radical.saga 0.60.0

A light-weight access layer for distributed computing infrastructure(http://radical.rutgers.edu/)

RADICAL-SAGA
============

[](https://travis-ci.org/radical-cybertools/radical.saga)


A light-weight access layer for distributed computing infrastructure

www: http://radical-cybertools.github.io/radical.saga/
wiki: https://github.com/radical-cybertools/radical.saga/wiki


Unit Tests
----------

The unit tests for radical.saga can be found in the tests/ subdirectory.
Instructions how to tun the tests are in tests/README.md.

RADICAL-SAGA requires Python version >= 2.7 and < 3.x.







- For a list of bug fixes, see
https://github.com/radical-cybertools/radical.saga/issues?q=is%3Aissue+is%3Aclosed+sort%3Aupdated-desc
- For a list of open issues and known problems, see
https://github.com/radical-cybertools/radical.saga/issues?q=is%3Aissue+is%3Aopen+


Version 0.60.0 Release 2019-04-10
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- radicalization! rename saga-python to radical.saga
- fix logger levels
- fix issue #661
- Adding missing flags for Summit. add test case
- fix job.cancel in some corner cases
- document missing path normalization
- add support for summit
- get hostname from env variable
- clean out unsupported jod description attributes
- LSF SMT level now defaults to 1 (summit)
- convert to new config file format (json)
- get unit tests back in working order
- gpu support for bridges
- linted, flaked, pepped, cleaned... a bit...
- make commtransparent flag optional
- remove topology restriction on BW
- sync torque and pbspro, remove deprecated pbs
- make job adaptors uniformely emit EPOCH timestamps


Version 0.50.5 2018-12-19
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- fixes in Slurm and Torque adaptor


Version 0.50.4 2018-12-12
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- fix version check in slurm adaptor


Version 0.50.3 2018-11-13
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- fix version check in face of git errors


Version 0.50.2 2018-11-13
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- fix version check for Stampede (#rp-1754) - thanks Ioannis!


Version 0.50.1 2018-10-26
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- Add Cheyenne suport - thanks Vivek!


Version 0.50.0 2018-0&-03
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- partial support for heterogeneous clusters (slurm)
- (origin/pr/637) more thorough handling of $PROMPT_COMMAND
- Fix #680 - Corrected Error on LSF: module object has no attribute Event
- Fix/issue 1514
- Fix/issue 662
- Fix/issue 663
- add gpu "support" to torque
- correctly interprete candidate_hosts on pbspro
- fix torque job name handling
- make sure theh default session also inherits the uid (#671)
- remove obsolete comment, add local GPUs
- sync pbspro and torque adaptor.


Version 0.47.6 2018-06-02
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- catch up with RU log, rep and prof settings


Version 0.47.5 2018-04-20
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- slurm uses '-N' on wrangler now.


Version 0.47.4 2018-04-09
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- trigger BW syntax based on version string


Version 0.47.3 2018-03-20
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- accept SID settings from upper layers (RP) (#654)
- add travis tests, badge
- cheyenne fix to pbspro
- get titan back to work (#664)
- fix task container get_state reval


Version 0.47.2 2018-02-28
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- accept SID settings from upper layers (RP) (#654)
- fix task container get_state reval


Version 0.47 2017-11-19
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- avoid use of `condor_history` if so configured
- cleaner recovery for `condor_hist` when its used
- be more resilient against `sacct` errors
- one more `PROMPT_COMMAND` setting


Version 0.46 2017-08-23
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- hotfix for RP #1415


Version 0.46 2017-08-11
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- Fix several debug messages
- Fix/621 experiment aimes (#622)
- Fixed run_job to run in service.py
- Properly support SGE job name. (#624)
- Anselm support in pbspro v.13 (#634)
- fix a condor script syntax error
- attempt to prevent job eviction
- be resiliant against lingering NFS locks (hi titan)
- clean bulk job info for condor
- clean up state management in condor adaptor,
- slim down condor log calls, simplify status updates, ensure output transfer
- container_cancel needs to accept timeout parameter (#633)
- don't barf on failing condor_history
- don't limit status check length
- iteration on slurm mpi support (#623)
- fix logic error in directive evaluation
- fix parsing of condor_history for multi-file staging
- fixes on src/tgt ordering in osg staging
- follow the rename of ru.Task to ru.Future
- follow the rename of ru.Thread to ru.Future
- implement bulk cancel for condor
- iteration on bulk submission, data staging
- iteration on run_job implementatio
- improve condor scaling / performance
- make sure we alsways have a valid transfer directive in condor
- make sure we do not fail on a missing exit code
- more clarity on file staging semantics, some cleanup
- better handling of $PROMPT_COMMAND
- resilience against condor_history errors
- update on torque to avoid triggering a check


