In other words you should still see:
CPPTRAJ configuration complete.
On Wed, Mar 9, 2016 at 11:06 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> 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
>>> >> >>
>>> >> >>
>>> >> >> _______________________________________________
>>> >> >> 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
>>>
>> _______________________________________________
>> 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)
--
-------------------------
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 - 10:30:06 PST
