Re: Current CVS broken? (SortedArray.h)

From: Chris Harrison (
Date: Tue Feb 05 2013 - 13:20:58 CST


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.


On Tue, Feb 5, 2013 at 12:52 PM, Michael Mazack <> 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_PLATFORM=\"Linux-x86_64-multicore\"
> -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:
> Web:

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       Voice: 773-570-6078                          Fax: 217-244-6078

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