<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Tatiana,<div><br></div><div>Thanks for trying running the "temporary.com" file directly. The fact that it runs means that your machine has no problem doing this job, at least in principle.</div><div><br></div><div>The installation problem you had with 1.4-85 is a problem we are currently trying to debug, as Ralf just replied to you about...</div><div><br></div><div>I am guessing that the run of autobuild has the same problem of deletion of files.</div><div><br></div><div>Can you try running your exact same job on a single machine with local disk, to see if it will run properly in this case?</div><div><br></div><div>All the best,</div><div>Tom T</div><div><br></div><div><div><div>On Jun 5, 2009, at 12:05 PM, Tatyana Sysoeva wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><br><span style="background-color: rgb(204, 204, 204);">On Wed, Jun 3, 2009 at 12:27 PM, Thomas C. Terwilliger <<a href="mailto:terwilliger@lanl.gov" target="_blank">terwilliger@lanl.gov</a>> wrote:</span><br style="background-color: rgb(204, 204, 204);"> <span style="background-color: rgb(204, 204, 204);">Hi Tatiana,</span><br style="background-color: rgb(204, 204, 204);"> <br style="background-color: rgb(204, 204, 204);"><span style="background-color: rgb(204, 204, 204);"> This may be a little difficult to debug on a cluster...but here goes.</span><br style="background-color: rgb(204, 204, 204);"> <br style="background-color: rgb(204, 204, 204);"><span style="background-color: rgb(204, 204, 204);"> The error message you got comes from</span><br style="background-color: rgb(204, 204, 204);"> <br style="background-color: rgb(204, 204, 204);"><span style="background-color: rgb(204, 204, 204);"> AutoBuild_run_1_/TEMP0/</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><span style="background-color: rgb(204, 204, 204);">AutoBuild_run_1_/TEMP0/</span><a style="background-color: rgb(204, 204, 204);" href="http://temporary.com/" target="_blank">temporary.com</a><br style="background-color: rgb(204, 204, 204);"> <br style="background-color: rgb(204, 204, 204);"><span style="background-color: rgb(204, 204, 204);"> You can see exactly what happens with that command file if you can log on</span><br style="background-color: rgb(204, 204, 204);"><span style="background-color: rgb(204, 204, 204);"> to a machine in the cluster:</span><br style="background-color: rgb(204, 204, 204);"> <br style="background-color: rgb(204, 204, 204);"><span style="background-color: rgb(204, 204, 204);"> cd AutoBuild_run_1_/TEMP0/</span><span style="background-color: rgb(204, 204, 204);">AutoBuild_run_1_/TEMP0</span><br style="background-color: rgb(204, 204, 204);"> <br style="background-color: rgb(204, 204, 204);"><span style="background-color: rgb(204, 204, 204);"> then copy </span><a style="background-color: rgb(204, 204, 204);" href="http://temporary.com/" target="_blank">temporary.com</a><span style="background-color: rgb(204, 204, 204);"> to </span><a style="background-color: rgb(204, 204, 204);" href="http://test.com/" target="_blank">test.com</a><span style="background-color: rgb(204, 204, 204);"> and edit </span><a style="background-color: rgb(204, 204, 204);" href="http://test.com/" target="_blank">test.com</a><span style="background-color: rgb(204, 204, 204);"> to replace all the</span><br style="background-color: rgb(204, 204, 204);"> <span style="background-color: rgb(204, 204, 204);"> material at the top of the file after #!/bin/csh -f (something like this</span><br style="background-color: rgb(204, 204, 204);"><span style="background-color: rgb(204, 204, 204);"> below) all the way down to "outputdir":</span><br style="background-color: rgb(204, 204, 204);"> <br style="background-color: rgb(204, 204, 204);"><span style="background-color: rgb(204, 204, 204);"> delete all this:</span><br style="background-color: rgb(204, 204, 204);"><span style="background-color: rgb(204, 204, 204);"> -------------</span><br style="background-color: rgb(204, 204, 204);"><span style="background-color: rgb(204, 204, 204);"> setenv CCP4_OPEN UNKNOWNsetenv SOLVEDIR</span><br style="background-color: rgb(204, 204, 204);"><span style="background-color: rgb(204, 204, 204);"> /Users/terwill/unix/PHENIX/</span><span style="background-color: rgb(204, 204, 204);">phenix-1.4-67/solve_resolve/</span><span style="background-color: rgb(204, 204, 204);">ext_ref_files</span><br style="background-color: rgb(204, 204, 204);"> <span style="background-color: rgb(204, 204, 204);"> setenv SYMOP</span><br style="background-color: rgb(204, 204, 204);"><span style="background-color: rgb(204, 204, 204);"> /Users/terwill/unix/PHENIX/</span><span style="background-color: rgb(204, 204, 204);">phenix-1.4-67/solve_resolve/</span><span style="background-color: rgb(204, 204, 204);">ext_ref_file</span><br style="background-color: rgb(204, 204, 204);"> <span style="background-color: rgb(204, 204, 204);"> s/symop.lib</span><br style="background-color: rgb(204, 204, 204);"><span style="background-color: rgb(204, 204, 204);"> /Users/terwill/unix/PHENIX/</span><span style="background-color: rgb(204, 204, 204);">phenix-1.4-67/build/mac-intel-</span><span style="background-color: rgb(204, 204, 204);">osx/solve_resolve/exe/r</span><br style="background-color: rgb(204, 204, 204);"> <span style="background-color: rgb(204, 204, 204);"> esolve <<EOD > AutoBuild_run_1_/TEMP0/image.