pass with flying colors.
* Add v1.1.26 and make crypto a variant
I need 1.1.26 for bcl2fastq2.
I also need to build it without crypto support.
* Initial support for bcl2fastq2
* Clean up commentary, messages, names
No substantial changes intended, just cleanup.
* fix flake8 and extra import
* The masked grammarian strikes again...
* Be normal (messages don't end in periods)
* When +crypto, add --with-crypto
Add `--with-crypto` to configure args when user hasn't explicitly set
`~crypto`.
* self.spec.satisfies is unsatisfying, in is in instead
See #4135, self.spec.satisfies has issues. @adamjstewart suggests
simply using in.
* added albacore package as well as dependency py-ont-fast5-api
* added py-cutadapt and dependency py-xopen
* made more changes to albacore and cutadapt as well as dependencies
* made changes again per @adamjstewart
* fixed by python n00b errors i think
* fixed?
* tw=79
* made changes to py-ont-fast5-api ont-albacore
* removed bad characters
* albacore requires setuptools as build and run dependency
* added vmd
* added back albacore
* removed vmd package
* added meme software
* libz is only needed as link depedency for meme
* added libxml2 libxslt libgcrypt as link dependencies
* added albacore package as well as dependency py-ont-fast5-api
* added py-cutadapt and dependency py-xopen
* made more changes to albacore and cutadapt as well as dependencies
* made changes again per @adamjstewart
* fixed by python n00b errors i think
* fixed?
* tw=79
* made changes to py-ont-fast5-api ont-albacore
* removed bad characters
* py-cdat-lite: a python package for managing and analysing climate science data
* py-cdat-lite: depends on py-numpy
* py-cdat-lite: flake8 compliance
* py-cdat-lite: provide a generic URL where multiple versions are listed
* py-cdat-lite: restrict python versions; python required at run-time
* py-cdat-lite: use URL under pypi.io for consistency with other packages
* py-cdat-lite: add run-time dependency on py-numpy
* Initial attempt at flann packaging.
Python2 somehow works. Python3 does not. Still debugging their
obscure setup.py configuration.
* Flann good enough. Python3 broken but close.
Flake8 checks in place. Unsure about CMAKE_BUILD_TYPE and default
spack behavior.
* spack uses RelWithDebInfo as default build type.
* builds py2/3, but direct site-packages install
* prefix working, empty python install dir
* flann package +python installs correctly
* str format {0} instead of {}
* potential doctest fix
* consistency of build env with PythonPackage
* fix python again, test deptype todo, build type
* potentially enable matlab, untested
* highfive: New package; this is a C++ wrapper for the HDF5 library
The C++ wrapper that is shipped with the HDF5 library has several shortcomings. The highfive library seems to avoid these.
* highfive: Make MPI variant default to true
* enable cuda support for suite-sparse
* do not use spec.satisfies
* cuda restructure, give clearer comment of why
* str format compatibility
* flake8 checks
* adding 0.5.1 and variant for uint8 bit stream word type
* Revisions as per davydden
* fixing style (flake8) issues
* - switched to derive from MakefilePackage
- fixed typo in variant check
- Confirmed installs correctly with bswtuint8 variant
* added build method; changed zfp_incdir to incdir
* * Adding uber fastmath package to support 'spack install fastmath'
* Adding dims variant boxlib to control compile-time spatial dimension count
* Explicitly disabling many parts of moab to get lib to build. Don't need tools yet.
* Add logic to spack/setup-env to not refer to $SYS_TYPE if its not defined.
* adding mesquite package
* * Added Chombo (still working on Fortran name mangling)
* Made mesquite depend on mpi
* Fixed use of boxlib's dims numerical variant
* adding PUMI
* flake8 compliance
* adding phasta
* fixing flake8 issues
* undue $SYS_TYPE protection change
* fixing install step for fastmath uber package; resolve issues requested by adamjstewart in PR
* revisions as per adamjstewart
* re-enabling trilinos and phasta dependencies
* all changes requested modulu values= and assert statement
* fixing cmake_args usage in pumi; fixing lib installs for chombo
* first pass at numerical variant
* fixing dims variant as per @adamjstewart
* fixing func/var name collision
* fixing means of disabling -Werror
* fix name collision for cmake_args var/func
* fixing chombo homepage/url; make FASTMath use chombo#3.2; remove extraneous comment about boxlib dim
* remove dummy fastmath package; switch to @BarrySmith soln for install of dummy bundle
* fix flake8 import os issue
* remove extraneous comment
* adding url for fastmath scidac site
* final fixes as per @adamjstewart
* adding 1 dims option for boxlib
* switching make(all) to gmake(all)
Added DFLAGS to the `make.inc` file being written.
These macros are also added to the language specific variables
like CFLAGS, CXXFLAGS and FCFLAGS. Changed `spec.satisfies('foo')`
with `'foo' in spec` in `intel-mkl`, see #4135. Added a basic
build interface to `intel-mpi`.
* Add GCC 7
* Allow users to build subset of GCC compilers with multi-value variant.
* Add comment explaining what 'all' actually means
* More specific golang support
* Only require Zip when building Java
* Comment out provide directives that don't currently work
* Add Ada support
* Use conflicts directive
* Fix joining of languages
* Need special flag to build jit
* Explicitly declare GNAT download extension
* Import tty, update lib64 to lib
* BRIG and Go are not supported on macOS
* Simplify formatting and imports
* JIT patch required for newer versions as well
