Tutorial-l Mailing List

From: Chris Harrison (charris5_at_gmail.com)
Date: Mon Jun 15 2009 - 06:32:56 CDT

Anna,

Did this produce a coredump file and did you configure with "--with-debug"
or using whatever debug flags are appropriate for the pg compiler?

Chris 

--
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu                            Voice: 217-244-1733
http://www.ks.uiuc.edu/~char               Fax: 217-244-6078
On Mon, Jun 15, 2009 at 3:49 AM, Anna Dejardin <anna.dejardin_at_ucl.ac.uk>wrote:
> Hi Peter,
>
> Thanks for your advice. I'm still having problems unfortunately. We've
> tried recompiling with TCL 8.4 support. My compiler is Portland Group 7.2-5
> and my operating system is Redhat Enterprise Linux 5. I'm still getting
> error messages when I try to run the tutorial programs. Example:
>
> Error: in routine alloca() there is a
> stack overflow: thread 0, max 10228KB, used 4KB, request -18888208B
>
> We are a bit stumped. Any ideas?
>
> Thanks so much
>
> Anna
>
>
> Peter Freddolino wrote:
>
>> Hi Anna,
>> it looks like your namd binary wasn't built with tcl support. While you
>> can get namd to work this way, many features will be disabled, and the
>> syntax in the tutorials assumes a fully functional build. I'd recommend
>> either rebuilding with tcl support or using one of the precompiled
>> binaries available on the namd website.
>> Best,
>> Peter
>>
>> Anna Dejardin wrote:
>>
>>
>>> Hi Peter,
>>>
>>> Here is the logfile:
>>>
>>> Charm++> Running on MPI version: 1.2 multi-thread support: 1/0
>>> Charm warning> Randomization of stack pointer is turned on in Kernel,
>>> run 'echo 0 > /proc/sys/kernel/randomize_va_space' as root to disable
>>> it. Thread migration may not work!
>>> Info: NAMD 2.6 for Linux-amd64-MPI
>>> Info:
>>> Info: Please visit http://www.ks.uiuc.edu/Research/namd/
>>> Info: and send feedback or bug reports to namd_at_ks.uiuc.edu
>>> Info:
>>> Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
>>> Info: in all publications reporting results obtained with NAMD.
>>> Info:
>>> Info: Based on Charm++/Converse 60000 for mpi-linux-amd64-pgf90-mpicxx
>>> Info: Built Tue May 5 12:36:23 BST 2009 by atg on reinette.lcn.ucl.ac.uk
>>> Info: 1 NAMD  2.6  Linux-amd64-MPI  1    reinette.lcn.ucl.ac.uk  acd
>>> Info: Running on 1 processors.
>>> Info: 1592 kB of memory in use.
>>> Info: Memory usage based on mallinfo
>>> Info: Changed directory to
>>> /homes/acd/NAMD2.6/namd-tutorial-files/1-2-sphere
>>> Info: Configuration file is ubq_ws_eq.conf
>>> ERROR: Expecting value and optional units for option 'temperature'
>>> ERROR: Expecting value and optional units for option 'langevinTemp'
>>> ERROR: The following variables were set in the
>>> ERROR: configuration file but are NOT VALID
>>> ERROR:    run
>>> ERROR:    reinitvels
>>> ERROR:    minimize
>>> ERROR:    set
>>> FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
>>> p0_14453:  p4_error: : 1
>>>
>>> Thanks
>>>
>>> Anna
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