Re: [AMBER-Developers] Amber and gcc6

From: Hai Nguyen <>
Date: Mon, 23 May 2016 18:59:34 -0400

*per pytraj issue*, did you `make distclean` before trying new compiler?

It's fine with gcc6.1 + linux (casegroup). I did `make clean distclean`

$ $CC --version
gcc (GCC) 6.1.0

haichit.casegroup ~/amber_git/amber/AmberTools/test (master) $ make
cd pytraj && make
make[1]: Entering directory
Testing pytraj
make[1]: Leaving directory

I have not tested OSX yet.

*Per BSC1*, I myself saw some tests failed with this too. (not sure if the
errors are the same as yours)


On Mon, May 23, 2016 at 5:57 PM, David A Case <>

> 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
> 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
> _______________________________________________
> AMBER-Developers mailing list
AMBER-Developers mailing list
Received on Mon May 23 2016 - 16:00:02 PDT
Custom Search