Sebenarnya sejak masuk ke lab komputasi dan bergelut dengan GAUSSIAN baik 98 maupun yang 03 saya penasaran mengapa setiap user bisa langsung menggunakan GAUSSIAN dan file-file scratchnya kok bisa langsung berada di folder /scratch. Penasaran ini masih terus terbawa sampai akhirnya saya melihat dosen saya menginstall GAUSSIAN. Kebetulan juga waktu itu ada teman yang baru saja masuk ke lab komputasi jadi oleh dosen saya diinstallkan GAUSSIAN 98. GAUSSIAN ADALAH SOFTWARE YANG HARUS DIBELI DARI gaussian, inc. saya sama sekali tidak menyarankan untuk membajak GAUSSIAN, jika tidak mampu membeli GAUSSIAN, gunakan saja software kimia komputasi yang bersifat free, bebas didistribusikan. GAUSSIAN yang digunakan di sini telah berbentuk file binary dan dipaket dalam bentuk tar.gz. Oke lah, tanpa basa basi lagi kita langsung coba.
Pertama-tama login lah dulu sebagai root atau bisa menggunakan perintah sudo.
$ su
Password:
#
kemudian pindahkan atau copy file tar.gz GAUSSIAN ke /usr/local dan kemudian ekstrak.
# cp g03.tar.gz /usr/local/
# cd /usr/local/
# tar zxfv g03.tar.gz
kemudian pindah ke /etc/profile.d
# cd /etc/profile.d/
Di sini kita akan membuat script untuk mengatur folder scratch GAUSSIAN dan agar GAUSSIAN bisa digunakan semua user di komputer kita.
Pertama-tama buat folder scratch dulu. Sebenarnya folder ini bisa di mana saja, bisa di bawah / atau di /home/user. Namun ada baiknya menempatkan folder scratch di partisi dengan kapasitas yang besar karena semakin kompleks perhitungan yang kita lakukan GAUSSIAN akan semakin membutuhkan space yang besar untuk meletakkan file-file rwf-nya. Setelah folder dibuat kemudian masuk ke /etc/profile.d dan buat 2 buah script g03.sh dan g03.csh, jika menginstall GAUSSIAN versi lain, tinggal sesuaikan saja nama scriptnya. Untuk g03.sh isinya seperti ini :
#! /bin/sh
export g03root=/usr/local
$g03root/g03/bsd/g03.profile
export GAUSS_SCRDIR=/home/$USER/scratch;
GAUSS_LFLAGS=’nodelist “linux-218f”‘
export GAUSS_LFLAGS
lalu untuk g03.csh
#! /bin/csh
setenv g03root /usr/local
source $g03root/g03/bsd/g03.login
setenv GAUSS_SCRDIR /home/$USER/scratch
setenv GAUSS_LFLAGS ‘-nodelist “linux-2i8f”‘
dua buah script ini saya ambil dari komputer teman, di mana hostnamenya linux-2i8f dan tampaknya diparalel dengan komputer lain. Setelah script ini dibuat kita perlu sedikit mengedit g03.profile dan g03.login agar sinkron dengan script yang telah kita buat tadi. Kedua file tersebut ada di folder bsd milik GAUSSIAN.
gr=$HOME
if [ "$g03root" ]
then gr=$g03root
fi
ubah folder utama GAUSSIAN dari $HOME ke /usr/local kemudian di-save. Di script g03.login juga dilakukan hal yang sama, ubah $HOME menjadi /usr/local
if ($?g03root) then
set gr=”$g03root”
else
set gr=”$HOME”
endif
Dari beberapa halaman web yang saya temui, memang terdapat beberapa cara untuk menginstall GAUSSIAN, salah satunya ada yang menyarankan jika telah terinstal adalah dengan mengetesnya dengan cara masuk ke folder g03 kemudian ./g03. Nah, jika ada pesan error semacam : error while loading shared libraries: util.so: cannot open shared object file: No such file or directory, copy util.so dan libpgc.so ke /usr/lib. Ada juga pesan eror yang menandakan bahwa file-file eksekusi GAUSSIAN tidak dikenal, maka tinggal ubah attribut semua file *.exe di folder g03 dengan cara
# chmod a+rx *.exe
Kira-kira kurang lebih begitu cara dosen saya memasang GAUSSIAN. Di web resmi GAUSSIAN, gaussian.com, terdapat system yang diperlukan untuk setiap masing-masing platform komputer begitu juga dengan library-library yang dibutuhkan, tapi ada baiknya juga jika di OS yang akan dipasang GAUSSIAN juga diinstal math library, entah BLAS, ATLAS, MKL, ACML dll. Untuk GAUSSIAN yang digunakan secara paralel dengan komputer lain, sampai saat ini saya masih belum tahu cara instalasinya, apakah sama ataukah berbeda. Jika folder scratch tidak diatur, maka secara otomatis GAUSSIAN akan membuat file-file rwf di folder tempat kita running.
