Finally everything works.
I thank everyone, especially Mengjuei Hsieh for patiently helping me along.
The main problem was that the Ambertools manual suggests to install amber11 as a subdirectory in /usr/local.
This causes all kinds of problems, and the error messages are not at all clear that privilege issues are at the core of it all.
Below is my final installation "guide" for Unix dummies like myself.
Installing Amber and AmberTools 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)
Erik R.P. Zuiderweg
Professor of Biological Chemistry
University of Michigan Medical School
4220D MSRB III,
1150 W. Medical Center Drive
Ann Arbor MI 48109-5605
Office Phone (734) 615 6365
Cell Phone (734) 276 4463
Lab Phone (734) 615 6378
zuiderwe.umich.edu
www-personal.umich.edu/~zuiderwe
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Received on Tue May 18 2010 - 09:30:04 PDT
