AMBER on Macintosh

Building AmberTools 1.5 on a 10.5.x or 10.6.x with gcc/gfortran 4.3

2011-04-23T16:10:00.000-07:00

I'll be using BASH environment in my examples here. Although I am a die-hard TCSH fan, I also speak BASH. I envision this document is for first time users who are somehow macports savvy. To learn more about macports, see http://guide.macports.org/ .

10.5.x / 10.6.x

Macports gcc45 is a set of stable compilers that you should be trying first. You are also advised to unset MKL_HOME since MKL gives some bad results for certain tests.

Supposed that you downloaded the source code of AmberTools 1.5 with your web-browser, the normal place of the source code archive file was saved is probably your own Downloads folder. ( ~/Downloads )

Now uncompress the archive and put it into the /opt directory. The reason that I chose this path is that I can always remove the whole contents of /opt folder without interfering your daily operations with your Macintosh.

 $ tar jxvf ~/Download/AmberTools-1.5.tar.bz2 -C /opt

Set up the environment variable, if these variables have already been set in your ~/.bashrc file, please just verify the values of variable and modify accordingly, and then open a new terminal session.

        $ export AMBERHOME=/opt/amber11
        $ export PATH="$AMBERHOME/bin:$PATH"
        $ export MPI_HOME=$AMBERHOME
        $ unset MKL_HOME
        (note: "unset" doesn't work on CSH, please use "unsetenv" instead)
        $ echo 'export AMBERHOME=/opt/amber11' >> ~/.bashrc
        $ echo 'export PATH="$AMBERHOME/bin:$PATH"' >> ~/.bashrc
        $ echo 'export MPI_HOME=$AMBERHOME' >> ~/.bashrc
        $ cd /opt/amber11/AmberTools/src

Configure for building serial amber

        $ ./configure -macAccelerate gnu

Build the serial AT15

        $ make

Test the serial build

        $ cd ../test

Clean the file after the serial build is finished.

        $ cd ../src
        $ make clean

Download the openmpi source code from open-mpi.org

        $ cd ~/Downloads
        $ curl -O http://www.open-mpi.org/software/ompi/v1.4/downloads/openmpi-1.4.3.tar.bz2

Uncompress this source archive

        $ cd /opt/amber11/AmberTools/src
        $ tar jxvf ~/Downloads/openmpi-1.4.3.tar.bz2

Build amber's own openmpi

        $ ./configure_openmpi

( If you use TCSH/CSH as your login shell, you'd need to run "rehash" command before continue following procedures. )

Configure parallel ambertools

        $ ./configure -mpi -macAccelerate gnu

Build some parallel components of ambertools

        $ make

Test parallel set

        $ cd ../test
        $ export DO_PARALLEL='mpirun -np 2'
        $ ./test_at_parallel.sh

Building AmberTools 1.5 on a 10.4.x Tiger with gcc/gfortran 4.3

2011-04-22T17:20:00.000-07:00

I'll be using BASH environment in my examples here although I am a die-hard TCSH fan, I also speak BASH. I envision this document is for first time users who are somehow macports savvy. To learn more about macports, see http://guide.macports.org/ .

The only reason that I am writing something for 10.4.x is that I have a intel-cpu 10.4.x box and "because I can". A very important limit of 10.4.x is that you can only build a gcc/gfortran as new as gcc43. So for a macports user like me, I just do "sudo port install gcc43 gcc_select". (After using macports with different compilers for a while, many people should be able to appreciate how handy gcc_select is...)

Supposed that you downloaded the source code of AmberTools 1.5 with your web-browser, the normal place of the source code archive file was saved is probably your own Downloads folder. ( ~/Downloads )

        $ tar jxvf ~/Download/AmberTools-1.5.tar.bz2 -C /opt

SERIAL AmberTools

Add "#include <unistd.h>" to AmberTools/src/ptraj/trajectory.c

        $ cd /opt/amber11/AmberTools/src/ptraj
        $ curl -O http://mjhsieh.github.com/a15_trajectory.patch
        $ patch -p0 < a15_trajectory.patch

Somehow my macports gcc43 doesn't understand off_t inside ptraj/trajectory.c. The situation is quite weird, since off_t is a posix standard, meaning that it should be a default everywhere. (updated: unistd.h is not included in ANSI standard.) Anyway, doing this doesn't hurt. (Updated: The reason that I didn't put this in the source tree was that I don't think 10.4.x tiger is a popular OS of choice for a Mac.)

Set up the environment variable, if these variables have already been set in your .bashrc file, please just verify the values of variable and modify accordingly, and then open a new terminal session.

        $ export AMBERHOME=/opt/amber11
        $ export PATH="$AMBERHOME/bin:$PATH"
        $ export MPI_HOME=$AMBERHOME
        $ echo 'export AMBERHOME=/opt/amber11' >> ~/.bashrc
        $ echo 'export PATH="$AMBERHOME/bin:$PATH"' >> ~/.bashrc
        $ echo 'export MPI_HOME=$AMBERHOME' >> ~/.bashrc
        $ cd /opt/amber11/AmberTools/src

For ambertools with xLEaP, we used default setting.

        $ ./configure gnu

For ambertools without xLEaP, generally good for 10.4.x, since many people probably didn't install the developers' tools with X11 option activated.

        $ ./configure -noX11 gnu

Build the serial AT15

        $ make

(cheering after it finished without problems)

Test the serial build

        $ cd ../test
        $ ./test_at_serial.sh

(cheering after it finished without problems)

Clean the file after the serial build is finished.

        $ cd ../src
        $ make clean

PARALLEL AmberTools

Download the openmpi source code from open-mpi.org

        $ cd ~/Downloads
        $ curl -O http://www.open-mpi.org/software/ompi/v1.4/downloads/openmpi-1.4.3.tar.bz2

Uncompress this source archive

        $ cd /opt/amber11/AmberTools/src
        $ tar jxvf ~/Downloads/openmpi-1.4.3.tar.bz2

Build amber's own openmpi

        $ ./configure_openmpi

(cheering after it finished without problems)

Configure parallel ambertools

        $ ./configure -mpi gnu

Build some parallel components of ambertools

        $ make

(cheering after it finished without problems)

Test

        $ cd ../test
        $ export DO_PARALLEL='mpirun -np 2'
        $ ./test_at_parallel.sh

There you have it!

AmberTools 1.5, the Intel compilers, and the Intel Math Kernel Library (MKL)

2011-04-18T10:17:00.000-07:00

We're pleased to announce the release of AmberTools 1.5, now available from the Amber website.

It includes several new packages:

MMPBSA.py, a much-expanded program for energetic analyses of trajectories
amberlite, a simplified interface for mm-pbsa analyses of protein-ligand interactions
MCPB, a platform for developing parameters for active sites of metalloproteins
cpptraj, an expanded trajectory analysis program
mdgx, a coding platform for explicit-solvent MD simulations
updates to GAFF (general Amber force field) and to the RNA force fields

You may install AmberTools 1.5 on top of an existing Amber 11 / AmberTools 1.4 installation. For instructions, please see the web site.

There are two traps I've discovered during the testing phase, related to AmberTools 1.5, the Mac, and the Intel compilers.

The first is that, if you're using the Intel compilers, it matters what version of the GNU compilers (gcc, etc.) you've selected. That's because parts of the code use the c++0x version of the C++ standard, and the version of the C++ header files becomes important. If you use the MacPorts GCC 4.4 or 4.5, you'll get ugly errors like this:

/opt/local/include/gcc44/c++/bits/stringfwd.h(67): error: identifier "char16_t" is undefined

    template<> struct char_traits<char16_t>;

                                  ^

/opt/local/include/gcc44/c++/bits/stringfwd.h(68): error: identifier "char32_t" is undefined
    template<> struct char_traits<char32_t>;                                   ^

The solution, if you get such errors, is to use the command sudo gcc_select, and choose a version of the GNU compilers that came with the XCode development tools. This will present the Intel compilers with a compatible version of the C and C++ headers.

A second problem is that some parts of Amber give bad results with the Intel MKL libraries. The solution here is simple: Don't use them. Make sure that the environment variables MKLROOT and MKL_HOME are unset (note: If they are set, the Amber configuration script will attempt to use an MKL in the location they point to). Instead, configure AmberTools with the –macAccelerate switch.

Amber Tutorial B6

2010-10-06T06:57:00.000-07:00

Some users have noticed that the menus in Sirius don't pop over the display window when working through tutorial B6 from ambermd.org. Here is a workaround:

Maximize the sirius window
Click on the gear button in the left hand pane.
Select the "Other" tab.
In the "Application look and feel" panel, select "Native look and feel".
Click on "OK".
Exit Sirius and restart the program.

Building AmberTools 1.4 with pre-built compilers on Mac OS X 10.6 Snow Leopard

2010-05-15T23:58:00.000-07:00

I have been using the pre-built compilers for Amber projects from time to time, but I've never settled down with any of these binary packages. The most obvious reason was that I really like to build it by myself, part of me deep inside my paranoid mind, I was just afraid of pre-built packages.

However when it comes to preparing documentation for the broad range of Amber users, suggesting an solution of requiring users to build compilers themselves seems to be ~~ridiculous in some level~~ a hassle for users. If you want to change the status quo, go to Apple's bugs report website and suggest them to bundle gfortran with Xcode. I can even envision Professors writing letter to Steve Jobs and having a very civilized discussion back and forth.

Before we convince Apple to begin hiring FORTRAN people, for users with limited experience of mac and unix, I can only introduce pre-built binary packages from third-party providers. Now I am going to write down the steps I have tried to work on Amber with a pre-built compiler package. Gaurav Khanna of "HPC on Mac OS X" project has done a great job providing binary packages for Mac community for a long time. To download the package, you can visit the homepage at http://hpc.sf.net and find the download link. My experience on the gfortran-only package was not successful, it failed on linking the fftw and nab. I also failed to finish the configure script with the other "llvm-gfortran-intel-bin.tar.gz" package. So I am going to recommend you to use the gcc+gfortran package.

