Frequently Asked Questions

Installation and Compilation

Tcl/FFTW not found

Question

configure complains that it can't find Tcl or FFTW!

Answer 1

Did you already install Tcl/Tk and FFTW3? If not, do so! Most Linux distributions provide packages for both.

Note that in many cases it is not enough to install the packages tcl and fftw that contain the libraries itself, but you will also need the development packages (e.g. tcl-dev and libfftw3-dev), that contain the header include files. Also, you need FFTW3. FFTW version 2 is not supported anymore. Unfortunately, FFTW2 still seems to be the standard FFTW package in Ubuntu.

Answer 2 (when it was installed in a non-standard location)

If you have installed the packages, but you couldn't install them into one of the default system paths (/usr or /usr/local), you'll have to pass the information where to find the packages to the configure script. To do that, you can pass additional include and library paths to the configure script via the variables CPPFLAGS and LDFLAGS, like

 configure CPPFLAGS="-I/path/to/tcl/include" LDFLAGS="-L/path/to/tcl/lib"

These and other variables are documented via

 configure --help

Answer 3 (when Tcl was built from source)

Out of whatever reason, the most recent Tcl versions do not by default build the static Tcl libraries anymore, which are required by ESPResSo. To get it to build the static libraries, you will have to pass the option --disable-shared to the configure script of the Tcl library only. Then, it will build the static library. Unfortunately, it will not build the dynamic library anymore. If you need both, you will have to configure, build and install Tcl twice.

Answer 4 (only on 64bit machines)

If you are using Linux on a 64bit machine (e.g. an AMD 64), ESPResSo will try to build a 64bit binary to obtain maximal efficiency. Unfortunately, it is still not uncommon that 64bit machines have a 32bit Linux and corresponding 32bit libraries (Tcl, FFTW).

You can check whether you have a 64bit machine by executing one of the commands

 cat /proc/cpuinfo
 uname -a
 gcc -dumpmachine

If you have a 64bit machine, you should check whether the Tcl library libtcl*.a and the FFTW library libfftw*.a are 64bit binaries via the file command:

 file libtcl.a

If they are not, you have a number of possibilities:

1. In fact, the best solution is to install a 64bit Linux on the machine. By using a 32bit Linux on a 64bit machine, you basically waste half of the machines capabilities!
2. Install 64bit versions of the libraries. Many Linux distributions allow to have at least 64bit versions of libraries in parallel to the 32bit versions and provide corresponding packages. If not, you will have to build the libraries yourself. To learn how to build 64bit libraries, refer to the corresponding documentation of the libraries.

How do I compile ESPResSo on a BlueGene/P System ?

Recently we got ESPResSo to compile and run on the BlueGene/P at the RZG of the Max Planck Society. We have not yet run any benchmarks on this system, so we can tell nothing about performance or scaling behaviour yet. Following is a description of what we had to do, to get ESPResSo to compile and run on the BlueGene/P:

1. Login to the front node "genius"

2. Set your CC environment variable CC to mpicc:

setenv CC mpicc

(where "which mpicc" should point to something similar to bgsys/drivers/ppcfloor/comm/bin/mpicc)

3. Get a tcl/tk source package, e.g. from sourceforge.net - we used tcl8.4.14-src.tar.gz, newer versions are likely to work too. After unpacking do the following:

cd tcl8.4.14/unix
./configure --prefix=$HOME/software --disable-shared --disable-threads --disable-load
make
make install

4. Enter the ESPResSo directory:

cd $SOMEPATH/espresso-2.1.2j
./configure CFLAGS="-I $HOME/software/include" LDFLAGS="-L $HOME/software/lib" LIBS="-lm -lc"
make

5. A job submit script could look like this:

#!/bin/ksh
# @ job_name = testjob
# @ error = $(job_name).$(jobid).out
# @ output = $(job_name).$(jobid).out
# @ environment = COPY_ALL
# @ wall_clock_limit = 00:30:00
# @ notification = error
# @ notify_user = your@email.address
# @ job_type = bluegene
# @ bg_size = 128
# @ queue = tiny_30m
#
#
P=/path/BlueGene/src/espresso-2.1.2j \
      mpirun -exe $P/obj-unknown-pc-linux/Espresso_bin \
      -env ESPRESSO_SCRIPTS=$P/scripts -mode VN -cwd $P \
      -args "$P/test_lj_liquid.tcl"

6. Now submit the job:

llsubmit test.job

Running

Why does the feature XYZ not work?

Question

I have read that ESPResSo supports the feature xyz. Now that I try, ESPResSo doesn't seem to be able to handle it!

Answer

Have you activated (i.e. compiled in) the corresponding feature? By default, ESPResSo only activates a certain number of features - not all features of ESPResSo are always compiled in. Out of efficiency reasons, it is recommended to only activate those features of ESPResSo, that you actually require.

To learn how to activate or deactivate features, read the section myconfig.h: Activating and deactivating features in the chapter Compiling and installing ESPResSo of the User's Guide (see Documentation).

I get a Segmentation Fault when running my script!

Question

Sometimes, when I run my script, I get a segmentation fault!

Answer

Please check what version of MPI (if any) you are using. If you are using OpenMPI of a version less than 1.4, it seems to be a bug in OpenMPI.

If you are not using OpenMPI, or a version 1.4 or later, then this is usually a sign of a bug in ESPResSo. Please write a mailing to the mailing list, or report a bug in the bug tracker (see Community)!

Analysis

Some coordinates are outside of the box!

Question

Why do the output files often contain particle coordinates that are outside the specified box size (box_l)? Why does part pid print pos return such coordinates?

Answer

In a periodic system, the particle positions are stored in absolute coordinates, i.e. when a particle crosses the boundary of a box, the coordinates are not folded back into the central image. However, all particles nonetheless interact with all images of all other particles, which is defined by the box size box_l. The reason for this behavior is, that it allows to compute observables like the mean square displacement of a particle after some time.

To get the coordinates of the central image of a particle, you can use the command

part <pid> print folded_pos