Tutorial-l Mailing List

From: Anna Dejardin (anna.dejardin_at_ucl.ac.uk)
Date: Mon Jun 15 2009 - 03:49:20 CDT

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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