IOINSTALLATION GAUSSIAN 03
  • Gaussian is a commercial software product and must be purchased from Gaussian, Inc. A CD-ROM with the Gaussian 03 Windows binary will be mailed to the customer.
  • Copy (under root) all *.taz file from your CD-ROM in /usr/local directory
  • Extract files :
    # cd /usr/local
    # tar -zxvf *.taz
  • Setup gaussian group and add authorized users to this group (under root) :
    # cd /etc
    # cp -p group groupOld
    # cp -p gshadow gshadowOld
    # groupadd -r gauss03                     “-> creation of gauss03 group”
    # usermod -a -G     gauss03 firstuser     ” ->add the ‘firstuser’ user to the gauss03 group”
    # usermod -a -G     gauss03 seconduser ” ->add the ‘seconduser’ user to the gauss03 group”by “usermod -a -G gauss03 ….” add all authorized users to this group
  • Change permissions for g03 directory
    # cd /usr/local
    # chown -R root:gauss03 g03
    # chmod -R o-rwx g03     “-> only the users of the gauss03 group are authorized to read/run g03″
    # cd g03    # echo ‘export g03root=/usr/local’ >> g03.shrc
    # echo ‘export GAUSS_SCRDIR=$HOME/tmp’ >>     g03.shrc
    # echo ‘. $g03root/g03/bsd/g03.profile    ‘  >> g03.shrc
    # echo ‘setenv g03root /usr/local’ >> g03.cshrc
    # echo ‘setenv GAUSS_SCRDIR=$HOME/tmp’ >>     g03.cshrc
    # echo ‘source $g03root/g03/bsd/g03.login    ‘  >> g03.cshrc
Each user should execute the following orders :
echo ‘. /usr/local/g03/g03.shrc’ >> .bashrc
echo ‘source /usr/local/g03/g03.cshrc’ >> .cshrc
exit
Gaussian 03 Installation Instructions for Linux
  • Obtain Gaussian 03
    Gaussian 03 is a commercial software product and must be purchased fromGaussian, Inc. Both source code and pre-compiled binary versions of Gaussian 03 are available.
  • Setup gaussian group and add authorized users to this group
    $ su
    # cd /etc
    # cp -p group group.bak
    # cp -p gshadow gshadow.bak
    # grep 499 group
    # groupadd -g 499 gaussian
    # usermod -a -G gaussian webmo
    # usermod -a -G gaussian smith
    # usermod -a -G gaussian jones
  • Copy binary distribution from CD-ROM
    # mount /mnt/cdrom
    # cd /usr/local
    # cp -p /mnt/cdom/tar/*.TAZ .
    # umount /mnt/cdrom
  • Extract files and change permissions
    # tar xzvf *.TAZ
    # chown -R root:gaussian g03
    # chmod -R o-rwx g03
    # exit
  • Optionally, setup gaussian environment
    $ cd ~
    $ mkdir g03
    $ cd g03
    $ vi g03setup_sh
    export g03root=/usr/local
    export GAUSS_SCRDIR=/tmp
    . $g03root/g03/bsd/g03.profile
  • Optionally, run a test job from the command line
    $ cd ~/g03
    $ cp -p /usr/local/g03/tests/com/test001.com test001.com
    $ cp -p /usr/local/g03/tests/sgi/test001.log test001.log.sgi
    $ . g03setup_sh
    $ g03 < test001.com > test001.log.linux
    $ tail test001.log.sgi
    $ tail test001.log.linux

Linux System Gaussian Installation and Error TroubleShooting

Installation method in 32-bit or 64-bit Red Hat Enterprise Linux operating systems tested for the Gaussian version of Gaussian 03 C02 for PC-Linux-IA32 and g03e01-em64t and so on.
