[phenixbb] not enough memory error in Resolve/AutobuildWizard
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>
This may be a little difficult to debug on a cluster...but here goes.
The error message you got comes from
> 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
> setenv SYMOP
> 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
> 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
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:
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.
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