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
