2: I made the replacement in the file sff/parm.c. I did this because it was
bailing on a command "fprintf(nabout, ....." without thinking any more
deeply on the matter.
1: A segfault does get triggered during the test cases, although it doesn't
seem to be directly related.
.
.
.
.
make[2]: Leaving directory `/home/josh/amber11/AmberTools/test/nab'
cd ptraj_rmsa && ./Run.rms
Segmentation fault
./Run.rms: Program error
make[1]: [test.ptraj] Error 1 (ignored)
cd ptraj_rms && ./Run.rms
ptraj: test rms and 2drms commands
Segmentation fault
./Run.rms: Program error
make[1]: [test.ptraj] Error 1 (ignored)
cd ptraj_matrix && ./Run.matrixptraj: analyze fluctuation matrices
diffing 1rrb_vac_distmat.dat.save with 1rrb_vac_distmat.dat
PASSED
.
.
.
I have to own up that I have been using nab a little bit differently to the
way it was probably intended, as a library of useful functions callable from
C++ programs rather than as a self-contained programming language. Perhaps
if I were doing things properly, which is to say having only .nab source
files, "nabout" would be automagically defined and I wouldn't have had this
error.
Looking at the documentation, it seems that MORT is intended more for this
purpose, but as both approaches lead back to the sff in the end I feel like
I might as well stick with nab, which I know my way around. Thanks for
indulging me.
Josh
On Wed, Jul 14, 2010 at 6:36 PM, case <case.biomaps.rutgers.edu> wrote:
> On Wed, Jul 14, 2010, Josh Berryman wrote:
>
> > Hello everyone. I have/had a problem with my AmberTools 1.4 install (new
> > and fully patched this morning); running on 64-bit ubuntu 10.04.
>
> >
> > I found that rdparm (called by the nab function readparm) was
> segfaulting.
> > Replacing all instances of "nabout" by "stdout" and recompiling seems to
> > fix this; although I am sure there are sound reasons for having a special
> > filepointer this is a good enough workaround for my personal use.
>
> Can you give some details?
>
> 1. Do any of the test cases fail? If not, can you post a small program
> that illustrates the problem?
>
> 2. When you say "replace all instances of nabout with stdout", in what
> file(s)
> did you make this replacement? What prompted you to think that this change
> would fix the problem?
>
> ...thx....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Jul 15 2010 - 05:00:05 PDT
