[gmx-users] Using the XTC library

[Joshua L. Phillips]

I looked into this today, and found the same error for C++. Fix: If you
are using C++, you need to add the -DCPLUSPLUS flag since this is used
to add the 'extern "C"' wrapper in xdrfile.h.

icpc -DCPLUSPLUS -I$HOME/apps/xdrfile/include/xdrfile \
     -L$HOME/apps/xdrfile/lib test.cpp -o test -lxdrfile

-- Josh

On Fri, 2011-05-06 at 22:22 -0700, Joshua L. Phillips wrote:
> You will need to link with the library as well (-lxdrfile)
> 
> Something like the following should work (if the paths that you provided
> are correct):
> 
> icpc -I$HOME/apps/xdrfile/include/xdrfile \
>      -L$HOME/apps/xdrfile/lib test.cpp -o test -lxdrfile
> 
> (Since, this is C++ code, then you should be using icpc instead of
> icc...)
> 
> -- Josh
> 
> On Sat, 2011-05-07 at 13:55 +1000, Mark Abraham wrote:
> > On 7/05/2011 1:31 PM, Ryan S Davis (rsdavis1) wrote:
> > > I am trying to use the XTC library in my code but I am just not good at this stuff.
> > > http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library
> > >
> > >
> > > I installed using
> > > ./configure --prefix=/$HOME/apps/xdrfile
> > 
> > This might not be the problem, but the HOME environment variable here 
> > and below will normally start with a slash, and so you should not 
> > preface it with another.
> > 
> > > make install
> > >
> > > everything seemed to go well and the make check said everything passed.
> > >
> > > So then I try a test code
> > >
> > >    1 #include<iostream>
> > >    2 #include "xdrfile_xtc.h"
> > >    3 using namespace std;
> > >    4
> > >    5 int main()
> > >    6 {
> > >    7
> > >    8      int natoms;
> > >    9      read_xtc_natoms("traj.xtc",&natoms);
> > >   10     return 0;
> > >   11 }
> > >
> > > and I compile with
> > >
> > > icc  -I/$HOME/apps/xdrfile/include/xdrfile  -L/$HOME/apps/xdrfile/lib/  test.cpp
> > >
> > > and i get an error saying...
> > >
> > > undefined reference to 'read_xtc_natoms(char *, int*)'
> > >
> > > I am sure that I am doing something stupid. I tried a C compiler and linking to few other random places but, like I said, this stuff (installing libraries and linking) is new to me.
> > > Please help.
> > 
> > icc  -I$HOME/apps/xdrfile/include/xdrfile test.cpp
> > 
> > will find $HOME/apps/xdrfile/include/xdrfile/xdrfile_xtc.h
> > 
> > Mark
> 
> -- 
> Joshua L. Phillips
> Ph.D. Candidate - School of Engineering
> University of California, Merced
> jphillips7 at ucmerced.edu
> 
> 

-- 
Joshua L. Phillips
Ph.D. Candidate - School of Engineering
University of California, Merced
jphillips7 at ucmerced.edu