FAQ

Table of Contents

Special Requests

Project Information

User Environment

General

Logging in

Data Transfer

Special Requests

How do I file a special request for longer wall time, higher priority, larger disk quota, etc.?

Special request forms are available on the special requests page. This page contains links to the different special request forms along with information on which form to submit for various requests.

Do I have a quota on my home directory? How much is it? Can it be increased?

All users start with a 2 GB quota on their home directory. We realize that this may not be sufficient for all users, but it is for most. If you absolutely must have more home disk space (remember you can use HPSS for archival purposes), then you will need to complete the relevant form on the special requests page.

You can check your home directory quota by first logging into the system home, and then running the quota command. You’ll get a response like the following:

$ quota
Disk quotas for user user1 (uid 12345):
     Filesystem  blocks   quota   limit   grace   files   quota   limit   grace
nccsfiler1a.ccs.ornl.gov:/vol/home
                  32500  2097152 2097152            2405  4294967295 4294967295

Project Information

How do I list all projects for which I am a member?

You can use the showproj utility to view all projects for which you are a member.

How do I view my allocation and usage?

Users can view their allocation and usage on allocated systems using the showusage utility. showusage returns year-to-date usage and allocation for the calling user’s allocated project(s). Usage is calculated from the first day of the fiscal year through midnight of the day before the request. The utility can be executed from the command line using the following arguments:

  1. h, -help: Lists available flags and usage.
  2. s <system>: Shows usage for specified system. Where system is “Jaguar,” “Phoenix,” “Ram,” or “all.” The “all” option will return usage for each of the listed systems. If -s is not specified, it will return usage for this system.
  3. p <project>: Shows usage for specified project. If -p is not specified, it will return all projects for which the calling user is a member.
  4. f: Lists usage for all members of a project. If not specified, only calling user’s usage is specified.

For example, to view your allocation and usage for all projects for which you are a member on Jaguar, use the following:

showusage -s jaguar

User Environment

I accidentally deleted some files. Can I get them back?

It depends on where the files were and how recently they were created. Scratch directories (/tmp/work/$USER) are not backed up at all, so any files deleted from those directories cannot be recovered. Home directories are different. Every user’s home directory contains a subdirectory, .yesterday. This is a read-only copy of the home directory from the previous day. (The backup is made each morning at 4 a.m.) If the files you deleted were created before that backup, you may be able to recover them from .yesterday.

How do I remove the Control-M characters in my text file?

Different operating systems use different methods of indicating the end of a line in a text file. UNIX uses only a new line, whereas Windows uses a carriage return and a line feed. If you have transferred text files from your PC to a UNIX machine, you may need to remove the carriage-return characters. (The line-feed character in Windows is the same as the new-line character under UNIX, so it doesn’t need to be changed.) Some systems provide a command dos2unix that can perform the translation. However, it can also be done with a simple perl command. In the following example, win.txt is the file transferred from your PC, and unix.txt is the new file in UNIX text format:

perl -p -e 's/r$//' <win.txt >unix.txt

How do I change my default limits for stack size, core file size, etc.?

When you connect to a system, your environment is set up with default limits for stack size, core file size, number of open files, etc. The system sets both soft and hard limits for these parameters. The soft limit is the actual limit imposed by the system. Thus, the soft stack limit is the maximum stack size the system will allow a process to use. However, users occasionally need to increase the default limits. This is where the hard limit becomes important. The system allows users to increase their soft limits, but it uses the hard limit as the upper bound. So, users cannot increase their soft limit to a value greater than their hard limit. Additionally, users cannot increase their hard limits (although they can decrease the hard limit). Note that if you decrease your hard limit, the restriction on increasing hard limits will apply to the value you set. Thus, if you reset your hard limit on stack size from unlimited to 128 MB, you will not be able to increase this hard limit beyond 128 MB (even though the original hard limit was unlimited). Once a hard limit has been decreased, the only way to return to the original value is to reconnect to the system.

The command to modify limits varies by shell. The C shell (csh) and its derivatives (such as tcsh) use the limit command to modify limits. The Bourne shell (sh) and its derivatives (such as ksh and bash) use the ulimit command. The syntax for these commands varies slightly and is shown below. More detailed information can be found in the man page for the shell you are using.

