On Wed, Jun 3, 2009 at 12:27 PM, Thomas C. Terwilliger <terwilliger@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

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 <<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"]
��� 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.