Re: [phenixbb] not enough memory error in Resolve/AutobuildWizard

On Wed, Jun 3, 2009 at 12:27 PM, Thomas C. Terwilliger wrote: Hi Tatiana, This may be a little difficult to debug on a cluster...but here goes. The error message you got comes from AutoBuild_run_1_/TEMP0/

AutoBuild_run_1_/TEMP0/temporary.com

You can see exactly what happens with that command file if you can log on to a machine in the cluster:

cd AutoBuild_run_1_/TEMP0/AutoBuild_run_1_/TEMP0

then copy temporary.com to test.com and edit test.com to replace all the material at the top of the file after #!/bin/csh -f (something like this below) all the way down to "outputdir":

delete all this: ------------- setenv CCP4_OPEN UNKNOWNsetenv SOLVEDIR /Users/terwill/unix/PHENIX/phenix-1.4-67/solve_resolve/ext_ref_files setenv SYMOP /Users/terwill/unix/PHENIX/phenix-1.4-67/solve_resolve/ext_ref_file s/symop.lib /Users/terwill/unix/PHENIX/phenix-1.4-67/build/mac-intel- osx/solve_resolve/exe/r esolve <<EOD > AutoBuild_run_1_/TEMP0/image.log access_file mirima.dat workdir AutoBuild_run_1_/TEMP0 outputdir /Users/Shared/unix/transfer/shiven/AutoBuild_run_6_ -------------

replace with:

phenix.resolve --huge <

and then run ./test.com ....it should bomb and tell you what is wrong.

It is possible that the size of your problem is too big for even the 8 GB of memory on your machine, but that would imply a pretty big cell and moderate or high resolution. Hopefully the output of that test will tell you...

Just to be sure, you might also go to the phenix web site and download a recent "nightly build" to make sure that there is not some other type of problem going on.

All the best, Tom T

Good afternoon! Thank you so much for the reply. I edited temporary.com and ran it, it reported no error. when I'm installing phenix 1.4-85, it stops at *................................. converting reflection_file_tools.html to reflection_file_tools.raw converting reflection_statistics.html to reflection_statistics.raw converting xtriage_gui.html to xtriage_gui.raw converting raw HTML files, creating tables-of-contents, and indexing* for "infinite" time. After Ctrl-C it continued and finished installation. I tried to run phenix.autobuild and it hangs in gui-output.log - *STEP: ImportRawData_output_files Run 1 List of files to convert to mtz format: File 1: e239a.hkl* in autobuild_run1.log - *ImportRawData_output_files ImportRawData Run 1 Thu Jun 4 21:54:11 2009 summary of input files: hklin : /home2/tas354/phenix_runs/20090603/e239a.hkl input labels:["FOBS", "SIGMA"] OUTPUT FILE NAME: /home2/tas354/phenix_runs/20090603/ImportRawData_run_1_/e239a_PHX.mtz SPACE GROUP NAME: P 21 21 2 CELL: [251.209, 242.58600000000001, 40.703000000000003, 90.0, 90.0, 90.0] *and after that it does not quit and seems to be doing nothing new for the rest of the available time.