Version 0.45.1 2017-02-28
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- hotfix to support CandidateHosts for LoadLeveler


Version 0.45 2017-02-28
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- Add srm adaptor - Thanks Mark!
- Add cobalt adaptor (blue gene/q) - Thanks Manuel!
- Add special case for Rhea
- Deal with timeouts.
- Don't want our jobs to restart after eviction (OSG)
- Make pty shell url configurable.
- Remove some more PBSPro remains.
- address #585
- fix #590
- check that prev_info exists before populating curr_info with its info in _job_get_info
- clean up slurm adaptor to get it fit for the split branch in RP
- fix state interpretation for pbspro
- make torque fit for rp split branch
- remove some debug logs
- some consistency fixes
- update slurm example in context of #611
- use `-o Port=%d` notation for ssh based channels
- backport ft and bulk ops for torque from osg_optimization


Version 0.44 2016-11-01
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- added basework_dir parameter to sge and proxy adaptors
- added new PBS versions to pbsnodes CPU count check
- changed the regular expression to find the job-id on LSF adaptor. Fixes #568
- re-enable fallback methods for slurm job containers, jd.name support for slurm
- fix for issue #586, removing invalid dirs from shell wrapper script file path
- fix parsing of file staging directives
- make shell job adaptor workdir configurable
- avoid double close for shell job service
- raise error on missing tools
- removed duplicate get_name function in job class
- add missing container method to get job states
- merged pull request #583
- enforce version in radical stack
- fix #555


Version 0.41.3 2016-07-07
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- still hating it...


Version 0.41.2 2016-07-07
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- I hate python deployment


Version 0.41.1 2016-07-07
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- hotfix: remove some debug code which causes trouble in multiuser envs


Version 0.41 2016-06-02
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- Feature/job name shell (#541)
- implementation of job names for shell job adaptor and on API level
- add job.name for condor
- address #552
- allow for non-interative local pty shells
- initialidir support for Condor
- change HOSTFILE settings

- fix missing var setting in aws example
- fix port opening directive, make sure port is opened just once
- fix regression in job cancellation
- fix rel path on open
- fix staging calls
- fix string formatting error
- fix ssh context to handle passwords containing spaces
- cleanup of the shell spawner, getting in sync with RP version
- implement dir.exists
- make sure we have a job description on reconnected jobs
- make task passing to async calls optional
- aws security group tweaking
- remove invalid obj redirection
- code simplification
- simplify local mkdir in shell file adaptor
- sync with updated benchmark tools
- use shared shell connection for FS ops


Version 0.40.2 2016-04-23
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- Hotfix release to avoid security warnings on Stampede


Version 0.40.1 2016-02-05
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- Hotfix release to address a tmp file race condition on file staging


Version 0.40 2016-01-19
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- Added job monitor state update fix to PBSPro adapter.
- Add session property to base class. Fix #480.
- add traceback property to exception
- support gsissh for condor job submission
- pass span parameter to LSF.
- support SLURM reservation.
- file staging for shell adaptor
- Fix #477, set session for shell job service
- Fixed job state monitor to correctly identify state changes.
- Fixed string formatting error.
- Fixes #501. Thanks Javi!
- fix session documentation. Thanks Jeremy!
- Fix to allow use of environment vars in ssh context key/cert property file paths.
- Implement bulk submit, states and wait for condor.
- Improve file staging directives handling.
- Logging goes into working directory.
- make ssh connection timeout configirable (defaults now to 10 seconds)
- Passing ssh_timeout param to ssh ConnectTimeout option
- Updated fix to #494 to take account of empty key/cert parameter.
- deprecate PBS adaptor


Version 0.39 2015-12-01
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- support dynamic adaptor loading
- fix #477, set session for shell job service (thanks Mehdi!)
- set session on file and directory instances, #480


Version 0.38.1 release 2015-11-11
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- fix 0.38 after botched merge


Version 0.38 release 2015-11-06
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- support for anaconda client install


Version 0.37 release 2015-10-15
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- scattered bug fixes


Version 0.36 release 2015-10-15
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- update of GO adaptor with recent GlobusOnline evolotion
- scattered fixes in GO adaptor


Version 0.36 release 2015-10-08
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Note that RADICAL_SAGA_VERBOSE should now be used instead of SAGA_VERBOSE (but
the latter will be supported for a while). PTY layer debug levels can
separately be enabled via RADICAL_SAGA_PTY_VERBOSE.

