Commonly used qstat options

Commonly used Qstat Options

 Options Description
qstat -i Display jobs that are non-running in alternative format
qstat -r Display jobs that are running
qstat -n In addition to basic information, it also provide information of nodes allocated to the job listed.
qstat -u users(s) Display jobs of a user or users
qstat -Q Status of queues
qstat -Q -f Full status of queues in the alternative format
qstat -q Status of queues in the alternative format
qstat -B Batch server status
qstat -B -f Full batch server status including configuration

High Performance Data Transfers on TCP/IP

This writeup is a summary of the excellent article from Pittburgh Supercomputing Centre “Enabling High Performance Data Transfers

According to the article, there are five networking options that should be taken into consideration

  1. “Maximum TCP Buffer (Memory) space: All operating systems have some global mechanism to limit the amount of system memory that can be used by any one TCP connection. [more][less]”
  2. “Socket Buffer Sizes: Most operating systems also support separate per connection send and receive buffer limits that can be adjusted by the user, application or other mechanism as long as they stay within the maximum memory limits above. These buffer sizes correspond to the SO_SNDBUF and SO_RCVBUF options of the BSD setsockopt() call. [more][less]”
  3. “TCP Large Window Extensions (RFC1323): These enable optional TCP protocol features (window scale and time stamps) which are required to support large BDP paths. [more][less]
  4. TCP Selective Acknowledgments Option (SACK, RFC2018) allow a TCP receiver inform the sender exactly which data is missing and needs to be retransmitted. [more][less]
  5. Path MTU The host system must use the largest possible MTU for the path. This may require enabling Path MTU Discovery (RFC1191, RFC1981, RFC4821). [more][less]

Under Linux Section, the article mentioned that for Linux

Recent versions of Linux (version 2.6.17 and later) have full autotuning with 4 MB maximum buffer sizes. Except in some rare cases, manual tuning is unlikely to substantially improve the performance of these kernels over most network paths, and is not generally recommended

Speeding up SSH connections

Suggestion 1: Resolving SLOW Login by turning off reverse DNS Lookup for OpenSSH

If you are facing slow login times, it might be due to reverse DNS is not responding quick enough. This system can show up on your log file

# tail -50 /var/log/secure

You will notice that there is a time lag from accepting the key to opening a session

Sep  6 10:15:42 santol-h00 sshd[4268]:
Accepted password for root from 192.168.1.191 port 51109 ssh2

Sep  6 10:15:52 santol-h00 sshd[4268]: pam_unix(sshd:session):
session opened for user root by (uid=0)

To fix the issue, you should modify the /etc/ssh/sshd_config file

# vim /etc/ssh/sshd_config

At /etc/ssh/sshd_config, change UseDNS  no

#ShowPatchLevel no
UseDNS no
#PidFile /var/run/sshd.pid

Restart the ssh service

# service sshd restart

Feel the login speed 🙂


Suggestion 2: Speeding up multiple ssh connections with ControlMaster

I’m assuming you are using OpenSSH 4.

If you are make multiple connections to the same server, you can enables the sharing of multiple sessions over a single network connections. In other words, the additional sessions will try to reuse the master instance’s connection rather than initiating new ones.

Step 1: Create a config file in your ~/.ssh directory. Make sure the permission is readable and writable by the owner only ie permission of 600

Step 2: Add the following lines

Host *
   ControlMaster auto
   ControlPath ~/.ssh/master-%r@%h:%p

ControlMaster auto Tries to start a master if there is no existing connection
or it will use an existing master connection.

ControlPath is the location socket for the ssh processes to communicate among
themselves. The %r, %h and %p are replaced with your user name, the host to which
you’re connecting and the port number—only ssh sessions from the same user to
the same host on the same port can or should share a TCP connection,
so each group of multiplexed ssh processes needs a separate socket.

