Amber 14 on Fujitsu Computers

Future of Amber

Future of Amber


Installation of Amber 14 on the Fujitsu Linux clusters

Decompress and untar distribution:

tar xvfj AmberTools14.tar.bz2

tar xvfj Amber14.tar.bz2

if tar does not support option “j” on a particular platform use:

bzip2 -d Amber14.tar.bz2

tar xvf Amber14.tar

bzip2 -d AmberTools14.tar.bz2

tar xvf AmberTools14.tar

Both distributions will unpack into the same directory tree, with amber14 at its root.

Set up the AMBERHOME environment variable to point to where the Amber tree resides on a machine. For example, using csh, tcsh, etc:

setenv AMBERHOME /path-to/amber14

or using sh/bash:

export AMBERHOME=/path-to/amber14

You should also add $AMBERHOME/bin to your PATH

Building serial version

To build Amber using Intel compilers:

setenv MKL_HOME $MKLROOT  # or export MKL_HOME=$MKLROOT

./configure intel

or for GNU compilers

./configure gnu

Then,

make install

will compile the codes. If this step fails, try to read the error messages carefully to identify

the problem. This can be followed by

for csh/tcsh

setenv LD_LIBRARY_PATH       $LD_LIBRARY_PATH:$AMBERHOME/lib

or for sh, bash, etc.

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$AMBERHOME/lib

and then finally

make test

which will run tests and will report successes or failures.

Where "possible FAILURE" messages are found, go to the indicated directory under $AMBERHOME/AmberTools/test or $AMBERHOME/test, and look at the "*.dif" files.

Differences should involve round-off in the final digit printed, or occasional messages that differ from machine to machine.

As with compilation, if you have trouble with individual tests, you may wish to comment out certain lines in the Makefiles (i.e., $AMBERHOME/AmberTools/test/Makefile or $AMBERHOME/test/Makefile), and/or

go directly to the test subdirectories to examine the inputs and outputs in detail.

For convenience, all of the failure messages and differences are collected in the $AMBERHOME/logs directory; you can quickly see from these if there is anything more than round-off errors.

Building parallel version of Amber

To compile parallel (MPI) versions of Amber:

cd $AMBERHOME

./configure -mpi intel

make install

To test installation:

setenv DO_PARALLEL ”mpirun -np 2”

make test

This assumes that you have installed MPI and that mpicc and mpif90 are in your PATH

Where "possible FAILURE" messages are found, go to the indicated directory under $AMBERHOME/AmberTools/test or $AMBERHOME/test, and look at the "*.dif" files.

Troubleshooting

Emap test of pmemd failure

It was reported the emap test failure of pmemd using the Intel Fortran compiler, version 14.0.0.080. The failure was reproduced make test using other 14.xx.xx versions. It was found out that a problem is in linking with options "-ipo -O3", i.e. if all source code is compiled with "-ipo -O3" but linked with "-ipo -O2" then a program will pass the tests.

So, a simple solution is either in linking with options "-ipo -O2" or in compiling & linking with options "-ip -O3".

The underlying reason of that is probably in some bug(s) in Intel 14.xx (and maybe 13.xx) compilers...