Here are the steps:

If you already tried MacPorts and fink, you should uninstall them to prevent them interfering your following procedures. (updated: no I am not bad mouthing MacPorts or fink in the previous version of the document, I was trying to be funny.)
If you want to keep your gcc/gfortran from MacPorts, try this:sudo gcc_select gcc42 sudo port deactivate gcc44 (for more information, do man gcc_select and man port, please.)
If you already install the package of "gfortran-snwleo-intel-bin.tar.gz (Snow Leopard gfortran only)", you should uninstall it. To uninstall it, do cd /; tar ztf ~/Downloads/gfortran-snwleo-intel-bin.tar.gz | grep -v -e '/$' -e '/\._' | xargs sudo rm -f
gcc+gfortran binary package "gcc-snwleo-intel-bin.tar.gz (Snow Leopard)" from the same site indeed does work, so you should download that gcc-snwleo-intel-bin.tar.gz file. To install it, do: sudo tar zxvf ~/Downloads/gcc-snwleo-intel-bin.tar.gz -C / (this will extract the files in /usr/local )

Now it comes to be the tedious part of the work, try to make sure you are running the right compilers when you type gcc and gfortran. First type gcc -v command, if your output looks like this, you are using the right C compiler:

[localhost:amber11/AmberTools/src] mjhsieh% 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)

If your gfortran -v output looks like this, you are using the right gfortran.

[localhost:amber11/AmberTools/src] mjhsieh% 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)

If they are not what you got, please make sure you have set the correct path environment variable, it should contain "/usr/local/bin"; my path variable looks like this:
% echo $PATH
/opt/local/bin:/opt/local/sbin:/opt/intel/Compiler/11.1/084/bin/intel64:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/usr/X11/bin:/Users/mjhsieh/bin
If you still can't have the correct output, ask us in the Amber mail reflector.

start to configure:

cd /usr/local/amber11
cd AmberTools/src; ./configure -macAccelerate gnu

If everything printed out looks okay, start building AmberTools by typing make install
Also go to the path where amber11 is at, start the building process: cd ../../src; make install
Now you have it, please make sure it passes the test cases in amber11/test and amber11/AmberTools/test.
GOOD LUCK playing AMBER/AMBERTOOLS!

This is my result:

Finished test suite for AmberTools at Sun May 16 02:58:11 PDT 2010.

     318 file comparisons passed
       0 file comparisons failed
       0 tests experienced errors

Finished serial test suite for Amber 11 at Sun May 16 03:53:37 PDT 2010.

     492 file comparisons passed
       0 file comparisons failed
       0 tests experienced errors

If you are not satisfied with this binary package, do this to uninstall: cd /; tar ztf ~/Downloads/gcc-snwleo-intel-bin.tar.gz | grep -v -e '/$' -e '/\._' | xargs sudo rm -f

AmberTools 1.4 and Amber 11 on Snow Leopard with the Intel compilers

2010-05-06T09:35:00.000-07:00

In this post, I describe how to compile and install Amber 11 on Snow Leopard with the Intel compilers. Some suggest that the Intel compilers should be passed over in favour of the GNU compilers for the time being; in my experience, on the whole, the two give comparable output. This post is written as though you have installed the most recent versions of the Intel Mac compilers, which at the time of writing are 11.1.088. For earlier (or later) versions, you will need to modify your paths accordingly. I also assume you have downloaded and installed the Intel compilers. The installation process for these is straightforward, and should in any case be documented by Intel.

Set up the Intel compiler environment. Note: These commands are intended for the Bourne shell and its variants (e.g., bash). If you are using the C shell or a variant (e.g., tcsh), you will need to use the scripts with a .csh extension instead of those ending in .sh. Also, if you are using an ia32 processor instead of a 64-bit processor, the argument to the script should be modified accordingly.

. /opt/intel/Compiler/11.1/088/bin/iccvars.sh intel64
. /opt/intel/Compiler/11.1/088/bin/ifortvars.sh intel64

If you wish to compile a parallel (MPI) version of Amber and/or AmberTools, download MPICH2 from here. WARNING: While other MPI implementations such as Open MPI exist, some are untested, and Open MPI fails.
Untar the mpich2 installation file:
tar xzvf mpich2-1.2.1p1.tar.gz
Configure MPICH2 for installation and build it:
cd mpich2-1.2.1p1 ./configure --prefix=your_chosen_mpich2_directory \ --enable-f77 --enable-f90 --enable-cxx \ CC=icc CXX=icpc F77=ifort F90=ifort
Follow the rest of the MPICH2 installation and testing instructions in the README file.
Make sure that your_chosen_mpich2_directory/bin and your_chosen_mpich2_directory/lib are in your PATH and DYLD_LIBRARY_PATH respectively, and that they are ahead of other possible MPI installations such as the default system MPI.
Follow steps 1 to 5 here. Step 6 should not be necessary.
Configure Amber:
./configure intel
Follow steps 8 to 10 here.
If you have also installed Amber 11, go to $AMBERHOME/src and run make there.
Before continuing, we recommend testing the serial executables, as outlined in the AmberTools and Amber documentation.
To build parallel, return to the AmberTools source directory and re-configure:
./configure -mpi intel
Clean up the previous object files by running make clean in both the AmberTools and Amber directories.
Make parallel executables by running make parallel in both the AmberTools and Amber directories.
Finally, test the parallel executables, as outlined in the AmberTools and Amber documentation.

If you have any questions, please feel free to direct them to the AMBER mailing list.

Step-by-Step AmberTools 1.4 Installation on Mac OS X 10.5/10.6 with GNU Compilers

2010-04-26T13:04:00.000-07:00

Here I am going to write something about the steps to install your own AmberTools 1.4 on your Mac OS X using GNU compilers. Previously we already had several blog entries about installing the compilers, so I am not going to spend too much effort on that issue. Now if you are not sure your Macintosh have the necessary compilers to build AmberTools, please read the previous posts in this blog and find some unix buddies to help. Also this tutorial is based on the assumption that you are using BASH as your default shell. For other shells, please consult your local unix guys or system administrator for equivalent commands.

If you have installed MacPorts but have not yet installed the gfortran:

sudo port install gcc44
sudo port install gcc_select
sudo gcc_select mp-gcc44

If you are using gfortran from fink, please note that you don't have gcc_select, but you can still use following steps to make sure you are using both gcc and gfortran from fink.

Of course, install gfortran with "sudo fink install gfortran".
Check which gcc is default in your environment:
"which gcc" and "gcc -v" commands.
If the result says "/usr/bin/gcc", and you later encounter this issue you probably need to change the configure script later in the directory of $AMBERHOME/AmberTools/src/ by replacing "gcc" to "gcc-4" and "g++" to "g++-4".

Now here comes the fun part, please make sure that you already downloaded the AmberTools (and also know where did the file you downloaded go!).

We first change the current directory to /usr/local,
```
cd /usr/local
```
and then extract the AmberTools archive you just downloaded, presumably at ~/Downloads/.
```
sudo tar xvfj ~/Downloads/AmbeTools-1.4.tar.bz2
```
And then fix the permission for you can build it without using root privilege:
```
sudo chown -R $USER:$GROUP amber11
```
Run this command and make sure to put this command to your $HOME/.bashrc:
```
export AMBERHOME=/usr/local/amber11
```
Change the current directory to where the configure script is:
```
cd amber11/AmberTools/src
```
Now it would be a good time to modify the configure script if you are required to do that because of this and that. THIS IS NORMALLY NOT NECESSARY.
```
perl -pi -e 's/cc=gcc/cc=gcc-4/;s/g++/g++-4/g' configure
```
Following the manual, do the configuration. This takes about 1~3 minutes to finish.
```
./configure -macAccelerate gnu
```
And start to build the program:
```
make install
```
This will take a while, make yourself a cup of tea. If you see any problem or message during the building process that prevent you from finishing, please report it to the Amber mail reflector.
After that, change your current directory to the testing directory:
```
cd ../test
```
And start testing!
```
make test
```

After finish building the AmberTools above, you might want to build a parallel version of some commands. About the decision of whether or not making a parallel version of them, please refer to the AmbetTools manual. If you want to build parallel version of AmberTools 1.4 or even Amber11 in general I'd recommend to build an openmpi software by yourself under the AMBER directory. Here is how to build an openmpi inside AMBER.

First change current directory to the AmberTools source:
```
cd $AMBERHOME/AmberTools/src
```
Important! Clean-up the left-over from previous non-parallel building work.
```
make clean
```
Then download the source code of openmpi from here and extract the files for openmpi.
```
tar xvfj ~/Downloads/openmpi-1.4.1.tar.bz2
```
Now start to build the openmpi:
```
./configure_openmpi gnu
```
Here comes the tricky part, by default your Mac OS X 10.6/10.5 bundled openmpi with the developer Tools without FORTRAN support (yes, sadly mpif90/mpif77 in the /usr/bin are disabled by Apple.), so you have to make sure $AMBERHOME/bin in the PATH and also it has to be prior to /usr/bin. If you have macports installed, your $PATH in the BASH should look something similar to this:
```
bash-3.2$ echo $PATH
/usr/local/amber11/bin:/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/usr/X11/bin
bash-3.2$ 
```
Now configure a parallel environment for building parallel commands in AmberTools:
```
env MPI_HOME=$AMBERHOME/AmberTools ./configure -mpi -macAccelerate gnu
```
And then build the things:
```
make parallel
```
Before you do some tests on parallel programs, be advised to turn off the firewall (consider this temporary), since the tests will give you a lot of pop-up prompts if you are using application based firewall rules...

And do some tests:

cd ../test
env DO_PARALLEL="mpirun -np 2" make test.parallel

Now you have it! If you still do not know what you are doing, please stop-by the Amber mail reflector and ask us questions and we are more than happy to help!

(Update: if your other compiling activities are broken by gcc_select, for example you no longer are able to build iphone app with Xcode, just do "sudo gcc_select gcc42" to reset the setting.)

Amber11 Released

2010-04-26T12:30:00.000-07:00

[AMBER] Announcement: release of Amber11 and AmberTools 1.4

David Case <email>

Mon, Apr 26, 2010 at 5:41 AM

Reply-To: AMBER Mailing List <amber@ambermd.org>

To: amber@ambermd.org, CHEMISTRY@ccl.net

I am pleased to announce the release Amber 11.