</span><span style="background-color: rgb(204, 204, 204);">log</span><br style="background-color: rgb(204, 204, 204);"><span style="background-color: rgb(204, 204, 204);"> access_file mirima.dat</span><br style="background-color: rgb(204, 204, 204);"><span style="background-color: rgb(204, 204, 204);"> workdir AutoBuild_run_1_/TEMP0</span><br style="background-color: rgb(204, 204, 204);"><span style="background-color: rgb(204, 204, 204);"> outputdir /Users/Shared/unix/transfer/</span><span style="background-color: rgb(204, 204, 204);">shiven/AutoBuild_run_6_</span><br style="background-color: rgb(204, 204, 204);"><span style="background-color: rgb(204, 204, 204);"> -------------</span><br style="background-color: rgb(204, 204, 204);"> <br style="background-color: rgb(204, 204, 204);"><span style="background-color: rgb(204, 204, 204);"> replace with:</span><br style="background-color: rgb(204, 204, 204);"> <br style="background-color: rgb(204, 204, 204);"><span style="background-color: rgb(204, 204, 204);"> phenix.resolve --huge <<EOD</span><br style="background-color: rgb(204, 204, 204);"> <br style="background-color: rgb(204, 204, 204);"><span style="background-color: rgb(204, 204, 204);"> and then run ./</span><a style="background-color: rgb(204, 204, 204);" href="http://test.com/" target="_blank">test.com</a><span style="background-color: rgb(204, 204, 204);"> ....it should bomb and tell you what is wrong.</span><br style="background-color: rgb(204, 204, 204);"> <br style="background-color: rgb(204, 204, 204);"><span style="background-color: rgb(204, 204, 204);"> It is possible that the size of your problem is too big for even the 8 GB</span><br style="background-color: rgb(204, 204, 204);"><span style="background-color: rgb(204, 204, 204);"> of memory on your machine, but that would imply a pretty big cell and</span><br style="background-color: rgb(204, 204, 204);"><span style="background-color: rgb(204, 204, 204);"> moderate or high resolution. Hopefully the output of that test will tell</span><br style="background-color: rgb(204, 204, 204);"><span style="background-color: rgb(204, 204, 204);"> you...</span><br style="background-color: rgb(204, 204, 204);"> <br style="background-color: rgb(204, 204, 204);"><span style="background-color: rgb(204, 204, 204);"> Just to be sure, you might also go to the phenix web site and download a</span><br style="background-color: rgb(204, 204, 204);"><span style="background-color: rgb(204, 204, 204);"> recent "nightly build" to make sure that there is not some other type of</span><br style="background-color: rgb(204, 204, 204);"><span style="background-color: rgb(204, 204, 204);"> problem going on.</span><br style="background-color: rgb(204, 204, 204);"> <br style="background-color: rgb(204, 204, 204);"><span style="background-color: rgb(204, 204, 204);"> All the best,</span><br style="background-color: rgb(204, 204, 204);"><span style="background-color: rgb(204, 204, 204);"> Tom T</span><br style="background-color: rgb(204, 204, 204);"> <div><div><span style="background-color: rgb(204, 204, 204);"> </span><br></div></div></blockquote>Good afternoon!<br><br><br>Thank you so much for the reply.<br>I edited <a href="http://temporary.com">temporary.com</a> and ran it, it reported no error.<br> <br>when I'm installing phenix 1.4-85, it stops at <br> <i>.................................<br> converting reflection_file_tools.html to reflection_file_tools.raw<br> converting reflection_statistics.html to reflection_statistics.raw<br> converting xtriage_gui.html to xtriage_gui.raw<br> converting raw HTML files, creating tables-of-contents, and indexing</i><br><br>for "infinite" time. After Ctrl-C it continued and finished installation.<br>I tried to run phenix.autobuild and it hangs <br> <br>in gui-output.log - <br><i>STEP: ImportRawData_output_files Run 1<br>List of files to convert to mtz format:<br>File 1: e239a.hkl</i><br><br>in autobuild_run1.log -<br><i>ImportRawData_output_files ImportRawData Run 1 Thu Jun 4 21:54:11 2009<br> summary of input files:<br>hklin : /home2/tas354/phenix_runs/20090603/e239a.hkl<br> input labels:["FOBS", "SIGMA"]<br> OUTPUT FILE NAME: /home2/tas354/phenix_runs/20090603/ImportRawData_run_1_/e239a_PHX.mtz<br> SPACE GROUP NAME: P 21 21 2<br> CELL: [251.209, 242.58600000000001, 40.703000000000003, 90.0, 90.0, 90.0]<br><br></i>and after that it does not quit and seems to be doing nothing new for the rest of the available time.<br> <br><br> _______________________________________________<br>phenixbb mailing list<br><a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a><br>http://www.phenix-online.org/mailman/listinfo/phenixbb<br></blockquote></div><br><div apple-content-edited="true"> <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 style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><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:<a href="http://www.phenix-online.org">www.phenix-online.org</a><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></div></span><br class="Apple-interchange-newline"> </div><br></div></body></html>