Basic Limit Operations

Operation sh/ksh/bash command csh/tcsh command
View soft limits ulimit -a
or
ulimit -S -a		 limit
View hard limits ulimit -H -a limit -h
Set stack size to 128 MB (131072 kB) ulimit -S -s 131072 limit stacksize 128m

By default, the ulimit command changes both hard and soft limits. Thus, if you were to use

ulimit -s 131072

both your hard and soft limits would be changed. In this case, you could change your hard limit because you are decreasing it. However, if you later realized that you needed 256 MB of stack size, you would have to log out and log back in so that you could change the stack size. This is because that command would have set the hard limit of your stack size to 128 MB, and users cannot increase a hard limit. To work around this, the -S flag should be used when changing limits via ulimit. The -S flag instructs ulimit to change only the soft limit. So, to set only your soft limit for stacksize, you would use

ulimit -S -s 131072

By default, the limit command changes only your soft limit. It must be called with the -h flag to change your hard limit. Thus, the command

limit stacksize 128m

will change only your soft limit. If you later need to increase the soft limit, you will be able to do so. However, when you use the -h flag, you will set the hard limit and will not be able to increase it later. The command

 limit -h stacksize 128m

sets the hard limit to 128 MB.

With any shell, you can always reset both soft and hard limits to their default values by logging out and back in.

How do I find out what macros are predefined by the compiler?

For the Cray systems (Phoenix and Jaguar) consult the “Cray online documentation” (http://www.cray.com/craydoc).

For C, search for the Cray “C and C++ Reference Manual”; and for Fortran, consult the “Cray Fortran Compiler Commands and Directives Reference Manual”.

How do I use the modules utility?

For information on modules, see the modules page.

Why doesn’t the backspace key work as expected?

If backspace produces ^? instead of what you expect, use the following to fix it at the command prompt:

stty erase <press backspace key>

You can put this in your .profile (ksh) or .login (csh) file so upon logging it automatically will be set. This stty command should also be executed only for interactive shells, not batch.

Another tactic is to change the configuration of your SSH client. For instance, if you are using Putty SSH from a Windows system, the default backspace key is <control>-?. This can be changed by going to the keyboard category and changing backspace to be <control>-H.

General

How do I activate and use my RSA SecurID?

For instructions on activating and using your RSA SecurID, see the connecting page.

Logging in

Why does my SSH connection fail? Why does SSH report that no authentication methods are available?

Your SSH client may not be set up to use the keyboard-interactive authentication method. You will need to use a client that supports the keyboard-interactive authentication method to connect to the NCCS computers. Different SSH clients will have different ways of setting the preferred authentication methods, so you may need to contact your system administrator to get your client set correctly.

Why do I get the error “init.c(375):ERROR:50: Cannot open file ” for ‘append’” when I log in?

This message usually means that you are at or near your home directory quota and that some part of the login process was trying to write there. This is often caused when the modules utility is loaded because it needs to write files to your home directory. You will need to reduce the usage in your home directory to log in successfully.

You may also notice that after getting this message, some commands cannot be found. This is due to the way C shell handles errors. For more information, see “I received an error when I logged in, and now the system can’t find commands. Why?“

I received an error when I logged in, and now the system can’t find commands. Why?

When the C shell (or one of its derivatives, such as tcsh) is starting up and encounters an error in one of its initialization files, it stops processing its initialization files. So, any aliases, environment settings, etc., that occur after the line that caused the error will not be processed. For help in troubleshooting the startup files, contact the User Assistance Center.

Data Transfer

How do I transfer data between the NCCS and other UNIX-based systems?

The SSH-based SCP and SFTP utilities can be used to transfer files to and from NCCS systems.

For larger files, the multistreaming transfer utility BBCP may be used. The BBCP utility is capable of breaking up your transfer into multiple simultaneously transferring streams, thereby transferring data faster than single-streaming utilities such as SCP and SFTP.

For more information on data transfers, see the remote data section of the data management page.

Why does SFTP exit with the error “Most likely the sftp-server is not in the path of the user on the server-side”?

See the answer to the next question.

Why does sftp exit with the error “Received message too long 1500476704″?

Examples of this error are

File transfer server could not be started or it exited unexpectedly.
Exit value 0 was returned. Most likely the sftp-server is not in the path of the user on the server-side.orReceived message too long 1500476704

These errors are usually caused by commands in a shell run-control file (.cshrc, .profile, .bashrc, etc.) that produce output to the terminal. This output interferes with the communication between the SSH daemon and the SFTP-server subsystem. Examples of such commands might be date or echo. If you use the mail command to check for mail, it can also cause the error.

You can check to see if this is likely the problem. If you are unable to SFTP to a machine, try to connect via SSH. If you are able to SSH, and you receive output to your terminal other than the standard login banner (for example, “You have mail”), then you need to check your run-control files for commands that might be producing the output.

To solve this problem, you should place any commands that will produce output in a conditional statement that is executed only if the shell is interactive. For C shell users, a sample test to put in your .cshrc file would be

if ($?prompt)
  date
endif

The equivalent command for your .profile file (ksh/bash) would be

if [[ -n $PS1 ]]; then
 date
fi