Backup diff of IT memo/linuxmemo vs current(No. 5)

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  • 2 (2006-08-23 (Wed) 22:01:01)
  • 3 (2006-09-06 (Wed) 19:44:09)
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  • 17 (2009-04-15 (Wed) 00:50:57)
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  • 19 (2009-04-15 (Wed) 14:46:57)

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* Setup of fuyu@SIO From 2006/06/01- [#faac4201]

#contents
** Specification [#w0d761af]

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

Renewed in 2009 Apr!!

 CPU: Intel Xeon2.0GHz Quad core x2
 RAM: 2.0GB x2
 HDD: 1.0TB x2
 OS: RedHat Enterprise Linux v5.3
 IP: 132.239.115.188 (fuyu.ucsd.edu)
** N-Bench2 result [#nc6af586]

 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 [#a8a066ad]

 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 ~/ 

  $ ln -s /mnt/usb01 ~/
** Japanization [#ra5c4fba]
 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 [#y3beea8a]
 Currently Impossible!!
 1280x1040 is the largest for the machine??
 Spec of VA912b says so...

** Installation of Applications [#m7912770]
***PGI Fortran/C 6.1.6 --> Into /usr/pgi [#ka4f3028]
 ***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.***

*** PGI updated to v7.2 on 2009/04/13 as fuyu's restoration [#mb0de2bb]

- Source codes are downloadable from http://www.pgroup.com
- Installation is automatic done by "install" script in the package.
- License ($PGI/license.dat) should be updated, too. (since MAC address has been changed.) 
+ Visit www.pgroup.com and login. (If you used to have your license.dat, you should have your account.) 
+ Select "Display PIN code" and enter PIN username and password (username starts with "pn") --> your 16 digits PIN code will be shown. 
+ Go to "Tie PIN to account" and enter PIN code. --> PGI PIN will be tied to your login account.
+ Go to "Create permanent keys" and select your PIN. 
+ In case you want to replace the old license file, chose "delete the license key" option. --> Deletion process will take a day. During this time, a trial license key can be issued.
***GrADS --> Into ~/GrADS [#z2b31b8a]
 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
 % setenv GADDIR /home/kyoshimura/GrADS/lib
  Or, if you are a super user
 # ln -s /home/kyoshimura/GrADS/lib /usr/local/lib/grads
***NetCDF 3.6.1 --> Into /usr/local [#f196b852]

 % 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***

***NetCDF 4.0.1 --> Into /usr/local on 2009/04/13 [#e5853499]
 % wget ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf.tar.gz
 % gunzip netcdf.tar.gz ; tar xvf netcdf.tar
 % setenv CC pgcc
 % setenv CXX pgCC
 % setenv FC pgf90
 % setenv CPPFLAGS -DpgiFortran
 % setenv CFLAGS -O
 % setenv FFLAGS -O -w
 % ./configure --prefix=/usr/local
 % make
 % make check
 % su
 # make install
***DCL 5.3.1 --> Into /usr/local/dcl-5.3.1 [#c175587c]

 % 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 [#i646c739]

 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 [#i91d0c38]

 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 [#beaab1bb]

 % 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 [#f54ba739]

 % 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 [#z1ef84b7]

 % 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)
     --> Add hostname(s) such as,
         "localhost 127.0.0.1 fuyu.ucsd.edu fuyu"
  c. Modify ~/.rhosts
    Finally, add hostname(s) and username to your .rhosts.
   $ vi ~/.rhosts
     --> Add "hostname username"
     --> Add "hostname username" such as,
         fuyu kyoshimura
         localhost kyoshimura
         fuyu.ucsd.edu kyoshimura

Using ssh instead of rsh
- It is generally better to disable rsh for security reason, so ssh should be used. You should generate a ssh key and place in authorized_keys file.
 $ cd ~/.ssh
 $ ssh-keygen -t rsa (or dsa)
 $ cat id_rsa.pub >> authorized_keyz
*** MPICH1.2.7 with PGI 7.2 or later [#fe25bfa0]
Just execute install_mpich in your PGI source code directory.
 # cd ~/PGI
 # ./install_mpich

