AMBER Archive (2009)

Subject: [AMBER] AmberTools modifications for Ubuntu 9.10

From: peker milas (pekermilas_at_gmail.com)
Date: Thu Dec 03 2009 - 15:58:31 CST

Recently we attempted to installed AmberTools 1.2 on Ubuntu 9.10
(Karmic) and experienced a few fairly straightforward issues during
configuration as well as compilation. First, the configuration script
appears to use a poor heuristic for identifying the g++ compiler
version, relying on `grep version` to identify the appropriate line in
the g++ -v output. Unfortunately, Ubuntu includes the
--with-pkgversion flag in the configuration command line, causing this
heuristic to fail. I worked around this with the following,

diff -r amber10/src/configure_at /amber/amber10/src/configure_at
476a477
>    return 0;
504c505
<         version=`$cplusplus -v 2>&1 | grep version | cut -d' ' -f3` 

---
>         version=`$cplusplus -v 2>&1 | grep ' version' | cut -d' ' -f3`

This patch also fixes a compiler warning due to incorrect test code
(the first chunk).

Secondly, g++ 4.4 is far stricter about standard library header files.
In particular, sprintf and the like require the <cstdio> header, which
is missing in amber10/src/gleap/mortsrc/common/fortran.cpp. This is
fixed by the following patch,

diff -r amber10/src/gleap/mortsrc/common/fortran.cpp
/amber/amber10/src/gleap/mortsrc/common/fortran.cpp
0a1
> #include <cstdio>

Please consider merging these patches into the upstream tree. Thanks,

- Ben Gamari

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