Conda Binary Distribution

PSI4 is available as a pre-compiled binary for Mac and Linux (and Windows, through the Ubuntu shell) architectures through Continuum Analytics, the company that produces Anaconda Python (a full-fledged scientific python environment with package manager conda) and, more particularly, Miniconda (a lightweight python distribution with same package manager conda). Some nice features for us:

  • cross-platform
  • no root, administrator, or sudo access required
  • built with high-performance math libraries
  • lightweight software stack (<100 MB w/o PSI4; ~1 GB including PSI4, numpy, and MKL)
  • updated nightly so new features accessible
  • standardizes python distribution so no need to find/install libpython packages
  • add-ons (plugins, extra features requiring Fortran compiler, etc.) can be made available as conda packages
  • develop PSI4 through plugins without a pre-existing development environment, see Creating a New Plugin Using a Conda Pre-compiled Binary.

The PSI4 binary repository is at Anaconda (formerly Binstar).

For commands to get a default installation, go to How to install a Psi4 binary with the Psi4conda installer, command-line or the psicode downloads page (pre-release downloads page). Users proficient with conda may prefer to consult What do the conda packages psi4 & psi4-dev and the installer psi4conda contain. For more flexibility and a detailed explanation, go to Detailed Installation of Miniconda and Detailed Installation of .

How to install a Psi4 binary with the Psi4conda installer, download site

Download one of the nine installers (Linux/Mac/Windows; Py27/35/36). bash it. Follow the prompts and do make the adjustments to PATH and PSI_SCRATCH that it suggests at the end. Test with psi4 --test. Done. Explicit commands at How to install a Psi4 binary with the Psi4conda installer, command-line.

How to install a Psi4 binary with the Psi4conda installer, command-line

Sequence of commands to get you to a working PSI4 on Linux, Mac, or Windows (Ubuntu shell for Windows accepts Linux installers). Installs Miniconda+Psi4+AddOns into $HOME/psi4conda and the PSI4 executable into the main conda environment at $HOME/psi4conda/bin/psi4.

# Linux
# py27|py35|py36 for alternate python versions
>>> curl -O "http://vergil.chemistry.gatech.edu/download/Psi4conda-latest-py35-Linux-x86_64.sh" --keepalive-time 2
>>> bash
>>> bash Psi4conda-latest-py35-Linux-x86_64.sh -b -p $HOME/psi4conda  # agrees to license terms
>>> echo "export PATH=$HOME/psi4conda/bin:\$PATH" >> ~/.bashrc
# log out, log back in so conda and psi4 in path
>>> psi4 --test

# Mac
# py27|py35|py36 for alternate python versions
>>> curl -O "http://vergil.chemistry.gatech.edu/download/Psi4conda-latest-py35-MacOSX-x86_64.sh" --keepalive-time 2
>>> bash
>>> bash Psi4conda-latest-py35-MacOSX-x86_64.sh -b -p $HOME/psi4conda  # agrees to license terms
>>> echo "export PATH=$HOME/psi4conda/bin:\$PATH" >> ~/.bash_profile
# log out, log back in so conda and psi4 in path
>>> psi4 --test

# Windows
# py27|py35|py36 for alternate python versions
>>> curl -O "http://vergil.chemistry.gatech.edu/download/Psi4conda-latest-py35-Windows-x86_64.sh" --keepalive-time 2
>>> bash
>>> bash Psi4conda-latest-py35-Windows-x86_64.sh -b -p $HOME/psi4conda  # agrees to license terms
>>> echo "export PATH=$HOME/psi4conda/bin:\$PATH" >> ~/.bashrc
# log out, log back in so conda and psi4 in path
>>> psi4 --test

That last command tested that psi4 is in your path, and it’s finding all the libraries it needs. It works because PSI_SCRATCH defaults to /tmp. Now you need only specify a permanent scratch directory (see Scratch Files and Elementary Restart) by replacing the placeholder in the following:

>>> echo "export PSI_SCRATCH=/path/to/existing/writable/local-not-network/directory/for/scratch/files" >> ~/.bashrc
# log out, log back in so variable takes effect

All done!

