Sciblade - User Guides

1. Account
2. Resource
3. System Access
4. Queuing system and job submission
5. File Transfer
6. Data Backup

1. Account

   Sciblade cluster is designed for research projects that require intensive computing power. Researchers of HKBU, CUHK, CityU, PolyU and HKUST required intensive computation are welcome to apply an account in the cluster. To apply for an account you must first contact your campus coordinator, followed by filling the online application form.

2. Resource

   Sciblade consists of 2048 processing cores in total.

   • Maximum number of job running in PBS per user = 8
   • Maximum number of CPUs used per user = 512
   • Default walltime in PBS = 8 hour
     
     

3. System Access

   Loggin in
   

   To login to the sciblade system, use one of the following hostnames or IP address:
   

   blade02.sci.hkbu.edu.hk
   158.182.11.182

   
   Only secured (ssh) connections to the sciblade system are supported. All insecure methods of connection (rlogin, rsh, telnet) are disabled. Users can login to the sciblade cluster using SSH as follows:

   ssh -I [login_name] blade02.sci.hkbu.edu.hk

   or

   ssh login_name@blade02.sci.hkbu.edu.hk

   For an example, ssh user@blade02.sci.hkbu.edu.hk will prompt the user of his/her password and get connected to the sciblade 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 [ Open SSH] before connecting to sciblade.
   For Microsoft Windows system, a free client called PuTTY is available here: http://www.chiark.greenend.org.uk/~sgtatham/putty/
   
   Changing Your Password
   

   You can change your password with the command passwd
   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.

4. Queuing system and job submission

• Queuing System, Sample PBS scripts and Job submission

5. File Transfer

   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 sciblade), 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. To use secure copy from Windows platforms, download a copy of WinSCP (freeware) or SSH Secure File Client.

6. Data backup

   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 sciblade 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. It is your responsibility to back up critical data! Please maintain your own copy of important data stored in the cluster. 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. The following example illustrates a directory move from a local machine to the cluster:

   1. Create a copy of the local directory with tar (the time to do this depends upon the sizes and number of files, etc.):

      % tar -cf name-of-your-file.tar directory_to_be_transfer

   2. Compress tar file with gzip (this step may not be necessary if your file is small):

      % gzip name-of-your-file.tar

      This creates a compressed tar file with the name name-of-your-file.tar.gz
   3. Use "scp" or "sftp" to move your data to sciblade

      % scp name-of-you-file.tar.gz your_login_name@sciblade.sci.hkbu.edu.hk:.

   4. Login sciblade, then uncompress tar file:

      %ssh sciblade.sci.hkbu.edu.hk
      %gunzip name-of-your-file.tar.gz

   5. Move tar file to the desired location on the cluster and untar:

      % tar -xf name-of-your-file.tar