Copyright 2008 Parallel Quantum Solutions, 2013 Green Acres Rd. Suite A, Fayetteville, Arkansas, USA. Phone: 1 479 521 5118, Fax: 1 479 521 5167 http://www.pqs-chem.com sales@pqs-chem.com ------------------------------------------------------------------------ PQS ab-initio Quantum Chemistry Software Package for Linux ------------------------------------------------------------------------ Table of Contents: ------------------ 1. Introduction 2. Software Requirements 3. Quick Install Guide 4. Installation 4.1 Installing From RPM 4.2 Installing From Tarball 5. Obtaining a License 6. Documentation 1. Introduction --------------- PQS is an ab-initio quantum chemistry molecular modelling software produced by Parallel Quantum Solutions. PQS is particularly efficient for SCF and DFT geometry optimisations, vibrational frequencies and NMR chemical shifts, and for MP2 single-point energy calculations. The program is avaliable as a single processor standalone executable. There are also parallel versions for both the Parallel Virtual Machine (PVM) and the Message Passing Interface (MPI) libraries. PQS optionally includes the NBO program of Prof. Frank Weinhold (University of Wisconsin) Other software available from Parallel Quantum Solutions include: PQSMOL: a fully functional Graphical User Interface (GUI) for PQS featuring a model builder with a large fragment library, two force fields for structure cleanup and pre optimization, PQS input generator, parallel job submission and post visualization of geometry, energy levels, electron density and molecular orbitals, electrostatic potential, NMR, IR, Raman and VCD spectra, animation of vibrational modes. SQM: an add-on module for PQS which scales forces constants to produce a Scaled Quantum Mechanical (SQM) force field. The method has considerable predictive power and is often of great help in understanding and assigning experimental vibrational spectra. Parallel Quantum Solutions manufactures parallel computers with integrated software for high-performance computational chemistry. Our offerings have an exceptional price/performance ratio, and are fully configured for parallel computations "straight out of the box". 2. Software Requirements ------------------------ Common to all versions: - Linux operating system - Bash command shell - Common utilities such as tar, gzip, grep, sed, ... Parallel PVM Version: - PVM message passing software. The program is linked against PVM v. 3.4.5 Parallel MPI1 Version: - MPI1 message passing software. The program is linked against MPICH1 v. 1.2.7p1. Parallel MPI2 Version: - MPI2 message passing software. The program is linked against MPICH2 v. 1.0.3. NOTE: MPI is a de facto standard for communication among processes for which there exist many implementations, both open source and commercial. Although all the MPI implementations adhere to the same application programming interface, the underlying details of each specific MPI flavor differ, and this might create portability issues. The PQS MPI executables that are currently available at the PQS web site are statically linked against the MPICH libraries (MPICH1 or MPICH2, see www-unix.mcs.anl.gov/mpi/mpich) for communication over ethernet interfaces, and there is no guarantee that they will work with a different MPI implementation, or for different hardware. Special combinations of MPI flavors/hardware might need an ad hoc version of the program. For enquires, contact the PQS customer support (tech@pqs-chem.com). 3. Quick Install Guide ---------------------- a) Installing from RPM: a.1) login as superuser root a.2) rpm -i pqs-.....rpm a.3) create user scratch directories, for instance: mkdir -p /scr/user1; chown user1.users /scr/user1 b) Installing from tarball: b.1) tar -xvzf pqs-.....tar.gz b.2) cd pqs-.... b.3) ./install.sh 4. Installation --------------- PQS is available as an RPM file or as a gzipped tar ball. The rpm package is very easy to handle, and will install the software in standard system directories that should be OK for most system configurations. You will need root access to your system and must have the rpm utility available in order to install the PQS rpm distribution. If you cannot meet the previous requirements, or you want to install PQS in a custom location (in particular, if you want to do a single user install, see below) you should download the gzipped tar distribution. As you will see in a moment, the PQS installation (either rpm or tar ball) is a very simple procedure. Before outlining it, howewer, it is useful to discuss the two main points of the PQS setup: 1) the PQS root directory and 2) the PQS scratch directory. 