Configuration for this set-up is summarized at How to run Psi4 as executable or Python module from conda installation.

Note

PSI4 installs a Python distribution alongside, so you should choose an installer based on the Python version you want, irrespective of any Python version you have.

Note

Above commands use bash for installation and set up your environment for bash at runtime. To use csh at runtime, follow the on-screen directions at the end of the installation or consult step 7 below.

How to install a Psi4 binary into an Ana/Miniconda distribution

Conda command to install the latest nightly build of PSI4 + compiled add-ons + runtime add-ons into an existing Anaconda or Miniconda distribution.

# Linux or Mac or Windows
# substitute x.x by 2.7|3.5|3.6 for alternate python versions
>>> conda create -n p4env python=x.x psi4 psi4-rt -c psi4/label/dev -c psi4

Activate environment and make the adjustments to PATH and PSI_SCRATCH that it suggests at the end. Test with psi4 --test. Configuration for this set-up is summarized at How to run Psi4 as executable or Python module from conda installation.

Details:

  • It is strongly recommended to place PSI4 into a conda environment where its libraries can’t interfere with other programs (on Linux/Windows, PSI4 installs a non-default gcc 5.2) rather than the main Anaconda or Miniconda environment. Hence the creation of the environment above, but the environment name (p4env above) can be substituted.
  • Only reason for psi4-rt package is to get the QC runtime add-ons; could say dftd3 gcp v2rdm_casscf instead of psi4-rt; or leave them out if you don’t want them.

How to update a Psi4 binary

Conda command to update an existing PSI4 conda installation to the newest stable release (roughly annually).

Warning

Until 1.1 is official, this pulls the July 2016 1.0 version. 1.0 and 1.1 really shouldn’t be mixed.

>>> conda update psi4 -c psi4

# if psi4 channel in defaults (true for Psi4conda installers)
>>> conda update psi4

Conda command to update an existing PSI4 conda installation to the latest development head (roughly nightly).

>>> conda update psi4 -c psi4/label/dev

# if add-on updates required, try
>>> conda update psi4 -c psi4/label/dev -c psi4

How to use conda to compile Psi4 faster and easier

# Linux or Mac or Windows
# substitute x.x by 2.7|3.5|3.6 for alternate python versions
>>> conda create -n p4dev python=x.x psi4-dev -c psi4

Same for Linux/Mac/Windows. Substitute desired python version: 2.7, 3.5, 3.6. Fine to choose your own env name. Activate environment, source activate p4dev. Go to where you’ve cloned psi4. Execute psi4-path-advisor. It gives you a basic cmake command covering python, sphinx, link-time qc addons, and run-time qc addons. There’s a help menu -h that gives more info. There’s other options that will also pre-configure compilers. For example, at GaTech psi4-path-advisor --intel works. On Macs with XCode, psi4-path-advisor --clang works. Just read the help. For DGAS, there’s a --disable-addons, but I don’t encourage it. It gives you a fully functional cmake command, but those are just setting up CMake cache — like the plugins you can always add your own CMake variables to the command.

For run-time, you may also wish to install NumPy and the executable add-ons (e.g., dftd3)

>>> conda install numpy psi4-rt

What do the conda packages psi4 & psi4-dev and the installer psi4conda contain

psi4 - has full-featured psi4 itself and necessarily all the link-time qc addons (e.g., chemps2). It has python, pytest, and numpy. Of gcc-ness, it has minimal, run-time libraries, not compilers, though, for Linux/Windows, full gcc and run-time gcc are the same. It doesn’t have the run-time qc addons psi4-rt (e.g., dftd3) or build tools (e.g., sphinx and cmake).

psi4-dev - does not have psi4 itself or the run-time addons psi4-rt or numpy (though fine to install them alongside). Does have all the link-time addons. Does have cmake and sphinx (and python). Of gcc-ness, has full packages, that is, compilers, not runtime packages.

