Does configure actually fail at that point? It should just disable
linking to the sander API.
On Wed, Mar 9, 2016 at 11:02 AM, Timothy Christopher Schutt
<tschutt.mymail.mines.edu> wrote:
> ./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
>> >> >>
>> >> >>
>> >> >> _______________________________________________
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>> >> >> 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
>>
> _______________________________________________
> 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)
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Received on Wed Mar 09 2016 - 10:30:05 PST