1) PQS root directory (PQS_ROOT hereafter). This is the directory containing the PQS software. This directory does not require large amounts of disk space (200MB should be more than enough), and its contents should be accessible to all the users that want to run PQS jobs. In a multi-user environment PQS_ROOT should thus be part of a system directory. In case PQS is to be used in a computer cluster, PQS_ROOT should be available to all the compute nodes, i.e., it should belong to a disk partition that is shared by all cluster node (the alternative to this would be to do a separate PQS install for each compute node). The default PQS_ROOT location (/usr/local/share/PQS) usually meets the requirements of a typical multi-user and/or cluster setup. The location of PQS_ROOT can be defined at runtime using the environment variable 'PQS_ROOT'. 2) PQS scratch directory (PQS_SCRDIR hereafter). This is the directory where the temporary files needed during a calculation are written. The amount of storage space used by PQS_SCRDIR will depend heavily on the type of calculation you are planning to run. Small and medium size jobs (up to 400-500 basis functions) can be run with less than 10 GB of scratch space (we recommend at least 2 GB as the very minimum), but large and very large jobs, specially large MP2 calculations, might require much more, say 100 GB. The efficiency of I/O intensive jobs (like MP2) can be increased by placing PQS\_SCRDIR on a fast-access storage device (for instance, a striped RAID array). In a multi-user setup it is desirable to have a separate PQS_SCRDIR for each PQS user, to avoid interference with each others' jobs. In a cluster environment, PQS_SCRDIR should be local to each compute node, in order to maximise the total storage available to the job and the efficiency of the calculation. The default location is PQS_SCRDIR=/scr/${USER} (e.g.: /scr/bob for user 'bob'). This value can be changed at runtime via the environment variable 'PQS_SCRDIR'. 4.1 Installing from RPM: Requires: root privileges, rpm utility program Defaults: PQS_ROOT=/usr/local/share/PQS, PQS_SCR=/scr/${USER} a) Single Processor Version: a.1 Download the main PQS rpm package for your architecture, for instance: pqs-3.3-1.x86_64.rpm (change version/architecture identifier as needed). a.2 As user root, type: 'rpm -ivh pqs-3.3-1.x86_64.rpm' (substitute the appropriate file name for the rpm package you have downloaded). a.3 Create a scratch directory for each PQS user: mkdir -p /scr/uname; chown uname.users uname where uname = user name to use a different location for PQS_SCRDIR you can set the environment variable PQS_SCRDIR, for instance (using bash syntax): export PQS_SCRDIR=/myscr/${USER} you can add a line similar to the above example to a system- wide configuration file, or instruct the users to modify their .bashrc files accordingly. b) Parallel Version: b.1 Make sure your system has a message passing parallel software such as PVM (recommended), MPICH1 or MPICH2 installed and properly configured. b.2 Install the PQS single processor version as explained in a) above. b.3 Download the parallel rpm for the message passing library you have chosen: (pqs_pvm-...rpm for PVM, pqs_mpi1-... for MPICH1, and so on) b.4 As user root, type: 'rpm -ivh pqs_pvm....rpm' (substitute the appropriate file name for the rpm package you have downloaded). 4.2 Installing From Tarball : If you chose to install from the tarball, you have the option of performing a multi-user install or a single-user install. The multi- user install (default) is suitable if there will be more than one user running PQS jobs. This is the installation method to use in a cluster environment. Root privileges are required. In case PQS is to be run by just one user and on only one compute node, you may chose the single-user install. This method does not requires root privileges, and the default locations are chosen so that the PQS software is installed under the user home directory. Make sure there is enough free disk space available to install and run PQS jobs. c) Multi-user install of Single Processor Version: Requires: root privileges, bash command shell, GNU utilities (tar, gzip, sed, etc.) Defaults: PQS_ROOT=/usr/local/share/PQS, PQS_SCR=/scr/${USER} c.1 Download the main PQS