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`DYLD_LIBRARY_PATH` can frequently break builtin macOS software when
pointed at Spack libraries. This is because it takes *higher* precedence
than the default library search paths, which are used by system software.
`DYLD_FALLBACK_LIBRARY_PATH`, on the other hand, takes lower precedence.
At first glance, this might seem bad, because the software installed by
Spack in an environment needs to find *its* libraries, and it should not
use the defaults. However, Spack's isntallations are always `RPATH`'d,
so they do not have this problem.
`DYLD_FALLBACK_LIBRARY_PATH` is thus useful for things built in an
environment that need to use Spack's libraries, that don't set *their*
RPATHs correctly for whatever reason. We now prefer it to
`DYLD_LIBRARY_PATH` in modules and in environments because it helps a
little bit, and it is much less intrusive.
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If a user invoked "spack env activate example-henv", Spack would
mistakenly interpret the "-h" from "example-henv" as the "-h" option.
This commit allows users to create and activate environments with
"-h" in the name.
This issue existed for bash shell support as well as csh support, and
this commit addresses both, along with some other unrelated csh
support issues.
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Previously the `spack load` command was a wrapper around `module load`. This required some bootstrapping of modules to make `spack load` work properly.
With this PR, the `spack` shell function handles the environment modifications necessary to add packages to your user environment. This removes the dependence on environment modules or lmod and removes the requirement to bootstrap spack (beyond using the setup-env scripts).
Included in this PR is support for MacOS when using Apple's System Integrity Protection (SIP), which is enabled by default in modern MacOS versions. SIP clears the `LD_LIBRARY_PATH` and `DYLD_LIBRARY_PATH` variables on process startup for executables that live in `/usr` (but not '/usr/local', `/System`, `/bin`, and `/sbin` among other system locations. Spack cannot know the `LD_LIBRARY_PATH` of the calling process when executed using `/bin/sh` and `/usr/bin/python`. The `spack` shell function now manually forwards these two variables, if they are present, as `SPACK_<VAR>` and recovers those values on startup.
- [x] spack load/unload no longer delegate to modules
- [x] refactor user_environment modification calculations
- [x] update documentation for spack load/unload
Co-authored-by: Todd Gamblin <tgamblin@llnl.gov>
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The pathadd function was using setopt to configure zsh for word
splitting, which leaks out of the function and breaks default
functionality in a number of external zsh plugins and packages. This
switches to emulate -L, just as the spack function uses, to keep the
setting local to the function.
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Dotkit is being used only at a few sites and has been deprecated on new
machines. This commit removes all the code that provide support for the
generation of dotkit module files.
A new validator named "deprecatedProperties" has been added to the
jsonschema validators. It permits to prompt a warning message or exit
with an error if a property that has been marked as deprecated is
encountered.
* Removed references to dotkit in the docs
* Removed references to dotkit in setup-env-test.sh
* Added a unit test for the 'deprecatedProperties' schema validator
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fixes #12915
closes #12916
Since Spack has support for specific targets it might happen that
software is built for targets that are not exactly the host because
it was either an explicit user request or the compiler being used is
too old to support the host.
Modules for different targets are written into different directories
and by default Spack was adding to MODULEPATH only the directory
corresponding to the current host. This PR modifies this behavior to
add all the directories that are **compatible** with the current host.
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Modify `setup-env.sh` to export fewer variables but to still set the module() function correctly.
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- `setup-env.sh` was not properly detecting a bash shell when bash was run
as /bin/sh.
- Detection routine now always reports bash when bash is run as sh, and
no longer parses the path to the executable indicated in `$BASH`.
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- Add set -u to the setup-env.sh test script
- Refactor lines in setup-env.sh that tested potentially undefined
variables to use the `[ -z ${var+x} ]` construct
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- replace use of [[ with [
- replace function foo { .. } with foo() { .. }
- wrap some long lines
- add lsof and /proc/fd magic so that we can find the sourced file even in dash
- only do the complicated shell checks in one place; test $_sp_shell
elsewhere.
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- We've seen this a few times now where users have set up `cd` to echo
the new directory, and it screws up `setup-env.sh`
- In the past we've said this is user error.
- Here, we just fix it by sending `cd` output to /dev/null where needed.
- this works in bash, zsh, and dash
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Usage of double quotes was preventing word-splitting when parsing
module roots in setup-env.sh, which lead to an error when multiple
module roots are used (in particular when Spack is pointed to use
an upstream module root in addition to its own).
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Still look for BASH_SOURCE[0] first, but if it's not set,
_sp_source_file is initialized to an empty value addressing the
unset parameter error (line 217).
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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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Spack shell detection in setup-env.sh was originally based on
examining the executable name of $$ (from "ps"). In some cases this
does not actually give the name of the shell used, for example when
setup-env.sh was invoked from a script using "#!". To make shell
detection more robust, this adds a preliminary check for shell
variables which indicate that the shell is bash or zsh; the
executable name of $$ is retained as a fallback if those variables
are not defined.
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- `spack env create <name>` works as before
- `spack env create <path>` now works as well -- environments can be
created in their own directories outside of Spack.
