I am trying to install Ambertools1.4 on a Intel MacbookPro , running
Os 10.6.
using the bash shell
I have the gnu compilers installed.
The configuration file is failing, WARNING: Unable to compile mixed C/
Fortran code. (see attached log)
The installation is failing because of a missing /usr/local/amber11/
lib/arpack.a file
(see attached log)
Your AMBERHOME environment variable should be set to /usr/local/amber11
ld: warning: in testp.f.o, file is not of required architecture
ld: warning: in /usr/local/lib/libgfortran.dylib, file is not of required architecture
Undefined symbols:
"_hello_", referenced from:
_main in testp.c.o
ld: symbol(s) not found
collect2: ld returned 1 exit status
Obtaining the gnu suite version:
gcc -v
The version is 4.2.1
Testing the gcc compiler:
gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c
OK
Validating the C++ compiler version:
g++ -v
The version is 4.2.1
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 -o testp testp.c.o testp.f.o -lgfortran -framework Accelerate
WARNING: Unable to compile mixed C/Fortran code.
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)
Error: NetCDF configure returned 1
NetCDF configure failed! Check the netcdf_config.log file.
Continuing but NetCDF will be skipped.
Configuring fftw-2.1.5; (may be time-consuming)
fftw-2.1.5 configure succeeded.
The configuration file, config.h, was successfully created.
The next step is to type 'make install'
Starting installation of AmberTools, version 1.4 serial at Thu May 13 09:54:25 EDT 2010.
(cd ucpp-1.3 && make install )
gcc -o ucpp mem.o nhash.o cpp.o lexer.o assert.o macro.o eval.o
mv ucpp /usr/local/amber11/bin
(cd byacc && make install )
mv yacc /usr/local/amber11/bin
(cd arpack && make install );
make[1]: Nothing to be done for `install'.
(cd lapack && make skip )
skipping compilation of LAPACK
(cd blas && make skip )
skipping compilation of BLAS
(cd c9x-complex && make skip )
using built-in (C99) complex.h functionality
(cd etc && make install )
cd ../lib && make sys2.a
make[2]: `sys2.a' is up to date.
gfortran -o ambpdb ambpdb.o forFIRSTtype.o forFIRSTbond.o forFIRSThbond.o forFIRSTteth.o forFIRSToutp.o forFIRSTsugar.o ../lib/sys2.a
gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o elsize elsize.o -lm
gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o molsurf molsurf.o -lm
gfortran -o add_pdb add_pdb.o ../lib/sys2.a
gfortran lapack.o resp.o -o resp
/bin/mv ambpdb elsize molsurf add_pdb resp /usr/local/amber11/bin
/bin/cp calcpka.pl cpinutil.pl CPin.pm lmodprmtop /usr/local/amber11/bin
(cd chamber && make install )
make chamber
gfortran -o chamber main.o psfprm.o psf_strings.o write_prmtop.o gbradii.o sort.o mkexcl.o cmap.o molnt.o
mv chamber /usr/local/amber11/bin
(cd pbsa && make install )
cd ../lib && make nxtsec.o
make[2]: `nxtsec.o' is up to date.
cd ../lapack && make skip
skipping compilation of LAPACK
cd ../blas && make skip
skipping compilation of BLAS
cd ../arpack && make install
make[2]: Nothing to be done for `install'.
gfortran -o pbsa dsvdc.o pbsa.o pb_read.o pb_write.o getcoor.o runmd.o runmin.o force.o pb_init.o sa_driver.o np_force.o pb_force.o pb_nlsolver.o pb_exmol.o pb_mpfrc.o pb_direct.o pb_list.o timer.o egb.o ene.o locmem.o myopen.o rdparm.o pb_lsolver.o decomp.o rgroup.o rfree.o debug.o ../lib/nxtsec.o /usr/local/amber11/lib/arpack.a -framework Accelerate
gfortran: /usr/local/amber11/lib/arpack.a: No such file or directory
make[1]: *** [pbsa] Error 1
make: *** [serial] Error 2
Please help!
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Received on Thu May 13 2010 - 14:00:06 PDT
