The National Institute for Computational Sciences


General: Why does my submitted job die with strange shell errors?

The shell initiation line in PBS scripts is not guaranteed to be used to determine the interpreting shell. The default behavior is to use the user's default login shell or the value of the PBS option -S (i.e. #PBS -S /bin/bash or qsub -S /bin/bash). If you are using a shell for a PBS script which is different than your default shell, please use the PBS -S option.

General: Why do I get 'no space left on device' error when writing from Fortran?

Your Fortran program may be writing a large file of stripe size 1, resulting in an error like:

forrtl: No space left on device, forrtl: severe (38): error during write, unit 12, file /lustre/medusa/$USER/...

Move the partially transferred file elsewhere or delete it. Then, cd to the directory where the partially transferred file once was. Issue the following command to change the striping of the directory:

lfs setstripe . -c 8

General: What should I do in the event of a lustre slowdown?

In the event of a lustre slowdown, there are many things to consider as lustre has many working parts and is shared by all users on the system. NICS continually monitors lustre's performance and seeks to improve researcher's data communications. If you notice your code's I/O performance or the lustre filesystem is slower than usual, please answer the following questions to the best of your knowledge and email XSEDE Help Desk your answers.

HPSS (Darter and Nautilus): How do I share my files on HPSS with other members of my research team ?

To find out what groups you are a member of on HPSS use the groups command.

K:[/home/username]: groups
K:HPSS Group List:
  1045: nsf008       1928: nsf008q4s 

This shows the user is a member of groups nsf008 and nsf008q4s.

If other members of your team are listed in the same group you can simply log into HPSS using HSI and change the group and permissions to share the files or directories.

For example, if both you and other members are all in nsf008q4s you will simply need to do a chgrp.

General: When should I use the PBS option '-V'?

The -V option tells the batch system to remember all of your environmental variables. For example, if I want to set OMP_NUM_THREADS to 4 and then submit the job, I need this flag so that OMP_NUM_THREADS is still set in the batch script. You can use it as a flag such as qsub -V ... or in your batch script like:


While this can be convenient, it is best practice not to use -V. Why?

General: Why can't I forward X11 connections with GSI on Mac OSX?

Apple handles the local "DISPLAY" variable necessary for X11 connections differently than Linux/Unix, therefore older versions of gsissh had trouble parsing the variable, yielding this error:

$ xlogo
/tmp/launch-xZ1piK/: unknown host. (no address associated with name)
X connection to localhost:14.0 broken (explicit kill or server shutdown).

Note that if the remote DISPLAY variable had been broken, it would have given the error "Can't open display".

HPSS (Darter and Nautilus): How do I verify the contents of an archive during creation?

HTAR provides the “-Hverify=option[,option...]” command line option, which causes HTAR to first create the archive file normally, and then to go back and check its work by performing a series of checks on the archive file. You choose the types of checks to be performed by specifying one or more comma-separated options. The options can be either individual items, or the keyword “all”, or a numeric level between 0, 1 or 2. Each numeric level includes all of the checks for lower-valued levels and adds additional checks. The verification options are:

HPSS (Darter and Nautilus): How do I retrieve a single file from HPSS?

Use hsi -ls to show the tar file in HPSS

>hsi ls -l file.tar
-rw-------   1 username     username          12800 Oct  2  2008 file.tar
Use "htar" to list the contents of the tar file:
> htar -tvf file.tar
HTAR: drwxr-xr-x  username/nicsstaff          0 2008-10-02 10:47  dir2/
HTAR: -rw-r--r--  username/nicsstaff       1492 2008-10-02 10:47  dir2/data.pbs
HTAR: -rw-r--r--  username/nicsstaff       1924 2008-10-02 10:47  dir2/mpi.pbs
Use "htar" to extract a single file (name must match what is listed by the above command):


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