- fix cray qsub arguments
- fix interpretation of relative / absolute URLs in some cases
- fix #449 - thanks jcohen02!
- keep up with logger changes in util
- properly detect failed jobs.
- follow changes on resource configurations (BW)
- remove dead code.
- fix state mapping in some queue adaptors
- clean torque/pbs separation


Version 0.35 release 2015-07-14
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- Add contexts to session at start of context list
- add tc.get_task(id)
- Add PROCESSES_PER_HOST to all job adaptors.
- sync an sdist naming fix
- Add dedicated PBS Pro adaptor.
- Get ppn from proccess_per_host.
- implement candidate_hosts for slurm adaptor
- processes_per_host for SLURM.


Version 0.29 release 2015-07-14
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- apply setup/git fix
- fix exception type exception
- convert to locking "with"/by context manager.
- only create parents for the dir part of a target.
- reentrant lock to guard concurrent cache writing.
- fix object._id format


Version 0.28 release 2015-04-16
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- set 'ssh_share_mode=no' on CentOS
- resilience against missing git in setup.py
- Prompt pattern for RSA SecureID (BW, Titan, etc.)
- cleaner version string
- treat empty strings as unset values in PBS job description
- fix slurm script generation
- implement discussed changes to job stdio inspection
- finish implementation of #202
- pre- and post-exec for shell job adaptor
- implement pre/post_exec, support in slurm, cleanup slurm submission
- clean up stdin/stdout/stderr/log handling for jobs
- sync setup.py with recent changes in RP
- Fix rounding up cores for blacklight
- ignore SIGHUP in the shell monitor -- fixes #415
- install sdist, export sdist location


Version 0.27 release 2015-03-25
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- fix rounding-up cores for blacklight


Version 0.26 release 2015-02-24
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- Major iteration on Globus Online adaptor, including tests and
examples
- move sources into src/
- short_version -> version
- long_version -> version_detail
- use DebugHelper in test suite
- implement #413
- Check status of task to be able to detect failure.
- fix to make async tasks working for methods which do not provide
metrics
- Fix ssh key logic.
- do not pick up pem certs by default
- Add "gres" (Generic Resource) query parameter.
- Add note about queue query parameter.
- fix syntax error in PBS variable spec
- Fix, cleanup and document qstat parsing.
- Document job states.
- stop job monitoring on continous errors (pbs)
- Support "bigflash" nodes selection on Gordon.
- make workdir for shell wrapper a parameter
- force copy shells to be non-posix (sftp)
- make sure that non-posix shells are excused from prompt triggering


Version 0.25 release 2014-12-17
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- hotfix for sftp problems on some client/server version
combinations which lead to data inconsistencies


Version 0.24 release 2014-12-08
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- make ssh share mode configurable
- Re-enable explicit_exec and add more explanation.
- Make setting job_type conditional on >1 cores.
- more variety in PBS "constants" (ha!)
- fix #401
- make sure the target dir for leased shells exists on
CREATE_PARENTS in dir ctor
- fix #400
- export PPN information to torque and pbs jobs
- merge and fix Danila's patch
- re-enable test for PBSPro_10
- added test config for archer
- re-enable test for PBSPro_10, as discussed with Ole.
- added test config for archer
- add missing error check on mkdir
- fix logical error on dir state recovery
- LoadLeveler support for BG/Q machines.