Amber is a suite of programs designed for molecular dynamics simulations of
biomolecules. For full information on what is new in Amber 11, and how to
order it, please visit:

http://ambermd.org/#Amber

I am also pleased are proud to announce the release of version 1.4 of
AmberTools.

AmberTools consists of several independently developed packages that
work well by themselves, and with Amber itself. Key facilities allow the
preparation of systems for MD simulations, and analysis of trajectories.
The suite can also be used to carry out complete molecular mechanics
investigations (using NAB), employing generalized Born, Poisson-Boltzmann
or 3D-RISM solvent models. AmberTools is released mainly using the GNU
General Public License (GPL), with some components using other open source
licenses.

For more information, and to download AmberTools, please visit:

http://ambermd.org/#AmberTools

...dave case
(For the Amber development team: http://ambermd.org/contributors.html )

_______________________________________________
AMBER mailing list
AMBER@ambermd.org

Some tips of Amber10 installation on Mac OS X 10.6 with GNU compilers

2010-01-28T18:52:00.001-08:00

The question was whether or not Amber10 is compatible with Mac OS X 10.6, Jason's answer from the Amber reflector mailing list is very sufficient:

Amber10 should work on Snow Leopard (as well as ambertools 1.3).However, you should make sure that you have compatible compilers (i.e. a gfortran compiler that builds 64-bit binaries, that you can get either from MacPorts or hpc.sourceforge.net).

I just want to add some extra tips for people wondering the same questions:

If you are using MacPorts, do what I did: install gcc44 and gcc_select and select mp-gcc44
do whatever manual told you to do, but right after the configure scripts (e.g. ./configure_amber or ./configure_at), get rid of every '-m32' from the config_amber.h and config.h files.
After that you are good to go.

Step-by-step procedure of building MacPorts gfortran and AmberTools 1.3 in Mac OS X 10.6

2009-12-23T02:00:00.000-08:00

This is what I would do if I got a brand new Mac OS X machine using gfortran to build AmberTools 1.3 on it.

Find the Mac OS X installation CDs/DVD, start to install Xcode Developer Tools.
If you left it at home, try to download it at the Apple Developer Connection site. Make sure you have installed "Unix Development" (default)
Download the MacPorts Disk Image from the MacPorts' website.
Mount the disk image and install the pkg, running the system's Installer by double-clicking on the pkg contained therein, following the on-screen instructions until completion.
Open a new shell window and do later stuff in this shell, this is to make sure that changes to the environment variables have taken effect.
check if your PATH environment variable really contains /opt/local/bin and /opt/local/sbin by running "echo $PATH"
check upgrades to MacPorts: "sudo port -v selfupdate"
run "sudo port install gcc44"
~~run "mkdir ${HOME}/bin"~~(not necessary)
append this line to the end your ~/.bashrc (If you are using CSH/TCSH, you must be very savvy, so you don't need no documentation... export PATH=${HOME}/bin:$PATH
run "export PATH=${HOME}/bin:$PATH"
~~run "ln -s /opt/local/bin/gfortran-mp-4.4 ~/bin/gfortran"~~
(Original steps were stupid, try following steps:) run "sudo port install gcc_select; sudo gcc_select mp-gcc44"
Download AmberTools from http://ambermd.org/#AmberTools (Safari will place it to ~/Downloads)
run "tar jxvf ~/Downloads/AmberTools-1.3.tar.bz2 -C ~/", this will extract an amber11 folder in your home directory.
Now it would be a good time to append this line to your ~/.bashrc export AMBERHOME=${HOME}/amber11
run "export AMBERHOME=${HOME}/amber11" as well
run "cd ~/amber11/src; ./configure -macAccelerate gnu"
run "make -f Makefile_at" and wait
After "make" stops, check to see if there is any error. If your building process indeed stopped prematurely, report it to the Amber mailing list. Please mention your OS version and compiler you used.
run "cd ~/amber11/test; make -f Makefile_at" to check the testing cases result. Please make sure your environment variable $AMBERHOME is correct before you run the test.

After thought

If you want to use macports without problem after above operation, make sure to "sudo gcc_select" back to gcc42 or llvm-gcc42, or you might encounter some incompatibility with building some certain ports.

Installing g95 or gfortran with MacPorts

2009-12-07T07:22:00.000-08:00

(Original blog entry posted on 7/27/09)

Besides a C compiler, AMBER installation requires a FORTRAN 90 compiler, this has been the case since AMBER 8. FORTRAN 90 compilers are not provided by Apple in developer environment therefore FORTRAN developers need to acquire a third party compiler by themselves. AbSoft PRO Fortran, NAG Fortran 90, IBM XL Fortran 9 and Intel Fortran are some fine compilers that require some funding. There are two popular open source licensed FORTRAN 90 compilers, g95 and gfortran. These two compilers originates from the same group of people but the diverged due to the difference of project managing styles. g95 is more conservatively and independently developed while gfortran integrates itself to the mothership -- gcc source tree. G95 has some advanced feature like coarrays, but gfortran does have something g95 doesn't have: OpenMP.

There are many ways to install these open source FORTRAN compilers on Mac OS X, you could build the compilers from the source or just install the binary packages, or from the way between: using porting system to build them automatically.

Before I write anything about the getting the compilers for your Mac OS X, you should at least have installed:

Apple's Xcode Developer Tools (at least version 3.2 for Snow Leaopard, version 3.1 for Leopard, or 2.4 for Tiger, ), found at the Apple Developer Connection site or on your Mac OS X installation CDs/DVD.
(You need this for Amber.) The X11 windowing environment (A.K.A. “X11 User”) and its related SDK package (“X11SDK”) for ports that depend on the functionality they provide to compile and run.
- the “X11 User” package is an optional installation on your system CDs/DVD for Panther and Tiger, enabled through the “Customize” button of the installer, whereas it is included by default on Leopard.
- the “X11 SDK” package from the Xcode installer will be automatically selected if “X11 User” is already installed, so be sure to install that first.

I personally recommend against porting things from the source trees. If you really do have that kind of skills and free time, you can skip this little note of mine, go ahead and do it already!

For the fans of binary packages, you should try the links from hpc.sourceforge.net/ or from MacResearch group, although I normally don't take this path, this is due to my inner geekiness that preventing me from installing 3rd party packages. Nevertheless, I strongly recommend this way to install your tools if you want to get over it fast.

For utilizing the porting system, you got the options of fink and macports. If you are a fan of Ubuntu or Debian Linux, you should try fink first. For me, I chose macports just because I got some friends in the founding team.

Here is how I did it:

Download the dmg file from http://www.macports.org/install.php, open and mount the dmg and launch the installer by double clicking the pkg file. This requires administrator's permission.
Read the port(1) manual page and http://guide.macports.org for help, http://www.macports.org/contact.php if you need to get in touch with The MacPorts Project.
$ sudo port install g95 g95 in latest macports repository seems to be broken in Tiger
$ sudo port install gcc45 +gfortran (gcc45 is an experimental version, please use gcc44 for stability.) On Mac OS X 10.4 Tiger, the only choices are gcc43 and gcc42.
Viola!

See the next note for more elaborated steps.

VMD 1.8.7 CUDA on Macbook Pro's Geforce 9400M and Snow Leopard

2009-10-10T14:02:00.000-07:00

For some reason, VMD 1.8.7 didn't pick up my 9400M video card.

With this message: No CUDA accelerator devices available.

I am not sure if it's something to do with Mac OS X 10.6 or else. I decided to take a look at CUDA's download page and got a hint that old run time library in VMD 1.8.7 might not work with 9400M+Mac OS 10.6. I started to install CUDA Driver and Toolkit but left the SDK alone. I happen to remember there were something CUDA in VMD's content, for example:

/Applications/VMD\ 1.8.7.app/Contents/vmd

So what I did was to remove the CUDA library files that came with VMD 1.8.7 and made symbolic links to the new runtimes I just installed.

$ cd /Applications/VMD\ 1.8.7.app/Contents/vmd
$ rm libcuda.dylib libcudart.dylib libtlshook.dylib
$ ln -s /usr/local/cuda/lib/libcuda.dylib
$ ln -s /usr/local/cuda/lib/libcudart.dylib
$ ln -s /usr/local/cuda/lib/libtlshook.dylib

Yay...

gcc 4.4 is not happy with sleap's boost source

2009-10-06T04:27:00.000-07:00

If by any chance you are using gcc 4.4 to compile sleap under gleap directory, you might encounter problems like this error:

../../ext/boost/mpl/apply_wrap.hpp:81:31: error: missing binary operator before token "("
../../ext/boost/mpl/apply_wrap.hpp:173:31: error: missing binary operator before token "("
....

This is due to some behaviors changes after gcc 4.4 that interpret C preprocessing macro differently. Here is a patch to workaround. We might need to use newer boost for or system's boost lib.

Using mddisplay with AMBER under Mac OS X

2009-10-04T03:17:00.000-07:00

Mddisplay is a neat tool by Chris Moth for molecular dynamics trajectory analysis. You can display the trajectory with an OpenGL window.

... a really nice program. I find the hardware stereo option very helpful, and the ptraj-like syntax very convenient... -- Dr. Meroueh

...a nice OpenGL based MD-viewer... -- Dr. Dawson

It's not difficult to build the program from the source on Mac OS X, I have tested it on Mac OS X 10.4, 10.5 and 10.6. However, I have submitted a ticket to create a new Macports port so it would be even easier to organize the software. (Check the website to know how to work with macports.)

If my porting setting got committed into Macports (Update: it got checked in to Macports collection), you should be able to install mddisplay under command line interface like this:

sudo port install mddisplay

Two programs would be installed, "preproc" and "mddisplay".

PLEASE BE SURE TO CHECK THE MANUAL!!

In order to display simulation frames in a time evolving way (movie), you can try to load AMBER topology and trajectories and convert it into mddisplay's movie data:

preproc -p 1enh.top -c 1enh.trj -n movie -f 100 (This generates three files: movie.cor, movie.bnd and movie.attr.)
Tips:
for trajectory with more than 100 frames, you might need to specify how many frame you need by "-f 888" if you need to load 888 frames.
use "-f 888%8" if you want to load 111 frame for every 8 frames of this 888 frame trajectory
multiple "-c" arguments are possible.
and .. you can use the name other than movie, it's okay.

