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* GapFiller.pl fixes: line endings, env perl, convert to Getopt::Std, requires perl with threads.
* GapFiller.pl fixed source path, install location.
* Fixed missing space.
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* Add version 3.10.1 to the PETSc spackage file.
* Makefile changes required for building PETSc native tests with the XL compiler.
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Also add zlib/bzip2 dependencies.
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Set default optimization level (-O2) if not specified in cflags.
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patch does not apply to 3.2.1 (released in late 2017).
Given that it fixes the issue discussed in May 2016, most likely
it shall apply only to 3.2
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Fix two bugs with module file parsing:
* Detection of the CRAY_LD_LIBRARY_PATH variable was broken by #9100.
This fixes it and adds a test for it.
* For module names like "foo-bar/1.0", the associated PACKAGE_DIR
environment variable name would be "FOO_BAR_DIR", but Spack was not
parsing the components and not converting "-" to "_"
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Building bazel yielded errors since commit cd9691d. The first commit
fixes the build for older bazel versions, the second commit adds new
versions and ports the patches to these versions.
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Lots of programs still have mpiexec/mpirun baked in.
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4.8 has c++11 support, and RHEL/Centos 7 still use 4.8.5
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* gmap-gsnap: Add variant for different cpu support.
* gmap-gsnap: fix flake8 error.
* gmap-gsnap: remove sys import.
* Change variant type to multi-valued.
* remove if-statement.
* gmap-gsnap: Build in seperate directories.
* gmap-gsnap: remove make distclean.
* gmap-gsnap: rewrite the recipe.
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Fixes #9166
This is intended to reduce errors related to lock timeouts by making
the following changes:
* Improves error reporting when acquiring a lock fails (addressing
#9166) - there is no longer an attempt to release the lock if an
acquire fails
* By default locks taken on individual packages no longer have a
timeout. This allows multiple spack instances to install overlapping
dependency DAGs. For debugging purposes, a timeout can be added by
setting 'package_lock_timeout' in config.yaml
* Reduces the polling frequency when trying to acquire a lock, to
reduce impact in the case where NFS is overtaxed. A simple
adaptive strategy is implemented, which starts with a polling
interval of .1 seconds and quickly increases to .5 seconds
(originally it would poll up to 10^5 times per second).
A test is added to check the polling interval generation logic.
* The timeout for Spack's whole-database lock (e.g. for managing
information about installed packages) is increased from 60s to
120s
* Users can configure the whole-database lock timeout using the
'db_lock_timout' setting in config.yaml
Generally, Spack locks (those created using spack.llnl.util.lock.Lock)
now have no timeout by default
This does not address implementations of NFS that do not support file
locking, or detect cases where services that may be required
(nfslock/statd) aren't running.
Users may want to be able to more-aggressively release locks when
they know they are the only one using their Spack instance, and they
encounter lock errors after a crash (e.g. a remote terminal disconnect
mentioned in #8915).
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* petsc: add new versions 3.9.4 and 3.10.0
* petsc:update superlu_dist dependency for version 3.10 [might have to change this later for xsdk]
* slepc: add in new releases 3.9.2 and 3.10.0
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compilers (#9316)
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- Many container builds are timing out frequently during Spack tests in
Travis CI.
- Travis recommends to try `sudo: required` to see whether this is an
infrastructure issue or something else.
- added `sudo: required` to all Linux builds.
- added --verbose to `spack test` invocation so that we can see more
easily what tests it's timing out on.
Signed-off-by: Todd Gamblin <tgamblin@llnl.gov>
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* adding r-animation package
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* Catch2: 2.3.0+
Add the latest two releases of Catch2.
In 2.3.0+, the include changed to a future-proof
`<catch2/catch.hpp>` path which dependent projects will break upon.
* openPMD-api: Catch2 2.3.0+
openPMD-api just updated to use the new, future-proof Catch2
headers `<catch2/catch.hpp>`.
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When a Spack Executable was configured to capture stderr and the
process failed, the error messages of the process were discarded.
This made it difficult to understand why the process failed. The
exception is now updated to include the stderr of the process when
the Executable captures stderr.
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Adds 'code' to the list of suffixes that are excluded from version
parsing of URLs, such that if a URL contains the string
'cistem-1.0.0-beta-source-code', a version X will substitute in to
produce a URL with cistem-X-source-code ('source' was already excluded).
The 'cistem' package version is updated to make use of this (and fix
a fetching bug with the cistem package). A unit test is added to check
this parsing case.
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