This is my first time using high performance machine. Although the machine is only for student, and of course, it is not good as those pro machines, it is still a good experience for me.
ssh remote machin, returns:
Last login: Wed Feb 17 15:02:15 2010 from nl103-144-35.student.uu.se
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__ __ ___
/\ \/\ \ /\_ \
\ \ \ \ \ __\//\ \ ___ ___ ___ ___ __
\ \ \ \ \ /’__`\\ \ \ /’___\ / __`\ /’ __` __`\ /’__`\
\ \ \_/ \/\ __/ \_\ \_ /\ \__/ /\ \L\ \/\ \/\ \/\ \ /\ __/
\ `\___/\ \____\/\____\\ \____\\ \____/\ \_\ \_\ \_\\ \____\
`\/__/ \/____/\/____/ \/____/ \/___/ \/_/\/_/\/_/ \/____/
__ _____ ____
/\ \__ /\ __`\ /\ _`\
\ \ ,_\ ___ \ \ \/\ \\ \,\L\_\
\ \ \/ / __`\ \ \ \ \ \\/_\__ \
\ \ \_ /\ \L\ \ \ \ \_\ \ /\ \L\ \
\ \__\\ \____/ \ \_____\\ `\____\
\/__/ \/___/ \/_____/ \/_____/
Interactive cluster at Uppmax, Uppsala Universitet
Access node; os1
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Hardware:
IBM X3455 dual Opteron 2220SE, 2.8GHz nodes. 4*10=40 cores
8GB RAM, Infiniband and Gigabit interconnect
Infiniband is not available for MPI programming due to system problems
Software:
Scientific Linux SL release 5.2, kernel 2.6.18-92.1.18.el5
SGE version 6.2, Grid Engine queue system
“man sge_intro” for an overview.
GCC version 4.3 c,c++,fortran and java
module load gcc
PGI version 7.2 & 8.0, 64 bit compilers (C,C++,F77,F95,HPF)
module load pgi
Intel version 10.1 & 11.1, 64 bit compilers (C,C++,Fortran)
module load intel
MPI, OpenMPI libraries, default 1.2.9, 1.3 available
module load pgi openmpi
module load gcc openmpi
mpicc or mpif90 to compile
mpirun to execute.
qsub -pe dmp8 16, to submit a 16 slot mpi job
openMP is available in pgi, intel and gcc
QUEUES and PEs:
os: 160 slots main queue (overbooked)
-pe dmp NN, distributed on nodes, 16 slots per node (4 cores)
-pe smp NN, shared memory, 1 single node for up to 16 threads (4 cores)
User Limits:
The login nodes are intended for short test runs only, max cputime is 30min
INTERACTIVE:
Use qsh to request a interactive job and recive a xterm.
e.g. qsh -l h_rt=01:00:20
**NB qlogin dont work at the moment use qsh**
(Use qlogin to execute an interactive session without starting a xterm. )
NB X-forwarding is working!
(If you have logged in with “ssh -X os.uppmax.uu.se” !!!)
Dont forget to request h_rt
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News:
2009-11-20 os6 restarted due to system problems
2009-10-7/8 Service stop
New file server “bubo” introduced for all uppmax storage.
Your home directory is now in /bubo/home/h?/user.
Refer to this using “$HOME” in your programs.
To ease the transition we have defined symbolic links so that the old
directory names are usable for a short time.
2009-07-07 Compilers: PGI is updated to 9.0, default is kept as 8.0
If you want the latest version use “module load pgi/9.0″
Intel is updated to 11.1 (build 038), 11.0 (build 084) is kept as default
If you want the latest version use “module load intel/11.1″
2009-03-17 Infiniband removed from openmpi due to stability problems
2008-11-28 OS-kluster is reinstalled with SL 5.2
R is now a module to run R please load the module first
“module load R”
Sun Grid Engine updated to 6.2
I use bold font to indicate hardware.
BTW, my knowledge of Vim helps me a lot. I like Vim 
