Center for Earth Surface System Dynamics (CESD) Network User's Guide
Contents
1.Overview of the Network
1.1.Overview of the network
A network for Center for Earth Surface System Dynamics (CESD) , Atmosphere and Ocean Research Institute, the University of Tokyo, can be pictured as follows (Figure 1).
Fig 1: Overview of the network
As in the figure 1, a network for CESD consists of a Mac OSX server, named “orange.local” and a data storage device (“star-pmds.local”).
A data storage device, “star-pmds.local”, is mounted on the server “orange3.local” on a directory “/archive/AORI0001” through “AORI0012”, though if there is no access from “orange3.local” for a certain period of time, the device automatically un-mounts for a power saving mode. Any users, who wish to store a data on the “star-pmds.local”, must be granted permission by administrator prior to their initial use. Basically, the “star-pmds.local” is not suited for a computational work, since it is a storage device (e.g., a frequent access may cause some strains on the machine; therefore, it is best to avoid heavy computations and frequent access to the “star-pmds.local”).
In addition, “orange3.local” has a storage space of 5.0 TB HDD attached to it at “/Volumes/HD1-HD3”. Every user has an access to these devices (HD2 or HD3), though its extensive use is highly discouraged (a large data set should be stored on the “star-pmds.local” instead). On using HDD space, users must create their own directory with their username and store all the files under the directory. The upper limit of use for the HDD device is set at 200 GB per one person, but you can ask the administrator to increase the disk amount. By the way, the upper limit of use for the home directory (/home/Users/) is set at 50 GB per one person, so that you should move your files to the HDD (/Volumes/HD2 or /Volumes/HD3) device if the amount on the home directory exceeds 50 GB.
When users do not input anything during more than three hours, they are forced to logout the system.
1.2.Profiles and directories on each server
orange3.local
- Mac OSX server 10.5
- 8 Intel core 3.00 GHz processors
- HDD are mounted on “/Volumes/HD1 – HD3”, which will be increased in near future.
- “star-pmds.local” is mounted on “/archive/AORI0001-AORI0012”
star-pmds.local
- A power saving data storage device
- Volumes “/archive/AORI0001” through “/archive/AORI0012” are mounted on to directories “/achive/AORI0001” through “/archive/AORI0012” of the “orange3.local”.
2.Understanding the CESD servers
2.1.General notes on how to use
- Please change the initial password (three different devices!) after you receive the e-mail from our administrator.
- Only login by a command “ssh” is allowed.
- Only a “scp” is allowed on file transfer from an external system (which you send us the fixed IP address).
- When users do not input anything during more than three hours, they are forced to logout the system
- Keep in mind that you cannot put large files (>50 GB) on the home directory.
- We don’t have any backup of your files.
- For a security purpose, users are not allowed to access to the storage “star-pmds.local” except when transferring a data file to the device.
2.2 User registration
Prior to new user registration, a system administrator needs to be informed of following information.
- Full name of a user
- Affiliation of a user
- Possible user id name (max: 8 characters)
- One static IP address of a computer that will be connected to the servers
- Contact information (phone number, email address and address)
Full in information above using the file (info_for_account.doc) and send it to Ms. Yamada ( mailto:hiro_yamada<at> aori.u-tokyo.ac.jp). Note that only the computer with a static IP address can be accessed to the CESD servers. Any computers with a dynamic IP address are not allowed to connect to the servers. When a registration process is finished, user accounts are created under an ID name in the servers (“orange3.local”) and a storage device (“star-pmds.local”).
2.3 Initial login
Only login by a command “ssh” is allowed, and if you are not given a prior permission, only a “scp” is allowed on file transfer from an external system.
To login from a registered computer, type a line in command prompt.
ssh –XY (User ID)@cesd2.aori.u-tokyo.ac.jp
Here –XY option is to allow users for use of XWindow. Then, users must type a password that was given by the administrator if you have not yet changed your password.
When the command is successfully executed, user will be in a login home directory of “/Users/(User ID)/”. This is your home directory and it is where you will put your “.bashrc” file and other shell start-up files. In this system, a “orange3.local” is the only server that is connected to the outside, and it is not possible to login directly to a “star-pmds.local” from the outside.
2.4 Initial settings
Initially, passwords are set by the administrator, but users need to create their own password. To do this, while logging in to a “orange3.local” server, write a command line:
passwd
This enables users to change their passwords. Similar steps apply for the “star-pmds.local”. First, by logging in from a “orange3.local” server using a “ssh” as follows:
ssh (user ID)@star-pmds.local (for login to a “star-pmds.local”)
After successfully logging in to a perspective server, again type a command line: “passwd” to change an initial password.
It must be noted that a new password has to be the same in these two machines (“orange3.local” and “star-pmds.local”); otherwise, an error will occurs when transferring a data to the “star-pmds.local”. Also, for this sole purpose of changing passwords, logging in to the system “star-pmds.local” is admitted.
2.5 Setting own working environment
If any user wishes to use some applications (programs or software) on the server, he/she needs to know a specific pass to the application. If such pass is included in the “.bashrc” file, one can only type a name of the application rather than whole path to the application. One such example is shown in a file:
“/Users/Shared/env.bashrc”
In this file, various paths to the applications are shown.
2.6 Data transfer to a storage device “star-pmds.local”
A data storage device “star-pmds.local” is mounted on the “orange3.local” server via network file system (NFS), and permits transferring files from the “orange3.local” using “cp” or “mv” commands. Or a command “scp” can be used to directly transfer files from your computer to the directory “/archive/AORI00**” in the “orange3.local” server. Such a command is shown below:
scp (filename) (user ID)@cesd2.aori.u-tokyo.ac.jp:/archive/AORI0001/…
When an attempt to access to the “star-pmds.local” fails and gives an error saying: “Permission denied”. It is likely that the cause is not due to a system failure, but rather due to a specific characteristic of the data storage itself. As an energy/cost efficient device, the data storage “star-pmds.local” automatically shuts down if there are no accesses to the storage for a longer period of time. And, it would take several minutes to boot up from such an energy saving mode. Thus, the error message will be displayed if the system is still in a middle of booting up. If you encounter such a trouble, the best way is to try an access again after few minutes of wait.
2.7 Running a computationally intensive task
In the machine (“orange3.local”), you can use the following applications: Intel fortran, g95, gnuplot, grads, etc.
2.8 Updating and installing your own software
It is possible to install necessary software under a login home directory, but since an administrator will not be responsible of taking back-ups of any kinds, please use it on your own risk.