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* preserve the order in which patches are applied by packages (in spite of grouping them by 'when')
* add tests confirming patch order
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* initial work to make use of an 'upstream' spack installation: this uses the DB of the upstream installation to check if a package is installed
* need to query upstream dbs when adding new record to local db
* prevent reindexing upstream DBs
* set prefix on specs read from DB based on path stored in install record
* check that Spack does not install packages that are recorded as installed in an upstream db
* externals do not add their path to install records - need to use 'external_path' to get path of upstream externals
* views need to check for upstream installations when linking metadata
* package and spec now calculate upstream installation properties on-demand themselves rather than depending on concretization to set these properties up-front. The added tests for upstream installations don't work with this new strategy so they need to be updated
* only refresh modules for local specs (not those in upstream packages); optionally generate local module files for packages installed upstream
* when a user tries to locate a module file for a package installed upstream, tell them to use the upstream spack instance to locate it
* support recursive upstream databases (allow upstream databases to use their own upstream databases)
* separate upstream config into separate file with its own schema; each entry now also includes a name
* metadata_dir is no longer customizable on a per-instance basis for YamlDirectoryLayout
* treat metadata_dir as an instance variable but dont set it from kwargs; this follows several other hardcoded variables which must be consistent between upstream and downstream DBs. Also update DirectoryLayout.metadata_path to work entirely with Spec.prefix, since Spec.prefix is set from the DB when available (so metadata_path was duplicating that logic)
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Prevents infinite recursion caused by sourcing `setup-env.sh` in bashrc
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Change the location of the CMake build area from the staged source
directory to the stage base directory.
This change allows CMake packages to refer to the build directory in
setup_environment (e.g. if tests need to have a directory in PATH):
Staging happens after the call to setup_environment(), and if the
stage area does not exist, then spec.stage.source_path returns None.
To accommodate this change, archived files (like config.log for
Autotools packages) are archived relative to the stage base directory
rather than the expanded source directory.
Other packages (those not using CMake) will still use the staged
source directory as the default working directory for builds (and
will still be unable to reference this directory in
setup_environment())
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When multiple instances of environment-modules were installed with
different architectures, Spack was not retrieving the installation
appropriate for the current architecture when finding the module
prefix.
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This allows shell commands for `spack edit` to be executed correctly if
they have quoted arguments.
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* Fixed some issues with CUDA-Intel compiler conflicts.
* Comment about expressing CUDA-compiler conflicts.
* More precise conflicts and also add support for Intel 19.0
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Patch extracted from #7536 courtesy of @mgsternberg
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If the user has set the environment variable VISUAL, it will be used
in preference to EDITOR for all Spack editing activities. If VISUAL
is not set or fails (perhaps due to a lack of graphical editing
capabilities),EDITOR will be used instead. We fall back to one of
several common editors if neither bears fruit.
This feature has been tailored to:
* Provide identical behavior to the previous implementation in the
case that VISUAL is not set.
* Not require any change to code utilizing the editor feature.
* Follow usual UNIX behavior concerning VISUAL and EDITOR.
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`string.find` is not part of Python 3 anymore.
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* Fix clearing EnvironmentModifications with python2
* Add EnvironmentModifications::clear unit test
Use re-assignment rather than del to clear array
* Fix flake issues
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Fixes #10191
* Add more regular expressions to detect clang versions that were
not being picked up
* Add a test for parsing versions from the output of Clang (this
does not run Clang, but rather uses example outputs from Clang)
* Separate Clang version parsing into its own method (to make it
easier to test)
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Currently, only C headers are considered, causing build failures for
packages depending on, e.g., netcdf-fortran and xerces-c. Additionally,
the regex used to look for the include path component did not consider
word boundaries, causing false matches.
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* Create option to build missing compilers and add them to config before installing packages that use them
* Clean up kwarg passing for do_install, put compiler bootstrapping in separate method
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Update documentation on getting started to mention that a "make"
executable is required to build packages with Spack.
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entry.
