Release 8th May, 2013.
Fixes to backup/restore study/workspace.
Removed OS test for SLC6 compatibility in run_six.

Release 2nd November, 2012.
A few minor improvements to check_locks and check_all_locks.

Release 10th October, 2012.
Added iplot and kvar to mywhich.
Fixed a couple of spelling errors.

Release 24th September, 2012.
run_results reports CPU time only
as Total Turns are no longer available.

Release 19th September, 2012.
Added the replacement of %NPART to mydorun_mad6t.
Changed all the mask/*.mask files to replace the NPART value
by the placekeeper %NPART. 
Changed mydocompare_results to use verify10.
Updated verify10 to also compare Word 59, Total Particle Turns.
Added a couple more variables to mymywhich.
Deleted create+protection_group and added add_boinc_user.
Updated allscripts to add mydocompare_results and add_boinc_user.

Release 20th August, 2012.
Changed . dot_profile . ./dot_profile in myunlock, mydot_env,
myset_env for users who do not have a . in their path.
Thanks Javier.

Release 11th August first for SVN.

Release 6th August, 2012. Changed log message levels and defaults.
Simplified locks to lock study but lock plot for run_post as well.
Added fort.15 to $Fileps as suggested by Massimo.

New Major Release 29th February matching SixDesk documentation 
and using study job_tracking with appropriate defaults.

Most/all commands now accept a study and optionally a
platform as parameters  to the command. This facilitates
running multiple studies in a workspace.

run_status still takes a long time for platform LSF but
the delays can be minimised but doing a run_status at regular
intervals.

Set up to use SIXTRACKEXE=SixTrack_pro (currently 4437)
Uses CASTOR_HOME and not nap.

Fixed a bug in sysenv for the new pts group specification.
Corrected messages in run_six when the one-turn jobs fail.
Modified run_post to use a working directory and to
NOT lock $sixdeskhome (the workspace).

Added pilot versions of compare_DA and plot_DA.
Some minor new messages to log normal completion.
Some improvements, 7th November, 2011.
Added batch_ join10|post|results|run
and the associated _template files.
Changed dot_boinc to use a per study sixdesktaskIds
directory to avoid locking the sixdeskTaskId.

New Major Release, 6th November, 2011.
Also:
 run_post and others: issue a message on completion
 run_status: puts missing_jobs in $sixdeskjobs
 run_results: issues only DIFF messages to sixdesklog when fort.10s are different
 dot_boinc: creates the results sub-directory
 dot_profile: issues sleep delay messages for locks
 Improved? lock handling everywhere
 Added bunch_charge
 short run remains an issue ????
 (Removed bnl options which can be restored)

Release 6th May, 2010.
Added new sixdeskenv variable bunch_charge for fort.3.mother1.
Added the BEAM block to fort.3.mother1_inj.
Added the correct tunes to the web.save file for run_post
Also added all this to update[d]_scripts.
and added the missing .save files as .mask:
beamweb.mask detuning.mask detuningh.mask detuningv.mask
tunedp.mask web.mask.
Fixed updated_scripts to add myrun_results, mydot_boinc, mydot_task,
(allmyseds and myrun_join10 seemed to be there already)
and the missing run_post files.
Fixed the "beam" control files as well.
Updated all executables to V4.2.09 (BNL).
Release 3rd March, 2010.
Just modified myrun_results to delete the BOINC .dec.done and
.zip in the boinc work directory (as left by Alex).
Release 18th January, 2010.
Added the new backup_study, backup_workspace,
recall_study and recall_workspace procedures.
Incorporates new SixTrack 4.2.06 for LSF and CPSS (NOT BOINC).
This version saves the closed orbit in sumda(53:58) and is thus
written out in fort.10.
Fixed sixdeskenv to include the chrom options described in the previous release.
Replaced the rfrm by nsrm -rf and the rfmkdir by nsmkdir.
Added a summary plot of DA over all seeds to run_post when kvar is 1.
Issue a warning when at least one seed is missing in plot_dyb summary.
Only plots down to minimum of writebinl turns from turnsl[e].
Corrected an error message in run_awk.
Corrected dot_bsub to ALWAYS save the .lsf job in the tree
and to ALWAYS delete the orginal.
run_missing_jobs sets sixdeskforce=2.
Made sixdeskerror.log and restart.log links to the same files
in $sixdesklogdir in mydot_env. Changed dot_profile to use
$sixdeskhome if $sixdesklogdir is undefined.
Corrected correct_cases.
Modified compare_workspaces to allow the username as a second parameter.
Moved README to scripts and put the link in sixjobs.
Several changes to correctly handle search for Runnam.
The following scripts were modified.
README (and was moved to the scripts directory).
In scripts:
allscripts check_sixdeskenv check_sysenv compare_workspaces exec_env
mybackup_study mybackup_workspace mycheck_incomplete mycheck_jobs
mycheck_locks mycheck_really mycompare_results mycorrect_cases
mydelete_study mydot_bsub mydot_env mydot_profile mymywhich
myrecall_study myrecall_workspace myrun_mad6t myrun_missing_jobs
myrun_post myrun_query myrun_six myrun_status myset_env
and finally plot/inc/plot_dyb and added plot/inc/minmax.awk

