./configure -amberlib -nobzlib gnu
Assuming 64 bit architecture.
Using BLAS/LAPACK/ARPACK/NetCDF libraries in /home/mtux7/Software/amber14
Not using bzip2
SANDER API will be used if found.
Using gnu compilers
Installing cpptraj binary to
/home/mtux7/Software/Betacpptraj/cpptraj-master/bin
Testing C compiler:
OK
Testing C++ compiler:
OK
Testing Fortran compiler:
OK
Checking ZLIB
OK
Checking NetCDF
OK
Checking LAPACK/BLAS
OK
Checking ARPACK
OK
Checking availability of the SANDER API from AmberTools
Using SANDER API from /home/mtux7/Software/amber14
./testp: error while loading shared libraries: libsander.so: cannot open
shared object file: No such file or directory
Warning: Compilation with the SANDER API failed. Error follows:
--------------------
--------------------
On Wed, Mar 9, 2016 at 8:41 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> Admittedly the configure process could (and should) be made a bit
> easier. By default cpptraj assumes you want certain libraries for full
> functionality. In this case, bzlib is for reading bzip2-compressed
> files (i.e. those with a .bz2 extension). The Amber configure script
> automatically disables this when bzlib is not available. You can
> either install the bzip2 development headers/libraries via your
> package manager (I think it's usually called libbz2-dev or
> bzip2-devel) or you can disable bzip2 support with '-nobzlib'. Typing
> ./configure --full-help will give you a full list of configure
> options.
>
> So try ./configure -amberlib -nobzlib gnu and see if that works.
>
> -Dan
>
>
> On Tue, Mar 8, 2016 at 11:43 PM, Timothy Christopher Schutt
> <tschutt.mymail.mines.edu> wrote:
> > I apologize for my slow reply - I did try that at first but it came up
> with
> > a BZLIB error. $AMBERHOME is set in the ~/.bashrc and the .bashrc is
> > sourced. This is what it gave me? I was lost so I went home and ate some
> > dinner first.
> >
> > xxxxx$ ./configure -amberlib gnu
> >
> > Assuming 64 bit architecture.
> > Using BLAS/LAPACK/ARPACK/NetCDF libraries in /home/mtux7/Software/amber14
> > SANDER API will be used if found.
> > Using gnu compilers
> > Installing cpptraj binary to
> > /home/mtux7/Software/Betacpptraj/cpptraj-master/bin
> >
> > Testing C compiler:
> > OK
> > Testing C++ compiler:
> > OK
> > Testing Fortran compiler:
> > OK
> > Checking BZLIB
> > ./configure: line 131: ./testp: No such file or directory
> > Error: Unable to compile using:
> > g++ -I/home/mtux7/Software/amber14/include -o testp testp.cpp
> > -lbz2
> > Please check your compiler settings or configure flags. Error follows:
> > --------------------
> > testp.cpp:2:19: fatal error: bzlib.h: No such file or directory
> > #include "bzlib.h"
> > ^
> > compilation terminated.
> > --------------------
> >
> > Thanks for all the help, all of you!!
> >
> > On Tue, Mar 8, 2016 at 9:43 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> >
> >> On Tue, Mar 8, 2016 at 6:05 PM, Timothy Christopher Schutt
> >> <tschutt.mymail.mines.edu> wrote:
> >> >
> >> > .Daniel: I'm having trouble compiling the beta cpptraj - I'm pretty
> new
> >> to
> >> > linux and command line stuff so I'm sure that part is just me being
> slow
> >> > but I'll figure it out here eventually.
> >>
> >> If you give some more specifics about what is going wrong I may be
> >> able to help. With the latest GitHub version of cpptraj with Amber
> >> already installed and AMBERHOME correctly set it should be as simple
> >> as:
> >>
> >> ./configure -amberlib gnu
> >>
> >> (Assuming of course you are using gnu compilers). Let me know if you
> >> need any more help,
> >>
> >> -Dan
> >>
> >> >
> >> > .Thomas: I just attempted the unwrap command and that totally worked!!
> >> > Thanks! I'll be sure to include that from now on. I didn't realize
> that
> >> was
> >> > required at first because the diffusion command automatically
> accounted
> >> for
> >> > wrapping around in one dimension at a time.
> >> >
> >> > On Tue, Mar 8, 2016 at 5:34 PM, David A Case <david.case.rutgers.edu>
> >> wrote:
> >> >
> >> >> On Tue, Mar 08, 2016, Timothy Christopher Schutt wrote:
> >> >> >
> >> >> > ...one molecule sitting on the box edge or corner happens to cross
> the
> >> >> > boundary in two different dimensions during the same frame change.
> In
> >> >> > this scenario the wrapping of the second periodic boundary is not
> >> >> > accounted for and the MSD jumps up by n * L^2/N (L= simulation box
> >> >> > length. n= number of molecules in the mask double wrapping that
> frame,
> >> >> > and N = the number of molecules in the mask).
> >> >>
> >> >> Are you trying to compute diffusion behavior from a trajectory that
> was
> >> >> originally created with iwrap=1? Or that has been subject to the
> >> "image"
> >> >> or
> >> >> "autoimage" command in cpptraj? Just trying to pin down possible
> >> sources
> >> >> of
> >> >> problems.
> >> >>
> >> >> ....dac
> >> >>
> >> >>
> >> >> _______________________________________________
> >> >> AMBER mailing list
> >> >> AMBER.ambermd.org
> >> >> http://lists.ambermd.org/mailman/listinfo/amber
> >> >>
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >>
> >>
> >> --
> >> -------------------------
> >> Daniel R. Roe, PhD
> >> Department of Medicinal Chemistry
> >> University of Utah
> >> 30 South 2000 East, Room 307
> >> Salt Lake City, UT 84112-5820
> >> http://home.chpc.utah.edu/~cheatham/
> >> (801) 587-9652
> >> (801) 585-6208 (Fax)
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Mar 09 2016 - 10:30:03 PST