Psi4conda installer - has full-featured psi4 itself, all link-time qc addons, all run-time qc addons, and minimal gcc runtime libraries. Developers should additionally install psi4-dev for build tools.

The How to install a Psi4 binary with the Psi4conda installer, command-line uses a conda constructor to package up Miniconda, the PSI4 conda package, the PSI4 add-on conda packages, dependencies thereof (possibly from particular channels), and the psi4 channel as a default. This is very convenient for novice users and robust against differing channel settings in ~/.condarc. But proficient conda users may prefer to treat psi4 as a normal conda package and not have another large Miniconda installation (including the hefty MKL) lying around just for PSI4. Installing just the psi4 package itself will get you PSI4, whatever add-ons require linking in to PSI4 (e.g., CheMPS2 and PCMSolver), and the correct versions of packages. However, just the psi4 package won’t get you add-ons that don’t need linking (e.g., DFTD3 and v2rdm_casscf).

Quick Installation

Sequence of commands to get you to a working PSI4. Installs Miniconda into $HOME/miniconda and the PSI4 executable into the main conda environment at $HOME/miniconda/bin/psi4.

# Linux or Mac, Py2 or Py3 for main environment (immaterial to Py for Psi4): select between four lines
# Windows: in Ubuntu shell, select either Linux line
>>> curl -o Miniconda-latest.sh "https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh"
>>> curl -o Miniconda-latest.sh "https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh"
>>> curl -o Miniconda-latest.sh "https://repo.continuum.io/miniconda/Miniconda2-latest-MacOSX-x86_64.sh"
>>> curl -o Miniconda-latest.sh "https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh"

>>> bash
>>> bash Miniconda-latest.sh -b -p $HOME/miniconda  # agrees to conda's license terms
>>> echo "export PATH=$HOME/miniconda/bin:\$PATH" >> ~/.bashrc  # Mac: use ~/.bash_profile
# log out, log back in so conda in path
>>> conda update --yes --all
>>> conda config --add channels http://conda.anaconda.org/psi4
>>> conda install --yes psi4
>>> psi4 "$(dirname $(which psi4))"/../share/psi4/samples/sapt1/test.in  # test installation. works b/c PSI_SCRATCH defaults to /tmp

That last command tested that psi4 is in your path, and it’s finding all the libraries it needs. Now you need only specify a scratch directory (see Scratch Files and Elementary Restart) by replacing the placeholder in the following:

>>> echo "export PSI_SCRATCH=/path/to/existing/writable/local-not-network/directory/for/scratch/files" >> ~/.bashrc
# log out, log back in so variable takes effect

All done!

Note

Above commands use bash for installation and set up your environment for bash at runtime. To use csh at runtime, follow the on-screen directions at the end of the installation or consult step 7 below.

Detailed Installation of Miniconda

  1. Sanity check. If you already have Miniconda or Anaconda, skip to step 5. The whole installation takes ~5 min; reading this page takes far longer.
  2. Get bzip2. You’ll need this slightly exotic command so run which to test for availability, and install from yum, source, etc. if unavailable. You’ll also need an internet connection for downloading; computers behind a firewall or with restricted login domains are eligible. So long as you can ssh into the computer to an account with write permissions and can connect to the internet from the computer, all is well.
# check
>>> which bzip2
/usr/bin/bzip2
>>> curl -O "http://psicode.org/psi4manual/master/introduction.html"
>>> ls -1
introduction.html
  1. Get Miniconda installer script. Either issue the command below or download from http://conda.pydata.org/miniconda.html by clicking on the appropriate link for your OS. If you already have or would prefer to use Anaconda rather than Miniconda, that’s fine. Locate or install Anaconda, check that conda is in your path, and skip to step 4.
>>> curl -O "http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh"
# check
>>> ls -1
Miniconda-latest-Linux-x86_64.sh
  1. Install Miniconda. Execute the script and answer its questions, particularly your choice of installation location. You may need to replace the filename below with the correct filename for the OS/version of installer you downloaded. Execute with bash regardless of csh/bash shell. If you’re a bash user, it’s convenient to agree to its offer to prepend conda commands to your PATH in ~/.bashrc. If you’re a csh/tcsh user, it’s convenient to do the same by hand to your ~/.tcshrc: setenv PATH /path/to/miniconda/bin:${PATH}. Further directions assume that the conda command is in your path; you may have to log out and log back in for which conda to return correctly.
>>> bash Miniconda-latest-Linux-x86_64.sh
# check
>>> which conda
/path/to/miniconda/bin/conda
  1. Update conda. This updates the package manager itself.
>>> conda update conda