To display the movie data, just do:

mddisplay -n movie and answer the questions. Here I used "b" for automatic coloring and ":" to assign every atom with this coloring style. I also used return key to tell mddisplay that's all my coloring style. Also the time frame and starting time were specified as default.

This will create a OpenGL window for you to control. Type "?" or click the help box for the controlling setting. You can blackout the side-chain atoms, filtering out the high frequency motions, or displaying averaged structure. Please refer to the manual.

The help window looks like this:

[FYI] my config_amber.h file

2009-08-04T13:53:00.000-07:00

Check this out if you like to install Amber10 with bundled lammpi source, g95, and Intel Math Kernel Library installed on your Mac OS X. download.

For non-parallel configureation: download it from here
This was tested on Mac OS X 10.4.9 with g95 0.91_1 and Intel MKL 10.0.4.022.

AmberTools 1.0 is now available!

2008-04-09T10:10:00.000-07:00

(Originally posted on 4/2/08, updated)

And AmberTools is now under GPL2! Go ahead and check it out!

Known macintosh-related issues on version 1.0

sleap crashs when launched (fixed in the current source tree, please wait for software update.)
antechamber crashs during several tests.

Coming up next: hardware accelerating PMEMD

2008-04-02T10:26:00.000-07:00

Just to show-off. Only vvexp, vvlog, vvrsqrt and vvrec are used in this test.

AMBER 9 PMEMD on the Mac

2008-03-26T12:16:00.000-07:00

Okay, this time I am going to do a step-by-step document of compiling AMBER 9 PMEMD on the Mac. But I still think compiling this kind of thing requires some consultant fees as a reward for your lovely technical guys around.

If you use intel ifort on Mac OS X, please refer the documentation of linux to use linux p4 option.

For g95/gfortran (intel), save this following piece of text into "pmemd/config_data/macosx_intel.g95", and run "./configure macosx_intel g95 nopar" to generate required config.h file. If you are using ppc CPU, just get rid of -msse3 and use the file of macosx_ppc.g95 and change the argument respectively.

DIRFRC_DEFINES = -DDIRFRC_COMTRANS -DDIRFRC_EFS
CPP = /usr/bin/cpp
CPPFLAGS = -traditional -P
F90_DEFINES = -DFFTLOADBAL_2PROC

F90 = g95
MODULE_SUFFIX = mod
F90FLAGS = -c
F90_OPT_DBG = -g -ftrace=full
F90_OPT_LO =  -O0
F90_OPT_MED = -O2
F90_OPT_HI =  -O3 -msse3
F90_OPT_DFLT =  $(F90_OPT_HI)

CC = gcc
CFLAGS = -DDBL_C_UNDERSCORE

LOAD = g95
LOADFLAGS =
LOADLIBS =

macosx_pcc.xlf90 file for Mac OS X 10.4 (tiger) ppc using IBM xlf90

setenv PREPROCFLAGS "-DDIRFRC_BIGCACHE_OPT -DNO_C_UNDERSCORE"

setenv CPP /opt/ibmcmp/xlf/8.1/exe/cpp

setenv OPT_LO  "xlf90 -qsuffix=f=f90 -qdpc -qmaxmem=-1 -qarch=auto -c"
setenv OPT_MED "xlf90 -qsuffix=f=f90 -qdpc -qmaxmem=-1 -O2 -qarch=auto -c"
setenv OPT_HI  "xlf90 -qsuffix=f=f90 -qdpc -qstrict -O3 -qarch=auto -c"

setenv LOAD "xlf90 -qdpc -qarch=auto"
setenv LOADLIB

g95 works on leopard now

2007-12-05T23:23:00.000-08:00

Ever since the release of Mac OS X 10.5 (leopard), g95 had been broken on Macintosh for a while, part of the reasons are some incompatibility issues of cctools. Although the MacPorts version is still broken, but I think Takeshi (the port maintainer) has already submitted the required patches so it's just a matter of time. If you want to skip MacPorts compiling and just want to install the binary built, it would be a good time to do it now.
Last night I checked the 2007-11-29 version of g95 and binary package started to work.
Get the binary from the g95 project now.

Bonus:

Recent version of g95 does having some annoying warning like this:

mjhsieh% /opt/g95-install/bin/i386-apple-darwin8.11.1-g95 hello.f90 -o f90hello.exe /var/folders/vQ/vQ6BYbLsHSGVwgPZR0sF6++++TI/-Tmp-//cc1UyeY8.s:59:indirect jmp without `*' /var/folders/vQ/vQ6BYbLsHSGVwgPZR0sF6++++TI/-Tmp-//cc1UyeY8.s:78:indirect jmp without `*' /var/folders/vQ/vQ6BYbLsHSGVwgPZR0sF6++++TI/-Tmp-//cc1UyeY8.s:97:indirect jmp without `*' /var/folders/vQ/vQ6BYbLsHSGVwgPZR0sF6++++TI/-Tmp-//cc1UyeY8.s:112:indirect jmp without `*'

You can use this script to get rid of the warning:

#!/bin/sh
myg95="/opt/g95-install/bin/i386-apple-darwin*g95"
exec 3>&1
$myg95 $* 2>&1 >&3 | grep -v "indirect jmp without " 1>&2
exec 3>&-

Save it as g95 in your path, make it executable and then you can run g95 without this kind of warnings.

[amber9] rdc test error with XL Fortran

2007-10-23T02:49:00.000-07:00

Yes, I am late reading the AMBER reflector again. This time Dr. Langsetmo brought up this issue in May 2007:

everything went well, and in the testing most things passed, till a failure at:
cd rdc; ./Run.dip
STOP 1
  ./Run.dip:  Program error
make: *** [test.sander.BASIC] Error 1
if look at rdc/gcg.dip.o i find at the end of the file:
Alignment info will be read from file: RST.dip
Here are comments from the alignment input file:
namelist reports error reading &align
i do have the environment variable:
XLFRTEOPTS=namelist=old:xrf_messages=no
so i don't understand the error. any help would be appreciated.

My PASSED rdc test on absoft Pro fortran compiled sander shows that the problem is on XL Fortran. After several small scale searches, I found that it can be avoid by getting rid of the old namelist compatible flag from the XLFRTEOPTS options. Normally the environment XLFRTEOPTS was set to "namelist=old:xrf_messages=no", I used "xrf_messages=no" for this test:

% env XLFRTEOPTS="xrf_messages=no" ./Run.dip
STOP 0
diffing gcg.dip.o.save with gcg.dip.o
PASSED
==============================================================

Old News: Discontinued XL Fortran and XL C/C++ on Macintosh

2007-10-22T14:47:00.000-07:00

The Announcement from IBM

Effective April 30, 2007, IBM is discontinuing program services for XL C/C++ Advanced Edition for Mac OS X V6.0 (5724-G12) and XL Fortran Advanced Edition for Mac OS X V8.1 (5724-G13).

[amber7] make: *** [test.sander] Error 1

2007-10-21T16:56:00.000-07:00

(I am sorry that I totally forgot this website project for quite a while, I am going to begin to review the problem from the AMBER reflector, if you found it still doesn't help, drop a note in the AMBER reflector or just comment in the guestbook for this blog.)
XLF/XLC on the Mac OS X is a little bit different, the exiting code might be different and the return value from the program might be mistaken as an error. From this 2004 post by Dr. Langsetmo in the Amber reflector:

i get the following error:
cd dmp; ./Run.dmp
  Program error
make: *** [test.sander] Error 1
however, if i go to the dmp directory and give the command "../dacdif mdout.dmp.save mdout" i get the answer:
PASSED

In my testing case, once Machines/Machine.rs6000 is taken as the MACHINE file, this problem is gone.

[test/]% env TESTsander=~/amber7/src/sander/sander Make test.sander
cd dmp; ./Run.dmp
STOP 0
diffing mdout.dmp.save with mdout
PASSED
==============================================================

not a Mach-O file

2007-10-16T00:46:00.001-07:00

From 2007 archive of the AMBER mail reflector:

Starting installation of Amber9 (serial) at Wed Oct 17 18:30:45 PDT 2007.
cd lib; make install
g95    -o new2oldparm new2oldparm.o nxtsec.o
ld: new2oldparm.o bad magic number (not a Mach-O file)
ld: nxtsec.o bad magic number (not a Mach-O file)
make[1]: *** [new2oldparm] Error 1

or in 2006

Starting installation of Amber8 (serial) at Mon Mar 27 14:42:01 EST 2006.
mkdir ../exe
mkdir: ../exe: File exists
make: [serial] Error 1 (ignored)
cd lib; make install
xlf90 -qextname=ddot:fdate:flush:lsame:dscal:dnrm2:idamax:drot:dswap:dspmv:daxpy:\
dspr2:dgemm:dcopy:dgemv:dtrmv:dtrmm:dger:lsame:dspev:dgeev:dspevd:dsyev:dppsv:\
dspsv:dlamch:dsteqr:dgeqr2:dorm2r:dlacpy:dlarnv:dlascl:dlaset:dlartg:dlanst:dlaev2:dlapy2:\
dlasr     -o new2oldparm new2oldparm.o nxtsec.o
/usr/bin/ld: new2oldparm.o bad magic number (not a Mach-O file)
/usr/bin/ld: nxtsec.o bad magic number (not a Mach-O file)
make[1]: *** [new2oldparm] Error 1
make: *** [serial] Error 2

This error is more likely due to the existing old *.o files from other computer. Please always do a

make clean

before you start to compile.

Problem PMEMD with MPI

2007-03-21T19:30:00.000-07:00

A friend of mine asked me about how come his PMEMD compiled with MPI doesnot contain suffix of .mpi that kind of thing. Actually if anyone check the Makefile of PMEMD, he/she will know that there is no such default filename suffix.

pmemd: $(NETCDF_MOD) $(OBJS)
        $(LOAD) $(LOADFLAGS) -o $@ $(OBJS) $(FFT_LIBS) \
        $(NETCDF_LIBS) $(MATH_LIBS) $(MPI_LIBS) $(LOADLIBS)

Where $@ means the name of this makefile rule, which is "pmemd".

