Installing The 3D Pipeline ZINC22

Installation of the 3D pipeline is somewhat tricky- the environment is very particular about which versions of which software should be used. It is thus easiest to copy the exact software packages we use from our servers- this should work provided they are installed in a 64-bit linux architecture, though depending on the distribution certain shared libraries may be missing.

Setting up the installation root

First find a suitable directory which will serve as the root of the installation- this should be a directory that is visible from all nodes in the cluster.

Within this directory, create two sub-directories:

$ROOT_DIR/
    soft
    licenses

Copy or link your openeye and chemaxon licenses to the licenses directory- name them ".oe-license.txt" and ".jchem-license.cxl", respectively.

Next, clone the submission scripts from github to this directory.

git clone https://github.com/docking-org/zinc22-3d-submit

I like to rename this repository directory to just "submit", leaving the installation looking like this:

$ROOT_DIR/
    soft
    licenses/
        .oe-license.txt
        .jchem-license.cxl
    submit

Finally, create the "env.sh" and "env.csh" scripts in the ROOT_DIR as follows:

#!/bin/bash
# env.sh
base=<<ROOT_DIR>>
export BINDIR=$base/submit
export SHRTCACHE=<<TEMPDIR 1>>
export LONGCACHE=<<TEMPDIR 2>>
export SOFT_HOME=$base/soft
export LICENSE_HOME=$base/licenses
export PATH=$PATH:$base/submit

#!/usr/bin/csh
# env.csh
set base=<<ROOT_DIR>>
setenv SHRTCACHE <<TEMPDIR 1>>
setenv LONGCACHE <<TEMPDIR 2>>
setenv BINDIR $base/submit
setenv SOFT_HOME $base/soft
setenv LICENSE_HOME $base/licenses
setenv PATH $PATH\:$base/submit

<<ROOT_DIR>> should be the installation directory you chose.

<<TEMPDIR 1>> and <<TEMPDIR 2>> should be temporary directories available to all nodes on the cluster- often in distributed computing environments there are special directories set aside for this purpose, e.g /scratch

<<TEMPDIR 1>> will be used for short-term storage of small job files- it is thus appropriate to set this to a faster-access lower-capacity location, like /dev/shm. using /dev/shm can introduce problems, so it is safest to use the same value as LONGCACHE

<<TEMPDIR 2>> will be used for long-term storage of software files- thus it is more appropriate to set this to a slower-access higher-capacity location, like /tmp or /scratch.