Connecting Infrastructure, Connecting Research

UEE Script Conventions

This page is primarily of interest to installers of Scientific software on the NGS. It describes the 'API' of the UEE (Uniform Execution Environment) scripts held at /usr/ngs/... on all NGS sites. It was last updated on 12 Sept 2008

This page describes the UEE script behaviour and naming conventions for applications installed on the NGS. Although the UEE script concept appears to be a very simple 'wrapper', there are at least three possible areas for misinterpretation that NGS site software installers need to be aware of:

  • Script name. : E.g. SIESTA or SIESTA-MPI for MPI (vs. serial) versions ?
  • Version number : E.g. Is Gaussian G03 C02, GAUSSIAN03_C02 or GAUSSIAN_03_C_02 ?
  • Script behaviour : E.g. Application with many binaries.
    One script "APPNAME_1_1 [bin arguments]"
    or many scripts "BIN-NAME_1_1 [bin arguments]"

The actual interpretation for a given application is irrelevant but all sites must adhere to the same naming and behaviour for resource brokering using the UI-WMS to work. At an NGS Ops meeting in July 2007 it was agreed that all sites would use the interpretation used by RAL for their initial portfolio and then new applications would follow the lead of the first installer (as defined by the NGS OPS board).

A-F G-M N-S T-Z

 
 In the table below <> signifies a required argument, [] signifies optional arguments.

Application Version UEE Name/version API Notes
Abaqus 6.7.1 ABAQUS_6_7_1 ABAQUS job=MyJobName input=std_inst -
Amber 9.0 AMBER_9_0 AMBER <amber-bin> [arguments] -
NCBI BLAST 2.2.26 BLAST-NCBI_2_2_16 BLAST-NCBI <blast-bin> [arguments] -
NCBI Blast Toolbox 25-03-07 BLAST_TOOLBOX
_NCBI_25032007		 BLAST_TOOLBOX_NCBI <binary> [argum ents] -
DLPOLY 2.16 DLPOLY2_2_16 DLPOLY2 [arguments] Dlpoly v2 and v3 are two different
programs not different versions.
DLPOLY 3.16 DLPOLY3_3_16 DLPOLY3 [arguments] Output is on stdout.
UCSF Dock 6.1 DOCK_6_1 DOCK <doc-bin> [arguments] Script selects serial or MPI version based
on environmental variable of number of
requested CPUs.
Emboss 4.1.0 EMBOSS_4_1_0 EMBOSS <emboss-bin> [arguments] Emboss consists of 173 binar ies.
Exonerate 1.4 EXONERATE_1_4 EXONERATE <binary> [arguments] Exonerate consists of 27 bi naries.
Fasta 1.4 FASTA_34_26_5 FASTA <binary> [arguments] FASTA consists of 26 binaries.
Gate 3.1.1 GATE_3_1_1 GATE [arguments] -
Gaussian G03 C02 GAUSSIAN03_C_02 GAUSSIAN03 [arguments] Gaussian 03 is different from 02.
Script sets up GAUSS_LFLAGS env, and scratch dir.
RAL script runs the Linda parallel version only.
Gaussian Utilities G03 C02 GAUSSUTILS03_C_02 GAUSSUTILS03 <binary> [arguments] Used to run formchk, rwfdump etc utilities that come with Gaussian03.
Gromacs 3.3.1 GROMACS_3_3_1 GROMACS <binary> [arguments] Gromacs package has 89 binari es.
GULP 3.1 GULP_3_1 GULP [arguments] Script could select serial or parallel version. RAL only has serial available now.
LAMMPS 10-Aug
-2007		 LAMMPS_070810 LAMMPS [arguments] Script needs to use '-in' argument n ot stdin for input.
MPI Blast 1.4.0 MPI_BLAST_1_4_0 MPI_BLAST <binary> [arguments] MPI Blast has 3 binarie s. Script creates the .ncbirc file
NAMD 2.6 NAMD_2_6 NAMD <binary> <input> [arguments] NAMD package has 5 binaries. Script assumes stdout but not stdin
R 2.4.1 R_2_4_1 R <binary> [arguments] R package has 25 binaries
Root 5.12 ROOT_5_12 ROOT <binary> [arguments] Root has 22 binaries
SABRE 4.0 SABRE_4_0 SABRE [arguments] Script selects serial or MPI version based
on envi ronmental variable of number of
requested CPUs.
v5.0 MPI version must use '-in' argument
Siesta 2.01 SIESTA_2_01 SIESTA <input file> <output file> Script requires input to be $1 and output $2 to launch MPI, not stdin/stdout.
WEKA 3.4.9 WEKA_3_4_9 WEKA [arguments] Script loads java 1.6.0_01 to run weka.
Java 1.6.0 JAVA_1_6_0 JAVA <binary> [arguments] Allows java, javac, javadoc etc from o ne UEE
Octave 2.1.73 OCTAVE_2_1_73 OCTAVE [arguments]  
Gamess-UK 7.0 GAMESS-UK_7_0 GAMESS-UK [arguments] Parallel version of Gamess-UK.
Input is assumed on stdin and output assumed on stdout
Gamess 7.0 GAMESS_7_0 GAMESS [arguments] Serial version of Gamess-UK.
Input is assumed on stdin and output assumed on stdout
PCGAMESS 7.1.4 PCGAMESS_7_1_4 PCGAMESS -i input -o output [arguments] Script overrides -t to set a unique slave-local tempdir based on jobid
CASTEP 4.2 CASTEP_4_2 CASTEP RunName -
CASTEPUTILS 4.2 CASTEPUTILS_4_2 CASTEPUTILS <binary> [arguments] e.g. pdb2cell
CosmoMC 200806 COSMOMC_200806 COSMOMC params.ini  
Bsoft 1.5.4 (64bit) BSOFT_1_5_4 BSOFT <binary> [arguments] e.g. bimg
Bsoft 1.5.4 (32bit) BSOFT32_1_5_4 BSOFT32 <binary> [arguments] e.g. bimg
PFT3DR(pft2) 2.0.4 PFT2_2_0_4 PFT2 [arguments]  
PFT3DR(em3dr2) 2.0.2 EM3DR2_2_0_2 EM3DR2 [arguments]  
Autodock 2.2.2.1 AUTODOCK_4_2_2_1 AUTODOCK [arguments] Autodock and Autogrid are part of the same pkg but have separate UEE's
Autogrid 2.2.2.1 AUTOGRID_4_2_2_1 AUTOGRID [arguments]  
Beast 1.5.3 BEAST_1_5_3 BEAST [arguments] (requires Java)

 

Applications Support

The NGS cannot offer scientific support for applications. However if you require further information or believe there is something wrong with the installation, please contact the NGS support centre.

Acknowledgements

Please note: When publishing work based on use of the NGS, users should acknowledge both the authors of any programs used (see the individual program web sites, or contact the authors directly) and the NGS directly using the following line:
"The authors would like to acknowledge the use of the UK National Grid Service in carrying out this work"
This line must also accompany any use of the NGS logos.

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