Getting Compilers for AMBER 9

2006-12-15T16:28:00.000-08:00

AMBER config.h for g95 on intel mac

2006-10-31T01:33:00.000-08:00

Just for your information:

AMBER_SRC=~/amber9/src
AMBERBUILDFLAGS=
LOCALFLAGS=
USE_BLASLIB=$(VENDOR_SUPPLIED)
USE_LAPACKLIB=$(VENDOR_SUPPLIED)
USE_LMODLIB=$(LMOD_UNAVAILABLE)
CC= gcc
CPLUSPLUS=g++
CFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -O2 -m32
CPPFLAGS= $(AMBERBUILDFLAGS)
FPPFLAGS= -P -xassembler-with-cpp -DHASSECOND $(AMBERBUILDFLAGS)
FPP= cpp -traditional $(FPPFLAGS)
FC= g95
FFLAGS= -O0 -fno-second-underscore $(LOCALFLAGS) $(AMBERBUILDFLAGS)
FOPTFLAGS= -O3 -fno-second-underscore $(LOCALFLAGS) $(AMBERBUILDFLAGS)
FREEFORMAT_FLAG= -ffree-form
LOAD= g95  $(LOCALFLAGS) $(AMBERBUILDFLAGS)
LOADCC= gcc  $(LOCALFLAGS) $(AMBERBUILDFLAGS)
LOADLIB=-Wl,-framework -Wl,Accelerate
LM= -lm
LOADPTRAJ= g95 $(LOCALFLAGS) $(AMBERBUILDFLAGS)
XHOME= /usr/X11R6
XLIBS= -L/usr/X11R6/lib
#------------------------------------------------------------------------------
#  Other stuff:
#------------------------------------------------------------------------------
.SUFFIXES:  .f90
EMPTY=
AR=ar rv $(EMPTY)
M4=m4
RANLIB=ranlib
SFX=
NETCDF=
NETCDFLIB=
MODULEDIR=-I
MAKEDEPEND=$(AMBER_SRC)/../bin/amber_makedepend
SLKO=skipDFTB

#  default rules for Fortran and C compilation:

.f.o:   $$<
        $(FPP) $$< $> _$$<
        $(FC) -c $(FFLAGS) -o $@ _$$<

.c.o:   
        $(CC) -c $(CFLAGS) $(CPPFLAGS) -o $@ $<

Reading AMBER Trajectory in MacPyMOL

2006-07-19T03:30:00.000-07:00

Ray passed me a question from Prof. P, about the right way to load the AMBER trajectory in PyMOL. Let me use MacPyMOL as an example. Since I have not taken too much attention on MacPyMOL's GUI, I won't bother trying find the right button in the menu. However, I do know how to type the commands...

So first of all, you need to rename the topology file to *.top and the trajectory file to *.trj. In many cases of AMBER tutorials, the topology file suffix are usually prmtop and trajectory are normally crd. So rename these files to their suffixes respectively.
Then you can double click the topology file, say, linear.top on your desktop. You can also launch MacPyMOL first and then File --> Open the file. (Or, drag the *.top and drop it on MacPyMOL....) The file will be loaded as an object called "linear".
After finished the loading, type the command (presumably your trajectory file is test.trj): load_trj ~/Desktop/test.trj, linear Watch the progress bar in the upper right, it indicates the loading progress.
There you have it. You can press play button to view the trajectory.

Site CSS Refactorizing

2006-07-10T03:58:00.000-07:00

This site is undergoing CSS refactorization, please be patient should there be formating problems in the blog entries.

Line Endings and LEaP programs

2006-06-25T18:33:00.000-07:00

AFAIK, Apple has not declared a standard line ending for Mac OS X even now. But the convention of MacOS 9 is using CR (a single Carriage-Return character) while the nature of UNIX in Mac OS X is favoring LF (a single Line-Feed character) as the default line ending. Also the line ending of DOS/Windows is CRLF (a Carriage-Return + Line-Feed pair).

Both DOS and MacOS 9 line endings show ^M under UNIX but different style. Therefore if you use LEaP to import text file (e.g. PDB file) from Windows or from Mac, it's highly possible that LEaP doesn't like the format at all. The "default" text editor in Mac OS X TextEdit.app can recognize either of the 3 kind of the line ending but it probably simply us CR.

From the AMBER Mail Reflector, Professor Di Giorgio complaint about the problem loading PDB file in LEaP program, and I checked the file the professor posted on the reflector, I not only found CR endings also separated LF endings! So I recommend to use a perl script (I call it: mac2unix) to fix the problem,

#!/usr/bin/perl -pi
chomp;
s/\r/\n/g;

Use nano command to create this file, and then chmod +x this file. Later you can just do ./mac2unix Desktop/znnew.pdb to convert the line endings.

References:

Apple Computer 2006. Changing Line Endings. In Xcode 2.3 User Guide.
Di Giorgio. 2006. Difficulty loading a pdb file. In The AMBER Mail Reflector

Single thread AMBER 9 with Absoft Pro Fortran

2006-06-07T17:48:00.000-07:00

Basically AMBER 9 compiles perfectly with Absoft Pro Fortran (my evaluation copy is version 9.2), you can just launch:

% ./configure -nopar absoft
% make serial

The binaries generated from here passed most of the test under amber9 except noesy related tests and antechamber tests. These two can be problematic even in other compilers, so I'll leave it there for now. If anyone has any further problem, just post in the amber user mailing list.

Building LAM-MPI Libraries without Root Permission

2006-05-15T14:25:00.000-07:00

This example has been tested on ppc machine with XL FORTRAN compiler. Strange enough, xlc is not working at this point, AMBER 9 only needs F90 compiler support from LAM anyway. These are the commands:
% env FC=xlf_r F77=xlf_r LDFLAGS=-lSystemStubs ./configure --with-rsh="/usr/bin/ssh -x" --prefix=/Users/johndoe/opt/lam --with-memory-manager=none % make % make install

Following example has been tested on intel core duo machine with Intel FORTRAN compiler. These are the commands:
% env FC=ifort F77=ifort ./configure --with-rsh="/usr/bin/ssh -x" --prefix=/Users/johndoe/opt/lam % make % make install

Later you just need to add ~/opt/lam into your path, no root permission needed.

Compiling AMBER 9 with xlf90 but without xlc

2006-05-10T17:45:00.000-07:00

AMBER 9 can be built with solely xlf90 but without xlc. In order to do so, just do ordinary ./configure -nopar xlf90_macosx and replace "xlc" in the config.h file with "gcc". But this probably will cause following problem when compiling ptraj:
/usr/bin/ld: warning multiple definitions of symbol _second second.o definition of _second in section (__TEXT,__text) /System/Library/Frameworks/Accelerate.framework/Versions/A/Fra meworks/vecLib.framework/Versions/A/libLAPACK.dylib(single mod ule) definition of _second /usr/bin/ld: Undefined symbols: _fprintf$LDBLStub _printf$LDBLStub _fscanf$LDBLStub _sprintf$LDBLStub _sscanf$LDBLStub _vfprintf$LDBLStub make: *** [rdparm] Error 1

For this, just try to add -Wl,-lSystemStubs in the LOADLIB parameter of config.h and we are all set. (I am guessing -lSystemStubs also works, but I am a little bit lazy, please test by yourself...)

Running Parallelly

2006-05-10T17:15:00.000-07:00

In order to use MPI programs, you need to make SSH works for you:

You need to connect to the computing nodes from job schedular server without entering password. So check out this great stuff that Warner wrote at his HPC homepage.
You also need to check out if your ssh is happy with the ssh fingerprint of every computing nodes. You can check this by manually ssh connecting every node you might use later for computation.
Using mpirun
lam-mpi
1. Make sure that lamboot/lamhalt is in your path
2. Manage machine file
```
# From $LAM_HOME/lam-7.1-xlf/etc/lam-bhost.def
#farq046c cpu=1
#murasaki cpu=2
localhost
# It's somehow okay to be lazy about cpu count, but it's
# highlyrecommended to add cpu={cpucount} when having 
# multiple nodes defined
```
  FYI: the host definition can be added to the /etc/hosts file or $LAM_HOME/etc/lam-hostmap.txt file.
3. % lamboot -v machinefile
4. SYSV (shared memory)
```
% mpirun -ssi rpi sysv -np 2 {command}
```
5. Overthenetwork
  % mpirun -ssi rpi tcp -np {# of cpus to run} {command}
  For manual test:
  % cd $AMBERHOME/test/4096wat % env TESTsander=../../exe/sander.MPI DO_PARALLEL="mpirun -ssi rpi sysv -np 2" ./Run.pure_wat
  or
```
% cd $AMBERHOME/test
% env DO_PARALLEL="mpirun -ssi rpi sysv -np 2" make test.parallel
```
6. Please remember to clean your mess with lamhalt
mpich
1. Still, make sure mpirun is in your path settings on the nodes. (just in case)
2. Write a machinefile defining available resources:
```
# hostname:{# of processors you want to run for this host}
# like:
# 192.168.0.1:2
# or just use multiple hostname like:
192.168.0.1
192.168.0.1
```
  These hostnames also imply the routing to the nodes in the case of running across the network...
3. shmem (shared memory) example:
  % cd $AMBERHOME/test % env DO_PARALLEL="/opt/mpich/bin/mpirun -arch smp -machinefile /tmp/machinefile -np 2" make test.sander.BASIC.MPI
4. Overthenetwork: normally you don't need to specify the arch argument, just to make sure that machinefile is correct.
5. Pass some options to mpirun for optimal socket efficiency, like adding 'env P4_SOCKBUFSIZE=524288' in front of the mpirun argument like this:
  % cd $AMBERHOME/test % env P4_SOCKBUFSIZE=524288 DO_PARALLEL="/opt/mpich/bin/mpirun -machinefile /tmp/machinefile -np 2" make test.sander.BASIC.MPI
6. use /opt/mpich/sbin/cleanipcs if your mpich program crashes in the middle.

While there may be a possibility using xgrid but since I am not familiar with the xgrid, I am not going to talk about it.

Building MPICH Libraries without Root Permission

2006-05-10T17:02:00.000-07:00

On PowerPC (G4/G5)

This article is based on Warner's documentation.

