Array jobs are not supported on NICS systems. The submission filter will reject jobs which make use of job arrays (i.e. #PBS -t or qsub -t). These jobs (if submitted) will not run and should be deleted.
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.
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
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.
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.
-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
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".
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:
Use hsi -ls to show the tar file in HPSS
Use "htar" to list the contents of the tar file:
>hsi ls -l file.tar
-rw------- 1 username username 12800 Oct 2 2008 file.tar
Use "htar" to extract a single file (name must match what is listed by the above command):
> 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
To retrieve a single directory from HPSS use the -R option. For example,
>get -R dir1