IT memo/linuxmemo

Setup of fuyu@SIO From 2006/06/01- †

Setup of fuyu@SIO From 2006/06/01-

Specification †

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)

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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.

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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 ~/

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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

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Enlargement of Monitor Resolution †

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

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Installation of Applications †

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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.***

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PGI updated to v7.2 on 2009/04/13 as fuyu's restoration †

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.

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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
% setenv GADDIR /home/kyoshimura/GrADS/lib
 Or, if you are a super user
# ln -s /home/kyoshimura/GrADS/lib /usr/local/lib/grads

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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***

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NetCDF 4.0.1 --> Into /usr/local on 2009/04/13 †

% 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

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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.

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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.

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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!

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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

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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!!

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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) 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" 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
```

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MPICH1.2.7 with PGI 7.2 or later †

Just execute install_mpich in your PGI source code directory.

# cd ~/PGI
# ./install_mpich

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MPICH1.2.7 with Intel compiler †

% 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

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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

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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.

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CMOR V1.2 --> ~/downloads/CMOR_V1.2 †

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

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UDUNITS 1.12.4 --> ~/downloads/udunits-1.12.4 and perl5 library †

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

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CDAT 4.1.2 --> ~/CDAT †

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

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IFORT 8.1 --> /opt/intel_fc_80 †

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.

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Intel compiler 11.0 --> /opt/intel (2009/04/13) †

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).

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NCL5.0(not OPeNDAP-enabled) --> ~/NCL †

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

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CDO1.3 --> ~/cdo (atlas) †

./configure --prefix=/home/kei/cdo --with-netcdf=/home/kei/nc
make
make install

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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)

firewall (by superuser)

# cd /etc/firewall
# vi host-list.txt  (edit the list)
# stop-firewall ; start-firewall
# service iptables save