Version 0.22 release 2014-11-03
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- Hotfix release fixing incompatbile sftp flag "-2"
- https://github.com/radical-cybertools/radical.saga/issues/397


Version 0.21 release 2014-10-29
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- scattered bug fixes related to connection caching
- configurable switch between scp and sftp
- tweak timeouts on ssh channels
- disable irods adaptor


Version 0.19 release 2014-09-15
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- LeaseManager for connection sharing.
- Improved file transfer performance
- Small improvements in PBS (esp. Cray) and LSF adaptors.
- Closed tickets:
- https://github.com/radical-cybertools/radical.saga/issues?q=is%3Aclosed+is%3Aissue+milestone%3A%22radical.saga+0.19%22+

Version 0.18 release 2014-08-28
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- scattered fixes and perf improvement

Version 0.17 release 2014-07-22
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- Improved prompt-detection and small bug fixes.
- Closed tickets:
- https://github.com/radical-cybertools/radical.saga/issues?milestone=20&state=closed

Version 0.16 release 2014-07-09
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- Several adaptor upddtes
- Addressed SSH caching and prompt-detection issues
- Closed tickets:
- https://github.com/radical-cybertools/radical.saga/issues?milestone=19&state=closed

Version 0.15 release 2014-06-18
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- Fixed issues with the shell aadaptor Directory.list() method:
- https://github.com/radical-cybertools/radical.saga/issues/330

Version 0.14 release 2014-05-07
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- Fixed TTY wrapper issues
- Migration to new GitHub repository
- Documentation now on ReadTheDocs:
http://radical.saga.readthedocs.org/en/latest/
- Integrated Mark's work on the Condor adaptor
- Closed tickets:
- https://github.com/radical-cybertools/radical.saga/issues?milestone=18&state=closed

Version 0.13 release 2014-02-27
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- Bugfix release.
- Closed tickets:
- https://github.com/radical-cybertools/radical.saga/issues?milestone=17&state=closed


Version 0.12 release 2014-02-26
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- Bugfix release + shell cleanup

Version 0.11 release 2014-02-25
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- Closed tickets:
- https://github.com/radical-cybertools/radical.saga/issues?milestone=16&state=closed

Version 0.10 release 2014-01-18
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- Changed versioning scheme from major.minor.patch to major.minor
due to Python's messed up installers
- Fixed job script cleanup:
https://github.com/radical-cybertools/radical.saga/issues?milestone=15&state=closed

Version 0.9.16 release 2014-01-13
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- Some improvements to sftp file adaptor
- Closed tickets:
- https://github.com/radical-cybertools/radical.saga/issues?milestone=14&state=closed

Version 0.9.15 release 2013-12-10
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- Emergency release to fix missing VERSION file

Version 0.9.14 release 2013-12-10
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- Migration to radical.utils
- Numerous SFTP file adaptor improvements
- Closed tickets:
- https://github.com/radical-cybertools/radical.saga/issues?milestone=13&state=closed

Version 0.9.13 release 2013-11-26
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- Added Platform LSF adaptor
- Closed tickets:
- https://github.com/radical-cybertools/radical.saga/issues?milestone=11&state=closed

Version 0.9.12 release 2013-10-18
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- Added iRODS replica adaptor
- Closed tickets:
- https://github.com/radical-cybertools/radical.saga/issues?milestone=10&state=closed

Version 0.9.11 released 2013-09-04
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- Bugfix release
- Closed tickets:
- https://github.com/radical-cybertools/radical.saga/issues?milestone=9&state=closed

Version 0.9.10 released 2013-08-12
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- Better support for Amazon EC2
- Fixed working directory handling for PBS
- Closed tickets:
- https://github.com/radical-cybertools/radical.saga/issues?milestone=3&state=closed

Version 0.9.9 released 2013-07-19
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- Hotfix release: bug in Url.__str__ and SFTP copy
- https://github.com/radical-cybertools/radical.saga/issues?milestone=8&state=closed

Version 0.9.8 released 2013-06-22
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- Hotfix release: critical bug in wait() signature
- https://github.com/radical-cybertools/radical.saga/issues?milestone=7&state=closed

Version 0.9.7 released 2013-06-19
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- Added resource package
- Added 'liblcoud' based adaptor to access Amazon EC2 clouds
- Closed issues:
- https://github.com/radical-cybertools/radical.saga/issues?milestone=5&state=closed

Version 0.9.6 released 2013-06-17
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- Hotfix release: critical PBS/TORQUE adaptor fixes
- https://github.com/radical-cybertools/radical.saga/issues?&milestone=6&state=closed

Version 0.9.5 released 2013-06-06
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- Hotfix release: critical SLURM adaptor fixes
- https://github.com/radical-cybertools/radical.saga/issues?milestone=4&state=closed