I am using mpich-1.2.7p1 from the mpich homepage. Here, C++ interface is disabled for now, I have no idea why xlc failed to be used as c++ compiler by the configure script.
% env FC=xlf_r CC=xlc_r F90=xlf90_r RSHCOMMAND=ssh SOCKSIZE=65536 ./configure --disable-cxx --without-romio --without-mpe --with-device=ch_p4 --with-device=ch_shmem --enable-sharedlib --prefix=/Users/johndoe/opt/mpich % make % make install % find /Users/johndoe/opt/mpich -name '*.a' -exec ranlib -c {} \;
(This is for just in case that linking problem shows up later in amber compilation. It might generate "no symbols" message, don't worry about it.)

Later I'll finish the part for Intel CPU based Macintosh.

env SOCKSIZE=65536 RSHCOMMAND=ssh CC=icc CXX=icpc FC=ifort F90=ifort ./configure --with-device=ch_p4 --with-device=ch_shmem --prefix=/home/software/mpich

Guestbook

2006-05-09T04:05:00.000-07:00

This entry is now dedicated to a guestbook function.

/usr/bin/ld: -L: directory name missing

2006-05-08T01:50:00.000-07:00

When compiling xleap under certain version of developer tools, you might encounter such error message:

gcc -o xaLeap basics.o sysdepend.o stringExtra.o varArray.o getline.o avl.o pdb_format.o pdb_read.o pdb_sprntf.o pdb_sscanf.o pdb_write.o vector.o zMatrix.o sort.o bag.o hash.o dictionary.o database.o nVector.o ring.o matrix.o fortran.o displayer.o assoc.o atom.o byteArray.o collection.o container.o internal.o list.o loop.o molecule.o oDouble.o oInteger.o oString.o objekt.o parmSet.o residue.o unit.o unitio.o tripos.o graphUtil.o select.o amber.o build.o elements.o library.o chirality.o minimizer.o model.o parmLib.o pdbFile.o tools.o variables.o parser.o help.o helptext.o octree.o commands.o mathop.o block.o restraint.o hybrid.o xTank.o xAction.o x3d.o xBasics.o xaLeapc.o xaUnitEditor.o xaTable.o xaAtomTable.o  XrawRegistr.o xaCommand.o xaTools.o xaAtomParmTable.o xaBondParmTable.o  xaAngleParmTable.o xaParmEditor.o xaTorsionParmTable.o xaImproperParmTable.o  xaHBondParmTable.o ../ Xraw/libXaw.a ../Wc/libWcLeap.a ../Xpm/libXpm.a ../Xmu/libXmu.a -L /usr/X11R6/lib -lXt -lXext -lSM -lICE -lX11 -lm -lpthread



/usr/bin/ld: -L: directory name missing

This is due to somehow more strict behavior in certain versions of ld (the ld on my iMac Core Duo and an user reported that an iMac G5 also has that.). ~~The manual solution is to modify your config.h file before issuing make command: to eliminate the space character between -L and /usr/X11R6/lib. This should solve the problem.~~ A better way to do it is to apply the bugfix.3 patch at AMBER 9 bugfixes page.

% cd amber9/src
% curl http://amber.scripps.edu/bugfixes/9.0/bugfix.3 -o /tmp/bugfix.3
% patch -p0 -N -r patch_rejects < /tmp/bugfix.3

Building AMBER 9 Parallel Ports with Pre-built MPI Libraries with XLF90

2006-05-07T07:20:00.000-07:00

For years my impression was that prebuilt binaries for something like MPI library only bring me troubles, therefore I normally recommend compiling MPI library by ourselves. Take this prebuilt mpich package from hpc.sourceforge.net for example:

This doesn't work with AMBER 9. Several reasons that this is not working with env MPI_HOME=/usr/local/mpich ./configure -mpich xlf90_macosx are:

the library function names have double-underscore tail xlf90 can not produce more than one underscore.
/usr/local/mpich/bin/mpif90 -show is not working, the configure script is not happy. (i.e. This mpich has to be configured with f90 option.)

When it goes to LAM-MPI, you might think that the official build from lam-mpi homepage should be working:

Unfortunately this doesn't work with AMBER 9, either. The reason is similar, no FORTRAN options were compiled into the package. (see the output of /usr/local/bin/mpif77 -showme)

Then I stumbled across another build from York University:

This seems to be working. These steps are required:

mkdir -p /Applications/Darwin; tar zxvf lam-7.1-xlf.tar.gz -C /Application/Darwin/ (Not everyone can write to /Applications/, so it's not very ideal for ordinary endusers of a Macintosh cluster.)
If you got this error when doing make parallel:
/usr/bin/ld: table of contents for archive: /Applications/Darwin/lam-7.1-xlf/lib/liblammpio.a is out of date; rerun ranlib(1) (can't load from it) /usr/bin/ld: table of contents for archive: /Applications/Darwin/lam-7.1-xlf/lib/liblamf77mpi.a is out of date; rerun ranlib(1) (can't load from it) /usr/bin/ld: table of contents for archive: /Applications/Darwin/lam-7.1-xlf/lib/libmpi.a is out of date; rerun ranlib(1) (can't load from it) /usr/bin/ld: table of contents for archive: /Applications/Darwin/lam-7.1-xlf/lib/liblam.a is out of date; rerun ranlib(1) (can't load from it) make[1]: *** [sander.MPI] Error 1 make: *** [parallel] Error 2
Don't panic, just do "ranlib /Applications/Darwin/lam-7.1-xlf/lib/*.a".
Please remember to put /Applications/Darwin/lam-7.1-xlf/bin in the path or lamboot won't start.

Some friends might find that the AMBER 9 compilation fails and gives some errors like this:
xlf90_r -qfree=f90 -o sander.MPI [skipped a lot of *.o obj] ../lmod/lmod.a ../lapack/lapack.a ../blas/blas.a ../lib/nxtsec.o ../lib/sys.a -L/usr/local/mpich/lib -lpmpich -lmpich -lpmpich -lmpich -Wl,-framework -Wl,Accelerate /usr/bin/ld: Undefined symbols: _mpi_bcast _mpi_irecv ********** ***OMIT*** ********** _mpi_waitany _mpi_waitall _mpi_type_free make[1]: *** [sander.MPI] Error 1 make: *** [parallel] Error 2
Here we need to check first of all if the library we are linking (red colored in the error log above.) exists. But in case you don't even have those red colored argument, your pre-built MPI library is not working. If the library files indeed exist, use "nm" command to check the names of the functions. For example:

nm /usr/local/mpich/lib/libmpich.a | grep mpi_type_free

If the result is 00000000 T _mpi_type_free_, then you can add some argument to tell xlf90 you need to add a trailing underscore to the function name you want to.

make -e AMBERBUILDFLAGS="-qextname=mpi_bcast:mpi_irecv:...skipped..."

but for 00000000 T _mpi_type_free__ (two trailing underscores), please just give up and build your own library instead.

Solving nmr_aux problem with IBM XL C compiler

2006-05-03T17:47:00.000-07:00

According to the AMBER reflector, there were several people reporting^{[1], [2]} compilation problem in nmr_aux directory.

/usr/bin/ld: can't open: NULL (No such file or directory, errno = 2)

Although for some reason it doesn't seem to be affecting me, but the solution can be found at ABSoft's technical archives^[3]. Basically it's like changing /etc/opt/ibmcmp/vac/6.0 from the line crtbegin = NULL to #crtbegin = NULL

Then try to compile it again. If you don't have the permission to change the file, you can copy the vac.cfg file to your own directory and modify that file. (say, your home directory) Then change the xlc argument to

xlc -F/Users/youraccountname/vac.cfg

in amber9/src/config.h file....

Benchmark

2006-04-10T03:21:00.000-07:00

The benchmark data goes here. (mjhsieh also gave his ifort testimonial to Intel, it probably will show up somewhere in their advertisements...)

Factor IX Benchmarks

iMac Core Duo 2.0GHz 512M RAM (Mac OS X 10.4.5) w/GNU Fortran 4.0.2/LAM 7.1.1 on share memory

	PMEMD 9.0		Sander 9.0
cpus	Ps/day	Speedup	Ps/day	Speedup
1	n/a	n/a	47.04	1.00
2	n/a	n/a	83.66	1.78

iMac Core Duo 2.0GHz 512M RAM (Mac OS X 10.4.5) w/Intel Fortran 9.1b/Intel MKL 8.1b/LAM 7.1.1 on share memory

	PMEMD 9.0		Sander 9.0
cpus	Ps/day	Speedup	Ps/day	Speedup
1	110.58	1.00	66.71	1.00
2	186.21	1.68	111.48	1.67

Jac Benchmarks

JAC benchmark with nstlim=10000 on sander of AMBER9 in current CVS repository. All binaries were compiled with ifort with/without math kernel. HTT means hyper-threading enabled (4 HTT cpus are actually 2 physical cpus).

4×2 Xeon 3G HTT | Total time 1993.87 (noMKL/MPICH/GbE)
4×  Xeon 3G HTT | Total time 3016.86 (w_MKL/MPICH/p4shmem)
2×  Core Duo 2G | Total time 3203.11 (w_MKL/LAM/SYSV)
2× Pentium D 3G | Total time 3389.14 (w_MKL/LAM/SYSV)
2× Pentium D 3G | Total time 3423.32 (w_MKL/MPICH/p4shmem)
1×  Core Duo 2G | Total time 5633.56 (w_MKL/noMPI)
1× Pentium D 3G | Total time 6367.24 (w_MKL/noMPI)

Compiling AMBER 9 on Intel based macintosh with Intel fortran

2006-04-10T02:10:00.000-07:00

Normally you just use following commands to compile AMBER 9 on intel based macintosh:

% ./configure -nopar ifort_macosx
% perl -pi -e 's/-L \/usr\/X11R6\/lib/-L\/usr\/X11R6\/lib/' config.h
% make serial

The reason getting rid of the space before /usr/X11R6/lib is that Mac OS X on intel based macintosh does not like space between the path and "-L"..... Don't blame me for forgetting this minor issue. It's more like to be fixed in next patch. :-) If you like to use intel math kernel library, use these:

% env MKL_HOME=$MKL ./configure -nopar ifort_macosx
% perl -pi -e 's/-L \/usr\/X11R6\/lib/-L\/usr\/X11R6\/lib/' config.h
% make serial

For compiling with parallel library, here is an example:

% env MPI_HOME=/opt/lam MKL_HOME=$MKL ./configure -lam ifort_macosx
% perl -pi -e 's/-L \/usr\/X11R6\/lib/-L\/usr\/X11R6\/lib/' config.h
% make serial

(My lam/mpi was installed at /opt/lam, change it to your own lam path.) For more information about the parallel library, try to figure it out from other macintosh resource, I can't promise writing one since it's a little bit tedious...

