Getting Started

Basic UNIX

Basic Comamands
Wildcards
Text Editors
Submitting Jobs

Basic Commands

These are some of the basic commands that you will be using in the shell on a daily basis.

ase-gui <file_name>

Graphical user interface for the Atomic Simulation Environment (ASE). This is the tool you will be using for viewing or setting up your structures.

cd ..

Move up one directory.

cd <directory_name>

Changes directory to the one provided. If no directory is given, the default is to return you to your home directory (/home/username/)

cp <source_file_with_path> <destination_path>

Copies files or directories from the source_file_with_path to the destination_path

cp -r <source_file_with_path> <destination_path>

Copy recursively. Useful for copying multiple files and directories (copies contents of the subdirectories).

cp -u <source_file_with_path> <destination_path>

Update. Copies only if the source file is newer than the destination file or the destination file does not exist.

mkdir <directory_name>

Create new a new directory.

mv <source_file> <destination_file>

Move or rename file.

ls <directory_name>

Lists the files and directories contained within the directory. Leave blank for present directory.

ls -t

List files in chronological order.

ls -la

List all files even those starting with a dot ‘.’ which are generally not listed.

ls | more

If the number of files in a directory is too large to fit in a single screen this command lists files and directories page after page on spacebar keystroke.

pwd

Provides the “present working directory,” i.e. the current folder.

rm <file>

Remove files. This is always permanent.

rm -r <file_or_directory_with_path>

Remove file or the directory and its contents recursively.

rmdir <directory_name>

Remove an empty directory. Use rm -r to remove recursively, such as if directory contains files (be careful).

cat <file_name>

Print out contents of a text file or files within the shell.

Wildcards

Wildcards can be used to perform commands on multiple files simultaneously.

Single character. Example: ag neb?.traj neb??.traj will use ag to open all files containing one or two characters between neb and .traj

Any number of characters. Example: ls *.traj will list all .traj files.

Text Editors

There are several text editors available. Popular ones include vim and nano. Most people at SUNCAT use vim. To open a file, use vim file.txt to open a file named file.txt.

Submitting Jobs

These instructions are specific to the Sherlock cluster. Instructions for the CEES cluster below.

sbatch <script_file>

Submit the job defined by the script file to the queue.

sbatch --job-name=$PWD <script_file>

I recommend specifying --job-name=$PWD so it will set the current directory as the job name. This way you will have this information in the email.

squeue

Check the status of your jobs. You will get something like the following:

             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON)
           1930211    normal slurm_jo   gunhan CG    2:00:20      1 sh-5-25
           1819909    normal feat5_st   cbohon PD       0:00      1 (Dependency)
           1819916    normal feat5_st   cbohon PD       0:00      1 (Dependency)
        1787348_10    normal      ida  reaganc PD       0:00     32 (Resources)
        1787348_11    normal      ida  reaganc PD       0:00     32 (Resources)
           1904877    normal cftr_ref  jadeshi PD       0:00      1 (QOSMaxCpusPerUserLimit)

squeue -u your_SUNETID

This will list your jobs.

squeue -u your_SUNETID -o '%.7i %.9P %.8j %.8u %.2t %.10M %.6D %R %Z'

Shows more useful details about the job, including the working directory of the script. For example

JOBID PARTITION     NAME     USER ST       TIME  NODES WORK_DIR
1948301      slac /scratch  ctsai89  R   23:24:47      8 /scratch/users/ctsai89/TS_CH3_Au111/N_NEB
1948505      slac /home/ct  ctsai89  R   19:57:06      1 /scratch/users/ctsai89/Class_remaining/Ag111/fbl
1948506      slac /home/ct  ctsai89  R   19:57:06      1 /scratch/users/ctsai89/Class_remaining/Ag211/fbl
1948302      slac /scratch  ctsai89  R   23:24:11      7 /scratch/users/ctsai89/TS_CH3_Au111/B_NEB

scancel <job_ID>

Delete your job. You can get the job ID from squeue

If you are using the CEES cluster, the command for submitting a job is

qsub <script_file>

where <script_file> is the name of your script (e.g. opt.py).

qstat