Lychee: Difference between revisions
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== Known Issues/Solving Problems == | == Known Issues/Solving Problems == | ||
=== High Load === | === High Load/Monitoring Network Traffic === | ||
The command /usr/sbin/iftop may be run by anyone in groups BMMG, MDGroup, SBeatson, KobeLab. This is to determine what the network traffic is doing. This was enabled by adding the following lines to /etc/sudoers: | The command /usr/sbin/iftop may be run by anyone in groups BMMG, MDGroup, SBeatson, KobeLab. This is to determine what the network traffic is doing (nfs activity can cause a high load). This was enabled by adding the following lines to /etc/sudoers: | ||
<code><pre> | <code><pre> | ||
%BMMG ALL=/usr/sbin/iftop | %BMMG ALL=/usr/sbin/iftop |
Revision as of 03:54, 3 June 2009
Lychee
lychee
is one of our servers. This document provides a full description of its services. If a service is moved to another server, please just move the corresponding description to its page.
Software
/marksw
/marksw/
contains a large selection of pre-compiled software for use by the group. Each package is found in /marksw/$NAME/$VERSION/
. The source code and details of how the software was built is in /marksw/$NAME/$VERSION/SOURCE
. In the bash (csh) configuration file /marksw/BASHRC
(/marksw/CSHRC
), is a simple shell function, module
, which can be used in the following ways:
module avail
module $NAME/$VERSION ...
The first use lists the possible $NAME/$VERSION
options for the second use. The second use simply adds for each $NAME/$VERSION
argument, /marksw/$NAME/$VERSION/bin
and /marksw/$NAME/$VERSION/sbin
to the beginning of the contents of the PATH environment variable; /marksw/$NAME/$VERSION/lib64
and /marksw/$NAME/$VERSION/lib
to the beginning of the contents of the LD_LIBRARY_PATH environment variable; and /marksw/$NAME/$VERSION/man
to the beginning of the contents of the MANPATH environment variable.
The module
command is sourced in the global bash configuration file /etc/bashrc
and in the global csh configuration file /etc/csh.local
.
Yum
Yum Repositories
Repository Software Installed
zsh yum-utils OpenIPMI OpenIPMI-tools
/opt
Rasmol
- Download source from [1]
- tar -xzvf RasMol_Latest.tar.gz
- cd Rasmol_2.7.4.2_23Mar08/src/
- Edit Imakefile:
- LDLIBS = -L/usr/lib64 '...'
- Make sure /usr/lib64/libforms.so exists (package xforms-devel doesn't actually create symbolic links correctly)
- ./build_all.sh
- Move rasmol_32BIT to /opt/bin/rasmol
Acrobat
- rpm -iv http://ardownload.adobe.com/pub/adobe/reader/unix/9.x/9.1/enu/AdbeRdr9.1.0-1_i486linux_enu.rpm
- ln -s /opt/Adobe/Reader9/bin/acroread /opt/bin/acroread
VMD
- Done by Mitch/AJ
Pymol
- Done by Mitch/AJ
AMD Core Math Library (ACML)
- Download from here
- Extract & run ./install-acml-4-2-0-gfortran-64bit.sh
- Licence? accept
- Location (/opt/acml4.2.0)? [Enter]
Install SystemImager Image Server (for Imaging Workstations)
The following relates to the once-off installation of systemimager for serving images. See CentosWorkstation for information as to the actual use of systemimager for getting the images onto the image server for serving.
- yum install perl-AppConfig
- rpm -iv systemconfigurator-2.2.11-1.noarch.rpm systemimager-common-4.1.6-1.noarch.rpm systemimager-server-4.1.6-1.noarch.rpm systemimager-x86_64initrd_template-4.1.6-1.noarch.rpm systemimager-x86_64boot-standard-4.1.6-1.noarch.rpm
- mkdir -p /systemimager/{images,overrides,tarballs,torrents}
- Edit /etc/systemimager/systemimager.conf:
- DEFAULT_IMAGE_DIR = /systemimager/images
- DEFAULT_OVERRIDE_DIR = /systemimager/overrides
- AUTOINSTALL_TARBALL_DIR = /systemimager/tarballs
- AUTOINSTALL_TORRENT_DIR = /systemimager/torrents
- Edit /etc/systemimager/pxelinux.cfg/syslinux.cfg to ensure boot CD has enough memory (otherwise we get
swapper: page allocation failure. order: 0, model: 0x20
errors):- Change ramdisk_size=120000
- Make sure firewall allows incoming connections to port 873/TCP (for serving images over rsync)
- We don't use the tftp server for network booting the workstations as we don't have access to the DHCP server for the MD VLAN, rather a boot CD is created (or Grub is used). See CentosWorkstation for details.
- Turn on image server for permanent operation:
- chkconfig systemimager-server-rsyncd on
Backups
- Root's crontab on lychee states:
0 23 * * sun /marksw/scripts/0.1/backup_dir /home/
0 22 * * sat updatedb
- This runs a very basic rsync copy of /home/ to cirrus.hpcu.uq.edu.au
- updatedb updates the file database used by the
locate
command
Known Issues/Solving Problems
High Load/Monitoring Network Traffic
The command /usr/sbin/iftop may be run by anyone in groups BMMG, MDGroup, SBeatson, KobeLab. This is to determine what the network traffic is doing (nfs activity can cause a high load). This was enabled by adding the following lines to /etc/sudoers:
%BMMG ALL=/usr/sbin/iftop
%MDGroup ALL=/usr/sbin/iftop
%SBeatson ALL=/usr/sbin/iftop
%KobeLab ALL=/usr/sbin/iftop
To read the network usage on the MD VLAN interface on lychee run:
sudo /usr/sbin/iftop -i eth0
To read the network usage on the cluster interface on lychee run:
sudo /usr/sbin/iftop -i eth2
Fedora-DS
Fedora-ds runs out of open file descriptors (default 1024) very quickly. The default value has been changed to 8192, allowing the system to survive longer but it still runs out after months. When this problem happens, all workstations freeze. Restarting fedora-ds will temporally fix the problem (/etc/init.d/fedora-ds restart
and wait a little while).
See here for reference.
NFS
If lychee is rebooted, NFS mounts from clients to lychee's NFS exports get stale. To fix this, you can try on the client:
mount -o remount -a
If this doesn't work the client has to be rebooted. Lychee's NFS can be restarted by /etc/init.d/nfs restart
.