Environment Variables

Configuring CRDS for pipeline or offsite personal use is accomplished by setting shell environment variables.

Basic Environment

By default, onsite at STScI, CRDS runs from a global cache with no connection to the CRDS Server and typically no user environment setup required to do basic best references.

For more personalized configurations or one designed for offsite use, the CRDS environment needs to define a CRDS server (CRDS_SERVER_URL) and a CRDS file cache directory (CRDS_PATH).

File Cache Location (CRDS_PATH)

CRDS stores reference files, rules files, and configuration information such as the current default context in a cache. The location of the CRDS cache is defined by the CRDS_PATH environment setting.

Default On Site CRDS_PATH

By default, CRDS behaves as if you set your environment like this:

$ export CRDS_PATH=/grp/crds/cache

/grp/crds/cache is on the Central Store and should be accessible to all users. It is a readonly cache containing all rule and reference files associated with all CRDS projects, now HST + JWST.

While it is configuration free and self-maintaining, limitations of the default cache include:

  1. A need for a direct connection to the STScI internal network
  2. Weak performance when accessed by VPN over the Internet
  3. Immutable files not well suited for experimentation

User Local CRDS_PATH

To avoid Internet inefficiencies, individual user’s can construct demand-based CRDS caches appropriate to their particular datasets. Personal CRDS caches also enable processing and many basic functions with no network access to the CRDS server. Rem

A remote or pipeline user defines a non-default CRDS cache by setting, e.g.:

$ export CRDS_PATH=$HOME/crds_cache

Using a personal cache also requires defining the CRDS server.

Server Selection (CRDS_SERVER_URL)

Since each project (and test system) is supported by a different CRDS server, a user must define any CRDS server they wish to use.

Default Server

By default, the CRDS client bestrefs functionality can run without a server provided they have access to an up-to-date CRDS cache.

By default CRDS behaves as if you set:

$ export CRDS_SERVER_URL=https://crds-serverless-mode.stsci.edu

Serverless mode limits CRDS to basic functions (bestrefs) but requires no server connection once the supporting CRDS cache has been synced.

HST Ops Server

A full featured CRDS configuration suitable supporting all server functions available for HST can be configured like this:

$ export CRDS_SERVER_URL=https://hst-crds.stsci.edu

JWST OPS Server

A full featured CRDS configuration suitable supporting all server functions available for JWST can be configured like this:

$ export CRDS_SERVER_URL=https://jwst-crds.stsci.edu

If CRDS cannot determine your project, and you did not specify CRDS_SERVER_URL, CRDS_SERVER_URL will be defaulted to:

$ export CRDS_SERVER_URL=https://crds-serverless-mode.stsci.edu

The serverless-mode URL directs CRDS to operate from the CRDS cache without contacting the CRDS server for updates. This works well with the default cache at /grp/crds/cache since it is kept up to date by the CRDS server. It is not possible to do cache updates while in serverless mode since no connection to the server is enabled.

Onsite CRDS Testing

For reference type development, updates are generally made and tested in the test pipelines at STScI. For coordinating with those tests, CRDS_PATH and CRDS_SERVER_URL must be explicitly set to a test cache and server similar to this:

$ export CRDS_PATH=${HOME}/crds_cache_test
$ export CRDS_SERVER_URL=https://hst-crds-test.stsci.edu

Alternative servers for JWST I&T testing are:

$ export CRDS_SERVER_URL=https://jwst-crds-b5it.stcsi.edu     # build-5
$ export CRDS_SERVER_URL=https://jwst-crds-b6it.stcsi.edu     # build-6
$ export CRDS_SERVER_URL=https://jwst-crds-dit.stcsi.edu      # build-7
$ export CRDS_SERVER_URL=https://jwst-crds-bit.stcsi.edu      # build-7
$ export CRDS_SERVER_URL=https://jwst-crds-cit.stcsi.edu      # build-7.2

After syncing this will provide access to CRDS test files and rules in a local cache:

# Fetch all the test rules
% crds sync --all

# Fetch specifically listed test references
% crds sync --files <test_references_only_the_test_server_has...>

Testing reference type changes (new keywords, new values or value restrictions, etc) may also require access to development versions of CRDS code. In particular, when adding parameters or changing legal parameter values, the certify tool is modified as “code” on the servers first. Hence distributed versions of CRDS will not reflect ongoing type changes. The test server Certify Files function should generally reflect the most up-to-date knowledge CRDS has about ongoing type changes. To see how new reference files stack up with changing CRDS code, try submitting the files to Certify Files on the test server or ask what the status is on redcat@stsci.edu.

NOTE: Without VPN or port forwarding, the test servers are not usable offsite.

Additional HST Settings

HST calibration software accesses reference files indirectly through environment variables. There are two forms of CRDS cache reference file organization: flat and with instrument sub-directories. The HST calibration software environment variable settings depend on the CRDS cache layout.

