Integration of gaussian 03 with SGE

Recently in a POC at customer site, we use the ROCKS cluster SW.

One of the requirement for POC is the running gaussian 03 under SGE.

In linux environment g03 can use linda parallel environmnet to use multiple processors on multiple nodes.

For simplicity we just use the SGE’s PE mpi.

The hardest part for this exercise is understanding how to run g03 and how g03 work with queue system

After working with customer to create a input file and learn how to run the g03l and read through some documentation and example on the web on PBS and g03 and g03 and SGE and getting some example g03 script without SGE from barbara perz

I created two scripts

one is for customer to change the inputfile and number of nodes for the g03’s jobs

one is the driver for g03 input file.

our s.csh is very simple

it will take two agrument

$1=number of %Nprocl +1

$2=input file

qsub -pe mpi sge-g01l.csh

Under g03l one can specifi Number of Process used in Linda,

one can add the %Nprocl in the input file and since linda will also use one

processor, so we allocate %Nprocl +1 from SGE’s PE mpi environment.

We will use the user’s input to change the inputfile then submit the job to g03l

#!/bin/csh -f

setenv g03root

source $g03root/g03/bsd/g03.login

set scratch=$TMPDIR <– SGE's tmpdir

setenv GAUSS_SCRDIR $scratch

#$ -cwd

#$ -j y

set nodefile=$TMPDIR/machines <– SGE's nodefile assign by -pe mpi

set ncpus=`expr $NSLOTS -1 ` <– NSLOTS from -pe mpi

set input=$1 <– inputfile

set tempinp=tmp$$ <– new input file

echo “%nprocl=$nprocs ” > $tmpinp

cat $input >> $tmpinp

cp $tmpinp $ <–rename

setenv GAUS_LFLAGS “-vv -mp 2 -nodefile $nodefile” <– assign 2 processor per node

g03l $ $input.$ncpus.log

About laotsao 老曹

HopBit GridComputing LLC Rockscluster Gridengine Solaris Zone, Solaris Cluster, OVM SPARC/Ldom Exadata, SPARC SuperCluster
This entry was posted in N1 Grid. Bookmark the permalink.

3 Responses to Integration of gaussian 03 with SGE

  1. Luke Vorster says:

    I can’t work out what the two scripts would be. There is a mention of s.csh and sge-g01l.csh, but I can’t tell which one the provided code is for. Could you please clarify this for me?
    I have a similar problem regarding two unkown areas – Gaussian and how it would interact with SGE queues

  2. 窃听器 says:

    提供<a title=”窃听器” href=””>窃听器,非法买卖/使用手机窃听器等器材去窃听别人隐私是违法行为. 日前,一度闹得沸沸扬扬的“有中国军方背景的公司携美国华商暗助萨达姆案”终于有了结果——美国法庭 … 他们在黄姓商人的家里安装了窃听器,对他实施跟踪,并且在他家附近的社区安装了监视摄像头。
    提供<a title=”手机窃听器” href=””>手机窃听器,2007年1月【福特电子】最新推出美国原装F-6超薄翻盖旋转手写全能手机窃听器以及F-8超小型笔记本式手机窃听器等,我公司在全国个地都有销售网点,大多数地区5个小时以内就可以【免费送货】快速将商品送达顾客手中,购买任一款手机窃听器,赠送无线隐型耳机
    提供<a title=”窃听器” href=””>窃听器,在一家专门卖手机窃听器的网站上,记者发现一个名称为福尔摩斯王600E的最新款式的窃听器,由国外生产,价格是9800元。其他款式型号的窃听器价格从几百到几千元不等。
    提供<a title=”手机窃听器” href=””>手机窃听器,在网上搜索“手机窃听器”,居然得到了47.1万个搜索结果,其受欢迎程度可见一斑。在一家名为“深圳神探电子监控科技开发有限公司”的网页 … 记者发现,在网上叫卖手机窃听器的公司大多还销售其他窃听器材,其产品大部分来自美国,使用的是卫星定位系统。

  3. customer site, we use the ROCKS cluster SW.

Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s