From: Michael Mazack (michael_at_mazack.org)
Date: Tue Feb 05 2013 - 14:24:42 CST
Chris,
Thanks for the reply. When I checkout namd2 from CVS (cvs.ks.uiuc.edu) I
don't currently see the update -- I'll try again tomorrow, as perhaps there
is some delay somewhere or things are still being checked-in/merged.
Though, I've also noticed that GCC is giving an error from flipdcd.c and
sortreplicas.c related to calling exit() and free(). Having these files
directly include stdlib.h fixes that problem.
Michael
On Tue, Feb 5, 2013 at 1:20 PM, Chris Harrison <charris5_at_gmail.com> wrote:
> Michael,
>
> Yes, we discovered the scope bug last night; the gcc compiler complains
> while the intel does not. It's been fixed and should be available in CVS,
> and in the nightly build tonight.
>
> Let us know if you continue to have problems.
>
> Chris
>
>
>
>
> On Tue, Feb 5, 2013 at 12:52 PM, Michael Mazack <michael_at_mazack.org>wrote:
>
>> Hi. I ran a CVS checkout on the namd2 source-tree yesterday, tried to
>> rebuild and was given a compiling error:
>>
>> g++ -m64 -O3
>> -I/home/michael/work/code/namd2/charm-6.5.0/multicore-linux64/include
>> -DCMK_OPTIMIZE=1 -Isrc -Iinc -Iplugins/include -DSTATIC_PLUGIN
>> -I.rootdir/tcl-threaded/include -DNAMD_TCL -I.rootdir/fftw/include
>> -DNAMD_FFTW -DNAMD_VERSION=\"2.9\"
>> -DNAMD_PLATFORM=\"Linux-x86_64-multicore\"
>> -DREMOVE_PROXYRESULTMSG_EXTRACOPY -DNODEAWARE_PROXY_SPANNINGTREE
>> -DUSE_NODEPATCHMGR -fexpensive-optimizations -ffast-math -o
>> obj/ComputeMoa.o -c src/ComputeMoa.C
>> In file included from src/HomePatchList.h:15:0,
>> from src/PatchMap.h:11,
>> from src/ComputeMoa.C:27:
>> src/SortedArray.h: In member function ‘int SortedArray<Elem>::index(const
>> Elem&)’:
>> src/SortedArray.h:77:42: error: ‘found’ was not declared in this scope
>> make: *** [obj/ComputeMoa.o] Error 1
>>
>> ---
>>
>> Using diff, it looks like "int found" was previously above "int isSorted"
>> as a protected variable in the declaration of template <class Elem> class
>> SortedArray: public SortableResizeArray<Elem> near the top of the old
>> SortedArray.h. With the new update in SortedArray.h, "int found" is not
>> declared as a class variable, but only as a local variable for a few
>> functions. Re-adding "int found" seems to make the code build fine, and it
>> seems to run this way too. However, the diff shows some significant
>> differences between the old SortedArray.h and new SortedArray.h, so I'm
>> unsure of any side effects by this "fix". Can anyone else confirm this?
>>
>> Michael
>>
>> --
>> Michael J. M. Mazack
>> Scientific Computation Program
>> University of Minnesota
>> Minneapolis, MN 55455
>> E-mail: michael_at_mazack.org
>> Web: http://mazack.org
>>
>
>
>
> --
> Chris Harrison, Ph.D.
> NIH Center for Macromolecular Modeling and Bioinformatics
> Theoretical and Computational Biophysics Group
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
>
> http://www.ks.uiuc.edu/Research/namd Voice: 773-570-6078
> http://www.ks.uiuc.edu/~char Fax: 217-244-6078
>
>
>
-- Michael J. M. Mazack Scientific Computation Program University of Minnesota Minneapolis, MN 55455 E-mail: michael_at_mazack.org Web: http://mazack.org
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