Release 22nd September, 2009.
Really tidied up (re-wrote) delete_study.
Added the -f flag to the rfrm of the "new" CASTORDIR in sixtracking.lsf.
Fixed sixtracking.lsf to copy only the four input files and to remove
any existing fort.10.gz; also added some ls and a tail -100 fort.6.
Added the extra chrom option for calculating it from two additional
one-turn runs. (Has a bug in sixdeskenv missing new chrom defs!)
Incorporates Frank's version 4.2.05 for LSF and CPSS (NOT BOINC).

Release 31st July, 2009.
Incorporates Frank's version 4.2.03 for LSF and CPSS (NOT BOINC).
Release 24th June, 2009.
Fixed the \n problem with ksh in run_post and plot/inc/plot_dyb
Release 27th, May 2009
Corrected chrom flag in sixdeskenv.
Modified run_six to handle chrom flag in one turn case.
Modified utilities/sixmedium.lsf.mask to properly handle sussix
(was wrong path, and myrun_six now defines the correct path).
Added another madX path to Version 3.04.53 and removed the -X flag.
This is meant to point to the previous production version
and should be updated when the default path is updated.
Added new option for turning off tune (tune).
Added new option for the mass of the proton (pmass).
Cleaned up "beam" option to specify null|b1|B1 for beam1 or
b2|B2 for beam2 with appropriate control_files; fixed a problem
affecting runtype injection with the b2 option which was using
a fixed "length" rather than the value returned from madX.
This might have affected studies concerning SUBRESONANCE CALCULATION,
RESONANCE COMPENSATION, SEARCH FOR THE BEST POSITIONS FOR 
COMPENSATION-ELEMENTS.
Fixed a bug in check_mad6t which was incorrectly concatenating
the MCSSX, MCOSX, MCOX, MCSX and MCTX error files when the
CORR_TEST option is selected.
Improved mydot_bsub to specify that LSF output should be returned
to the track hierarchy in Rundir; after submission moved the actual
job to the Rundir as well. Improves scalability.
Fixed the error message on job submission.
Greatly improved run_awk to handle only the specified files (angles)
and to clear the .plot file.
Added a new check_locks command.
Added a new compare_workspaces script.
Updated the sixtrack_da executable.
Fixed bug with chrom=0 in run_six one turn.

Release 16th March, 2009.
Added \* to find in run_status/run_results to help Tatiana
with the "e" field which can now be any number of digits.
(Not checked really for post-processing etc.)
Tidied up the sixdesk.log links and directories.
Modified test for current directory to be anything followed
by $workspace/sixjobs. (Fixes annoying problem with a link.)
Modified create_protection_group for two new users.
Modified myrun_six to better handle errors in producing
the betavalues. fort10 is saved as fort.10_old and any (wrong)
betavalues file is also renamed to make sure we try again.

Release 5th March, 2009.
Got rid of some bin links to non-existent files.
Got rid of local cronlogs sixdesklogs directories.
Redefined logs to have workspace sub-directory.
Modified delete_study for the new log directories.

Release 13th February, 2009.
Added new CASTOR V2 environment variables to myrun_results.
Changed uploadWorkunit to submit only 2 copies of the work
with a 3-day deadline (instead of 2 weeks).

Release 28th August, 2008.
Just changed sixdeskenv comment about sixdeskpairs
to report that it may now be varied between 1 and 32

Release 26th August, 2008.
Fixed a problem with incomplete_cases in dot_bsub, dot_boinc and dot_task.
Changed to use mychecktens to handle Version No in Word 52 fort.10.
Free the locks correctly (rather than by default) in run_six.

