On Thu, Oct 4, 2012 at 2:40 AM, Sajeewa Pemasinghe <sajeewasp.gmail.com>wrote:
> Hi all,
>
> I am trying to install Amber12 and AmberTools12 in parallel. I already have
> a working mpi installation which is in
> "/usr/mpi/intel/openmpi-1.3.3/bin/mpirun".
>
> I already have set
>
> export AMBERHOME=/wsu/home/ej/ej02/ej0271/amber12
> export LD_LIBRARY_PATH=$LD_LIBRARY_PATH\:$AMBERHOME/lib
> export MPI_HOME=/usr/mpi/intel/openmpi-1.3.3/
>
> in the~/.bashrc file.
>
> When I do
>
> ./configure -mpi gnu it gives the following output.
>
> Checking for updates...
> AmberTools13 is up to date
> Amber13 is up to date
>
> Searching for python2... Found python2.7: /usr/local/bin/python2.7
>
> Obtaining the gnu suite version:
> gcc -v
> The version is 4.1.2
>
> Testing the gcc compiler:
> gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c
> OK
>
> Testing the gfortran compiler:
> gfortran -O0 -o testp testp.f
> OK
>
> Testing mixed C/Fortran compilation:
> gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -c -o testp.c.o
> testp.c
> gfortran -O0 -c -o testp.f.o testp.f
> gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c.o
> testp.f.o -lgfortran -w
> OK
>
> Testing pointer size:
> gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o test_pointer_size
> test_pointer_size.c
> Detected 64 bit operating system.
>
> Testing flex: OK
>
> Configuring NetCDF (may be time-consuming)...
>
> NetCDF configure succeeded.
>
> Checking for zlib: OK
>
> Checking for libbz2: testp.c:2:19: error: bzlib.h: No such file or
> directory
> testp.c: In function 'main':
> testp.c:5: error: 'BZFILE' undeclared (first use in this function)
> testp.c:5: error: (Each undeclared identifier is reported only once
> testp.c:5: error: for each function it appears in.)
> testp.c:5: error: 'infile' undeclared (first use in this function)
> ./configure2: line 1884: ./testp: No such file or directory
> Not found.
>
> Configuring fftw-3.3 for mdgx (may be time-consuming)...
>
> fftw-3.3 configure succeeded.
>
> The configuration file, config.h, was successfully created.
>
> The next step is to type 'make install'
>
> Cleaning the src directories. This may take a few moments.
> Configure complete.
>
> My questions are
>
> 1) Can the configuration be considered successful?
>
Sure. You don't have bzlib, so cpptraj will not be able to read bzipped
ASCII trajectories. This is not a big deal if you don't plan on using
bzipped trajectories (NetCDF trajectories are far superior even to bzipped
ASCII trajectories).
2) Would the following lines indicate or cause a problem in the future?
>
> Checking for libbz2: testp.c:2:19: error: bzlib.h: No such file or
> directory
> testp.c: In function 'main':
> testp.c:5: error: 'BZFILE' undeclared (first use in this function)
> testp.c:5: error: (Each undeclared identifier is reported only once
> testp.c:5: error: for each function it appears in.)
> testp.c:5: error: 'infile' undeclared (first use in this function)
> ./configure2: line 1884: ./testp: No such file or directory
> Not found.
>
See my comments above. If you have root privileges on the machine you're
trying to build on, you can always try to install the BZ2 libraries from
your package manager. If you have Ubuntu, SUSE, or Debian, you can see
http://jswails.wikidot.com/#toc6 for a list of packages you should install
for Amber (and how to install them).
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Oct 04 2012 - 05:30:03 PDT
