<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Tatyana,<div><br></div><div>I think we have the autobuild and PHENIX installation hanging problem figured out now. There was a problem in deleting system files (.nfsxxxxxx) in temporary directories that caused PHENIX to hang. Now we are able to either ignore them or delete them and it seems to work fine on a system where we could make this problem happen. The next nightly build (tonight) should have this fix in it.</div><div><br></div><div>Thanks very much to all those reporting the problems and I hope that this will fix it!</div><div>All the best,</div><div>Tom T</div><div> <br><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>