QUEEN

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Description

Nuclear Overhauser effect (NOE) data are an indispensable source of structural information in biomolecular structure determination by NMR spectroscopy. Program QUEEN serves for quantitative evaluation of experimental NMR restrains. Program QUEEN for proper running needs program X-Plor.

Availability

Version 1.1

Use

Load module queen ("module ad queen") and run queen (in case you are using CHARON system, you have to use command "metamodule" to load this program). some solved questions are available on the FAQs.

Way of loading a configuration

In original program file queen.conf is read from the directory with program, in installed version you are allowed to set a path to you own configuration file into environment variable QUEEN_CONF. In case that standard configuration comply with all you needs except of settings of project directory, you can set this directory into environment variable Q_PROJECT and make no changes into QUEEN_CONF.

For program efective running you have to put subdirectory "log" in assigment (item Q_LOG in queen.conf) into the fastest storage -- e.g. on a scratch volume (in a directory dedicated for a job -- identified by the $SCRATCHDIR environment variable) or in a /storage volume.

There are available a standard program queen.py and new created script "queen", which after setting the same parametres as in the one processor job, make initialization of MPI, parallel computing on all processor which was mentioned in the assigment of the job and finally cancel MPI environment (cancel assistant processes)

Suppored platforms

QUEEN is availaible (and runs in primary mode) for all platforms in MetaCentrum exept of SGI (so in: 386, x86_64 a ia64 (Itanium)) and runs also for paralell running (through more processors or more nodes).

Documentation

http://www.cmbi.ru.nl/software/queen/

Program administrator

meta@cesnet.cz

Homepage

http://www.cmbi.ru.nl/software/queen/

FAQs

Q:I can not run queen properly at testing example (see /home/pavelm/queen/test) In case I run queen locally in directory /home/pavelm/queen/test (by command "queen --Iuni example noe") the job runs properly, in case I want to queue the job, it fails with error message: "ERROR - Dictionary /home/pavelm/queen/test/queen.conf could not be read. Script has been stopped." I tryied to run this script by psubmit and also by qsub in normal queue ("qsub -q normal run" nebo "psubmit normal run"). Script contains both "metamodule add queen" and setting of path to configuration file into environment variable QUEEN_CONF ("QUEEN_CONF=/home/pavelm/queen/test/queen.conf;export QUEEN_CONF"). Script to execute is following:

metamodule add queen

Q_PROJECT=/home/pavelm/queen/test/ export Q_PROJECT QUEEN_CONF=/home/pavelm/queen/test/queen.conf export QUEEN_CONF

  1. export Q_PROJECT=/home/pavelm/queen/test/
  2. export QUEEN_CONF=/home/pavelm/queen/test/queen.conf

queen --Iuni example noe Unfortunatelly I can not learn why my configuration file can not be read.

A:Path which is set into QUEEN_CONF must be available from machine, where PBS ran your job (in case of parallel jobs from all nodes), so path /home/pavelm/... is local for clusters (leads on different clusters to different disks) Either put queen.conf into your directory in AFS(/afs/ics.muni.cz/home/pavelm, or /home/pavelm/shared) this directory is seen from all MetaCentrum machines, or limit running of job just to machines, which have access to your directory. E.g: by option PBS -l brno (-l ...:brno) if you have it in /home on skirit or perian.

...For program efective running you have to put subdirectory "log" in assigment (item Q_LOG in queen.conf) into the fastest storage -- e.g. on a scratch volume (in a directory dedicated for a job -- identified by the $SCRATCHDIR environment variable) or in a /storage volume.

Q:I linked through Q_LOG on $SCRATCHDIR ... I want to ask, if I can apply above described use of $SCRATCHDIR to parallel job in program xplor-nih.


A:According documentation (/afs/ics.muni.cz/software/xplor-nih-2.20/parallel.txt) you have to have a directory shared by all used nodes using program xplor in parallel mode. The best way should be to use the shared scratch volume (available just at the mandos cluster -- the dedicated space is identified by the $SCRATCHDIR environment variable), or to use a NFSv4 volume within the /storage directory. By the way, QUEEN must be able to read assingment from all nodes (e.g. it could be copied for just for reading), but subdirectory log could and it is sufficient to be on each node local, because some parts of a job run in it as separely runned xplor instance which communicate with queen local processes through files. Result of whole job is written just by main process.