On May 18, 2010, at 11:14 AM, erik zuiderweg wrote:
> 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.
>
I think there could possibly be something included to suggest people use
sudo -s -E
before trying to install AT into /usr/local on Mac OS X.
Additionally, there should be something about changing the ownership of the test/ to facilitate running the parallel tests, as some MPIs don't eagerly run as root, unless you jump through hoops to make a private/public key pair for root... and that's something that's better NOT done, in my opinion:
chown -R youraccount:youraccount $AMBERHOME/test/
Well, there you have it.
>
> 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 - 09:30:05 PDT