* Rework of buildcache creation and install prefix checking using the functions introduced in
https://github.com/spack/spack/pull/9199
Instead of replacing rpaths with placeholder and then checking strings, make use of the functions
relocate.is_recocatable and relocate.is_file_relocatable to decide if a package needs the allow-root option.
This fixes a problem where the placeholder path was not in the first rpath entry. This was seen in c++ libraries and binaries because the compiler was outside the spack install base path and always appears first in the rpath.
Instead of checking the first rpath entry, all rpaths have the placeholder path and the old install path (if it exists) replaced with the new install path.
* flake8
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* Added the `spack buildcache preview` sub-command
This is similar to `spack spec -I` but highlights which nodes in a DAG
are relocatable and which are not.
spec.tree has been generalized a little to accept a status function,
instead of always showing the install status
The current implementation works only for ELF, and needs to be
generalized to other platforms.
* Added a test to check if an executable is relocatable or not
This test requires a few commands to be present in the environment.
Currently it will run only under python 3.7 (which uses Xenial instead
of Trusty).
* Added tests for the 'buildcache preview' command.
* Fixed codebase after rebase
* Fixed the list of apt addons for Python 3.7 in travis.yaml
* Only check ELF executables and shared libraries. Skip checking virtual or external packages. (#229)
* Fixed flake8 issues
* Add handling for macOS mach binaries (#231)
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The environment modules package has been updated to include
versions up to 4.0.0. The url of the package and the homepage
have been updated accordingly.
The `spack bootstrap` command now builds version 3.2.10 of
the environment-modules package, and will do until #10708
is fixed.
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This restores the use of Package.headers when computing -I options
for building a package that was added in #8136 and reverted in
#10604. #8136 used utility logic that located all header files in
an installation prefix, and calculated the -I options as the
immediate roots containing those header files.
In some cases, for a package containing a directory structure like
prefix/
include/
ex1.h
subdir/
ex2.h
dependents may expect to include ex2.h relative to 'include', and
adding 'prefix/include/subdir' as a -I was causing errors,
in particular if ex2.h has the same name as a system header.
This updates header utility logic to by default return the base
"include" directory when it exists, rather than subdirectories.
It also makes it possible for package implementers to override
Package.headers to return the subdirectory when it is required
(for example with libxml2).
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- Switch all libhio tarball listings to sha256 checksums
- Correct typo in alert message in /lib/spack/spack/util/module_cmd.py: fucntion -> function
https://github.com/hpc/libhio/releases
Released 2019-02-01
Verification builds on LANL Darwin:
**Intel Xeon**
Architecture: x86_64
CPU op-mode(s): 32-bit, 64-bit
Byte Order: Little Endian
CPU(s): 40
On-line CPU(s) list: 0-39
Thread(s) per core: 2
Core(s) per socket: 10
Socket(s): 2
NUMA node(s): 2
Vendor ID: GenuineIntel
CPU family: 6
Model: 63
Model name: Intel(R) Xeon(R) CPU E5-2660 v3 @ 2.60GHz
Stepping: 2
CPU MHz: 1198.779
CPU max MHz: 3300.0000
CPU min MHz: 1200.0000
BogoMIPS: 5193.70
Virtualization: VT-x
L1d cache: 32K
L1i cache: 32K
L2 cache: 256K
L3 cache: 25600K
NUMA node0 CPU(s): 0-9,20-29
NUMA node1 CPU(s): 10-19,30-39
Flags: fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc cpuid aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 sdbg fma cx16 xtpr pdcm pcid dca sse4_1 sse4_2 x2apic movbe popcnt aes xsave avx f16c rdrand lahf_lm abm cpuid_fault epb invpcid_single pti intel_ppin tpr_shadow vnmi flexpriority ept vpid ept_ad fsgsbase tsc_adjust bmi1 avx2 smep bmi2 erms invpcid cqm xsaveopt cqm_llc cqm_occup_llc dtherm ida arat pln pts
`