JWST calibration code refers to explicit cache paths at runtime and does not require these additional settings.

Flat Cache Layout for /grp/crds/cache

The flat cache layout places all references in a single directory. The shared group cache at /grp/crds/cache has a flat organization:

export iref=${CRDS_PATH}/references/hst/
export jref=${CRDS_PATH}/references/hst/
export oref=${CRDS_PATH}/references/hst/
export lref=${CRDS_PATH}/references/hst/
export nref=${CRDS_PATH}/references/hst/
export uref=${CRDS_PATH}/references/hst/
export uref_linux=$uref

By-Instrument Cache Layout

The default cache setup for newly created caches for HST is organized by instrument.

Unless you reorganize your cache using the crds.sync tool, these are the settings that are most likely to be appropriate for a personal HST cache.

For HST calibration software to use references in a CRDS cache with a by-instrument organization, set these environment variables:

export iref=${CRDS_PATH}/references/hst/iref/
export jref=${CRDS_PATH}/references/hst/jref/
export oref=${CRDS_PATH}/references/hst/oref/
export lref=${CRDS_PATH}/references/hst/lref/
export nref=${CRDS_PATH}/references/hst/nref/
export uref=${CRDS_PATH}/references/hst/uref/
export uref_linux=$uref

Reorganizing CRDS References

The crds.sync tool can be used to reorganize the directory structure of an existing CRDS cache. These organizations determine whether or not reference files are partitioned into instrument-specific sub-directories.

To switch from flat to by-instrument:

crds sync --organize=instrument

To switch from by-instrument to flat:

crds sync --organize=flat

JWST Context

The CRDS context file defines a version of CRDS rules used to assign best references.

The CRDS context used to evaluate CRDS best references for JWST defaults to jwst-operational. This is an indirect name for the context in use or soon-to-be in use in the archive pipeline.

During development jwst-operational corresponds to the latest context which is sufficiently mature for broad use. Use of jwst-operational is automatic.

The context used for JWST can be overridden to some specific historical or experimental context by setting the CRDS_CONTEXT environment variable:

$ export CRDS_CONTEXT=jwst_0057.pmap

CRDS_CONTEXT does not override command line switches or parameters passed explicitly to the crds.getreferences() API function.

Advanced Environment

A number of things in CRDS are configurable with environment variables, most important of which is the location and structure of the file cache.

CRDS Cache Locking

CRDS cache locking has been added to support JWST association calibration multi-processing for users who set up personal demand-based CRDS Caches. Cache locking prevents simultaneous transparent CRDS Cache updates from multiple JWST calibration processes.

Single Shell Locking

By default, CRDS uses Python’s built in multiprocessing locks which are robust and suitable for running multiprocesses within a single shell or terminal window:

$ crds list --status
CRDS Version = '7.2.0, 7.2.0, 139bbcb'
...
Cache Locking = 'enabled, multiprocessing'
...
Readonly Cache = False

However, this default CRDS cache locking is not suitable for running calibrations in multiple terminal windows or for pipeline use.

File Based Locking

Since Python’s default multiprocessing locks cannot support multiple process trees or terminal windows, CRDS also supports file based locking by setting appropriate configuration variables:

$ export CRDS_LOCKING_MODE=filelock
$ crds list --status
CRDS Version = '7.2.0, 7.2.0, 139bbcb'
...
Cache Locking = 'enabled, filelock'
...
Readonly Cache = False

File based locking is not used by default for several reasons:

1. They introduce a dependency on a 3rd party package.
2. File locks created on network or other virtualized file systems may be unreliable.
3. File lock behavior is OS dependent.

Restrictions on Locking

There are multiple conditions in CRDS that determine when locking is really used:

1. CRDS_READONLY_CACHE must be undefined or 0
2. The CRDS cache must be writable as determined by file system permissions
3. The CRDS_LOCK_PATH directory (nominally /tmp) should already exist
4. For file based locking,  a lock must be successfully created
5. CRDS_USE_LOCKING must be undefined or 1
6. For file based locking,  the lockfile or filelock Python package must be installed

The readonly nature of:

*/grp/crds/cache*

prevents the use of locking for typical onsite users. None should be required.

It should be noted that the existence of any lock file directory is itself a concurrency issue, so it must be created or otherwise available before cache synchronization takes place.

The CRDS command:

$ crds sync --clear-locks

can be used to remove orphan locks (due to some unexpected failure) that are blocking processing.

Locking requires installation of the lockfile package and CRDS-7.1.4 or later.

