Python module for quantum chemistry

2017-01-04

• 1.3 alpha
• Stable release 1.2.1
• Changelog
• Documentation (PDF)
• Installation
• Features

• 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 lib
    mkdir build; cd build
    cmake ..
    make
  

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

    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
      ...
  

• Error message "Library not loaded: libcint.2.9.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.2.8.dylib
  Referenced from: xxx/pyscf/lib/libcgto.dylib
  Reason: unsafe use of relative rpath libcint.2.8.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.2.8.dylib xxx/pyscf/lib/deps/lib/libcint.2.8.dylib xxx/pyscf/lib/libcgto.dylib
    $ install_name_tool -change libcint.2.8.dylib xxx/pyscf/lib/deps/lib/libcint.2.8.dylib xxx/pyscf/lib/libcvhf.dylib
    $ install_name_tool -change libcint.2.8.dylib xxx/pyscf/lib/deps/lib/libcint.2.8.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

This problem relates to MKL v11.1 on intel64 architecture. Currently, there is no solution for the combination of Python + MKL 11.1 + AVX. You need either change to other MKL version (10.*, 11.0, 11.2) or disable mkl_avx:

    cmake -DBLA_VENDOR=Intel10_64lp_seq .. -DDISABLE_AVX=1

• Runtime error message

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

This is MKL 11.* bug for "dlopen" function. Preloading the two 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:$MKLROOT/lib/intel64/libmkl_sequential.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

Qiming Sun osirpt.sun@gmail.com