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FAQ

See also: Kraken FAQ.

Table of Contents

Project Information

User Environment

General

Logging in

Data Transfer

Project Information

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

You can use the showusage 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 kraken;: Shows usage for Kraken.
  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 Kraken, use the following:

showusage -s kraken

User Environment

How do I change my shell?

Users may use the default bash or tcsh login shell. To change your login shell, use the ldap_chsh command. You will be prompted for your password—enter your static password, the one you would use to log in to the *-pwd nodes. It will then prompt you for the shell you wish to use, enter /bin/bash or /bin/tcsh.

Other shells (such as ksh, zsh) are available for scripts and interactive use (type ksh), but not as login shells.

Vi is unresponsive

If vi appears to hang, but other commands (ls, cat, etc) work normally, try renaming the the .viminfo file:

mv ~/.viminfo ~/.viminfo.bak

This file saves the state of vim, but can sometimes appear to get corrupted. It may be that the old version of vim on the XT4 is unable to read the .viminfo created by the new version on the XT5.

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 (/lustre/scratch/$USER) are not backed up at all, so any files deleted from those directories cannot be recovered. Home directories are different. Please contact NICS support if you have inadvertently deleted a file in your home area.

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. For example, 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. Users cannot increase their hard limits. They can decrease the hard limit, but its not recommended.

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.

Limit commands

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

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 Kraken consult the “Cray online documentation” (http://docs.cray.com).

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.

How can I set my environment using .modulerc??

Some sites recommend using the .modulerc file to set your default modules. Do not do so on Kraken: the .modulerc file is read every time module is called. This causes issues with some of the Cray software, the global default module list, and can lead to unexpected results (if you unload a module in the .modulerc file, it will be re-loaded next time you use the module command). Instead, set your default environment in your .bashrc file (or analogue). It is best to send the output (stderr in particular) to a log or /dev/null to prevent .bashrc from printing anything, which may cause errors.

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 NICS 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.

I am trying to use GridFTP/GSISSH and I am getting an error: "Untrusted self-signed certificate in chain with hash..." What is going wrong?

Globus is unable to find the correct certificate to authenticate: most likely, you have a ~/.globus/certificates directory which is overriding the system defaults. If this directory exists, rename it and try again. Within the TeraGrid, these certificates are managed for you, so you should not need a certificates directory.

If you do need it for regular transfers to non-TG sites, you can generally get the certificate from the /etc/grid-security/certificates directory—the name of the file is given by the error message: Untrusted self-signed certificate in chain with hash <filename>. 

cp /etc/grid-security/<filename> ~/.globus/certificates

These certificates may be changed without notice, so you will periodically have to remove and replace expired certificates.

Data Transfer

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

The SSH-based SCP and SFTP utilities can be used to transfer files to and from NICS 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