[phenixbb] Autobuild error - bash/dash/sh

[Stephen Graham]

Hi Tom,

Thanks for the info.  I think the command is the '>&' redirect of
stdout and stderr on line 5 of the generated script.  If my sh memory
is correct, the same should be achievable with:

phenix.autobuild /path/to/TEMP0/PARAMS_1.eff
write_run_directory_to_file=/path/to/TEMP0/INFO_FILE_1 >
/path/to/TEMP0/RUN_FILE_1.log 2>&1

i.e. redirect stdout to the RUN_FILE_1.log, and then redirect stderr
to the same place using '2>&1'

I've done a quick test and this seems to give the expected behaviour.

Cheers,

Stephen

On 26 October 2010 13:08, Thomas C. Terwilliger <terwilliger at lanl.gov> wrote:
> Hi Stephen,
> I'm sorry about the problem! I put in the "sh" with a bash system as you
> guessed, and I must have used a non-generic command. I will have to check
> this out on an ubuntu system.
>
> No, unfortunately there is no easy way to get rid of the sh completely
> (this is all there because I was trying to get rid of csh which is not in
> ubuntu at all).  You can however go back to the last release version of
> phenix (which used csh), then download csh and you should be in business.
>
> On the sequence file, both fasta and pir should work...but try just a
> plain sequence of letters, no headers, and that might solve the gui part
> of this.
>
> All the best,
> Tom T
>
>
>>> Hi there,
>>>
>>> Apologies if this has been reported before, but the autobuild job I
>>> tried to run last night failed after a short while...
>>>
>>> The job was started from the command line using:
>>>
>>> phenix.autobuild data=../mydata_free.mtz seq_file=../protein.fasta
>>> map_file=../ccp4i/protein_phaser.1_parrot2.mtz
>>> input_map_labels='parrot.F_phi.F parrot.F_phi.phi None'
>>>
>>> And it got to the point where it was trying to submit the three jobs
>>> before it died as follows:
>>>
>>> Splitting work into 3 jobs and running with 1 processors using sh
>>> background=False in
>>> /home/stepheng/Projects/my_protein/autobuild/AutoBuild_run_3_/TEMP0
>>>
>>> Starting job 1...Log will be:
>>> /home/stepheng/Projects/my_protein/autobuild/AutoBuild_run_3_/TEMP0/RUN_FILE_1.log
>>> *************ERROR ENDING *******************
>>>
>>> ********************************************************************************
>>> Failed to carry out AutoBuild_build_cycle:
>>>
>>> child process stderr output:
>>>   command: 'sh
>>> /home/stepheng/Projects/my_protein/autobuild/AutoBuild_run_3_/TEMP0/RUN_FILE_1'
>>>   /home/stepheng/Projects/my_protein/autobuild/AutoBuild_run_3_/TEMP0/RUN_FILE_1.sh:
>>> 5: Syntax error: Bad fd number
>>> ********************************************************************************
>>>
>>> *************ERROR ENDING *******************
>>>
>>> I think the problem might be that the RUN_FILE_1.sh script seems to
>>> use a bash command/redirection that is not implemented in plain old
>>> 'sh' spec, and thus not supported by dash (the lean version of sh that
>>> ships with ubuntu)?  If I change the #! line of RUN_FILE_1.sh to call
>>> /bin/bash rather than /bin/sh the script seems to run to completion...
>>>
>>> Is there any easy way to change the script template to use /bin/bash
>>> or remove the offending command?  I'm running phenix dev-550 on an x86
>>> ubuntu 10.10 machine.
>>>
>>> Thanks,
>>>
>>> Stephen
>>>
>>> P.S.  The reason I'm trying to run autobuild from the command line
>>> rather from the GUI is that the GUI seems to crash every time I give
>>> autobuild a sequence file in either the FASTA or PIR format.  Is there
>>> another format I should be using?
>>>
>>> --
>>> Dr Stephen Graham
>>> 1851 Research Fellow
>>> Cambridge Institute for Medical Research
>>> Wellcome Trust/MRC Building
>>> Addenbrooke's Hospital, Hills Road
>>> Cambridge, CB2 0XY, UK
>>> Phone: +44 1223 762 638
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>>
>
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>



-- 
Dr Stephen Graham
1851 Research Fellow
Cambridge Institute for Medical Research
Wellcome Trust/MRC Building
Addenbrooke's Hospital, Hills Road
Cambridge, CB2 0XY, UK
Phone: +44 1223 762 638