[+] /scratch/users/dantopa/new-spack/strawman.pr.libhio/opt/spack/linux-centos7-x86_64/gcc-4.8.5/libhio-1.4.1.3-s4fnmesfp65trhks5qi3it5p73ssfpsp
[+] /scratch/users/dantopa/new-spack/strawman.pr.libhio/opt/spack/linux-centos7-x86_64/gcc-4.8.5/libhio-1.4.1.2-fkgh5vqpijvwqywffmokgmsglqxwfrtl
`
**Arm**
Architecture: aarch64
Byte Order: Little Endian
CPU(s): 256
On-line CPU(s) list: 0-255
Thread(s) per core: 4
Core(s) per socket: 32
Socket(s): 2
NUMA node(s): 2
Model: 0
BogoMIPS: 400.00
L1d cache: 32K
L1i cache: 32K
L2 cache: 256K
L3 cache: 32768K
NUMA node0 CPU(s): 0-127
NUMA node1 CPU(s): 128-255
Flags: fp asimd evtstrm aes pmull sha1 sha2 crc32 atomics cpuid asimdrdm
`
[+] /scratch/users/dantopa/new-spack/strawman.pr.libhio/opt/spack/linux-rhel7-aarch64/gcc-4.8.5/libhio-1.4.1.3-q6nnwiy6bi7ktnghdsngwamom23zpmgy
[+] /scratch/users/dantopa/new-spack/strawman.pr.libhio/opt/spack/linux-rhel7-aarch64/gcc-4.8.5/libhio-1.4.1.2-y6nwovff3qbdy242zc4x2toloz6xpcvm
`
2019-02-25
Signed-off-by: Daniel Topa <dantopa@lanl.gov>
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* Add /hash to spack help --spec
* Make /hash gray, add ^/hash
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Spack warns users when a dependency package updates CPATH. This
warning message is generating bug reports and alarm in cases where
there is no problem. For now this downgrades the warning message to
the debug level, so it only shows up if something goes wrong for the
user and they ask for more information from Spack.
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This spack command adds a new schema for a file which describes the
builder containers available, along with the compilers availabe on
each builder. The release-jobs command then generates the .gitlab-ci.yml
file by first expanding the release spec set, concretizing each spec
(in an appropriate docker container if --this-machine-only argument is
not provided on command line), and then combining and staging all the
concrete specs as jobs to be run by gitlab.
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Adds four new sub-commands to the buildcache command:
1. save-yaml: Takes a root spec and a list of dependent spec names,
along with a directory in which to save yaml files, and writes out
the full spec.yaml for each of the dependent specs. This only needs
to concretize the root spec once, then indexes it with the names of
the dependent specs.
2. check: Checks a spec (via either an abstract spec or via a full
spec.yaml) against remote mirror to see if it needs to be rebuilt.
Comparies full_hash stored on remote mirror with full_hash computed
locally to determine whether spec needs to be rebuilt. Can also
generate list of specs to check against remote mirror by expanding
the set of release specs expressed in etc/spack/defaults/release.yaml.
3. get-buildcache-name: Makes it possible to attempt to read directly
the spec.yaml file on a remote or local mirror by providing the path
where the file should live based on concretizing the spec.
4. download: Downloads all buildcache files associated with a spec
on a remote mirror, including any .spack, .spec, and .cdashid files
that might exist. Puts the files into the local path provided on
the command line, and organizes them in the same hierarchy found on
the remote mirror
This commit also refactors lib/spack/spack/util/web.py to expose
functionality allowing other modules to read data from a url.
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- add CombinatorialSpecSet in spack.util.spec_set module.
- class is iterable and encaspulated YAML parsing and validation.
- Adjust YAML format to be more generic
- YAML spec-set format now has a `matrix` section, which can contain
multiple lists of specs, generated different ways. Including:
- specs: a raw list of specs.
- packages: a list of package names and versions
- compilers: a list of compiler names and versions
- All of the elements of `matrix` are dimensions for the build matrix;
we take the cartesian product of these lists of specs to generate a
build matrix. This means we can add things like [^mpich, ^openmpi]
to get builds with different MPI versions. It also means we can
multiply the build matrix out with lots of different parameters.
