Re: [AMBER-Developers] Problem installing Amber12

From: Jason Swails <>
Date: Thu, 11 Oct 2012 09:28:05 +0200

On Thu, Oct 11, 2012 at 3:22 AM, Sajeewa Pemasinghe <>wrote:

> Hi all,
> I am trying to install amber12 using pgi 11.5. I am first trying to install
> serial and try to go parallel. Following is my config.log for the serial
> installation.

> Checking for updates...
> AmberTools13 is up to date
> Amber13 is up to date

Just a clarification -- this is *not* Amber 12 -- this is a developer
version of Amber.

>From a warning in your compile log, I can tell you that your problem will
be virtually impossible to debug. The warning I'm talking about is this:

"CharBuffer.cpp", line 199: warning: pointless comparison of unsigned
          with zero
    if (n_char_written<0 || n_char_written >= n_chars_left) {

In the developer version, CharBuffer.cpp no longer exists (which means that
your source code is substantially out-of-date and fails compiling a package
that is rapidly changing right now). Furthermore, line 199 in Amber 12 is

if (n_char_written<0 || n_char_written >= n_chars_left) {

it is

char *DoubleToBuffer(char *buffer, double *X, int N, const char *format,

(in fact, that line doesn't even exist in amber12 from what I can tell).
 Therefore, you're not using the amber12 cpptraj, either. Given that your
code no longer exists and has never been released, I can't imagine any
effort being put into debugging it (since we would first have to find out
exactly what version it *is*).

You will need to update to the latest developer version or back up to a
released version of Amber 12 in order to get any support for build issues.


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER-Developers mailing list
Received on Thu Oct 11 2012 - 00:30:03 PDT
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