Working on Linuxs Machines
Working on the center for scientific computing descktops requires the researcher to become familiar with Linux as an operating system.This imposes on the researcher to use alternative softwear on Linuxs which have the same appication as on windows.The mentioned programs are the substitue programs used on windows:
1-You can use kwrite as some thing similar to notpad in windows.
2-For cd writting K3B the CD and DVD Kreator.
3-Emacs is used for bash scripting , when submitting jobs for a parrallel job.
4-Open office is the alternative for windows office on Linuxs.
5-File manger is used for looking inside different folders.
6-Wine is a programe used for an instalation of a softwear on your computer.
Regular used commands on Linuxs:
1-Using emaxs needs typing emacs.
2-To accses the bash script editor type :qsub filename.pbs. Another used command :less filename.pbs.e77968.
3-Checking the statues of your calculation type:qstat. Another used command: watch qstat -u espdf
4-Editting input file content is by using program called kate or vi, just by typing Kate or vi.
5-Using the make or the make clean commmand.
6-Using the rm fort.* command is to remove generated files from a previous run due to that some times the code wouldnt work if the files are located on the folder.
7-Using the pwd command.
8-Using the copy command :cp fort.99 /home/eng/espdf/Desktop/foldername
9-The cat command: cat ~/.bashrc.
10-accessing the required cluster to work on: ssh esrpdf@brenda.
11-creating a file and assigning it a name: mv fort.99 test.gr.
12-working on code: ./jan10<input_file_name.in>output_file_name.out.
13-Loading the required compiler :module load intel/ompi/1.4.2.
Calculation Command Procedure for a Large Job:
1-Creat input in your home.
2-Log in Brenda,menerva,francesca.
3-cd /gpfs/eng/esrpdf/code_folder_name
4-cp <home/input_file>
5-modfiy bash_script_file.pbs, inside the bash script file change the name of the input file depending on the studied case, note that for an mpi code you need to add the comment of run mip.
------------------------------------------------------------------------------------
#!/bin/bash
#PBS -1 nodes=1:ppn=1,pvmem=1000mb,walltime=08:00:00
#PBS -V
cd $PBS_O_WORKDIR
runmpi ./jan09<input_file_name.in>output_file_name.out
-------------------------------------------------------------------------------------
7-Loading code compilier : Modlual load MPI
8-qusb bash_script_file_name.pbs
Steps taken for Planning to run a simulation:
1-Thinking of what initial condition would be choosen.
2-Dimension of domain and number of nodes used.
3-How many time steps are required, and specfiying them in your input file.
4-Documenting the input file name and date, to get back to it after a while and check quikly what was done.
5-Running the simualtion and allocating the required data storage space and having its back up.
Some Commands that may become handy at some point:
1-To find out how much space i have on my disc drive:
esrpdf@grub:~>quta -S
esrpdf@grub:~>quta -QS
2-To find the list of folders i have:
esrpdf@grub:~>ls -1ha
3-To remove dumped data
esrpdf@grub:~>rm.xsession-errors
4-accessing my account from personal computer:
ahmed@linux-gotg:~>vi .ssh/known_hosts
ahmed@linux-gotg:~>ssh brenda.csc.warwick.ac.uk
ahmed@linux-gotg:~>ssh godzilla
ahmed@linux-gotg:~>vi .ssh/known_hosts
ahmed@linux-gotg:~>ssh exodar.csc.warwick.ac.uk
then you will be asked for password
5-Copying files from desktop to laptop
ahmed@linux-gotg:~>ssh yalda.csc.warwick.ac.uk
6-Fileing a report on bugzelia requires:
Login: Warwick_User_Email@warwick@ac.uk
Password:windows2011
the link to bugzellia.
7-To show the list of files and their details in a list:
ahmed@linux-gotg:~>du -ha
2-For cd writting K3B the CD and DVD Kreator.
3-Emacs is used for bash scripting , when submitting jobs for a parrallel job.
4-Open office is the alternative for windows office on Linuxs.
5-File manger is used for looking inside different folders.
6-Wine is a programe used for an instalation of a softwear on your computer.
Regular used commands on Linuxs:
1-Using emaxs needs typing emacs.
2-To accses the bash script editor type :qsub filename.pbs. Another used command :less filename.pbs.e77968.
3-Checking the statues of your calculation type:qstat. Another used command: watch qstat -u espdf
4-Editting input file content is by using program called kate or vi, just by typing Kate or vi.
5-Using the make or the make clean commmand.
6-Using the rm fort.* command is to remove generated files from a previous run due to that some times the code wouldnt work if the files are located on the folder.
7-Using the pwd command.
8-Using the copy command :cp fort.99 /home/eng/espdf/Desktop/foldername
9-The cat command: cat ~/.bashrc.
10-accessing the required cluster to work on: ssh esrpdf@brenda.
11-creating a file and assigning it a name: mv fort.99 test.gr.
12-working on code: ./jan10<input_file_name.in>output_file_name.out.
13-Loading the required compiler :module load intel/ompi/1.4.2.
Calculation Command Procedure for a Large Job:
1-Creat input in your home.
2-Log in Brenda,menerva,francesca.
3-cd /gpfs/eng/esrpdf/code_folder_name
4-cp <home/input_file>
5-modfiy bash_script_file.pbs, inside the bash script file change the name of the input file depending on the studied case, note that for an mpi code you need to add the comment of run mip.
------------------------------------------------------------------------------------
#!/bin/bash
#PBS -1 nodes=1:ppn=1,pvmem=1000mb,walltime=08:00:00
#PBS -V
cd $PBS_O_WORKDIR
runmpi ./jan09<input_file_name.in>output_file_name.out
-------------------------------------------------------------------------------------
7-Loading code compilier : Modlual load MPI
8-qusb bash_script_file_name.pbs
Steps taken for Planning to run a simulation:
1-Thinking of what initial condition would be choosen.
2-Dimension of domain and number of nodes used.
3-How many time steps are required, and specfiying them in your input file.
4-Documenting the input file name and date, to get back to it after a while and check quikly what was done.
5-Running the simualtion and allocating the required data storage space and having its back up.
Some Commands that may become handy at some point:
1-To find out how much space i have on my disc drive:
esrpdf@grub:~>quta -S
esrpdf@grub:~>quta -QS
2-To find the list of folders i have:
esrpdf@grub:~>ls -1ha
3-To remove dumped data
esrpdf@grub:~>rm.xsession-errors
4-accessing my account from personal computer:
ahmed@linux-gotg:~>vi .ssh/known_hosts
ahmed@linux-gotg:~>ssh brenda.csc.warwick.ac.uk
ahmed@linux-gotg:~>ssh godzilla
ahmed@linux-gotg:~>vi .ssh/known_hosts
ahmed@linux-gotg:~>ssh exodar.csc.warwick.ac.uk
then you will be asked for password
5-Copying files from desktop to laptop
ahmed@linux-gotg:~>ssh yalda.csc.warwick.ac.uk
6-Fileing a report on bugzelia requires:
Login: Warwick_User_Email@warwick@ac.uk
Password:windows2011
the link to bugzellia.
7-To show the list of files and their details in a list:
ahmed@linux-gotg:~>du -ha
Unless otherwise noted, all content on this site is @Copyright by Ahmed Al Makky 2012-2013 - http://cfd2012.com