- `spack install` will look for a `spack.yaml` file in the current
directory, and will install the entire project from the environment
- The Environment class has been refactored so that it does not depend on
the internal Spack environment root; it just takes a path and operates
on an environment in that path (so internal and external envs are
handled the same)
- The named environment interface has been hoisted to the
spack.environment module level.
- env.yaml is now spack.yaml in all places. It was easier to go with one
name for these files than to try to handle logic for both env.yaml and
spack.yaml.
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- `spack env activate foo`: sets SPACK_ENV to the current active env name
- `spack env deactivate`: unsets SPACK_ENV, deactivates the environment
- added support to setup_env.sh and setup_env.csh
- other env commands work properly with SPACK_ENV, as with an environment
arguments.
- command-line --env arguments take precedence over the active
environment, if given.
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setup-env includes a call to 'ps' to determine what shell is being
used. 'ps' can be instructed to use a different default output format
via the 'PS_FORMAT' env variable. Thus unset this variable before
calling 'ps'.
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- remove the old LGPL license headers from all files in Spack
- add SPDX headers to all files
- core and most packages are (Apache-2.0 OR MIT)
- a very small number of remaining packages are LGPL-2.1-only
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When using zsh, trying to shift when there are no arguments left results
in warnings like this: spack:shift:22: shift count must be <= $#
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As requested in the review all the commands meant to manage module
files have been grouped under the `spack module` command.
Unit tests have been refactored to match the new command structure.
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fixes #2215
fixes #2570
fixes #6676
fixes #7281
closes #3827
This PR reverts the use of `spack module loads` in favor of
`spack module find` when loading module files via Spack. After this PR
`spack load` will accept a single spec at a time, and will be able
to interpret correctly the `--dependencies` option.
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This reverts commit 732c24f603864ec7dbec425ac4507b47fdb7a641.
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- The setup-env.sh script currently makes two calls to spack, but it
should only need to make one.
- Add a fast-path shell setup routine in `main.py` to allow the shell
setup to happen in a single, fast call that doesn't load more than it
needs to.
- This simplifies setup code, as it has to eval what Spack prints
- TODO: consider eventually making the whole setup script the output of a
spack command
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- replace `spack.config.get_configuration()` with `spack.config.config()`
- replace `get_config`/`update_config` with `get`, `set`
- add a path syntax that can be used to refer to specific config options
without firt getting the entire configuration dict
- update usages of `get_config` and `update_config` to use `get` and `set`
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Fix `spack load` with extended packe specifications those includes spaces.
Solved by using perfectly parameter forwarding via temporary array.
example:
```
$ spack install zlib
$ spack install zlib cppflags='-O3 -march=native'
$ spack install zlib cppflags='-O2 -march=native'
$ spack find -d -L -f zlib
==> 3 installed packages.
-- linux-linuxmint18-x86_64 / gcc@5.4.0 -------------------------
k5hg4kkxiutkfl6n53ogz5wnlbdrsdtf zlib@1.2.11%gcc
mse2fyzdxciszdhiqi4b5kl6fxkps3fh zlib@1.2.11%gcc cppflags="-O2 -march=native"
vrnvj2fikcbxqxrymctnlpmud7wbuahk zlib@1.2.11%gcc cppflags="-O3 -march=native"
$ spack load zlib cppflags='-O3 -march=native'
==> Error: Unexpected token
['zlib', 'cppflags=-O3', '-march=native']
```
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* Reduce the calls to the python interpreter during initialization
This should reduce the delay the users experience when sourcing the
setup file to activate shell support. It works by generating at once
all the commands that needs to evaluated (they are stored in
a string and later `eval`ed by the shell).
* setup_env.sh: changed `read` with an equivalent magic
For some reason `read` breaks when sourced from a running script.
Change the incantation we use to construct the unique python command
that will be evaluated.
* setup_env.sh: python command now constructed with `printf` for portability
This recovers the support for `zsh` that was broken in previous commits.
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We moved to a new GitHub org! Now make the code and docs reflect that.
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type's output can be localized, causing the grep to fail.
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setup-env.sh adds the 'module' command to the user's environment
if it is not defined and if there is a Spack installation of
environment-modules available. This commit updates that logic to
perform these checks and updates quietly.
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On OSX, the shell detection code may get a preceding dash, like
"-bash". This adds a filter to remove it.
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These were discovered with bash 4.1.2.
Add quotations around a variable to prevent the destruction of a
newline. Without this fix a conditional doesn't work properly.
Remove square brackets around a conditional meant to be evaluated based
on the return code of a command. This wasn't working properly with an
old bash.
Fix a typo.
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Renames the existing bootstrap command to 'clone'. Repurposes
'spack bootstrap' to install packages that are useful to the
operation of Spack (for now this is just environment-modules).
For bash and ksh users running setup-env.sh, if a Spack-installed
instance of environment-modules is detected and environment modules
and dotkit are not externally available, Spack will define the
'module' command in the user's shell to use the environment-modules
built by Spack.
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* Return an error exit code if spack cd does not succeed.
* Reducing amount of return statements in spack cd exit code.
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* Revert "Add lmod files to MODULEPATH (#3912)"
This reverts commit 186d1f4511c8aa3bc5ce661b1e883db10e20958a.
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