*** MPICH1.2.7 with Intel compiler [#u45c4d41]
 % wget ftp://ftp.mcs.anl.gov/pub/mpi/mpich.tar.gz
 % tar tvfz mpich.tar.gz
 % cd mpich-1.2.7-p1 
 % setenv FC ifort
 % setenv F77 ifort
 % setenv F90 ifort
 % setenv CC icc
 % setenv CXX icc
 % ./configure --enable-debug --prefix=/usr/local/mpich
 % make
 # make install
***CCSR/NIES AGCM 5.6b [#n58f974d]

 % 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 [#p1ce5e45]
- Download from http://www.openoffice.org/index.html
 % tar xvfz OO***.tar.gz
 % su
 # cd RPMS
 # rpm -Uivh *.rpm
- Change individual preferences.

*** CMOR V1.2 --> ~/downloads/CMOR_V1.2 [#w821020a]
- Download from http://www-pcmdi.llnl.gov/software-portal/cmor/download
 % tar xvfz cmor.tar.gz
 % cd CMOR_V1.2
 % cp makefiles/Makefile.Linux-PGI ./Makefile
 edit Makefile (e.g. netcdf library)
 % make install

*** UDUNITS 1.12.4 --> ~/downloads/udunits-1.12.4 and perl5 library [#n5ac5a75]
- Download from http://www.unidata.ucar.edu/downloads/udunits/index.jsp
 % umcompress udunits.tar.Z
 % tar xvf udunits.tar
 % cd udunits-1.12.4/src
 % setenv CC gcc
 % setenv CFLAGS '-O -fno-builtin -D_POSIX_SOURCE'
 % setenv CPPFLAGS '-UNDEBUG -Df2cFortran'
 % ./configure
 % make
 % make test
 % su
 # make install

*** CDAT 4.1.2 --> ~/CDAT [#kb547100]
- Download from http://sourceforge.net/project/showfiles.php?group_id=11356&package_id=19190
- unsetenv FC, FFLAGS, etc.
 % tar xvfz CDAT-4.1.2-everything.tar.gz
 % cd CDAT-4.1.2
 % express-install ~/CDAT
*** IFORT 8.1 --> /opt/intel_fc_80 [#a0d64240]
You may be able to obtain this software (in other versions, too) freely for non-commercial purpose after registration. All procedures as follows: 
- Registration
+ Visit http://www.intel.com/cd/software/products/asmo-na/eng/compilers/284264.htm 
+ Choose "Free Non-Commercial Download" and Click "accept".
+ Choose product you want. (say "Fortran Compiler for Linux")
+ Input your e-mail address and country, then submit information.
+ You will get an e-mail with Download Site, Serial Number, and License File.
- Installation
+ Visit the Download Site, and download package(s). The Serial Number will be required.
+ Untar the package 
+ Copy the license file to the untared directory.
+ type ./install.sh (in case of ifort 8.1), and follow the instruction.

*** Intel compiler 11.0 --> /opt/intel (2009/04/13) [#ge38b0a5]
- Visit http://software.intel.com/en-us/articles/non-commercial-software-download/ for registration and download.
- Most of installation processes are the same as the former version (see above).
*** NCL5.0(not OPeNDAP-enabled) --> ~/NCL [#jf6f09d1]
+ Get account on the ESG (http://www.earthsystemgrid.org/)
+ Download binary files that suite for your environment from ESG ("latest NCL release" of the pull down menu in the middle of the home page). For my case (Xeon-RHLinux), "NCL 5.0.0 32-bit binary for i686 chips for LINUX (compiled with gcc 3.x)" is the one.
+ gunzip & untar the file into ~/NCL
+ setenv NCARG_ROOT ~/NCL
+ make .hluresfile as written [[here:http://www.ncl.ucar.edu/Document/Graphics/hlures.shtml]]

*** CDO1.3 --> ~/cdo (atlas) [#f8618315]
 ./configure --prefix=/home/kei/cdo --with-netcdf=/home/kei/nc
 make
 make install
***Other [#a46c1eba]
-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)
-firewall (by superuser)
 # cd /etc/firewall
 # vi host-list.txt  (edit the list)
 # stop-firewall ; start-firewall
 # service iptables save