Python-based Simulations of Chemistry Framework

2017-10-05

• Stable release 1.4
• Changelog
• Documentation
• Installation
• Features

Installation

• Prerequisites

  • Cmake 2.8 or higher
  • Python 2.6, 2.7, 3.2, 3.3, 3.4
  • Numpy 1.8.0 or higher
  • Scipy 0.10 or higher (0.12.0 or higher for python 3.3, 3.4)
  • h5py 2.3.0 or higher (requires HDF5 1.8.4 or higher)

• Compile core module

    cd pyscf/lib
    mkdir build; cd build
    cmake ..
    make
  

  Note during the compilation, external libraries (libcint, libxc, xcfun) will be downloaded and installed. If you want to disable the automatic downloading, this document is an instruction about how to manually build these packages.

• To make python find pyscf, edit environment variable PYTHONPATH, e.g. if pyscf is installed in /opt, your PYTHONPATH should be

    export PYTHONPATH=/opt/pyscf:$PYTHONPATH
  

• Use Intel MKL as BLAS library. cmake with options -DBLA_VENDOR=Intel10_64lp_seq

    cmake -DBLA_VENDOR=Intel10_64lp_seq ..
  

  If cmake does not find MKL, you can define BLAS_LIBRARIES in CMakeLists.txt

    set(BLAS_LIBRARIES "${BLAS_LIBRARIES};/path/to/mkl/lib/intel64/libmkl_intel_lp64.so")
    set(BLAS_LIBRARIES "${BLAS_LIBRARIES};/path/to/mkl/lib/intel64/libmkl_sequential.so")
    set(BLAS_LIBRARIES "${BLAS_LIBRARIES};/path/to/mkl/lib/intel64/libmkl_core.so")
    set(BLAS_LIBRARIES "${BLAS_LIBRARIES};/path/to/mkl/lib/intel64/libmkl_avx.so")
  

• Using DMRG as the FCI solver for CASSCF. There are two DMRG solver interfaces avaialbe in pyscf. Block (http://chemists.princeton.edu/chan/software/block-code-for-dmrg) CheMPS2 (https://github.com/SebWouters/CheMPS2) After installing the DMRG solver, create a file future/dmrgscf/settings.py to store the path where the DMRG solver was installed.

• Using FCIQMC as the FCI solver for CASSCF. NECI (https://github.com/ghb24/NECI_STABLE) After installing the NECI, create a file future/fciqmc/settings.py to store the path where the NECI was installed.

• Using optimized integral library on X86 platform. Qcint (https://github.com/sunqm/qcint.git) is a branch of libcint library. It is heavily optimized against X86_64 platforms. To replace the default libcint library with qcint library, edit the URL of the integral library in lib/CMakeLists.txt file

    ExternalProject_Add(libcint
      GIT_REPOSITORY https://github.com/sunqm/qcint.git
      ...
  

• Using pyberny (https://github.com/azag0/pyberny) as geometry optimizer. After downloading pyberny

  git clone https://github.com/azag0/pyberny /path/to/pyberny
  

  edit the environment variable to make pyscf find pyberny

  export PYTHONPATH=/path/to/pyberny:$PYTHONPATH
  

Known problems

• Error message "Library not loaded: libcint.3.0.dylib" On OS X. libcint.dylib is installed in pyscf/lib/deps/lib by default. Add "/path/to/pyscf/lib/deps/lib" to DYLD_LIBRARY_PATH

• On Mac OSX, error message of "import pyscf"

  OSError: dlopen(xxx/pyscf/lib/libcgto.dylib, 6): Library not loaded: libcint.3.0.dylib
  Referenced from: xxx/pyscf/lib/libcgto.dylib
  Reason: unsafe use of relative rpath libcint.3.0.dylib in xxx/pyscf/lib/libao2mo.dylib with restricted binary

It is only observed on OSX 10.11. One solution is to manually modify the relative path to absolute path

    $ install_name_tool -change libcint.3.0.dylib xxx/pyscf/lib/deps/lib/libcint.3.0.dylib xxx/pyscf/lib/libcgto.dylib
    $ install_name_tool -change libcint.3.0.dylib xxx/pyscf/lib/deps/lib/libcint.3.0.dylib xxx/pyscf/lib/libcvhf.dylib
    $ install_name_tool -change libcint.3.0.dylib xxx/pyscf/lib/deps/lib/libcint.3.0.dylib xxx/pyscf/lib/libao2mo.dylib
    ...

Running script pyscf/lib/_runme_to_fix_dylib_osx10.11.sh can patch all required dylib files.

• Fails at runtime with error message

  OSError: ... mkl/lib/intel64/libmkl_avx.so: undefined symbol: ownLastTriangle_64fc

or

  MKL FATAL ERROR: Cannot load libmkl_avx.so or libmkl_def.so.

This is MKL 11.* bug for "dlopen" function. Preloading MKL libraries works fine with most system:

  export LD_PRELOAD=$MKLROOT/lib/intel64/libmkl_def.so:$MKLROOT/lib/intel64/libmkl_core.so

or

  export LD_PRELOAD=$MKLROOT/lib/intel64/libmkl_avx.so:$MKLROOT/lib/intel64/libmkl_core.so

• h5py installation. If you got problems to install the latest h5py package, you can try the old releases: https://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.12/ https://github.com/h5py/h5py/archive/2.3.1.tar.gz

• If you are using Intel compiler (version 16, 17), compilation may be stuck at

[ 95%] Building C object CMakeFiles/cint.dir/src/stg_roots.c.o

This code is used by F12 integrals only. If you do not need to use F12 methods, the relevant compilation can be disabled, by searching DWITH_F12 in file lib/CMakeLists.txt and setting it to -DWITH_F12=0.

Citing PySCF

The following paper should be cited in publications utilizing the PySCF program package:

• The Python-based Simulations of Chemistry Framework (PySCF), Q. Sun, T. C. Berkelbach, N. S. Blunt, G. H. Booth, S. Guo, Z. Li, J. Liu, J. McClain, E. R. Sayfutyarova, S. Sharma, S. Wouters, G. K.-L. Chan, WIREs Comput Mol Sci 2017, DOI: 10.1002/wcms.1340

Bug report

Qiming Sun osirpt.sun@gmail.com