Re: [AMBER-Developers] Amber and gcc6

From: Nhai <>
Date: Mon, 23 May 2016 19:14:08 -0400

> dlopen(/home/case/amber16/lib/python2.7/site-packages/pytraj/, 2):
Symbol not found: __ZN8Topology7AddBondEii

This is common error when cpptraj breaks its API (for good). Recently Dan made changes topology parsing (to handle million atoms) and the api change a bit. So pytraj needs to update its code. Sometimes I pulled pytraj code to master branch before Dan pull his code (or in opposite).


> On May 23, 2016, at 5:57 PM, David A Case <> wrote:
> Hi everyone:
> Gcc version 6 was released at the end of April, so we can expect people to
> start using it on our code soon. Here's what I know so far:
> 1. reduce and pytraj are the two parts that don't build for me (using
> the MacPorts version of gcc 6.1). In reduce, if I add "#define OLD_STD_HDRS 1"
> to pdb++.h, that gets rid of many (but not all) the problems. Not sure that
> this is the best fix; these changes mostly arise from changes in how
> iostreams are handled, particular in casting iostream results to things like
> bool variables. Since iostreams are evil anyway, and I am not much of a C++
> person, others will have to look at this.
> 2. In line 12 of cphstats/utilities.cpp, changing "return f" to
> "return static_cast<bool>( f );" seems to help. But Dan says he found a
> better way to handle the same problem in cpptraj, so there could be another
> solution there.
> 3. If one skips reducen and pytraj, everything builds.
> 4. Serial test results: good, except for the very common pytraj problem:
> ImportError:
> dlopen(/home/case/amber16/lib/python2.7/site-packages/pytraj/, 2):
> Symbol not found: __ZN8Topology7AddBondEii
> Plus some file diffs in leap/4PY5 and leap/BSC1 that I get with almost
> all compilers: has anyone else seen these?
> Anyone wishing to tackle the pytraj and reduce problems are welcome to have a
> go!
> ....dac
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Received on Mon May 23 2016 - 16:30:03 PDT
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