|
Q: Why
are my sessions getting killed?
Q: Where
do I compile code?
Q: How do I
submit a job?
Q: How
long does each job run?
Q: What
sort of performance can I get?
Q: What
useful commands are there for checking job status?
| qstat -n |
Lists nodes on which jobs are running. |
| qstat -a |
Shows all running PBS jobs |
Q: How
come my files on the scratch file systems were deleted?
The scratch file systems are kept below 80% utilization
automatically by a tidying program that runs nightly. The program
deletes oldest files first. If you have datasets that you wish to
retain for long periods on the cluster then the unix command touch
can be used to indicate which these files are by setting the
file age to a recent date. However,
 | the scratch file systems are never backed up and so they are
not intended for permanent archival. |
| if too many files are marked for retention with touch
then the tidying system will still remove the oldest of these. |
The scratch directories from which files are automatically
deleted are shown on the Hardware
Layout diagram. The only user directories on the cluster that
are backed up regularly are the home space directories.
Q: Is
there a parallel Matlab on the cluster?
Coming soon .......
Q:
I am getting
a strange error message, what should I do?
You should feel free to send e-mail to cg01-admin@techsquare.com
containing the error message. It is also often very useful to paste
the error message into a search engine such as Google
to see if this is a well known problem.
Q: How do
I modify my MANPATH variable to include the PBS help pages?
The usual way to do this is to edit your shell startup settings
file. To do this for the default shell of /bin/tcsh you edit the
file .tcshrc in your home directory to contain a line like the
following:
setenv MANPATH /usr/man:/usr/X11R6/man:/usr/local/man:/usr/pbs/man
Q: What
are the names of the different machines in the cluster?
The Hardware Layout section
includes a diagram showing the names of the machines in the cluster.
The technical specifications of the machines is presented in textual
form in the Technical Specs section.
Q: What
options do I need in the MITgcm genmake file for compiling?
The genmake options for compiling MITgcm on the myrinet-3 cluster
with the Portland group compiler and using the Myrinet optimized MPI
are shown below. Note - the compilation should execute on a
myrinet-3 cluster node.
|
MITgcm genmake options for myrinet-3
nodes with the Portland group compiler using the Myrinet
optimized MPI. |
case cg01+pgi:
set LN = ( '/bin/ln -s' )
set CPP = ( '/lib/cpp -traditional -P' )
set INCLUDES = ( '-I/usr/local/pkg/mpi/mpi-1.2.4..8a-gm-1.5/pgi/include' )
set DEFINES = ( ${DEFINES} '-DWORDLENGTH=4' )
set FC = ( '/usr/local/pkg/mpi/mpi-1.2.4..8a-gm-1.5/pgi/bin/mpif77' )
set FFLAGS = ( '-byteswapio -r8 -Mnodclchk -Mextend' )
# set LIBS = ( '-L/home/cnh/src/gm-1.4/libgm')
set FOPTIM = ( '-tp p6 -v -O2 -Munroll -Mvect=cachesize:512000,transform -Kieee' )
set LINK = ( '/usr/local/pkg/mpi/mpi-1.2.4..8a-gm-1.5/pgi/bin/mpif77' )
breaksw |
Q: I am
using the Myrinet MPI with PBS and sometimes my jobs don't terminate
when I expect. Instead they run to the PBS time limit and then stop.
Whats happening?
If the timeout on the --gm-kill option of the
mpirun.ch_gm command is set too low (for example --gm-kill 1)
the startup script for mpi execution may hang, even though the
compute processes have terminated. To work around this problem set
the timeout value larger (for example --gm-kill 5).
The timeout value needed increases with the number of processes. For
thirty-two processes a value of 5 seems to work robustly.
Q: I
am getting a license manager error using the Portland Group
compilers (pgf77, pgf90, etc...). What should I do?
If the environment variable PGI is not set correctly then the
Portland compilers (pgf77, pgf90) and the mpi compilations scripts
based of these compilers give the error message:
LICENSE MANAGER PROBLEM: Cannot find license
file
To fix this set the environment variable to the
correct value.
Q: What
are useful environment variable/shell startup (.cshrc) settings for
using the cluster?
|
Environment variable name and
c-shell setting syntax. |
Meaning |
setenv PATH ${PATH}:/usr/pbs/bin |
Sets command search path to include PBS
commands. |
setenv MANPATH /usr/man:/usr/X11R6/man:/usr/local/man:/usr/pbs/man |
Sets man page search path to include PBS help
pages (the command should be entered on a single line). |
setenv PGI /usr/local/pgi |
Sets the location of the Portland group
compilers, needed for compilation to work with pgf77 or pgf90. |
|
