Installation¶

These intructions provide more details on the compilation and installation of QUIP (Fortran library and main programs) and quippy (Python interface).

Precompiled Containers¶

If you have access to Docker or Singularity, you can try one of the precompiled images to get up and running quickly.

Compilation Instructions¶

First try the quickstart below, which should work with most Linux systems. For Mac systems, have a look at Installing on Mac OS X with macports first.

Quick start¶

Install [1] the prerequisites: GCC, gfortran, Python, and the linear algebra libraries. For example, on Ubuntu, do (in a terminal):

$ sudo apt-get install gcc gfortran python python-pip libblas-dev liblapack-dev

For other systems, replace the apt-get part with your system package manager. Beware that the packages might also have slightly different names; these can usually be found with a quick search.

Don’t forget the quippy prerequisites:

$ pip install numpy
$ pip install ase

Now you can get the code and compile:

$ git clone --recursive https://github.com/libAtoms/QUIP.git
$ export QUIP_ARCH=linux_x86_64_gfortran
$ export QUIPPY_INSTALL_OPTS=--user  # omit for a system-wide installation
$ make config

Answer all the questions with their defaults (by pressing enter) for now, just to get things working.

$ make
$ make install-quippy

And now open a Python terminal and see if it works:

$ python
>>> import quippy
>>>

If the import completes successfully (i.e. with no output) then the installation was successful. You may want to continue with Installing the Jupyter notebook to run the interactive tutorials.

[1]	If this isn’t your machine and you don’t have root access, these packages might already be installed by the system administrator. If not, ask them.

Step by step¶

If that didn’t work, try these step-by-step instructions instructions excerpted from the top-level README. The README file is the most up-to-date source of installation information.

If that still doesn’t work or you’re using a nonstandard architecture, try looking at Custom settings and Common Problems. As a last resort you can consult the issue tracker on Github.

Installing the Jupyter notebook¶

Jupyter is an environment for interactive computing that makes using Python much easier and more intuitive. Especially useful is its notebook environment, which provides a handy way to experiment with code, see the results, and have a record of your progress. The interactive getting-started tutorial is a Jupyter notebook that you can run and modify yourself.

To get Jupyter up and running, the following should suffice [2]:

$ pip install jupyter
$ jupyter notebook

This will open a new window in your browser that you can use to navigate through your filesystem. To access the interactive tutorials, you can run the jupyter notebook command from your QUIP/doc/Examples directory (or any enclosing directory) then navigate to the notebooks and open Introduction.ipynb to get started.

[2]	This assumes you’ve already run `sudo apt-get install python-pip; pip install numpy; pip install ase` as in the Quick start.

Custom settings¶

MATHS_LINKOPTS

Library options needed to link to BLAS and LAPACK libraries. Any working BLAS/LAPACK installation is fine. If you are using Linux, ATLAS is a good option, and you should use something like the following:

-L/usr/local/atlas -llapack -lf77blas -lcblas -latlas

On Mac OS X, there are build in LAPACK libraries in the Accelerate framework, which you can use by entering

-framework Accelerate

FOX_LIBDIR, FOX_INCDIR and FOX_LIBS

Directories containing FoX libraries and header files, and required link options. Should be read automatically from QUIP Makefiles.

QUIPPY_FCOMPILER

Fortran compiler to use. The shell command:

$ f2py -c --help-fcompiler

will print a list of detected compilers on your system. Use gnu95 for gfortran, intel for ifort on 32-bit platforms and intelem for ifort on 64-bit platforms.

QUIPPY_DEFINES Preprocessor macros which should be defined

when compiling quippy. Note that since the Fortran source files are preprocessed before being scanned by f90doc, it’s important to put all the -D options needed here and not in QUIPPY_F90FLAGS.

QUIPPY_F90FLAGS and QUIPPY_F77FLAGS

Extra flags to pass to Fortran 90 and 77 compilers

QUIPPY_OPT

Optimisation settings for Fortran compiler

QUIPPY_DEBUG

Set this to 1 to include debugging information in the compiled extension code. This also disables optimisation.

QUIPPY_CPP

Fortran preprocessor to use. Default is system cpp.

QUIPPY_INSTALL_OPTS

Installation options, e.g. specify --user to install for the current user --prefix=${PREFIX} to install in a non-default location.

QUIPPY_NO_TOOLS

If set to 1, omit compilation of extra tools such as the elasticity module.

QUIPPY_NO_CRACK

If set to 1, omit compilation of crack utilities.

HAVE_NETCDF4

Should be set to 1 to enable NetCDF4 support. Should be read automatically from QUIP.