Version 0.9.4 released 2013-06-01
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- jd.working_directory now gets created if it doesn't exist
- Support for older Cray systems running PBS Pro 10
- Job state callback support for the PBS adaptor - others to follow
- A simple HTTP protocol file adaptor
- Fixed some issues with user-pass and X.509 security contexts
- Over 40 bugfixes and improvements:
- https://github.com/radical-cybertools/radical.saga/issues?milestone=2&state=closed

Version 0.9.3 released 2013-04-08
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- Added SFTP adaptor
- Added tutorial examples
- Closed issues:
- https://github.com/radical-cybertools/radical.saga/issues/78
- https://github.com/radical-cybertools/radical.saga/issues/73
- https://github.com/radical-cybertools/radical.saga/issues/72
- https://github.com/radical-cybertools/radical.saga/issues/71
- https://github.com/radical-cybertools/radical.saga/issues/69
- https://github.com/radical-cybertools/radical.saga/issues/66
- https://github.com/radical-cybertools/radical.saga/issues/63
- https://github.com/radical-cybertools/radical.saga/issues/62
- https://github.com/radical-cybertools/radical.saga/issues/61
- https://github.com/radical-cybertools/radical.saga/issues/60
- https://github.com/radical-cybertools/radical.saga/issues/58
- https://github.com/radical-cybertools/radical.saga/issues/57
- https://github.com/radical-cybertools/radical.saga/issues/56
- https://github.com/radical-cybertools/radical.saga/issues/55
- https://github.com/radical-cybertools/radical.saga/issues/22
- https://github.com/radical-cybertools/radical.saga/issues/51
- https://github.com/radical-cybertools/radical.saga/issues/53
- https://github.com/radical-cybertools/radical.saga/issues/26
- https://github.com/radical-cybertools/radical.saga/issues/49
- https://github.com/radical-cybertools/radical.saga/issues/50
- https://github.com/radical-cybertools/radical.saga/issues/47
- https://github.com/radical-cybertools/radical.saga/issues/45
- https://github.com/radical-cybertools/radical.saga/issues/46
- https://github.com/radical-cybertools/radical.saga/issues/43
- https://github.com/radical-cybertools/radical.saga/issues/27

Version 0.9.2 released 2013-03-11
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- Hotfix release

Version 0.9.1 released 2013-03-03
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- Major re-write of engine and adaptor interface
- Support for asynchronous operations
- Improved PTYWrapper for ssh/gsissh remote execution
- Added SLURM job adaptor
- Added Condor job adaptor

Version 0.2.7 released 2012-11-09
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- Fixed errors related to pbs://localhost and sge://localhost
URLs that were caused by a bug in the command-line wrappers.

Version 0.2.6 released 2012-10-25
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- HOTFIX: credential management for SGE and PBS. both adaptors now
iterate over SSH and GSISSH contexts as well as consider usernames
that are part of the url, e.g., pbs+ssh://[e-mail]...

Version 0.2.5 released 2012-10-24
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- Changed documentation to Sphinx
- Removed object_type API. Python buildins can be used instead
- Updates to Filesystem API
- Added JobDescription.name attribute (as defined in DRMAA)
- Introduced stateful SSH connection substrate for PBS, SGE, etc
- Introduced support for GSISSH: pbs+gsissh://, sge+gsissh://
- Re-implementation of a (more Python-esque) attribute interface
- Fixed JobID issues, i.e., job.job_id returns 'None' in case the
job is not running instead of
- Introduced dynamic, fault-tolerant plug-in loader. If anything
goes wrong during loading of a specific plug-in (i.e.,
dependencies on 3rd party modules cannot be fulfilled, the plug-in
will just get skipped and the remaining ones will still get
loaded. Previously, a single problem during plug-in loading would
take radical.saga down.

