I suggest to install Amber11, I just went through all the hoops to get that done, and it works.
************************
Installing Amber11 and AmberTools1.4 on a
Macbook Pro with 64-bit 2.4 Ghz Intel Core 2 Duo, running OS 10.6.3 (snowleopard)
(1) make the latest OS upgrades
(2) get the latest version of X-tools (3.2.2)
(3) get the latest compilers (4.5). You need gcc and gfortran.
The package vgcc-snwleo-intel-bin.tar.gz from
http://HPC.sf.net is working.
(4) This package unpacks as a usr/local directory wherever you unpacked it
(5) sudo copy the contents of the individual subdirectories in to your "real"
usr/local subdirectories
(6) Make sure the executables are found by your PATH --
(a) add /usr/local/bin to your PATH in
IN .cshrc like
setenv PATH ${PATH}:/usr/local/bin
BE CAREFUL!: this should be one long line.
IN .bash_profile as
PATH="/usr/local/bin:${PATH}"
(b) make sure there are NO compilers in /usr/bin -- they will take precedence over the ones just installed
(7) check the compilers:
which gcc
/usr/local/bin/gcc
gcc -v
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/local/libexec/gcc/x86_64-apple-darwin10/4.5.0/lto-wrapper
Target: x86_64-apple-darwin10
Configured with: ../gcc-4.5-20100107/configure --enable-languages=fortran --host=x86_64-apple-darwin10 --build=x86_64-apple-darwin10 : (reconfigured) ../gcc-4.5-20100107/configure --enable-languages=fortran,c++ --host=x86_64-apple-darwin10 --build=x86_64-apple-darwin10
Thread model: posix
gcc version 4.5.0 20100107 (experimental) (GCC)
which gfortran
/usr/local/bin/gfortran
gfortran -v
Using built-in specs.
COLLECT_GCC=gfortran
COLLECT_LTO_WRAPPER=/usr/local/libexec/gcc/x86_64-apple-darwin10/4.5.0/lto-wrapper
Target: x86_64-apple-darwin10
Configured with: ../gcc-4.5-20100107/configure --enable-languages=fortran --host=x86_64-apple-darwin10 --build=x86_64-apple-darwin10 : (reconfigured) ../gcc-4.5-20100107/configure --enable-languages=fortran,c++ --host=x86_64-apple-darwin10 --build=x86_64-apple-darwin10
Thread model: posix
gcc version 4.5.0 20100107 (experimental) (GCC)
(8) create a home directory for AMBER. DONOT CREATE IT IN /usr/local AS SUGGESTED IN THE MANUAL -- THIS WILL CAUSE HOURS OF
MISERY. I put it in my home directory: /Users/erikzuiderweg/AMBER_DIR
(9) put both Amber downloads there, and unpack them with tar xvfj xxxxxxx.tar.bz2
(10) in .cshrc set:
setenv PATH ${PATH}:/usr/local/bin:/Applications/Sparky.app/Contents/MacOS:$AMBERHOME
setenv AMBERHOME /Users/erikzuiderweg/AMBER_DIR/amber11
in .bash_profile set:
export AMBERHOME=/Users/erikzuiderweg/AMBER_DIR/amber11
(11) cd /Users/erikzuiderweg/AMBER_DIR/amber11/AmberTools/src
(12) ./configure -macAccelerate gnu (takes 30 seconds)
(13) make (takes 20 minutes)
(14) cd /Users/erikzuiderweg/AMBER_DIR/amber11/AmberTools/test
(15) make test (takes 45 minutes)
(16) cd /Users/erikzuiderweg/AMBER_DIR/amber11/src
(17) make sure it contains a config.h file (generated by AmberTools)
(18) make serial (takes 5 minutes)
(19) cd /Users/erikzuiderweg/AMBER_DIR/amber11/test
(20) make test (takes 45 minutes)
********************************************************************
On May 24, 2010, at 1:39 PM, case wrote:
> On Mon, May 24, 2010, Aurora Clark wrote:
>>
>> I have read through the archives and followed the instructions posted for
>> compiling Amber10 on Mac running Snow Leopard (10.6) using gcc/gfortran,
>> but am running into an undefined symbols error when compiling just the
>> serial version of Amber10 (ambertools 1.4 and 1.3 compiled just fine).
>
> Note that Amber10 requires you to have AmberTools1.2 (which you can download
> from the Amber web site). Both AmberTools 1.2 and Amber10 should be extracted
> under the amber10 tree. Don't try to use AmberTools 1.3 or 1.4 with Amber 10.
>
>> Undefined symbols:
>> "_ambsecond_", referenced from:
>> _dsaupd_ in lmod.a(dsaupd.o)
>
> _ambsecond_ should be in ../lib/sys.a. You can type "nm sys.a | grep second"
> in amber10/src/lib to see what might be happening.
>
>>
>> Note that I had to modify the Makefile in /sander because it was pointing to
>> the wrong path for lapack.a and blas.a, as when the lapack and blas
>> subdirectories get compiled the .a files get moves to the amber11/lib
>> directory.
>
> This sounds dangerous, maybe a result of combining the wrong versions of
> Amber10 and AmberTools?
>
> [If you can, consider getting Amber11 -- a lot of Mac related things are much
> more straightforward now. OSX 10.6 was released after amber10 but before
> amber11, so we could address many issues.]
>
> ....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Mon May 24 2010 - 11:30:03 PDT
