AMBER Archive (2009)

Subject: [AMBER] problem in installing amber tools on Mac OSX 10.6

From: Chun-Wei Pao (barbarossapao_at_gmail.com)
Date: Mon Dec 28 2009 - 01:54:26 CST

Hi

I am trying to install Amber Tools 1.3 on my Mac Pro. However, I found I had problems in both configuring the system and compile the codes. I doubt that the problems are related with the 64-bit in the new MacOSX. Can any one help me? I tried to install everything on a linux cluster without any problems at all.

When doing ./configure process, I typed ./configure -macAccelerate gnu
and I got the following :

Setting AMBERHOME to /Users/mac/Codes/amber11
 

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 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.
 
The configuration file, config.h, was successfully created.
 
The next step is to type 'make -f Makefile_at'
=======================================================

The last few lines of the netcdf_config.log file reads

checking CC CFLAGS... gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
checking type gcc... gcc is hashed (/usr/bin/gcc)
checking CXX... g++
checking CXXFLAGS... -g -O2
checking type g++... g++ is /usr/bin/g++
checking FC... gfortran
checking FFLAGS... -O3 -mtune=generic
checking type gfortran... gfortran is /usr/local/bin/gfortran
checking F90... gfortran
checking F90FLAGS... -O3 -mtune=generic
checking type gfortran... gfortran is /usr/local/bin/gfortran
checking AR... ar
checking ARFLAGS...
checking type ar... ar is /usr/bin/ar
checking NM... /usr/bin/nm
checking NMFLAGS...
checking for /usr/bin/nm... /usr/bin/nm
checking nm flags...
checking for C-equivalent to Fortran routine "SUB"... sub_
checking for Fortran "byte"... yes
checking for Fortran "integer*2"... yes
checking if Fortran "byte" is C "signed char"... configure: error: Could not link conftestf.o and conftest.o
=======================================================

Then, I tried to compile the code and found the error following (only the last part is shown):

cd ../lib && make sys2.a
cpp -traditional -P -DNO_SANDER_DIVCON sys.f > _sys.f
gfortran -c -O0 -o sys.o _sys.f
gcc -c -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o wallclock.o wallclock.c
cpp -traditional -P -DNO_SANDER_DIVCON random.f > _random.f
gfortran -c -O0 -ffree-form -o random.o _random.f
cpp -traditional -P -DNO_SANDER_DIVCON veclib.f > _veclib.f
gfortran -c -O0 -ffree-form -o veclib.o _veclib.f
cpp -traditional -P -DNO_SANDER_DIVCON amopen.f > _amopen.f
gfortran -c -O0 -o amopen.o _amopen.f
cpp -traditional -P -DNO_SANDER_DIVCON mexit.f > _mexit.f
gfortran -c -O0 -o mexit.o _mexit.f
cpp -traditional -P -DNO_SANDER_DIVCON nxtsec.f > _nxtsec.f
gfortran -c -O0 -o nxtsec.o _nxtsec.f
cpp -traditional -P -DNO_SANDER_DIVCON rgroup.f > _rgroup.f
gfortran -c -O0 -o rgroup.o _rgroup.f
cpp -traditional -P -DNO_SANDER_DIVCON rfree.f > _rfree.f
gfortran -c -O0 -o rfree.o _rfree.f
cpp -traditional -P -DNO_SANDER_DIVCON matinv.f > _matinv.f
gfortran -c -O0 -o matinv.o _matinv.f
ar rv sys2.a sys.o wallclock.o random.o veclib.o amopen.o mexit.o nxtsec.o rgroup.o rfree.o matinv.o
ar: creating archive sys2.a
a - sys.o
a - wallclock.o
a - random.o
a - veclib.o
a - amopen.o
a - mexit.o
a - nxtsec.o
a - rgroup.o
a - rfree.o
a - matinv.o
ranlib: archive member: sys2.a(wallclock.o) cputype (16777223) does not match previous archive members cputype (7) (all members must match)
ranlib sys2.a
ranlib: archive member: sys2.a(wallclock.o) cputype (16777223) does not match previous archive members cputype (7) (all members must match)
make[2]: *** [sys2.a] Error 1
make[1]: *** [syslib] Error 2
make: *** [serial] Error 2
=======================================================

Thank you guys very much for any useful feedbacks!!

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