* Fix crashes when running spack install under nohup
Fixes#4919
For reasons that I do not entire understand, duplicate_stream() throws
an '[Errno 22] Invalid argument' exception when it tries to
`os.fdopen()` the duplicated file descriptor generated by
`os.dup(original.fileno())`. See spack/llnl/util/lang.py, line
394-ish.
This happens when run under `nohup`, which supposedly has hooked
`stdin` to `/dev/null`.
It seems like opening and using `devnull` on the `input_stream` in
this situation is a reasonable way to handle the problem.
* Be more specific about error being handled.
Only catch the specific error that happens when trying to dup
the stdin that nohup provides.
Catching e as a StandardErorr and then
`type(e).__name__` tells me that it's an OSError.
Printing e.errno tells me that it's 22
Double checking tells me that 22 is EINVAL.
Phew.
* 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.
- Remove `special_types` dict in spec.py, as only 'all' is still used
- Still allow 'all' to be used as a deptype
- Simplify `canonical_deptype` function
- Clean up args in spack graph
- Add tests
* 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.
* Disable spec colorization when redirecting stdout and add command line flag to re-enable
* Add command line `--color` flag to control output colorization
* Add options to `llnl.util.tty.color` to allow color to be auto/always/never
* Add `Spec.cformat()` function to be used when `format()` should have auto-coloring
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