Detailed Installation of PSI4

  1. Subscribe to PSI4. Subscribe to our channel at http://anaconda.org/psi4 that contains the PSI4 package and several dependency packages. Make sure this shows up in your ~/.condarc file.
>>> conda config --add channels http://conda.anaconda.org/psi4
# check
>>> cat ~/.condarc
channels:
  - http://conda.anaconda.org/psi4
  - defaults
  1. Install PSI4. You can install into the main conda environment so that whenever commands conda or (Ana/Miniconda’s) python are available, then psi4 is available, too.
>>> conda install psi4
# check
>>> which psi4
/path/to/miniconda/bin/psi4

Or, you can install into a conda environment that places PSI4 and its dependencies (including python) into a sandbox unaffected by any other software installed in Ana/Miniconda. This is recommended for developers to avoid interference between multiple versions (including github/conda versions) or to test python versions, etc.. If your main conda is not python=2.7, then PSI4 must be installed into a conda environment. In practical terms, installing into a conda environment means you can turn PSI4‘s availability on/off by switching conda environments without turning on/off the whole Ana/Miniconda installation. Below, PSI4 is installed into an environment called p4env. Then the environment is activated, removing the main Ana/Miniconda bin and adding envs/p4env/bin to PATH. The activate command only works in bash, so csh/tcsh will need corresponding adjustments.

>>> conda create -n p4env psi4
>>> source activate p4env
# check
>>> which psi4
/path/to/miniconda/envs/p4env/bin/psi4

The output for either of the installation commands above looks like the following. It checks what packages are needed, gets your approval for downloading them, fetches and installs them, prints out some useful information, and runs a PSI4 test case to check that all’s well.

>>> conda install psi4
Using Anaconda Cloud api site https://api.anaconda.org
Fetching package metadata: ......
Solving package specifications: .........

Package plan for installation in environment /theoryfs2/ds/cdsgroup/miniconda/envs/tpsi4:

The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    psi4-0.4.322               |    py27_g84b3aa1        44.4 MB  http://conda.anaconda.org/psi4/linux-64/

The following NEW packages will be INSTALLED:

    psi4: 0.4.322-py27_g84b3aa1 http://conda.anaconda.org/psi4/linux-64/

Proceed ([y]/n)? y

Fetching packages ...
psi4-0.4.322-p 100% |####################################################################################| Time: 0:00:08   5.77 MB/s
Extracting packages ...
[      COMPLETE      ]|#######################################################################################################| 100%
Linking packages ...


  Thank you for installing psi4. Additional resources:
    Website: www.psicode.org
    Inputs:  /theoryfs2/ds/cdsgroup/miniconda/envs/tpsi4/share/psi4/samples
    Manual:  http://psicode.org/psi4manual/master/index.html
    GitHub:  https://github.com/psi4/psi4/wiki
    Binary:  https://anaconda.org/psi4
    Youtube: https://www.youtube.com/user/psitutorials

