[phenixbb] not enough memory error in Resolve/AutobuildWizard
terwilliger at lanl.gov
Fri Jun 5 11:37:34 PDT 2009
Thanks for trying running the "temporary.com" file directly. The fact
that it runs means that your machine has no problem doing this job, at
least in principle.
The installation problem you had with 1.4-85 is a problem we are
currently trying to debug, as Ralf just replied to you about...
I am guessing that the run of autobuild has the same problem of
deletion of files.
Can you try running your exact same job on a single machine with local
disk, to see if it will run properly in this case?
All the best,
On Jun 5, 2009, at 12:05 PM, Tatyana Sysoeva wrote:
> On Wed, Jun 3, 2009 at 12:27 PM, Thomas C. Terwilliger <terwilliger at lanl.gov
> > wrote:
> Hi Tatiana,
> 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
> material at the top of the file after #!/bin/csh -f (something like
> 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
> 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
> converting reflection_statistics.html to
> converting xtriage_gui.html to xtriage_gui.raw
> converting raw HTML files, creating tables-of-contents, and
> for "infinite" time. After Ctrl-C it continued and finished
> 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
> summary of input files:
> hklin : /home2/tas354/phenix_runs/20090603/e239a.hkl
> input labels:["FOBS", "SIGMA"]
> OUTPUT FILE NAME: /home2/tas354/phenix_runs/20090603/
> SPACE GROUP NAME: P 21 21 2
> CELL: [251.209, 242.58600000000001, 40.703000000000003, 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.
> phenixbb mailing list
> phenixbb at phenix-online.org
Thomas C. Terwilliger
Mail Stop M888
Los Alamos National Laboratory
Los Alamos, NM 87545
Tel: 505-667-0072 email: terwilliger at LANL.gov
Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov
PHENIX web site: http:www.phenix-online.org
ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu
TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB
CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the phenixbb