This was resolved off-line, but in case anyone else has similar problems with Phaser or any other program launched from ccp4i, it’s probably worth sharing this with the rest of the BB.
We worked out that there was no way the Phaser interface distributed with ccp4-6.4.0 could generate the “PACK 10” command, which is old syntax that had to be updated as new features were added. So the question was how ccp4i could be using an old version of the interface.
Ed tracked it down to an old version of the phaser_MR interface installed under his home directory, in $HOME/.CCP4/CCP4I_TOP. Apparently this is where the interface goes when you install a task into the user’s local ccp4i area. It’s nice to have a mechanism to do this, but apparently when you subsequently install a new version of CCP4 (potentially with updated programs that are no longer compatible with the old interface), the old interface files in the user’s local directory still take precedence.
I think the CCP4 folk are looking into whether there would be a way to detect such potential conflicts when new versions are installed, but in the meantime if anyone discovers a mismatch between commands generated by ccp4i and the commands expected by the installed executable, for any CCP4 program, this would be a good place to look.
Best wishes,
Randy Read
On 21 Apr 2014, at 00:19, Edward A. Berry <[log in to unmask]> wrote:
> I seem to have a version incompatibility between phaser 2.5.6
> and the current ccp4 (updated today and restarted before testing)
>
> If i try to allow a few clashes in a simple autoMR job,
> it dies immediately with:
>
> The program run with command: /sw/lnx/ccp4-6.4.0/bin/phaser
> has failed with error message child process exited abnormally
>
> The script generated by the gui includes the command:
>
> PACK 10
>
> To which phaser 2.5.6 responds:
> SYNTAX ERROR: Use (optionally) SELECT CUTOFF DISTANCE QUICK TRACE or COMPACT
>
> And the phaserwiki gives the syntax:
> PACK SELECT [ 1BEST | 2ALLOW | 3PERCENT | 4ALL ]
> PACK CUTOFF <ALLOWED_CLASHES>
> .
> .
>
> So if I "run and view commands" and change to "PACK CUTTOFF 10"
> now it works.
>
> ===========================
> This happened originally with re-running a job that had been
> generated on a previous version of the GUI and PHASER (and worked).
> But i generated an all-new job doing the same thing, and got the
> ame syntax and same error.
> Still i suppose it may have something to do with running different
> versions (on different hosts) sharing the same user database.
>
> Hard to believe I'm the only one who tried to allow clashes -
> or that the fix is so obvious that no one bothered to report it.
>
> eab
------
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research Tel: + 44 1223 336500
Wellcome Trust/MRC Building Fax: + 44 1223 336827
Hills Road E-mail: [log in to unmask]
Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
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