Re: [AMBER-Developers] AmberTools19: release candidate 1

From: David Cerutti <>
Date: Fri, 5 Apr 2019 03:24:41 -0400

OK, I can add the first ticket item, here.

As it is in master, and now in my two mdgxCuda and mdgxMods branches that
have recently merged in code from master, if one attempts to configure
-noopt and -debug options, this somehow short-circuits the -fPIC flag and
the result is that FFTW, or the final linking step that binds everything
together, is compiled without -fPIC. The symptom is that cpptraj fails to
compile, with the error message:

/usr/bin/ld: /home/cerutti/AT19/amber18/lib64/libfftw3.a(apiplan.o):
relocation R_X86_64_32 against `.rodata' can not be used when making a
shared object; recompile with -fPIC
/home/cerutti/AT19/amber18/lib64/libfftw3.a: error adding symbols: Bad value
collect2: error: ld returned 1 exit status

If I try to push through this and go straight to AmberTools/src/mdgx to
compile, I get the same error. Configuring without these debugging flags
produces a clean build.

Scott Brozell was very helpful today in tracking down the fault in one of
my branches, but there it was because of something particular that I was
doing, which I have since fixed. The underlying problem seems to be more
pervasive, however, so we're hopefully close to a general fix.


On Thu, Apr 4, 2019 at 10:26 PM David Case <> wrote:

> Hi everyone:
> Here is a link to release candidate 1 (04apr19) for AmberTools19:
> Please download and give this a try. Remember that it is this tarfile
> (in its final version) and not what is in the git repo, that users will
> see.
> In particular, I'd like to have people using OSX to kick the tires.
> Helpful if (a) you have Mojave, but have never installed Amber on that
> machine; or (b) you have a pre-mojave version.
> Other good tests would include various gcc compilers, Intel, etc.
> Enter your summaries here:
> ...thanks!...dac
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Received on Fri Apr 05 2019 - 00:30:02 PDT
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