How to Use Fujitsu PRIMEPOWER HPC2500

September 1, 2005
Tatsuki Ogino

The new supercomputer system of the Information Technology Center, 
Nagoya University was begun to operate on March 1, 2005. It is 
scalar-parallel supercomputer, Fujitsu PRIMEPOWER HPC2500. 

you can connect the supercomputer by telnet as
     telnet hpc.cc.nagoya-u.ac.jp 
     or (telnet 133.6.1.153)

Fujitsu PRIMEPOWER HPC2500 23 nodes and 1536 cpu's
  Host name:  hpc.cc.nagoya-u.ac.jp
  IP address: 133.6.1.153
    23 nodes
    64 cpu/512 GB memory  x      22 nodes
    128 cpu/512 GB memory x       1 node
    Total performance:           12 Tflops
    Total memory:              11.5 TB
    Disc capacity:               50 TB
  
  Operation system: Solaris9

Job Class
  Queue  No. cpu  cpu time  upper limit  elapsed time
                   (hours)  of cpu time      (hours)
  a8        8         10        10               2                     
  p8        8         10     unlimited          20 
  p16      16        200     unlimited         100 
  p64      64        200     unlimited         200 
  p128    128        200     unlimited         336 
  p256    256        200     unlimited         336 
  p1024  1024        200     unlimited         336

  TSS     128          2     unlimited          - 

  *) Cpu time is the sum of cpu time by all processors.

Connection of server and file system

  hpc.cc.nagoya-u.ac.jp   -----  /home
                                 /large0  /large1
                                 /large_tmp0  /large_tmp1
                                
  gpcs:/home/usrN/user-id   -->     /home/usrN/user-id
  vpp:/home/usrN/user-id    -->     /home/vpp/usrN/user-id
  vpp:/home/dpfs/usrN       -->     /large0/usrN/user-id
                                    /large1/usrN/user-id

Command of compile
  Fortran:     frt
  XPFortran:   xpfrt  (succession from VPP Fortran)
  C:           fcc
  C++:         FCC
  MPI Fortran  mpifrt
  MPI C        mpicc

Options of compiler
  -Kfast_GP2=3
  -Klargepage=2   :use largepage
  -KV9            :use SPARC V9
  -X9             :Fortran95
  an example of compile
  frt -Knolargepage -o prog_nlg prog.f

Command of NQS (Network Queuing System)
  qsub
  qstat
  qdel
  qcat
--------------------------------------------------
(A1) Compile and execution of MPI Fortran program
    use 8 processors
    8 process parallel

mpifrt -Lt progmpi.f -o progmpi08 -Kfast_GP2=3,V9,largepage=2 -Z mpilist
qsub mpi_lim08y20.sh

hpc% more mpi_lim08y20.sh
#  @$-q p8 -lP 8 -eo -o pexecmpi08.out
#  @$-me -lT 20:00:00 -lM 7gb
cd ./vpp05a/mearthb3
mpiexec  -n 8  -mode limited ./progmpi08

(A2) Compile and execution of MPI Fortran program
    use 128 processors
    128 process parallel

mpifrt -Lt progmpi.f -o progmpi128 -Kfast_GP2=3,V9,largepage=2 -Z mpilist
qsub mpiex_0128th01.sh

hpc% more mpiex_0128th01.sh
#  @$-q p128 -lP 128 -eo -o progmpi128.out
#  @$-lM 8.0gb -lT 600:00:00
setenv  VPP_MBX_SIZE  1128000000
cd ./mearthd4/
mpiexec -n 128 -mode limited ./progmpi128

(A3) Compile and execution of MPI Fortran program
    use 128 processors
    32 process parallel
     4 thread parallel (sheared memory)

mpifrt -Lt progmpi.f -o progmpi128th04 -Kfast_GP2=3,V9,largepage=2 -Kparallel -Z mpilist
qsub mpiex_0128th04.sh

#  @$-q p128 -lp 4 -lP 32 -eo -o progmpi128th04.out
#  @$-lM 8.0gb -lT 600:00:00
setenv  VPP_MBX_SIZE  1128000000
cd ./mearthd4/
mpiexec -n 32 -mode limited ./progmpi128th04

(1) Compile and execution of MPI Fortran program
    use 16 processors
    16 process parallel

mpifrt -Lt progmpi.f -o progmpi -Kfast_GP2=3,V9,largepage=2 -Z mpilist
qsub mpiexec_pp0016k1.sh

hpc% more mpiexec_pp0016k1.sh
#  @$-q p16 -lP 16 -eo -o pexecmpi16.out
#  @$-lM 10.0gb -lT 16:00:00
setenv  VPP_MBX_SIZE  1256000000
cd /home/usr6/vpp/usr6/a41456a/mearthd3/
mpiexec -n 16 -mode limited ./progmpi
 
(2) Compile and execution of MPI Fortran program with automatic 
    parallel procedure
      use 128 processors
      32 process parallel   (distributed memory)
       8 automatic parallel or thread parallel (sheared memory)

mpifrt -Lt progmpi.f -o progmpi128s4 -Kfast_GP2=3,V9,largepage=2 -Kparallel -Z mpilist
qsub mpiex_0128k2s4.sh 

hpc% more mpiex_0128k2s4.sh
#  @$-q p128 -lp 4 -lP 32 -eo -o pexecmpi128s4.out
#  @$-lM 10.0gb -lT 2000:00:00
setenv  VPP_MBX_SIZE  1256000000
cd /home/usr6/vpp/usr6/a41456a/mearthd3/
mpiexec -n 32 -mode limited ./progmpi128s4

(3) Compile and execution of Fortran program (single)

qsub -q p8 -eo -o comp.out comp.sh
qsub -q p8 -eo -o exec.out exec.sh

hpc% more comp.sh
cd /home/usr6/vpp/usr6/a41456a/mearthd3
frt -o prog prog.f
hpc% more exec.sh
#  @$ -lt 10:00
#  @$-q x  -eo
cd /home/usr6/vpp/usr6/a41456a/mearthd3
timex prog
--------------------------------------------------
(4) How to Use XPFortran 

XPFortran is succession from VPP Fortran.

Compile
xpfrt -o xprog xprog.f

Execution
xpfexec -vp NP -m MODE prog
  NP:   number of processors
  MODE: full or limited
  prog  name of execution file (pass + file name)

Execution by full mode (xp_prog)
qsub xpf_full.sh
Set number of cpu in -lP is added by 1 cpu to the number of cpu to use.

more xpf_full.sh
#  @$-q p8 -eo -o xpf_full.out
#  @$-lP 5
xpfexec -vp 4 ./xp_prog

Execution by limited mode (xp_prog)
qsub xpf_limited.sh

more xpf_limited.sh
#  @$-q p8 -eo -o xpf_lim.out
#  @$-lP 4
xpfexec -vp 4 -mode limited ./xp_prog
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