tar.gz package for your architecture, for instance: pqs-3.3-1.x86_64.tar.gz (change version/architecture identifier as needed). c.2 Unpack the file: tar -xvzf pqs-3.3-1-x86_64.tar.gz (change version/architecture identifier as needed). This will create a directory named pqs-... (the name of the tar file without the .tar.gz extension) c.3 Enter the newly created directory: cd pqs-... You should see the following files: README.PQS (this file) install.sh installation script pqs-dist....tar.gz distribution file c.4 As user root, type: './install.sh'. You will be prompted for a choice of the installation type: chose multi-user. The installation procedure will guide you through the process of defining PQS_ROOT and PQS_SCRDIR and (optionally) creating separate scratch directories for each PQS user d) Single-user install of Single Processor Version: Requires: bash command shell, GNU utilities (tar, sed, etc.) Defaults: PQS_ROOT=${HOME}/PQS, PQS_SCR=$(HOME}/pqsscr d.1 Download the main PQS tar.gz package for your architecture, for instance: pqs-3.3-1.x86_64.tar.gz (change version/architecture identifier as needed). d.2 Unpack the file: tar -xvzf pqs-3.3-1-x86_64.tar.gz (change version/architecture identifier as needed). This will create a directory named pqs-... (the name of the tar file without the .tar.gz extension) d.3 Enter the newly created directory: cd pqs-... You should see the following files: README.PQS (this file) install.sh installation script pqs-dist....tar.gz distribution file d.4 Type: './install.sh'. You will be prompted for a choice of the installation type: chose single-user. The installation procedure will guide you through the process of defining PQS_ROOT and PQS_SCRDIR. e) Parallel Version: e.1 Make sure your system has a message passing parallel software such as PVM (recommended), MPICH1 or MPICH2 installed and properly configured. e.2 Install the PQS single processor version as explained in c) or d) above. e.3 Download the parallel tar ball for the message passing library you have chosen: (pqs_pvm-...tar.gz for PVM, pqs_mpi1-... for MPICH1, and so on) e.4 Unpack the file: tar -xvzf pqs_pvm....tar.gz (change version/architecture identifier as needed). This will create a directory named pqs_pvm... (the name of the tar file without the .tar.gz extension) e.5 Enter the newly created directory: cd pqs_pvm... You should see the following files: README.PQS (this file) install.sh installation script pqs_pvm-dist....tar.gz distribution file e.6 Type: './install.sh'. When prompted, enter the location of PQS_ROOT, You might need root privileges according to your chosen setup. 5. Obtaining a License ---------------------- After you have installed the software you need to obtain a license in order to run PQS calculations. You can run small single-processor jobs without a license, but in order to run larger calculations, or to use the parallel version or any other PQS software, a license file is required. The first step in obtaining a license is generating the lockcode file. To do this type: 'pqs -lockcode'. This command should produce a file called 'pqs_lockcode' containing the lockcode for your host. If you are in a cluster environment, you need to repeat this procedure for every compute node in which you want to be able to run PQS jobs. You might want to use a script for this, for instance (bash syntax): for node in n1 n2 n3 n4 n5 n6 n7 n8; do rsh $node pqs -lockcode done All the corresponding lockcodes will be appended to the existing pqs_lockcode file. Once you have the pqs_lockode file, edit it with a text editor and fill in the contact information in the header, then e-mail the file to licenses@pqs-chem.com. A license file will be e-mailed back to you. Once you have received the license file, you should save it in the PQS_ROOT directory. The license file must be named 'pqs_lic'. Once you have installed the license, you can test it by typing 'pqs -check'. NOTE: The 'pqs -check' command will check for the PQS license proper, and also for the license for the NBO module. NBO is an optional add-on module to the PQS program, and its license is sold separately. The NBO license is not needed for the normal operation of PQS. It is needed only to access the functionality of the NBO module. 6. Documentation ---------------- The electronic documentation for the PQS software is located in PQS_ROOT/DOC. To order paper copies of the PQS manuals visit our web site (www.pqs-chem.com) or contact PQS.