Re: [AMBER] Issue installing Amber18 pbsa.cuda

From: Ruxi Qi <>
Date: Thu, 11 Jul 2019 11:34:08 +0800

Hi Mahesh,

Sorry for late reply. This error is not pbsa specific, as you still
encountered it with pmemd after turning off pbsa.cuda build. The
potential cause is a library you are trying to link was compiled by an
older gcc rather than gcc 5 you are using. I guess your CUDA 8 was not
built by gcc 5. If that's the case, a easy fix for you may be re-compile
Amber with an older gcc version, e.g. gcc 4.8. Some other workaround is
to reset a macro value with linking stage inside all the Makefiles you
are seeing errors. Let me know whether an older gcc can fix your issue.



On 6/25/2019 8:51 PM, Ray Luo wrote:
> Dave,
> We'll take a look ...
> Ray
> --
> Ray Luo, Ph.D.
> Professor of Structural Biology/Biochemistry/Biophysics,
> Chemical Physics, Biomedical Engineering, and Chemical Engineering
> Department of Molecular Biology and Biochemistry
> University of California, Irvine, CA 92697-3900
> On Tue, Jun 25, 2019 at 8:04 PM David A Case <> wrote:
>> On Tue, Jun 25, 2019, Mahesh kumar Teli wrote:
>>> We are using gcc5.4 in our system. I have followed the suggested
>>> instruction and still, installation is not completed and giving the
>>> following error-
>>> /home/surendra/amber18/lib/libemil.a(setup.o): In function
>>> `hsc::setUpNew(double*, double*, double*, double*)':
>>> setup.C:(.text+0x151d): undefined reference to `VTT for
>>> std::__cxx11::basic_stringstream<char, std::char_traits<char>,
>>> std::allocator<char> >'
>> Just a note to Ray and UCI folks: your pbsa.cuda target does the link
>> with "-lstdc++". Are you sure this is correct? Do you not need
>> something like "-std c++11"? All these errors are related to lack of
>> cxx11 constructs, so my WAG is that this may require either more recent
>> compilers, or more suitable linking flags.
>> ...dac

AMBER mailing list
Received on Wed Jul 10 2019 - 21:00:03 PDT
Custom Search