- Add a schema format for spec-sets
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Fixes #10617
Fixes #10624
Closes: #10619
#8136 dependended entirely on spec.libs to retrieve library directories
from dependencies. By default this function only retrieves libraries if
their name is something like lib<package> (e.g. "libfoo.so" for a
package called "Foo"). This unconditionally adds lib/lib64 directories
for each dependency as link/rpath directories.
This also filters system paths from link/rpaths/include directories and
removes duplicated paths that #8136 could add.
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If the -f <specyamlfile> argument to install is used (rather than
providing package specs on the command line), CDash throws an exception
due to missing the installation command (the packages targeted for
install). This fixes that behavior so CDash reporting succeeds in
either case.
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fixes #10601
Due to a bug this attribute is wrong for packages that use directories
as namespaces. For instance it will add "<boost-prefix>/include/boost"
instead of "<boost-prefix>/include" to the include path.
As a minor addition a few loops in the compiler wrappers have been
simplified.
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Fixes #7855
Closes #8070
Closes #2645
When searching for library directories (e.g. to add "-L" arguments to
the compiler wrapper) Spack was only trying the "lib/" and "lib64/"
directories for each dependency install prefix; this missed cases
where packages would install libraries to subdirectories and also was
not customizable. This PR makes use of the ".headers" and ".libs"
properties for more-advanced location of header/library directories.
Since packages can override the default behavior of ".headers" and
".libs", it also allows package writers to customize.
The following environment variables which used to be set by Spack
for a package build have been removed:
* Remove SPACK_PREFIX and SPACK_DEPENDENCIES environment variables as
they are no-longer used
* Remove SPACK_INSTALL environment variable: it was not used before
this PR
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* fix permission setter
Fix a typo in islink test when applied to files.
* os.walk explicitly set not to follow links
The algorithm strongly rely on not following links.
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* Spack debug output now includes microsecond-granularity timestamps.
* Timestamps can also be enabled with the `--timestamp` command line argument.
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* Note that `none` is the default for lmod autoload
Save a bit of confusion by *explicitly* pointing out that `none` is
the default value for autoload in the lmod module file generator.
* Add a tip re building software externally
Add a tip about using `autoload: all` when building packages outside
of the tree that use artifacts (e.g. libraries, includes) within the
tree.
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CMake supports the notion of secondary generators which provide extra
information to (e.g.) IDEs over and above that normally provided by
the primary generator. Spack only supports the 'Unix Makefiles' and
'Ninja' primary generators but was not parsing out the primary
generator when a secondary generator was also included (e.g. for
a generator attribute like 'Codeblocks - Ninja'). This adds a regex
for extracting the primary generator for validation.
Since the secondary generator is irrelevant to a Spack build, it is
passed on to CMake without further validation.
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Add x86_64 as a target for the Cray platform, and also designate it
as the default front_end target.
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* CUDA compiler conflicts for Linux.
* Add Volta and Turing GPUs.
* Add mandatory conflict for Volta and Turing GPUs.
* Revert "CUDA compiler conflicts for Linux."
This reverts commit 7d4ff654ac53aad272c59e9f7f8bb3fbb32bcec4.
* Compiler conflicts introduced from previous commit into CUDA packaged moved and integrated into CUDA build system.
* More conversative with compiler conflicts for cuda 10.0.130, since I don't know what will happen with future cuda 10.x releases.
* Correct off-by-one errors in clang conflicts for x86_64 Linux.
* No restrictions on Apple Clang compiler until we are able to distinguish Xcode clang from github clang more easily. Note to fix this in the future.
* Change comment to clarify that github clang refers to LLVM clang.
* Fix and simplify index range.
* Fix overlapping conflicts for CUDA 10.0.130
* Removed extra ^cuda from conflict.
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Debug output now includes the output of modulecmd executions. Only
output module content when a failure occurs; always report when a
module is loaded/unloaded.
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