[phenixbb] not enough memory error in Resolve/AutobuildWizard

Tatyana Sysoeva tatyanasysoeva at gmail.com
Fri Jun 5 11:05:14 PDT 2009

On Wed, Jun 3, 2009 at 12:27 PM, Thomas C. Terwilliger <terwilliger at lanl.gov>
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/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:
> -------------
> /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 <<EOD
> 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"]
 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.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20090605/236eac35/attachment-0003.htm>

More information about the phenixbb mailing list