* Setup of fuyu@SIO From 2006/06/01- [#faac4201]
#contents
** Specification [#w0d761af]
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 ~/
** 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) 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
*** 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