Compiling AMBER 9 on g4/g5 with XL compiler

2006-04-10T00:31:00.000-07:00

Basically AMBER9 provides you an out of box compatibility on PPC Macintosh if you use IBM XL compilers. What you need to do is:

% ./configure -nopar xlf90_macosx
% make serial

With this modification, the test (make test.serial) passes without failure. However, even if you don't apply this patch, you can still get an almost working config.h ...

One noticeable change of this patch is that the underscore extension name for blas/lapack function calls are no long required probably because the current library provided by Apple (10.4.5) already took care of that.

If you don't have XL C compiler, you might have trouble compiling it. This issue is fixable, but if you are having trouble modifying config.h by yourself, please drop your question in the AMBER mail reflector.

For parallel computing, I recommend LAM-MPI for now. See Warner's tutorial when compiling LAM. As to the linking issue, I'll address this more later.

Also some might experience the problem of not finding a NULL file with XL C. Please read the later post here.

AMBER 8 PMEMD Benchmarks on Xserve G5 Cluster

2005-07-20T17:30:00.000-07:00

(2005-07-01 11:41:03 Update: The original benchmark did not use any code modifications for G5. New benchmark is faster.)(Update: files posted)
The contributions have been made by Apple Computer are really nice! Thank you guys!

Recently I got some chances to access Xserve G5 clusters in UC Irvine and in Apple Computer. The Research Computing group in Apple Computer is kind enough to share their progress on optimizing PMEMD with me. The modification seems to be very nice also maintaining good double precision accuracy. Here is a tarball of the files got modified during this test: pmemd_modification.tgz. Of course, md5 and filelist are here

MD5 (pmemd_modification.tgz) = 4600a2f66e40995bb087e6eb21b8a360
pmemd/configure
pmemd/src/ew_direct_cit.f90
pmemd/src/short_ene_G5_opt.f90
pmemd/config_data/macosx_g4.xlf90.nopar
pmemd/config_data/macosx_g5.xlf90.lam
pmemd/config_data/macosx_g5.xlf90.mpich_gm
pmemd/config_data/macosx_g5.xlf90.nopar

Also, the usages of this modified configure script for the g5 can be found here:

./configure macosx_g4 xlf90 nopar
./configure macosx_g5 xlf90 nopar
./configure macosx_g5 xlf90 lam
./configure macosx_g5 xlf90 mpich_gm

*Important* Please make sure to backup the old source files before untar this tarball.

As to the AltiVec patch I proposed last year, I don't think it really matters because of the precision issue --- AltiVec is a floating point monster, but it's not even a double precision animal.

This benchmark is following the way we do in AMBER 8 benchmark page. In default JAC benchmark, the simulation undergoes 1 pico second time scale. So the performance measure ppd (ps per day) would be the ratio of 86400 over the time consumed by the simulation.

This plot clearly shows that the code optimization for G5 does improve the performance. It also tells us that mpich-gm scales pretty well.

In this table, NACS_UCI is the demo Xserve Dual G5 cluster hosted by Research Computing Support, NACS, UC Irvine while RC_AAPL is the demo Xserve Dual G5 cluster kindly provided by the Research Computing group in Apple Computer.

  =============================================================================
  "jac" == Joint Amber/Charrm DHFR benchmark.  This is the protein DHFR,
  solvated with TIP3 water, in a periodic box.  There are 23,558 total atoms,
  and PME used with a direct space cutoff of 9 Ang.  This is the benchmark
  in benchmarks/jac subdirectory of the Amber 8 distribution.  Results
  here are for pmemd.

  --------------------------------------------------------------------------------
  name   date      CPU              OS         compiler  npcu    ps per day
  --------------------------------------------------------------------------------
NACS_UCI  6/05 2.0 Ghz G5        MacOS X 10.3   xlf8.1    2        336
               GbE, LAM/MPI
 RC_AAPL  7/05 2.0 Ghz G5        MacOS X 10.3   xlf8.1    1        180
               GbE, LAM/MPI                               2        324
                                                          4        561
                                                          6        758
                                                          8       1005
                                                         10       1168
                                                         12       1290
                                                         14       1440
                                                         16       1516
 RC_AAPL  7/05 2.0 Ghz G5        MacOS X 10.3   xlf8.1    1        180
               myrinet, MPICH-GM                          2        325
                                                          4        596
                                                          6        873
                                                          8       1094
                                                         10       1371
                                                         12       1600
                                                         14       1878
                                                         16       2057

% process_mdout: Permission denied

2004-10-14T15:10:00.000-07:00

Problem Description: user copied process_mdout.perl from a workstation to a local macintosh with Mac OS X, user encountered:

% process_mdout.perl model1min2.out
% process_mdout: Permission denied.

This can be solved either by % chmod +x process_mdout.perl and then run the command like % ./process_mdout.perl model1min2.out or just do % perl process_mdout.perl model1min2.out

Early AMBER8 PMEMD bench with AltiVec wrapper.

2004-05-22T00:00:00.000-07:00

(originally posted on 05/19 18:32)
(updated 05/22) Added single precision modification version with vecLib support!
(updated 05/20) Finally I realized that I didn't successfully link to vecLib for PMEMD. We will see if we can do it later.

  =============================================================================
  "jac" == Joint Amber/Charrm DHFR benchmark.  This is the protein DHFR,
  solvated with TIP3 water, in a periodic box.  There are 23,558 total atoms,
  and PME used with a direct space cutoff of 9 Ang.  This is the benchmark
  in benchmarks/jac subdirectory of the Amber 8 distribution.  Results
  here are for pmemd.

  --------------------------------------------------------------------------------
  name   date      CPU              OS         compiler  npcu    ps per day
  --------------------------------------------------------------------------------
bluefish 12/03 SGI Origin 3800                  f90      2        115
  loyd    4/04 2.4 Ghz PIV Xeon   RH 9          ifc8     2        210
  apple   5/04   2 Ghz G5        MacOS X 10.3   xlf8.1   2        293 (double)
  apple   5/21   2 Ghz G5        MacOS X 10.3   xlf8.1   2        324 (single)
 unc/duke 4/04 3.2 GHz PIV Xeon  RH E3smp       ifc7     2        330
  apple   5/21   2 Ghz G5        MacOS X 10.3   xlf8.1   2        344 (single)*
  yt      2/04 altix/itanium 1.3GHz linux       ifort8   2        465

single precision means partial of the variables in short_ene are real*4.
G5 results were pmemd results.
*: altivec was used.
2 cpu results were done with LAM/MPI library.

AMBER 8 PMEMD Benchmark Done During RECOMB04 Meeting

2004-03-31T09:04:00.000-08:00

If you are looking for current AMBER 8 PMEMD benchmark, please visit here

I always want to do some AMBER 8 benchmark on Apple's G5 machines, but apparently there is no G5 nearby, *sigh*.

Recently I got a chance to access powermac G5 (sponsored by Apple) in the RECOMB04. I wasn't able to run sander on those G5 email console because my old binaries still need IBM's dynamic libraries. Later I finally found the way to build static binary (Yes, I already tried "-Wl,-static".) with xlf 8.1beta on my powerbook. Here is how:

1. mkdir /opt/ibmcmp/lib_save/
2. mv /opt/ibmcmp/lib/*.dylib /opt/ibmcmp/lib_save/
3. echo "int mjhsiehkickme(){}" > test.c
4. xlc -c test.c -o test.o
5. ar rvs test.a test.o; ranlib test.a
6. mv test.a /opt/ibmcmp/lib/libxlomp_ser.a
7. Then you now can make a static binary with xlf.

By the way, remember to add this to your shell's environment variables:
setenv XLFRTEOPTS "namelist=old:xrf_messages=no"

I only tested it on jac and gb_mb because there were too many people eager to use these consoles and I still haven't gotten a chance to use it again.

=============================================================================
  "jac" == Joint Amber/Charrm DHFR benchmark.  This is the protein DHFR,
  solvated with TIP3 water, in a periodic box.  There are 23,558 total atoms,
  and PME used with a direct space cutoff of 9 Ang.  This is the benchmark
  in benchmarks/jac subdirectory of the Amber 8 distribution.
-------------------------------------------------------------------------------
  name   date      CPU              OS         compiler  npcu    ps per day
-------------------------------------------------------------------------------
RECOMB04  3/31   1.8 Ghz G5   MacOS X 10.3   IBM XLF 8.1b  1       138 (sander)
 mjhsieh  3/18   400 Mhz G4   MacOS X 10.3   IBM XLF 8.1b  1        25 (sander)
 mjhsieh  3/18   400 Mhz G4   MacOS X 10.3   IBM XLF 8.1b  1        26 (pmemd)

============================================================================
  "gb_mb" == Generalized Born myoglobin simulation.  This protein has 2492
  atoms, and is run with a 20 Ang. cutoff and a salt concentration of 0.2 M,
  with nrespa=4 (long range forces computed every 4 steps.)  This is the
  test case in the benchmarks/gb_mb subdirectory of the Amber 8 distribution.
-------------------------------------------------------------------------------
  node-name        CPU                 OS         compiler  npcu  ps-per-day
-------------------------------------------------------------------------------
RECOMB04  3/31   1.8 Ghz G5   MacOS X 10.3   IBM XLF 8.1b  1       184
 mjhsieh  3/18   400 Mhz G4   MacOS X 10.3   IBM XLF 8.1b  1        23

============================================================================
  "fix": This is a factor_ix benchmark, from Bob Duke, also a protein
  solvated with TIP3 water, in a periodic box.  There are 90,906 total atoms,
  and PME used with a direct space cutoff of 8 Ang.  This test is in
  amber8/benchmarks/factor_ix.  This uses dt=0.0015, so the conversion is
  ps-per-day = 129.6/(time-per-step)
-------------------------------------------------------------------------------
  name   date      CPU              OS         compiler  npcu   ps-per-day
-------------------------------------------------------------------------------
 mjhsieh  3/18   400 Mhz G4   MacOS X 10.3   IBM XLF 8.1b  1        10

============================================================================
   "hb": This is a hemoglobin benchmark, also a protein solvated with TIP3
   water, in a periodic box.  There are 44,247 total atoms, and PME used
   with a direct space cutoff of 8 Ang.  This 500-step test is in
   amber8/benchmarks/hb; it uses a truncted octahedral box, and nrespa=2.
-------------------------------------------------------------------------------
  name   date      CPU              OS         compiler  npcu    ps-per-day
-------------------------------------------------------------------------------
 mjhsieh  3/18   400 Mhz G4   MacOS X 10.3   IBM XLF 8.1   1        16

Porting resp to MacOS X with plep Source

2004-02-19T11:03:00.000-08:00

Last night I got an email from York University asking how to compile resp of AMBER software on their G5. Min, the person who sent the email, was using the MACHINE file I posted on my weblog. Min couldn't use my MACHINE file for compiling resp.

