Hi Tatiana,
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,
Tom T
On Jun 5, 2009, at 12:05 PM, Tatyana Sysoeva wrote:
On Wed, Jun 3, 2009 at 12:27 PM, Thomas C. Terwilliger <[email protected]> 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.
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