General Questions
Q: How do I get an account on hpcsim?
Hpcsim cluster is reserved for research project. Application must be under the advice of the Project Leader with Assistant Lecturer grade or above.
To apply for an account, you must contact the hpcsim administrators.
Q: How do I connect to hpcsim system?
Only Secured (ssh) connections to the hpcsim system are supported. All insecure methods of connection (rlogin, rsh, telnet) are disabled.
From any computer, issuing the command
ssh [-I login_name] hpcsim.sci.hkbu.edu.hk
or
ssh login_name@hpcsim.sci.hkbu.edu.hk
For an example, ssh user@hpcsim.sci.hkbu.edu.hk
will prompt the user of his/her password and get connected to the hpcsim system. You will log on to the master node and you should be in your home directory which is also accessible by compute nodes.
If your local computer system does not support SSH, please install the SSH software [
SSH or Open SSH] before connecting to hpcsim.
For Microsoft Windows system, a free client called PuTTY is available here:
http://www.chiark.greenend.org.uk/~sgtatham/putty/
Q: How do I change my password?
Use the command "passwd"
% passwd
Every user is recommended to change the password at his/her very first login to the system, as well as at regular intervals.
A good password will have a mix of lower- and upper-case characters, numbers, and punctuation marks, and should be at least 6 characters long. Some people like to put a punctuation mark/number in the middle of a word, e.g., Ha&pp6Y.
Q: How do I transfer files between hpcsim and another computer system?
You must use a utility that used the SSH protocol. Examples are Secure CoPy (scp)and SSH File Transfer Protocol (sftp).
Using "scp", you can use be very flexible in moving data from one computer system to another.
For example, if you want to copy files from the system where you issue the command to a remote destination system, you may use the command
% scp filename1 filename2 user@remote_host:/dest/dir/for/file/
You may also copy a directory recursively, using the option "-r", for example,
% scp -r directory user@remote_host:/dest/dir/
Of course, using "scp" you can also copy files from a remote system to the computer you are logged in. The command would be
% scp user@remote_host:/dir/remotefile /dest/dir/file
Another powerful tool for file transfer is "sftp". Not only "sftp" is secure, it is also much more convenient due to its recursive transfer of directories. On the machine where you are logged in (such as hpcsim), just issuing the command
% sftp remote_host
will establish the connection. Then, if you use the sftp command
sftp> get dir_of_files
you will get all the files under the directory dir_of_file recursively. The sftp commands are very similar to the conventional "ftp". The only thing one should pay particular attention to is that "sftp" must be connected to a machine which is running ssh2 service.
Q: How do I get files from the web to hpcsim?
You can use the command "wget":
% wget http://www.abc.com/file1.doc
Q: Where can I find news about hpcsim?
Read the login message of the day (motd). This is one forum where important changes are announced. We also send out announcement to all users by e-mail about important modifications (such as software upgrade) of the system. We also announced planned system downtimes beforehand so that users can get prepared.
Q: Where should a new hpcsim user get started?
New hpcsim users should read through the HPCSIM web page,
including this FAQ, to familiarize themselves with the system.
Q: Is the data stored on hpcsim automatically backed up?
All the data are backed up by the administrators daily on a backup server. Nevertheless, we should emphasize the different levels of importance of computer data. Most of the data on hpcsim are generated by programs, and could be regenerated, in case of necessity. The source code, on the other hand, are very precious to the developers, and could not easily be regenerated. The users are highly recommended to do everything possible for ensuring those critical material (programs etc.) never be lost. For example, the users should keep multiple copies of these important files on different computer systems, including users' local system. Use "scp" or "sftp" to move your data off hpcsim.
Q: Where can I run X-windows applications from?
Normally, only from master, the hpcsim front-end. This includes: emacs, vim, etc. Please realize that these applications soak up considerable bandwidth. Having to share bandwidth is one of the reasons such applications do not always run smoothly.
Q: How can I remote login to hpcsim through GUI?
You can connect to hpcsim through GUI using VNC viewer. If your local computer is using Windows environment, you can download vncviewer from
http://www.uk.research.att.com/vnc/.
Then you can connect the the cluster by following the instruction listed in this file. Set your research machine hostname as "hpcsim.sci.hkbu.edu.hk".
Q: Can I install software on hpcsim?
Please minimize the installation of downloaded software for personal use. If it is reasonable software to have, it should be installed in /u1/local. Please contact administrator to request software that you need to use.
Q: My job did not clean up correctly what do I do?
Please email to administrator and request that your job be cleaned up. Be sure to include your job ID and do not start any new jobs until the administrator has cleaned up your jobs for you. Also, if you have more than one job running and you wish for the administrator to clean up a subset of the compute nodes please specify which nodes that you want cleaned.
Q: How do I monitor the cluster?
The "frontend" node of the hpcsim cluster serves a set of web pages to monitor its activities and configuration.
(See the hpcism webpage: http://hpcsim.sci.hkbu.edu.hk/.)
The web pages available from this link provide a graphical interface to live cluster information provided by Ganglia monitors running on each cluster node.
The monitors gather values for various metrics such as CPU load, free Memory, disk usage, network I/O, operating system version, etc.
Q: How do I run a shell command on all the compute nodes?
Use the command: cluster-fork [COMMAND]
For example, to check the load on all compute nodes, you would type this:
% cluster-fork uptime
To execute "ps" on all the nodes and check the processes for USER, you would type this:
% cluster-fork ps -U$USER
Q: How do I run a shell command to check the processes on all the compute nodes?
Use the command: cluster-ps [PATTERN]
For example, to check processes of user Sam on all the compute nodes, you would type this:
% cluster-ps Sam (similar function as "cluster-fork ps -USam")
To check which compute nodes are running matlab processes, you would type:
% cluster-ps matlab
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