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Non-Distribution Software management VASP

Source codes and corresponding makefiles are located in /usr/local/vasp on all Wolverton clusters. On opteron machines (Barcelona or Shanghai cores), the following combination performs the best: Pathscale compiler suite, GotoBLAS, fftw3, and ATLAS optimized LAPACK, while on intel machines (Clovertown or Nehalem cores) intel products (intel compiler suite, MKL optimized fftw, LAPACK and BLAS) warrants the best performance.

Math libraries

fftw

fftw3 is installed as a package on all clusters. fftw2 is installed on /opt/fftw. A makefile for fftw2 can be found in /repository/cluster/math/make.fftw on josquin. Untar fftw-2.X.X.tar.gz and run make.fftw script the directory and it is installed on /opt/fftw. To link fftw3 or fftw2, one can use -lfftw3 or -lfftw, respectively, in a makefile.

ATLAS

ATLAS optimized LAPACK and (C)BLAS are also installed as a package on all clusters. To use ATLAS optimized lapack and blas, one can use -llapack and -lcblas, respectively.

MKL (Math Kernel Library) from intel

Intel math library is also installed as a package on all clusters at /opt/intel/mkl/{version}. Intel optimized fftw library interface can be found in /opt/intel/mkl/{version}/lib/em64t.

kaien@josquin /opt/intel/mkl/10.0.5.025/lib/em64t $ ls -al libfftw*

-rw-r--r-- 1 root root 102342 May 30 2009 libfftw2xc_gnu.a

-rw-r--r-- 1 root root 94998 Jan 18 16:41 libfftw2xc_intel.a

-rw-r--r-- 1 root root 151160 May 30 2009 libfftw2xf_gnu.a

-rw-r--r-- 1 root root 134232 Jan 18 16:41 libfftw2xf_intel.a

-rw-r--r-- 1 root root 318538 May 30 2009 libfftw3xc_gnu.a

-rw-r--r-- 1 root root 288306 Jan 18 16:40 libfftw3xc_intel.a

-rw-r--r-- 1 root root 520504 May 30 2009 libfftw3xf_gnu.a

-rw-r--r-- 1 root root 443844 Dec 18 10:48 libfftw3xf_intel.a

Gallery

Gallery is also installed as an ubuntu package on /var/www/gallery. Administrator account info is admin/Znj8c7t7. When upload photos on the gallery page, it is recommended to upload a zip file on local directory via secure copy, such as /home/kaien/photos/group_photo.zip, and specify its absolute address in the URL tab.

Refbase

Publications menu in group webpage is running via Refbase and it is installed from tar ball, and linked to /var/www/refbase on encina. Refbase also uses MySQL and following is the MySQL information for refbase on encina:

// The host name of your MySQL installation:

$hostName = "localhost"; // e.g.: "localhost"

// The name of the MySQL database that you're planning to use with the

// refbase package:

// Note: - if there's no existing database with the specified name,

// the 'install.php' script will create it for you

$databaseName = "literature"; // e.g.: "literature"

// The name of the MySQL user that's going to be used with your MySQL

// literature database:

// Note: - this user should be a separate MySQL user (different from the

// user that has full administrative privileges like the root user!)

// - if there's no existing MySQL user with the specified name,

// the 'install.php' script will create this user for you

$username = "litwww"; // e.g.: "litwww"

// The password by which the above MySQL user will be granted access to

// your MySQL literature database:

$password = "%l1t3ratur3?"; // e.g.: "%l1t3ratur3?"

Backup

Local backup

All files on /etc, /home directories are locally backup on /backup (victoria) and /repository (josquin/byrd). Backup script that uses rsync is located in /etc/cron.daily.

josquin cron.daily # cat josquinbackup

#!/bin/bash

# excludes file - this contains a wildcard pattern per line of files to exclude

EXCLUDES=/etc/cron.daily/excludes

for i in /etc /boot /home /opt /usr/local /var

do

rsync -avu --delete --delete-excluded --exclude-from=$EXCLUDES $i --backup /repository/josquin_local > /dev/null 2>&1

done

Certain files are excluded from backup and the exclusion list is in /etc/cron.daily/excludes.

Cross backup between clusters

Wolverton clusters are being cross backuped for emergency situation, or for carelessly lost data.

Note: Data is backed up along the direction of the arrow, i.e. Josquin is backed up on Palestrina. A directory can be found in /backup partition that is being backed in all cluster.

Please refer ‘Unattended rdiff-backup HOWTO’ for details of implementation.

Postfix (mail-server)

Since the internal name of our clusters is all set as master.cl.northwestern.edu, so if one uses normal MTA software, such as sendmail or qmail, then email will be bounce at northwestern server since it cannot find a registered server named master.cl.northwestern.edu. So we use postfix MTA to make an alias. Once install postfix on a cluster, and then modify configuration files (main.cf and master.cf) in /etc/postfix directory (http://www.gentoo.org/doc/en/virt-mail-howto.xml, also refer configuration files on existing clusters). You should be able to start postfix service without any problem.

kaien@josquin ~ $ sudo /etc/init.d/postfix start

* Starting postfix (/etc/postfix) ... [ ok ]

Afterwards, generic file in /etc/postfix has to be updated to create aliases for user address in a cluster.

kaien@josquin ~ $ sudo tail /etc/postfix/generic

wenhao@master.cl.northwestern.edu wenhao@josquin.northwestern.edu

defarr@master.cl.northwestern.edu defarr@josquin.northwestern.edu

wacounts@master.cl.northwestern.edu wacounts@josquin.northwestern.edu

zhang@master.cl.northwestern.edu zhang@josquin.northwestern.edu

daidhy@master.cl.northwestern.edu daidhy@josquin.northwestern.edu

hahansen@master.cl.northwestern.edu hahansen@josquin.northwestern.edu

yongli@master.cl.northwestern.edu yongli@josquin.northwestern.edu

aii982@master.cl.northwestern.edu aii982@josquin.northwestern.edu

jwd686@master.cl.northwestern.edu jwd686@josquin.northwestern.edu

sjk648@master.cl.northwestern.edu sjk648@josquin.northwestern.edu

Make sure that the user list is up-to-date, and don’t forget to recreate generic.db whenever you make a change.

victoria ~ # postmap /etc/postfix/generic