Start with something simple, and grow your suppose run from there.
For example, start with 2 or 3 .pdbs only - and ensure that they have
the same topology. Or, input the same (identical) .pdb three times -
and you should get 0.0s out.
My point is that when I run into segfault problems with nab (and
"suppose" by extension), starting with a simple system, and growing from
there, is the most productive way to move forward.
Also, try a simpler match string than ":15-18,106-109:C*,N*,O*,P" and
build up from there.
I believe you can source-debug the code with
nab -g suppose.nab -o suppose
gdb ./suppose
set arg -fit ":15-18,106-109:C*,N*,O*,P" ./oldpdb/*.pdb
run
Then, when it crashes, you can use "bt" to possibly figure out where it
died - but I'd only get into that when you try the "start simple and
grow" approach first.
On 12/09/2014 02:27 PM, Yu Chen wrote:
> Hello, All
>
> I am having trouble with "suppose" program (in AmberTools/example/suppose).
> I have tried both AmberTools12 and AmberTools14 and all with updated bug
> fixes on OS X 10.6 and OS X 10.10.
>
> On OS X 10.6.8, I used macports gcc45. The compiling went without any
> problems. (make suppose). But when I try to run it with some pdb files
> (./suppose -fit ":15-18,106-109:C*,N*,O*,P" ./oldpdb/*.pdb or similar
> command), it just dies with "Segmentation fault".
>
> On OS X 10.10.1, I used macports gcc49. Again, compiling was fine. When
> running, it dies with a little bit different message: "Segmentation fault:
> 11".
>
> Could anyone give me any suggestions/advices?
>
> Thanks in advance!
>
> Best
> Chen
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Received on Tue Dec 09 2014 - 14:00:02 PST
