Backup of IT memo/linuxmemo (No. 6)

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---

Setup of fuyu@SIO From 2006/06/01- †

Specification †

CPU: Intel Xeon3.2G dual core x2
RAM: 2.0G
HDD: 400G x2
OS: Redhat AS3
IP: 132.239.115.188 (fuyu.ucsd.edu)

N-Bench2 result †

BYTEmark* Native Mode Benchmark ver. 2 (10/95)
Index-split by Andrew D. Balsa (11/97)
Linux/Unix* port by Uwe F. Mayer (12/96,11/97)
 
TEST                : Iterations/sec.  : Old Index   : New Index
                    :                  : Pentium 90* : AMD K6/233*
--------------------:------------------:-------------:------------
NUMERIC SORT        :          774.36  :      19.86  :       6.52
STRING SORT         :          107.64  :      48.10  :       7.44
BITFIELD            :      3.6896e+08  :      63.29  :      13.22
FP EMULATION        :          78.169  :      37.51  :       8.66
FOURIER             :           16597  :      18.88  :      10.60
ASSIGNMENT          :          25.538  :      97.18  :      25.21
IDEA                :            2144  :      32.79  :       9.74
HUFFMAN             :          1348.7  :      37.40  :      11.94
NEURAL NET          :          18.864  :      30.30  :      12.75
LU DECOMPOSITION    :          1003.7  :      52.00  :      37.55
==========================ORIGINAL BYTEMARK RESULTS==========================
INTEGER INDEX       : 42.964
FLOATING-POINT INDEX: 30.982
Baseline (MSDOS*)   : Pentium* 90, 256 KB L2-cache, Watcom* compiler 10.0
==============================LINUX DATA BELOW===============================
CPU                 : 4 CPU GenuineIntel Intel(R) Xeon(TM) CPU 3.20GHz 3200MHz
L2 Cache            : 2048 KB
OS                  : Linux 2.4.21-40.ELsmp
C compiler          : gcc version 3.2.3 20030502 (Red Hat Linux 3.2.3-54)
libc                : ld-2.3.2.so
MEMORY INDEX        : 13.537
INTEGER INDEX       : 9.001
FLOATING-POINT INDEX: 17.184
Baseline (LINUX)    : AMD K6/233*, 512 KB L2-cache, gcc 2.7.2.3, libc-5.4.38
* Trademarks are property of their respective holder.  

Installation of 1.2TB USB HDD †

1.Connect the device (power and USB), and turn it on.
2.Check the auto device detector message by
 # dmesg
   and find the device address (for example /dev/sdc1)
 2'. format the disk. (if the disk is new or differently formatted)
  # /sbin/mkfs.ext3 /dev/sdc1
3. Make the mountpoint directory.
 # mkdir /mnt/usb01 (for example)
4. Mount it.
 # mount -t ext3 /dev/sdc1 /mnt/usb01
5. Change owner
 # chown -R kyoshimura:users /mnt/usb01
6. Make link (for example)
 $ ln -s /mnt/usb01 ~/

Japanization †

Finally it is impossible to enable Japanese server in English environment. 
So, I change the language setting only when I login to the server.
Language --> Japanese --> Login

Enlargement of Monitor Resolution †

Currently Impossible!!
1280x1040 is the largest for the machine??
Spec of VA912b says so...

Installation of Applications †

PGI Fortran/C 6.1.6 --> Into /usr/pgi †

***ATTENTION: You should not be in Japanese environment!!***
   If you are using X, please make a session in English. 
   (Other languages are not checked)
Visit http://www.pgroup.com and get latest package.
# cd ~/downloads/tmp/
# ./install
Visit http://www.pgroup.com again and assign for new license.
Change $PGI/license.dat
***Note: Only kyoshimura has right to use.***

GrADS --> Into ~/GrADS †

Visit http://www.iges.org/grads/downloads.html and get the appropriate one.
gunzip, untar
% set path = ( /home/kyoshimura/GrADS/bin $path )
% setenv GASCRP /home/kyoshimura/GrADS/lib
# ln -s /home/kyoshimura/GrADS/lib /usr/local/lib/grads

NetCDF 3.6.1 --> Into /usr/local †

% wget ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf.tar.gz
% gunzip netcdf.tar.gz ; tar xvf netcdf.tar
% setenv CC gcc
% setenv CXX g++
% setenv FC pgf77
% setenv F90 pgf90
% setenv CPPFLAGS -DpgiFortran
% setenv CFLAGS -O
% setenv FFLAGS -O -w
% ./configure --prefix=/usr/local
% make
% make check
% make extra_check
% su
# make install
make PATH and MANPATH in your environmental settings.
***A logfile is in /home/kyoshimura/downloads/netcdf-3.6.1/src/netcdf.log***

DCL 5.3.1 --> Into /usr/local/dcl-5.3.1 †

% wget http://www.gfd-dennou.org/arch/dcl/dcl-5.3.1.tar.gz
% gunzip dcl-5.3.1.tar.gz
% tar xvf dcl-5.3.1.tar
% export FC=pgf77
% export CC=gcc
% export DCLDIR=/usr/local/dcl-5.3.1
% ./configure --prefix=/usr/local/dcl-5.3.1 --disable-gtk --disable-gtk2
% make
% su
# make install ; exit
% cd demo
% make
% cd gokuraku/hop ; ./hop --> X window should pop out. 

