[AMBER] Problem in Installing Amber12/Tools in parallel

From: Sajeewa Pemasinghe <sajeewasp.gmail.com>
Date: Thu, 4 Oct 2012 02:40:55 -0400

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?

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.

Thank you

Sajeewa Dewage
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Received on Thu Oct 04 2012 - 00:00:02 PDT
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