Installation

Quick instructions

If you are feeling lucky:

tar xzf ape<-version>.tar.gz
cd ape-<version>
./configure
make
make install

This may not work but, before giving up, just read the following paragraphs.

Long instructions

The code is written in standard Fortran 2003, with some routines written in C. To build it you will need both a C compiler (gcc works just fine), and a Fortran 2003 compiler (gfortran also works fine).

Besides the compiler, you will also need:

  1. make: most computers have it installed, otherwise just grab and install the GNU make.

  2. cpp: GNU cpp is just fine, but any cpp that accepts the -C flag (preserve comments) should work just as well.

  3. GSL: The GSL is heavily used in APE. If you don’t have it already installed in your system, you can obtain GSL from here. You will need version 1.0 or higher.

  4. Libxc: Libxc is a library of exchange and correlation functionals. If you don’t have it already installed in your system, you can obtain it here.

First you should obtain the code file, ape<-version>.tar.gz, (you probably have already done this). The code is freely available, and can be downloaded from the APE website or from Gitlab. Uncompress and untar it

tar xzf ape<-version>.tar.gz

In the following, APE-HOME denotes the home directory of APE, created by the tar command.

APE-HOME contains the following subdirectories:

  • autom4te.cache, build: contains files related to the building system. May actually not be there. Not of real interest for the plain user.

  • doc: The documentation of APE in Markdown format.

  • liboct_parser: The parser used by APE. This is the parser from Octopus.

  • sample: Sample input files for APE.

  • src: Fortran 2003 source files. Note that these have to be preprocessed before being fed to the Fortran compiler, so do not be scared by the # directives.

  • testsuite: APE regression testsuite.

Before configuring you can (should) setup a couple of options. Although the configure script tries to guess your system settings for you, we recommend that you set explicitly the default Fortran 2003 compiler and the compiler options. For example, in bash you would typically do:

export FC=gfortran
export FCFLAGS="-O3 -Wall"

if you are using the GNU Fortran compiler on a Linux machine. Also, if you have some of the required libraries in some unusual directories, these directories may be placed in the variable LDFLAGS (e.g., export LDFLAGS="-L/opt/lib/").

You can now run the configure script1

./configure

There are some options you can use with the configure script. To obtain a full list just type

./configure --help

Some commonly used options include:

  • --prefix=PREFIX: Change the base installation dir of APE to PREFIX. The executable will be installed in PREFIX/bin, the libraries in PREFIX/lib and the documentation in PREFIX/info. PREFIX defaults to the home directory of the user who runs configure.

  • --with-gsl-prefix=DIR: Installation directory of the GSL library. The libraries are expected to be in DIR/lib and the include files in DIR/include. The value of DIR is usually found by issuing the command gsl-config --prefix. (If the GSL library is installed, the program gsl-config should be somewhere.)

  • --with-libxc-prefix=DIR: Installation directory of the Libxc library. The libraries are expected to be in DIR/lib and the include files in DIR/include.

Then compile the code and launch the testsuite by running

make
make check

If all tests were passed, you can then install the code with

make install

If everything went fine, you should now be able to run APE.

Troubleshooting

So, something went wrong. Here is a list of things that might have gone wrong.

Some tests of the testsuite fail: When running the testsuite, one or more tests fail.

  • Is the test failing because of a very small numerical difference? While running a test, if a test case is failed, the code will print some extra information about the failure, namely the calculated value, the reference value, and the allowed tolerance. This should look like this:

      Match Failed
       Calculated value : -24.344302
       Reference value  : -24.344198
       Difference       : 0.000104
       Tolerance        : 8e-5
    

If the difference is slightly larger than the tolerance, like in the previous example, and if the same happens for all the failed test cases, then it is likely that there is nothing wrong with your compilation.

Could not find GSL library: We assume that you have already installed GSL but, for some reason, you were not able to compile the code.

  • Did you pass the correct --with-gsl-prefix to the configure script? If your library is installed in a non-standard directory (like /opt/gsl), you will have to pass the script the location of the library (in this example, you could try ./configure --with-gsl-prefix=/opt/gsl.

Could not find Libxc library: We assume that you have already installed libxc but, for some reason, you were not able to compile the code.

  • Did you pass the correct --with-libxc-prefix to the configure script? If your library is installed in a non-standard directory (like /opt/libxc), you will have to pass the script the location of the library (in this example, you could try ./configure --with-libxc-prefix=/opt/libxc.

  • Did you use the same Fortran compiler when compiling Libxc? Unfortunately the compilation of Fortran modules generates compiler dependent files (usually with the .mod extension). Since APE uses the Fortran interface of Libxc, it is required that you use the same Fortran compiler for APE and Libxc.

Error while loading shared libraries: You have already compiled the code, but it fails to run, giving an error message about a failure in locating some shared object file.

  • Did you set the LD_LIBRARY_PATH environment variable? If some of the libraries used to compile APE are installed in a non-standard directory (like /opt/libxc), you will have to add the path to the directory where the library objects are installed to the LD_LIBRARY_PATH environment variable. If you are using bash, this is done with the following command:
export LD_LIBRARY_PATH=/path/to/libxc/lib:$LD_LIBRARY_PATH

Fatal Error: Sometimes the code stops after issuing a Fatal Error message. Here is a list of some of the most common errors and a brief explanation of their origin and some possible solutions.

  • Unable to bracket eigenvalue for state xxx. This error occurs when the eigensolver is unable to find the eigenvalue for a given orbital. Most of the times this will happen when an occupied orbital becomes unbound.

  • Generation of pseudopotentials from spin-polarized calculations is not implemented! You are trying to generate a pseudopotential from a spin-polarized calculation, but this is not possible in APE. Although there are schemes to generate spin-dependent pseudopotentials, for most applications, spin-polarized calculations can be performed using pseudopotentials generated for a spin-unpolarized atom. This is because spin-polarization should come from the valence electrons. Furthermore, spin-dependent pseudopotentials cannot be used in the same way as spin-independent ones and most DFT codes don’t know how to handle them.

Whatever went wrong...: If something else went wrong, please send an e-mail to the APE-users mailing list (ape-users at tddft.org). Note that you have to be subscribed to the mailing list in order to be able to post a message.


[1] If you downloaded the git version, you will not find the configure script. In order to compile the development version you will first have to run the GNU autotools. This may be done by executing the command autoreconf -i. Note that you need to have working versions of the automake (1.11), autoconf (2.68) and libtool (2.4) programs (the versions we currently use are between parentheses). Note that autoreconf will likely not work if you have (much) older versions of the autotools.