[phenixbb] Autobuild error - bash/dash/sh

Tom Terwilliger terwilliger at lanl.gov
Fri Oct 29 08:49:01 PDT 2010


Hi Stephen,

Thanks very much again for pointing out this problem!  I have changed this so that all versions of phenix starting now should run on your machine with '2>&1' instead of '>&' for redirecting stderr to the output file. Let me know if this doesn't do it!

All the best,
Tom T

On Oct 26, 2010, at 9:54 AM, Stephen Graham wrote:

> 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


Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545

Tel:  505-667-0072                 email: terwilliger at LANL.gov
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