Release 15th August, 2008.
(Finally?) Fixed problem with delete_study.
Implemented sixdeskpairs by using it in inc/prepare_fort.3 to set %nss.
Modified utilities/sixtracking.lsf and run_six to honour 
the CASTOR flag for LSF jobs.
Fixed run_status to update my[in]complete[d]_cases for LSF.

Release 27th June, 2008.
Thanks to Massimo I added the "beam" option to sixdeskenv
and the two fort.3.mother2_col.B2  fort.3.mother2_inj.B2
files to the control_files.

Release 17th June, 2008.
Updates mydot_bsub, task, boinc to update myincomplete_tasks.
Removed a lot of useless DEBUG messages and added the
"stat" command to try and find the AFS/Linux problem
with run_results. It exits with 999 but should still be OK
for production. 
 
Release 9th June, 2008
More debug code added. Look for DEBUGZ in the sixdesk.log.
Maintain a parallel databse with mycompleted_cases and 
myincomplete_cases in $sixdeskwork updated by subroutine update_cases.
Now treats all CPSS download failures as errors.
A new script correct_cases which regenerates the correct
completed|incomplete_cases for the workspace by checking for fort.10.gz. 

Release 2nd June, 2008
Some debug code in myrun_results for finding AFS problem.
Moved the tmp file in myupdate_incomplete

Release 17th March, 2008
Two new scripts delete_study and check_incomplete.
New option run_mad6t -i to make the mad6t runs interactively
when the batch queues are blocked.
New mad6t option "beam" which is appended to the "runtype" for the 
mother filenames.
Easier to run multiple studies simultaneously in the same workspace.
run_results (as called by get_wlhc) accepts STUDY and PLATFORM as options:
e.g. run_results lhc boinc or run_results lhc cpss irrespective of current
settings in sixdeskenv.
dot_env initialises track to current study and logfiles are now in the
cronlogs and sixdesklogs directories. 
run_status reporting tidied up.
Fixed nasty bug with duplicate BOINC TaskIds and improved run_results to handle them.
  
Release 11th July, 2006
Fixes missing ./ for exec_end in [my]dot_env since lxplus
now removes . from PATH
Sets kvar to 0 with a comment

Release 11th May, 2006
Now added support for "short" and "DA" studies.
Handle the BOINC directories ACL using the 
AFS_GROUP feature. Cleaned up the "utilities".
Corrected plot/inc/plot_dyb for these new studies.
Removed all references to TARGETDIR in the batch jobs.
Use a temporary SIXDA executable until we move to
the next SixTrack version with newcrlibm etc.

The scripts modified in sixjobs/scripts: README \
mydot_bsub \ myrun_status \ mycheck_mad6t \
myrun_six \ myrun_post \ myrun_mad6t \ exec_env \
myrun_join10 \ mydot_env \ mydot_profile \
and
plot/inc/plot_dyb \ sixdeskenv \ sysenv. 

Current executables in ~/sixdesk/slap/Bin are:
For LSF, one turn, etc:
-rwxr-xr-x    1 mcintosh c3        5276057 Mar 22  2005 SixTrack62v4004lsf
For CPSS:
-rwxr-xr-x    1 mcintosh c3        2526836 Mar 23  2005 SixTrack71v4004.exe
For DA runs
-rwxr-xr-x    1 mcintosh c3        4871142 Jan 27 12:09 SixTrack_da_frs
For BOINC we use the compatible version 4004.

(Still to add additional mad6t checks, tune overlaps,
and a generic run_results workspace platform (parallel?)).

Release 1st July, 2005
Incorporates "BOINC" support using new names with "%" converted
to "__" for Markku.
Handle most errors automatically, but keep info in "problems".

The scripts modified in sixjobs/scripts: README \
mydot_bsub \ mydot_boinc \ myrun_status \ myrun_query \ mycheck_mad6t \
myrun_six \ myrun_results \ myrun_post \ myrun_incomplete_cases \
myrun_incomplete_tasks \ mydot_boinc


The scripts modified in sixjobs AND scripts:
sedboincnames \ dot_bsub \ dot_boinc \ run_status \
run_query \ check_mad6t \ run_six \ run_results \ run_post \
run_incomplete_cases \ run_incomplete_tasks \ dot_boinc


First Release for Dobrin  24th May, 2005
All the scripts are now stored in workspace/sixjobs/scripts.
They are listed in the file "allscripts" which is used
for maintenance and support. All changes should be made in 
that directory. The script domyseds expands macros in the "my" source files using the
"allmyseds" directives and copies all executables to sixjobs.
A backup is made in the "backup" sub-directory.