FOR IMMEDIATE RELEASE
PRLog (Press Release) – Jul. 27, 2011 – Installation method in 32-bit or 64-bit Red Hat Enterprise Linux operating systems tested for the Gaussian version of Gaussian 03 C02 for PC-Linux-IA32 and g03e01-em64t and so on.
One would g03d02.tar.gz extract to / home / userid /, we obtain / home/userid/
g03 folder (where userid for the current user name). Extracted command: tar zxvf g03_c02_lin.taz
Two in the Linux system to install Gaussian03
1 in / home/userid/g03 / established under the scratch folder as your temporary files directory.
2 Open bashrc file. Methods:
Open a terminal, enter the command vi / home / userid / .bashrc
3 In. Bashrc file add the following statement at the end and save:
# For Gaussian.03.C02
G03ROOT = / home/userid/g03
GAUSS_EXEDIR = $ G03ROOT
GAUSS_SCRDIR = / tmp/userid/g03
LD_LIBRARY_PATH = $ G03ROOT /: $ LD_LIBRARY_PATH
PATH = $ G03ROOT /: $ PATH
export G03ROOT GAUSS_EXEDIR GAUSS_SCRDIR LD_LIBRARY_PATH PATH
Description: G03ROOT defined as g03 decompressed root directory, which is g03, l502.exe so a lot of the directory where the executable program;
GAUSS_EXEDIR for the gaussian path to the executable program, usually G03ROOT the same;
GAUSS_SCRDIR for storing temporary files directory, where the hard disk space should be relatively large, generally need to scratch in the root directory of the tmp or create their own subdirectory, it can also be set to / home/userid/g03/scratch;
LD_LIBRARY_PATH defined gaussian functions needed for the operation of some of the library location, generally with G03ROOT;
PATH is also gaussian executable path, but different functions and GAUSS_EXEDIR variables. It is a system variable that defines the future, no matter where you run gaussian03, just type “g03″ on it, eliminating the need to enter the absolute path of trouble.
Usually installed when the user only needs to modify G03ROOT and GAUSS_SCRDIR path.
If the shell is csh, edit the. Cshrc file, the variable definition is similar, but use setenv instead of export, form: setenv variable name assignment
Note: If you do not know how to edit the vi, you can enter after press “i”, then paste the above statement to the end, finished press the ESC key to finish editing the return to command state. In this state, enter “: x” or “: wq” and press Enter to save and exit. Bashrc file editing.
4 automatically returned to the terminal command line mode, enter “bash”, if you do not set an error general it means success.
Third, the method of running Gaussian03
Open terminal, cd to the directory storing the input file, input “g03 test.gjf &” to run after the carriage return, pay attention to input the background operator “&.”
After installing run the Gaussian gaussian error and possible solutions
1 appears “cannot execute binary file” error prompt
Gauss likely installed linux system with the current version does not meet the number of bits, such as Gaussian packed in 64-bit 32-bit systems will be out this error. There may be errors or operating system installation files are missing some libraries.
View the current redhat Linux version is 32-bit or 64-bit command: use getconf LONG_BIT, rather than getconf WORD_BIT. 32-bit model, generally ILP32, that int, long, pointer are 32 bits long; 64-bit model, generally LP64, that long, pointer is 64 bits, and may still be 32-bit int, it could be 64. You can also use the command “uname-a” or “uname-m”, if the result there, said the current i386 or i686 32-bit Linux systems, if the result is that there is x86_64 64-bit.
2. “Probably out of disk space” error
Specifically:
Erroneous write during file extend. Write 448 instead of 4096
Probably out of disk space.
Write error in NtrExt1: No such file or director
There may be some corresponding GAUSS_SCRDIR temporary folder permission problems with chmod 777-R foldername command can solve the permissions problem. In addition, if it is Red Hat’s case, as root, enter the following statement or in the / etc / rc.local file adding at the end:
echo 0> / proc / sys / kernel / randomize_va_space
3.no such file or directory
Installed when running the g03 a “bash: ./userid/g03/g03/bsd/g03.profile: no such file or directriy” or “g03: commands is not found” error messages, there may not be set correctly Gaussian path. According to re-set on the last re-source about bash or csh file.
In addition, if not in / tmp / file to create the file, as long as the / tmp / under a new read and write permissions to delete a directory named userid can solve the problem. userid refers to the currently logged on the computer’s user name.