After a hour or so, I figured out some problems and their solutions.

Min's error log suggests that neither MACHINE file nor Compile script is working:

$ make
cd ../lib ; ./Makelist ../lib/mexit.o ../lib/amopen.o ../lib/lapack.o
make[1]: `mexit.o' is up to date.
make[1]: `amopen.o' is up to date.
./Compile L2 -P -DDPREC -o lapack.o lapack.f
csh: L2: Undefined variable.
make[1]: *** [lapack.o] Error 1
make: *** [libobj] Error 1

Unfortunately, I never used resp command nor ever tried to compile it before. Therefore I need to start from beginning in order to find out what happened. The clue is that Min was using the resp source in plep package of AMBER, which is kinda free in the InterNet. After a short google search, I found it's in the file repository of AMBER.

The hierarchy of this distribution of plep is from AMBER 5 but it only includes crucial files. The immediate trouble inside src/ is the directory Machine/, the script "Compile" requires a symbolic linked file call "MACHINE". If you are familiar with HFS+ that MacOS X uses, you probably already know the filesystem is not case-sensitive. Because "MACHINE" is equal to "Machine", we need to rename "Machine/" to "Machines/". Of course, you need to check the "Compile" script and the "MACHINE" files later we'll mention to see if you need to rename the fixed variable.

Then I copy the "Machines/Machine.bsd" file to my customized file, say, "Machines/Machine.macosx" and modify the "Machine.macosx" file. One of the things you need to check is that the C preprocessor is located at "/usr/bin/cpp", not "/lib/cpp" as the old setting suggested. After then, you might need to change f77 to g77 because the c-shell script "Compile" seems to be not recognizing the f77 aliases you might have for your tcsh. Oh, don't forget running this "ln -s Machines/Macine.macosx ./MACHINE".

Another thing that maybe very important is that G5 is a big-endian machine, the related issues is addressed in the "mksrc" file, although we don't need it to compile resp. So you can enter the "resp" directory, and run "make bigsource" command. In this case, the command only generates a file called "resp_all.for" without actually compiling it. You might want to modify the "Makefile" file adding some rules. But right now, you can just use "g77 -O2 resp_all.for -o resp" to create the resp program.

If any of my reader of this blog entry has questions about compiler "g77" or "XLF/XLC", don't ask me, do ask the technical support of Apple or IBM.

Supplemental Materials:
1. diff file between Machine.bsd and Machine.macosx
2. My result:

[mjhsieh:plep/src/resp] mjhsieh% make bigsource
SYSDIR=`../sysdir dir` ; cd $SYSDIR ; make sys.f
make[1]: `sys.f' is up to date.
SYSSRC=`../sysdir src` ; ../Compile CPPONLY -o resp_all.f
                 resp.f ../lib/mexit.f ../lib/amopen.f ../lib/lapack.f $SYSSRC ;
                 ../Compile L1 -P resp_all.f ;
                ../Compile LOAD -o resp resp_all.o
Making source: machine is Generic BSD Unix
cat resp.f | /usr/bin/cpp -P -I/mjhsieh/plep/src/lib
     -DBSD -DISTAR2 -DREGNML -DEWALD   >>  resp_all.f
cat ../lib/mexit.f | /usr/bin/cpp -P -I/mjhsieh/plep/src/lib
     -DBSD -DISTAR2 -DREGNML -DEWALD   >>  resp_all.f
cat ../lib/amopen.f | /usr/bin/cpp -P -I/mjhsieh/plep/src/lib
     -DBSD -DISTAR2 -DREGNML -DEWALD   >>  resp_all.f
cat ../lib/lapack.f | /usr/bin/cpp -P -I/mjhsieh/plep/src/lib
     -DBSD -DISTAR2 -DREGNML -DEWALD   >>  resp_all.f
cat /mjhsieh/plep/src/Machines/bsd/sys.f | /usr/bin/cpp -P -I/mjhsieh/plep/src/lib
     -DBSD -DISTAR2 -DREGNML -DEWALD   >>  resp_all.f
Made source for machine: Generic BSD Unix
cat resp_all.f | /usr/bin/cpp -I/mjhsieh/plep/src/lib -P
     -DBSD -DISTAR2 -DREGNML -DEWALD   > _resp_all_.f
g77 -c _resp_all_.f
g77 -o resp resp_all.o
[mjhsieh:plep/src/resp] mjhsieh% ls 
0README     files.h     resp*       resp_all.f
Makefile    readit.f    resp.f      resp_all.o

DHFR benchmark of Amber 7 on Macintosh

2003-09-11T21:09:00.000-07:00

According the method came with the amber package, I did two benchmarks, this time it would be more serious than previous one and also comparable to Amber 7 Benckmarks page.

The measurement should be more accurate because the time step is longer. Please check the table below.

Special thank to professor Eric Mockensturm at Penn State University for his help on G5 machine.

=============================================================================
"jac" == Joint Amber/Charrm DHFR benchmark.  This is the protein DHFR,
solvated with TIP3 water, in a periodic box.  There are 23,558 total atoms,
and PME used with a direct space cutoff of 9 Ang.  This is the benchmark
in benchmarks/jac subdirectory of the Amber 7 distribution.

--------------------------------------------------------------------------------
node-name        CPU                 OS         compiler  npcu   time-per-step
--------------------------------------------------------------------------------
mjhsieh      400 MHZ G4            MacOS X      g77 3.4    1       5.644
Prof. E. M.    2 GHZ G5 (dual)     MacOS X      g77 3.4    1       1.275
Prof. E. M.    2 GHZ G5 (dual)     MacOS X      XLF 8.1b   1       0.777

=============================================================================
"gb_mb" == Generalized Born myoglobin simulation.  This protein has 2492
atoms, and is run with a 20 Ang. cutoff and a salt concentration of 0.2 M,
with nrespa=4 (long range forces computed every 4 steps.)  This is the
test case in the benchmarks/gb_mb subdirectory of the Amber 7 distribution.

--------------------------------------------------------------------------------
node-name        CPU                 OS         compiler  npcu   time-per-step
--------------------------------------------------------------------------------
mjhsieh      400 MHZ G4            MacOS X      g77 3.4    1       4.857
Prof. E. M.    2 GHZ G5 (dual)     MacOS X      g77 3.4    1       0.697
Prof. E. M.    2 GHZ G5 (dual)     MacOS X      XLF 8.1b   1       0.543

AMBER7: XLF performance on powerbook G4, PowerMac G5 and Pentium4

2003-09-10T00:45:00.000-07:00

I did a performance comparison of AMBER 7 main program sander compiled with GNU fortran compiler (g77 3.1) and IBM XLF v8.1beta on my powerbook G4-400 and from other machines including new G5. WARNING: the time measured may not be accuray and should be just for your information. (I don't have time to use longer time steps.)

Speed comparisons (the more the better)

g77 (G4-400) : xlf (G4-400) = 1 : 1.337
g77 (G4-400) : ifc (P4-1.7G) = 1 : 3.213
g77 (G4-400) : ifc (Opteron-1.4G) = 1 : 4.473
g77 (G4-400) : ifc (Xeon-2G) = 1 : 4.562
g77 (G4-400) : g77 (G5-2G) = 1 : 4.808
g77 (G4-400) : ifc (P4-2.4G) = 1 : 5.810
g77 (G4-400) : xlf (G5-2G) = 1 : 7.118

The binaries on G4-400 are not optimized for vecLib framework on BLAS and LAPACK, but it seems that sander uses very few BLAS and LAPACK functions. It doesn't make any difference in running time on G4 and G5 after replacing BLAS/LAPACK with vecLib. Advanced analysis of the code would be necessary if we want to improve it.

Hopefully Apple can have time to help us to optimize the sander code.

Technical Details

g77: MACHINE file (no altivec)
XLF: MACHINE file for g4 and MACHINE file for g5. We also need to setenv XLFRTEOPTS NAMELIST=OLD in order to run sander.
And, of course, the MACHINE file of Intel compiler optimized for Petium4/Opteron.

Molecular dynamics Input file: benchmd.in

g77_g4_0.4.out:       352.98 (G4-400)
xlf_g4_0.4.out:       245.16 (G4-400)
ifc_p4_1.7.out:       102.03 (P4-1.7G)
ifc_p4_2.4.out:       60.75 (P4-2.4G)
g77_g5.out:           73.42 (G5-2Gx2 on single cpu)
xlf_g5_2.out:         54.79 (G5-2Gx2 on single cpu)
xlf_g5_2_unroll.out:  49.59 (G5-2Gx2 on single cpu)
ifc_opteron_1.4.out:  78.91 (Opteron-1.4Gx2 on single cpu)
ifc_xeon_2.out:       77.37 (Xeon-2Gx2 on single cpu)

Speed is refered to be inverse of time in seconds.
Special thank to professor Eric Mockensturm at Penn State University for his help on G5 machine.

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Speed comparisons (the more the better)

Technical Details