<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>