NETCDF4_LIBS, NETCDF4_FLAGS

Linker flags for compiling with NetCDF4 support, and flags for finding header files. Should be read automatically from QUIP.

Common Problems¶

Permission errors when installing¶

If you are installing as root, you may need to make sure the value of the QUIP_ARCH gets through to the install script, e.g.

sudo QUIP_ARCH=darwin_x86_64_gfortran make install-quippy

Installing on Mac OS X with macports¶

Macports requires various packages to be installed to compile everything, and may require extra linking arguments. See the README.macports for the latest details.

RuntimeError when importing¶

If, after installing quippy, you get the error shown below when you try to import it for the first time, then you are a victim of a bug in early versions of Python 2.6.

>>> import quippy
Traceback (most recent call last):
 File "<stdin>", line 1, in <module>
 File "/home/ab686/QUIP/Tools/quippy/quippy/__init__.py", line 31, in
<module>
   _quippy.system.verbosity_push(0)
RuntimeError: more argument specifiers than keyword list entries
(remaining format:'|:_quippy.system.verbosity_push')

The solution is either to compile your own Python from the current svn snapshot, or to update numpy to workaround the fix. This can be done either by compiling numpy from source from an up-to-date svn snapshot, or by applying the patch manually.

ImportError when importing¶

If you get an ImportError with a message about unresolved dependancies then something went wrong with the linking process - check that all the libraries you’re linking against are correct. You can used ldd on Linux of otool -L on Mac OS X to check which libraries the _quippy.so Python extension is linked against.

Possible problems installing atomeye module¶

If you get an ImportError with a message ::

>>> import atomeye
ImportError: dlopen(/Users/silvia/lib/python/_atomeye.so, 2): Symbol not found: _Config_load_libatoms
Referenced from: /Users/silvia/lib/python/_atomeye.so
Expected in: flat namespace
in /Users/silvia/lib/python/_atomeye.so

be sure that you have set QUIP_ROOT variable before starting the compilation. If not make clean and recompile again

If you get an ImportError with a message ::

>>> import atomeye
ImportError: dlopen(/Users/silvia/lib/python/_atomeye.so, 2): Symbol not found: __gfortran_adjustl
Referenced from: /Users/silvia/lib/python/_atomeye.so
Expected in: flat namespace
in /Users/silvia/lib/python/_atomeye.so

be sure that the gfortran libraries are properly set in ATOMEYE_LIBS in Makefile.atomeye

Error compiling IPModel_GAP¶

If you get the following error during compilation:

/src/Potentials/IPModel_GAP.f95:51.22:

use descriptors_module
                      1
Fatal Error: Can't open module file 'descriptors_module.mod' for reading at (1): No such file or directory

The GAP_predict module is not publicly available, so the Makefile.inc must contain HAVE_GP_PREDICT = 0, and HAVE_GP_TEACH = 0.

Warning about `quippy.castep` when importing quippy¶

If you get the following warning message when importing quippy:

$ python
>>> from quippy import *
WARNING:root:quippy.castep import quippy.failed.

then don’t worry, the quippy.castep module is not redistributed with the main code. The rest of quippy works fine without it.

Internal compiler error with ifort¶

If you see an error like the following when using the Intel fortran compiler:

fortcom: Severe: **Internal compiler error: internal abort** Please
report this error along with the circumstances in which it occurred
in a Software Problem Report.
 Note: File and line given may not be explicit cause of this error.

ifort: error #10014: problem during multi-file optimization compilation (code 3)
backend signals

Then the problem is due to bugs in the compiler. As a workaround, setting QUIPPY_NO_CRACK =1 in Makefile.inc should solve the problem, at the cost of excluding the fracture utilities from quippy.

Linking error on Mac OS X¶

When recompiling quippy on top of a previous compilation, you may see errors like this:

collect2: ld returned 1 exit status ld: in
/QUIP/build.darwin_x86_64_gfortran/libquiputils.a, malformed
archive TOC entry for  ___elasticity_module_MOD_einstein_frequencies,
offset 1769103734 is beyond end of file 1254096

This seems to be a Mac OS X Lion problem with rebuilding static libraries (.a files). Removing the static libraries with rm ../../build.${QUIP_ARCH}/*.a and recompiling should solve the problem.

Segmentation Faults with OpenBLAS¶

The threading in OpenBLAS can interfere with the OpenMP resulting in segfaults. Either recompile OpenBLAS with USE_OPENMP=1 or disable threading with export OPENBLAS_NUM_THREADS=1 at runtime.