Multi-Project Caches

CRDS_PATH defines a cache structure for multiple projects. Each major branch of a multi-project cache contains project specific sub-directories:

/cache
    /mappings
        /hst
            hst mapping files...
        /jwst
            jwst mapping files...
    /references
        /hst
            hst reference files...
        /jwst
            jwst reference files...
    /config
        /hst
            hst config files...
        /jwst
            jwst config files...
  • mappings contains versioned rules files for CRDS reference file assignments
  • references contains reference files themselves
  • config contains system configuration information like operational context and bad files

Inidivdual branches of a cache can be overriden to locate that branch outside the directory tree specified by CRDS_PATH. The remaining directories can be overriden as well or derived from CRDS_PATH.

CRDS_MAPPATH can be used to override CRDS_PATH and define where only mapping files are stored. CRDS_MAPPATH defaults to ${CRDS_PATH}/mappings which contains multiple observatory-specific subdirectories.

CRDS_REFPATH can be used to override CRDS_PATH and define where only reference files are stored. CRDS_REFPATH defaults to ${CRDS_PATH}/references which contains multiple observatory specific subdirectoriers.

CRDS_CFGPATH can be used to override CRDS_PATH and define where only configuration information is cached. CRDS_CFGPATH defaults to ${CRDS_PATH}/config which can contain multiple observatory-spefific subdirectories.

Specifying CRDS_MAPPATH = /somewhere when CRDS_OBSERVATORY = hst means that mapping files will be located in /somewhere/hst.

While it can be done, it’s generally considered an error to use a multi-project cache with different servers for the same observatory, e.g. both hst-test and hst-ops.

Single Project Caches

CRDS_PATH_SINGLE defines a cache structure for a single project. The component paths implied by CRDS_PATH_SINGLE omit the observatory subdirectory, giving a simpler and shallower cache structure:

/cache
    /mappings
        mapping_files...
    /references
        reference files...
    /config
        config files...

It’s an error to use a single project cache with more than one project or server. It is inadvisable to mix multi-project (no _SINGLE) and single-project (_SINGLE) configuration variables, set one or the other form, not both.

As with CRDS_PATH, there are overrides for each cache branch which can locate it independently.

CRDS_MAPPATH_SINGLE can be used to override CRDS_PATH and define where only mapping files are stored. CRDS_MAPPATH_SINGLE defaults to ${CRDS_PATH}/mappings but is presumed to support only one observatory.

CRDS_REFPATH_SINGLE can be used to override CRDS_PATH and define where only reference files are stored. CRDS_REFPATH_SINGLE defaults to ${CRDS_PATH}/references but is presumed to support only one observatory.

CRDS_CFGPATH_SINGLE can be used to override CRDS_PATH and define where only server configuration information is cached. CRDS_CFGPATH_SINGLE defaults to ${CRDS_PATH}/config but is presumed to support only one observatory.

Specifying CRDS_MAPPATH_SINGLE = /somewhere when CRDS_OBSERVATORY = hst means that mapping files will be located in /somewhere, not in /somewhere/hst.

Miscellaneous Variables

CRDS_VERBOSITY enables output of CRDS debug messages. Set to an integer, nominally 50. Higher values output more information, lower values less information. CRDS also has command line switches –verbose (level=50) and –verbosity=<level>. Verbosity level ranges from 0 to 100 and defaults to 0 (no verbose output).

CRDS_ALLOW_BAD_RULES enable CRDS to use assigment rules which have been designated as bad files / scientifically invalid.

CRDS_ALLOW_BAD_REFERENCES enable CRDS to assign reference files which have been designated as scientifically invalid after issuing a warning.

CRDS_IGNORE_MAPPING_CHECKSUM causes CRDS to waive mapping checksums when set to True, useful when you’re editing them.

CRDS_READONLY_CACHE limits tools to readonly access to the cache when set to True. Eliminates cache writes which occur implicitly. This is mostly useful in CRDS server user cases which want to ensure not modifying the server CRDS cache but cannot write protect it effectively.

CRDS_MODE defines whether CRDS should compute best references using installed client software only (local), on the server (remote), or intelligently “fall up” to the server (when the installed client is deemed obsolete relative to the server) or “fall down” to the local installation (when the server cannot be reached) (auto). The default is auto.

CRDS_CLIENT_RETRY_COUNT number of times CRDS will attempt a network transaction with the CRDS server. Defaults to 1 meaning 1 try with no retries.

CRDS_CLIENT_RETRY_DELAY_SECONDS number of seconds CRDS waits after a failed network transaction before trying again. Defaults to 0 seconds, meaning proceed immediately after fail.

CRDS_USE_LOCKING boolean enabling/disabling CRDS cache locking, currently only used for JWST and defaulting to enabled. File locking is currently limited to JWST calibrations so HST sync and bestrefs tools must be run in single processes or with CRDS_READONLY_CACHE=1.

CRDS_LOCKING_MODE chooses between multiprocessing, filelock, or lockfile based locks. multiprocessing is the default. To support multiple terminal windows or pipeline processing, file based locking must be used with filelock recommended and known problems having been observed with the lockfile package.