February 16, 2010

High performance machine

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

Interactive cluster at Uppmax, Uppsala Universitet
Access node; os1

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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\n 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
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
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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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\n 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.