  For csh/tcsh command-line use, add to shell or ~/.tcshrc file:
    unsetenv PSIDATADIR
    setenv PATH /theoryfs2/ds/cdsgroup/miniconda/envs/tpsi4/bin:$PATH
    setenv PSI_SCRATCH /path/to/existing/writable/local-not-network/disk/for/scratch/files

  For sh/bash command-line use, add to shell or ~/.bashrc file:
    unset PSIDATADIR
    export PATH=/theoryfs2/ds/cdsgroup/miniconda/envs/tpsi4/bin:$PATH
    export PSI_SCRATCH=/path/to/existing/writable/local-not-network/disk/for/scratch/files

  Report problems at http://forum.psicode.org/t/report-conda-update-psi4-oddities-here/32


    Nuclear Repulsion Energy..........................................PASSED
    SAPT0 Eelst.......................................................PASSED
    SAPT0 Eexch.......................................................PASSED
    SAPT0 Eind........................................................PASSED
    SAPT0 Edisp.......................................................PASSED
    SAPT0 Etotal......................................................PASSED

[      COMPLETE      ]|#######################################################################################################| 100%
  1. Configure environment. Preceding steps have placed conda and psi4 in your PATH, either permanently through rc-files or temporarily in this terminal session. You can keep or undo these changes. For general psi4 use, you must enable the psi4 executable to be found through any of:
  1. prepending to PATH in shell, ~/.bashrc, ~/.tcshrc, or PBS cmd file
  2. activating the conda environment (p4env above) in shell, ~/.bashrc, or PBS cmd file
  3. supplying full path to executable (shell or PBS cmd file)

Similarly, the scratch directory (see Scratch Files and Elementary Restart) must be specified through:

  1. defining PSI_SCRATCH in shell, ~/.bashrc, ~/.tcshrc, or PBS cmd file

Suitable values for these variables have been printed to screen during installation (see last codeblock in step 6).

Useful Commands

  • Update to latest PSI4 version

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    >>> conda update psi4

  • Install into a conda environment “p4env” instead of “root”. Second command only works on bash; for csh/tsch, setenv PATH /path/to/miniconda/envs/p4env/bin:$PATH instead. This creates a sandbox with just PSI4 and python (loaded as dependency).

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    >>> conda create -y -n p4env psi4
>>> source activate p4env

  • Install a particular PSI4 version

    1
    >>> conda install psi4=0.1.12

  • Uninstall PSI4 from current environment

    1
    >>> conda remove psi4

Troubleshooting

  • If the target computer doesn’t have libc >= 2.7 (released c.2007; for reference, 2.10 is newer than 2.7; unlike most libraries, libc generally not available in multiple versions on a computer), the PSI4 conda package won’t work.

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    # unsuitable computer
>>> ldd --version
ldd (GNU libc) 2.5
# suitable computer
>>> ldd --version
ldd (GNU libc) 2.17

  • It is of greatest importance that the PSI4 executable be linked against conda libpython.so not against any system libpython.so. This is arranged by setting RPATH to seek libraries relative to executable (thanks, conda binary relocation routine!). The conda PSI4 executable is not vulnerable to interference from your LD_LIBRARY_PATH settings. Below shows a well-linked executable.

    • no libraries “not found”
    • fundamental libraries like libc, ld-linux, pthreads found system libraries to link against
    • libpython linked against conda python not system python
    • libm is linked against conda or system
    • blas, c++, and gcc libraries are absent because statically linked
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    >>> conda install conda-build  # needed for next command
>>> conda inspect linkages psi4
python-2.7.9-2:
  libpython2.7.so.1.0 (lib/libpython2.7.so.1.0)
system-5.8-1:
  libm.so.6 (lib/libm.so.6)
system:
  libc.so.6 (/lib64/libc.so.6)
  libdl.so.2 (/lib64/libdl.so.2)
  libpthread.so.0 (/lib64/libpthread.so.0)
  librt.so.1 (/lib64/librt.so.1)
  libutil.so.1 (/lib64/libutil.so.1)
  linux-vdso.so.1 ()
not found: