<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Stephen,<div><br><div>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!</div><div><br></div><div>All the best,</div><div>Tom T</div><div><br><div><div>On Oct 26, 2010, at 9:54 AM, Stephen Graham wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi Tom,<br><br>Thanks for the info. I think the command is the '>&' redirect of<br>stdout and stderr on line 5 of the generated script. If my sh memory<br>is correct, the same should be achievable with:<br><br>phenix.autobuild /path/to/TEMP0/PARAMS_1.eff<br>write_run_directory_to_file=/path/to/TEMP0/INFO_FILE_1 ><br>/path/to/TEMP0/RUN_FILE_1.log 2>&1<br><br>i.e. redirect stdout to the RUN_FILE_1.log, and then redirect stderr<br>to the same place using '2>&1'<br><br>I've done a quick test and this seems to give the expected behaviour.<br><br>Cheers,<br><br>Stephen<br><br>On 26 October 2010 13:08, Thomas C. Terwilliger <<a href="mailto:terwilliger@lanl.gov">terwilliger@lanl.gov</a>> wrote:<br><blockquote type="cite">Hi Stephen,<br></blockquote><blockquote type="cite">I'm sorry about the problem! I put in the "sh" with a bash system as you<br></blockquote><blockquote type="cite">guessed, and I must have used a non-generic command. I will have to check<br></blockquote><blockquote type="cite">this out on an ubuntu system.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">No, unfortunately there is no easy way to get rid of the sh completely<br></blockquote><blockquote type="cite">(this is all there because I was trying to get rid of csh which is not in<br></blockquote><blockquote type="cite">ubuntu at all). You can however go back to the last release version of<br></blockquote><blockquote type="cite">phenix (which used csh), then download csh and you should be in business.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">On the sequence file, both fasta and pir should work...but try just a<br></blockquote><blockquote type="cite">plain sequence of letters, no headers, and that might solve the gui part<br></blockquote><blockquote type="cite">of this.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">All the best,<br></blockquote><blockquote type="cite">Tom T<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Hi there,<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Apologies if this has been reported before, but the autobuild job I<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">tried to run last night failed after a short while...<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">The job was started from the command line using:<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">phenix.autobuild data=../mydata_free.mtz seq_file=../protein.fasta<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">map_file=../ccp4i/protein_phaser.1_parrot2.mtz<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">input_map_labels='parrot.F_phi.F parrot.F_phi.phi None'<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">And it got to the point where it was trying to submit the three jobs<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">before it died as follows:<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Splitting work into 3 jobs and running with 1 processors using sh<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">background=False in<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">/home/stepheng/Projects/my_protein/autobuild/AutoBuild_run_3_/TEMP0<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Starting job 1...Log will be:<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">/home/stepheng/Projects/my_protein/autobuild/AutoBuild_run_3_/TEMP0/RUN_FILE_1.log<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">*************ERROR ENDING *******************<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">********************************************************************************<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Failed to carry out AutoBuild_build_cycle:<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">child process stderr output:<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> command: 'sh<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">/home/stepheng/Projects/my_protein/autobuild/AutoBuild_run_3_/TEMP0/RUN_FILE_1'<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"> /home/stepheng/Projects/my_protein/autobuild/AutoBuild_run_3_/TEMP0/RUN_FILE_1.sh:<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">5: Syntax error: Bad fd number<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">********************************************************************************<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">*************ERROR ENDING *******************<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">I think the problem might be that the RUN_FILE_1.sh script seems to<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">use a bash command/redirection that is not implemented in plain old<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">'sh' spec, and thus not supported by dash (the lean version of sh that<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">ships with ubuntu)? If I change the #! line of RUN_FILE_1.sh to call<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">/bin/bash rather than /bin/sh the script seems to run to completion...<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Is there any easy way to change the script template to use /bin/bash<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">or remove the offending command? I'm running phenix dev-550 on an x86<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">ubuntu 10.10 machine.<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Thanks,<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Stephen<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">P.S. The reason I'm trying to run autobuild from the command line<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">rather from the GUI is that the GUI seems to crash every time I give<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">autobuild a sequence file in either the FASTA or PIR format. Is there<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">another format I should be using?<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">--<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Dr Stephen Graham<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">1851 Research Fellow<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Cambridge Institute for Medical Research<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Wellcome Trust/MRC Building<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Addenbrooke's Hospital, Hills Road<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Cambridge, CB2 0XY, UK<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Phone: +44 1223 762 638<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">_______________________________________________<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">phenixbb mailing list<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><a href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a><br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">_______________________________________________<br></blockquote><blockquote type="cite">phenixbb mailing list<br></blockquote><blockquote type="cite"><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br></blockquote><blockquote type="cite"><a href="http://phenix-online.org/mailman/listinfo/phenixbb">http://phenix-online.org/mailman/listinfo/phenixbb</a><br></blockquote><blockquote type="cite"><br></blockquote><br><br><br>-- <br>Dr Stephen Graham<br>1851 Research Fellow<br>Cambridge Institute for Medical Research<br>Wellcome Trust/MRC Building<br>Addenbrooke's Hospital, Hills Road<br>Cambridge, CB2 0XY, UK<br>Phone: +44 1223 762 638<br></div></blockquote></div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0; "><div><div><div><div><div><br>Thomas C. Terwilliger<br>Mail Stop M888<br>Los Alamos National Laboratory<br>Los Alamos, NM 87545<br><br>Tel: 505-667-0072 email: <a href="mailto:terwilliger@LANL.gov">terwilliger@LANL.gov</a><br>Fax: 505-665-3024 SOLVE web site: <a href="http://solve.lanl.gov">http://solve.lanl.gov</a><br>PHENIX web site: http:www.phenix-online.org<br>ISFI Integrated Center for Structure and Function Innovation web site: <a href="http://techcenter.mbi.ucla.edu">http://techcenter.mbi.ucla.edu</a><br>TB Structural Genomics Consortium web site: <a href="http://www.doe-mbi.ucla.edu/TB">http://www.doe-mbi.ucla.edu/TB</a></div><div>CBSS Center for Bio-Security Science web site: <a href="http://www.lanl.gov/cbss">http://www.lanl.gov/cbss</a><br><br></div></div></div></div><br></div></span><br class="Apple-interchange-newline">
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