Step 3a: To test the configuration, start an ssh session and keep it connected, you should see something like

...........
debug1: setting up multiplex master socket
debug1: channel 0: new [client-session]
...........

Step 3b: Launch another ssh connection to a the same server with the same userid

....................
debug1: auto-mux: Trying existing master
...................

Much of the materials come from  Speed Up Multiple SSH Connections to the Same Server (Linux Journal).


Suggestion 3: Speeding and Compressing X forwarding Traffic

To run the an X application over SSH connection, you can use the

$ ssh -X user@computername.com

Do note that for the remote Server shich you are connecting to must have X forwarding enabled. To configure, go to /etc/ssh/ssh_config/

X11Forwarding yes

If the SSH is setup with trusted X11 Forwarding ie in the /etc/ssh/ssh_config file,

ForwardX11Trusted yes

You can compress and speed up the X forwarded connection

$ ssh -Y -C user@computername.com
  • -Y to enable trusted X11 forwarding. Trusted X11 forwardings are not subjected to the X11 SECURITY extension controls. So it will boost speed.
  • -C to compress the data

Suggestion 4: Tuning TCP/IP and Patching SSH with HPN-SSH

Good read-up to tune your SSH connections.

  1. High Performance Data Transfers on TCP/IP
  1. High Performance SSH/SCP – HPN-SSH

Installing Grace (xmgrace) on CentOS 5 and 6

For further information on what is Grace ( xmgrace ) and some notes during installation. Do read the blog entry

  1. Grace plotting tool for X Window System 
  2. Compiling Grace: checking for a Motif >= 1002 compatible API… no

For installing in a nutshell on CentOS 5 and CentOS 6.

./configure --enable-grace-home=/opt/grace \
--with-extra-incpath=/usr/local/include:/opt/include \
--with-extra-ldpath=/usr/local/lib:/opt/lib \
--prefix=/usr/local

–enable-grace-home=DIR      define Grace home dir [PREFIX/grace]
–with-extra-incpath=PATH    define extra include path (dir1:dir2:…) [none]
–with-extra-ldpath=PATH     define extra ld path (dir1:dir2:…) [none]

 

Compiling,

make

Testing

make tests

Installation

make install

Making links

make links

References:

  1. Encountering the pars.yacc:5426 error when installing Grace 5.1.23 on CentOS 5

Understand parameters in /etc/fstab

Exemplar for fixed media file system

Read an interesting article from Dr. Brown’s Administration (January 2012 Edition). I have used the material inside to

If you look at your /etc/fstab file,  you may be wondering what are those parameter settings in the

LABEL=/home             /data                   ext3    defaults        1 2

Column 1 (“LABEL=/home“) – Label assigned to the filesystem when it was created

Column 2 (“/data“) – Mount point within the directory

Column 3 (“ext3“) – Type of filesystem. Supported types includes ext2, ext3, ext4, reiserfs, isi9660,nfs etc

Column 4 (“defaults”) – Mount Options. Valid options depend on the filesystem type

Column 5 (“1”) – Interpreted by the dump command if you use it to make backup (1 = Make backups, 0 = Do not)

Column 6 (“2”) –  The order in which fsck will check the filesystem at boot time. ( 1 = the root partition, >1 = non-root partition), 0 = no check which is appliable for removable media or NFS)

 

Exemplar for movable media

/dev/sdd    /media/dvdrom    auto   ro, noauto, user 0 0

Column 1 (“/dev/sdd”) – The name of the dvd-rom device

Column 2 (“/media/dvdrom”) – The mount point

Column 3 (“auto”) – Tell the kernel to determine the filesystem type automatically

Column 4 (“ro, auto, user”) –

  • ro -> read only
  • noauto -> don’t mount boot time
  • user non-root users can mount it (for security, the following option are implied
    • nosuid (do not honour the set-user-id bit on files)
    • nodev  (do not honour device file entries)
    • noexec (do not treat files as executable)

Column 5 and Column 6 as above.