Version 0.2.4 released 2012-7-10
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- Added unit-tests for SPMDVariation
- Added 'mpirun' support for local job plug-in (via SPMDVariation)
- Added some of the missing methods and flags to filesystem package
- An URL object can now be constructed from another URL object
- Fixed job.cancel()
- Wildcard support for Directory.list()

Version 0.2.3 released 2012-6-26
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- Fixed query support for URL class (issue #61)
- Improved logging. No root logger hijacking anymore (issue #62)
- Fixed job.Description.number_of_processes (issue #63)
- Less chatty SSH plug-in (issue #51)

Version 0.2.2 released 2012-6-12
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- job.Decription now accepts strings for int values. This has been
implemented for backwards compatibility
- Fixed resource.Compute.wait() timeout issue
- Removed excessive SGE/PBS plug-in logging
- job.Service can now be created from a resource.Manager
- Implemented deep copy for description objects
- Runtime now supports multiple plug-ins for the same schema

Version 0.2.1 released 2012-5-16
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- Fixed https://github.com/radical-cybertools/radical.saga/issues/5
- Fixed https://github.com/radical-cybertools/radical.saga/issues/13

Version 0.2.0 released 2012-5-15
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- SFTP support for local <-> remote copy operations, mkdir, get_size
- Added supoprt for ssh re-connection after timeout (issue #29)
- Abandoned 'Exception' filenames and API inheritance. The radical.saga
interface looks much cleaner now. Compatibility with previous
versions has been ensured
- Improved (inline) API documentation
- Swapped urlparse with furl in saga.Url class This hopefully fixes
the problem with inconsistent parsing accross different Python
versions
- Added SGE (Sun Grid Engine) plug-in (issue #11)
- Removed sagacompat compatibility API
- Log source names now all start with 'radical.saga.'. This should make
filtering much easier
- Moved SD package into development branch features/servicediscovery

Version 0.1.19 released 2012-02-29
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- Hotfix - removed experimental Resource plug-in from release

Version 0.1.18 released 2012-02-29
--------------------------------------------------------------------------------

- Fixed issue with plugin introspection
- Added template for job plug-in

Version 0.1.17 released 2012-01-04
--------------------------------------------------------------------------------

- Hotfix

Version 0.1.16 released 2012-01-03
--------------------------------------------------------------------------------

- Fixed issue: https://github.com/oweidner/radical.saga/issues/9

Version 0.1.15 released 2012-01-03
--------------------------------------------------------------------------------

- Fixed issue: https://github.com/oweidner/radical.saga/issues/8
- Fixed issue: https://github.com/oweidner/radical.saga/issues/6
- First version of a bigjob plugin. See wiki for details.
- Fixed Python 2.4 compatibility issue

Version 0.1.14 released 2011-12-08
--------------------------------------------------------------------------------

- Added bliss.sagacompat module for API compatibility.
- API documentation:
http://oweidner.github.com/bliss/apidoc-compat/
- Added examples for 'compat' API, e.g.:
https://github.com/oweidner/bliss/tree/master/examples/job-api/compat/
- Added configuration files for epydoc

Version 0.1.13 released 2011-12-07
--------------------------------------------------------------------------------

- Fixed executable & argument handling for the local job plugin
- Added support for jd.output and jd.error to local job plugin

Version 0.1.12 released 2011-12-06
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- Fixed bug in URL.get_host()
- Fixed issues with extremely short running PBS jobs in conjunction
with scheduler configruations that remove the job from the queue
the second it finishes execution.
- First working version of an SFTP file API plugini based on
Paramiko
- Two advance bfast examples incl. output file staging:
https://github.com/oweidner/bliss/blob/master/examples/advanced/bfast_workflow_01.py
https://github.com/oweidner/bliss/blob/master/examples/advanced/bfast_workflow_02.py

Version 0.1.11 released 2011-11-28
--------------------------------------------------------------------------------

- Fixed issues with PBS working directory
- Added simple job API example that uses BFAST:
https://github.com/oweidner/bliss/blob/master/examples/job-api/pbs_via_ssh_bfast_job.py
- Updated apidoc: http://oweidner.github.com/bliss/apidoc/
- First prototype of a job container. Example can be found here:
https://github.com/oweidner/bliss/blob/master/examples/job-api/pbs_via_ssh_container.py
- Implemented CPU and Memory information via PBS service discovery
- Changed job.Description.walltime_limit to
job.Description.wall_time_limit

Version 0.1.10 released 2011-11-16
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- Fixed issue with local job plugin

Version 0.1.9 released 2011-11-16
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- Prototype of a Service Discovery packages
- PBS/SSH support for service discovery

Version 0.1.8 released 2011-11-09
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- Fixed issue with PBS plugin job.wait()

Version 0.1.7 released 2011-11-09
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- More or less stable job API
- First functional PBS over SSH plugin


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