GTOOL 3.5 --> Into /usr/local/gtool3.5 †

Get the package from http://gcm.tokyo.rist.or.jp/gcm/
Because of license problem (only kyoshimura has right to use PGI fortran), 
untar the file to /usr/local but permission is all kyoshimura.
# cd /usr/local
# tar xvf gtool3.5.tar
# chown -R kyoshimura:users ./gtool3.5 ; exit
% setenv GTOOLDIR /usr/local/gtool3.5
% cd $GTOOLDIR
% setenv DCLDIR /usr/local/dcl-5.3.1
% ln -sf $GTOOLDIR/libsrc/dcl531-gtool $GTOOLDIR/libsrc/dcl-gtool
% vi $GTOOLDIR/libsrc/sysmake/Makedef.Linux-pgi
 --> Modify FC/CC/FLAGS etc.
% vi $GTOOLDIR/Mkinclude
 --> Modify PERLPATH, DCLLIBNAME, etc.
% make
% make install
*** A logfile is in $GTOOLDIR/gtool.log***

Also get the man package (gtooldoc-0.1.tar.gz) from the site above.
1. gunzip and tar xvf
2. makeman.sh
3. copy the man directory to your local directory.

GMT 4.1.3--> ~/downloads/GMT4.1.3 †

Visit http://gmt.soest.hawaii.edu/ and get a file "install_gmt"
% ftp://ftp.soest.hawaii.edu/gmt/install_gmt
Follow instructions. (Just default is fine)
--> Success! 

wgrib2 --> Into ~/downloads/grib2/wgrib2 †

% wget ftp://ftp.cpc.ncep.noaa.gov/wd51we/wgrib2/wgrib2.tar
% tar xvf wgrib2.tar ; cd grib2 ; make
% ln -s ~/downloads/grib2/wgrib2 ~/bin  # make a link 

Image Magick --> Into ~/downloads/IM6.2.8 †

% wget ftp://ftp.imagemagick.org/pub/ImageMagick/ImageMagick-6.2.8-0.tar.gz
% gunzip ImageMagick-6.2.8-0.tar.gz ; tar xvf ImageMagick-6.2.8-0.tar
% cd ImageMagick-6.2.8
% mkdir ~/downloads/IM6.2.8
% su
# ./configure --prefix=/home/kyoshimura/downloads/IM6.2.8
# make install
# make check
Says "Failed 1/27 test scripts, 96.30% okay. 1/356 subtests failed, 99.72% okay."
-->Never mind!!

MPICH 1.2.7-p1 --> /usr/local/mpich †

% wget ftp://ftp.mcs.anl.gov/pub/mpi/mpich.tar.gz
% tar tvfz mpich.tar.gz
% cd mpich-1.2.7-p1 

% setenv FC pgf77
% setenv F77 pgf77
% setenv F90 pgf90
% setenv CC pgcc
% setenv CXX pgCC
% setenv CFLAGS "-Msignextend -tp p7"
% setenv FFLAGS "-fast -tp p7"　  
% setenv F90FLAGS "-fast -tp p7"   
% setenv CXXFLAGS "-fast -tp p7" 
% setenv CPP "pgCC -E"       
% setenv OPTFLAGS "-fast"   

% ./configure --enable-debug --prefix=/usr/local/mpich

% make
% make install
 -> it causes some errors, but main parts look OK.

*** To use same options of PGI, you should install MPICH by the PGI compilers***

You need followings
1. machine.LINUX in $MPIDIR/util/machine
 --> But, I don't know whether is is really effective or not.
2. activate rsh service.
 --> in /etc/xinetd.d/rsh, "disable=no" 
 # service xinetd restart
 But, it causes serious security hole. So,
3. make a permission to use rsh.
 a. Use iptables
  # iptables -L (check current status)
    You need to add your IP to be accepted as well as "localhost"
  # iptables -I INPUT -p udp -s fuyu.ucsd.edu -j ACCEPT
  # iptables -I INPUT -p tcp -s fuyu.ucsd.edu -j ACCEPT
  # /etc/init.d/iptables save
 b. Use TCPwrapper
  Also, if you activate rsh service, servers that already allowed can use rsh.
  So, use TCPwrapper to deny. 
  # vi /etc/hosts.deny
    --> Add "in.rshd : ALL"
  # vi /etc/hosts.allow
    --> Add "in.rshd : localhost 127.0.0.1 fuyu.ucsd.edu fuyu : ALLOW"
  # vi /etc/hosts.equiv
    --> Add hostname(s)
 c. Modify ~/.rhosts
   Finally, add hostname(s) and username to your .rhosts.
  $ vi ~/.rhosts
    --> Add "hostname username"

CCSR/NIES AGCM 5.6b †

% wget http://hydro.iis.u-tokyo.ac.jp/~kei/tmp/agcm5.6_test.tar.gz
% wget http://hydro.iis.u-tokyo.ac.jp/~kei/tmp/agcm5.6_test_std.tar.gz

OpenOffice-2.0.3 †

• Download from http://www.openoffice.org/index.html

  % tar xvfz OO***.tar.gz
  % su
  # cd RPMS
  # rpm -Uivh *.rpm

• Change individual preferences.

Other †

• Scanner

  EPSON Perfection 3490 --> Cannot be detected... 
   Maybe because installed  sane-backends is old?

• Benchmark using CCSR/NIES AGCM5.6b

  GSWP2 run, single cpu   : 1579 sec (Sun V440  6147 sec, SGI shui N/A sec, HP 1081 sec)
  GSWP2 run, 4-parallel   :  819 sec (Sun V880  2606 sec, SGI shui 303 sec, HP  351 sec)
  Standard run, single cpu: 2141 sec (Sun V440 11313 sec, SGI shui N/A sec, HP 1829 sec)
  Standard run, 4-parallel: 1122 sec (Sun V880  3044 sec, SGI shui 305 sec, HP  439 sec)