This tutorial is intended to walk you through the required steps to install software packages on the FAS-RC Cannon cluster available as pre-compiled binaries. The software apps are frequently packaged in archives with extensions, such as .tar, .tar.gz, .zip, etc.
The installation process is best illustrated by a specific example. Suppose, you need a tool to extract files packaged as .rar archives. Although, readily available on Windows and MAC computers, such a tool is not available on the cluster out of the box. One such tool that works from the command-line can be downloaded from RARLAB. Here are the exact steps to make this work:
First we need to locate the package we need. Going to the Downloads page at the RARLAB's website, we locate the package we need, RAR 6.12 for Linux x64. We get the package's URL (right-click and then "Copy Link Address") and download it with wget in a selected directory for this purpose.
$ mkdir -p $HOME/Software
$ cd $HOME/Software
$ wget https://www.rarlab.com/rar/rarlinux-x64-612.tar.gzThe above commands will result in the file rarlinux-x64-612.tar.gz which can be unpacked with the tar command, e.g.,
$ tar xvfz rarlinux-x64-612.tar.gz
rar/
rar/unrar
rar/acknow.txt
rar/whatsnew.txt
rar/order.htm
rar/readme.txt
rar/rar.txt
rar/makefile
rar/default.sfx
rar/rar
rar/rarfiles.lst
rar/license.txtThis results in the rar/ directory with the above contents. The next step is to examine its contents and to configure the binary for use.
At this stage the binaries are usually ready for use. If you go to the unpacked directory and list its contents, you will see something like the below:
$ cd rar/
$ ls -lh
total 1.4M
-rw-r--r-- 1 pkrastev rc_admin 2.7K May 4 14:22 acknow.txt
-rwxr-xr-x 1 pkrastev rc_admin 199K May 4 14:22 default.sfx
-rw-r--r-- 1 pkrastev rc_admin 6.6K May 4 14:22 license.txt
-rw-r--r-- 1 pkrastev rc_admin 428 May 4 14:22 makefile
-rw-r--r-- 1 pkrastev rc_admin 3.3K May 4 14:22 order.htm
-rwxr-xr-x 1 pkrastev rc_admin 624K May 4 14:22 rar
-rw-r--r-- 1 pkrastev rc_admin 1.2K May 4 14:22 rarfiles.lst
-rw-r--r-- 1 pkrastev rc_admin 105K May 4 14:22 rar.txt
-rw-r--r-- 1 pkrastev rc_admin 692 May 4 14:22 readme.txt
-rwxr-xr-x 1 pkrastev rc_admin 348K May 4 14:22 unrar
-rw-r--r-- 1 pkrastev rc_admin 28K May 4 14:22 whatsnew.txtThe executable files of interest are rar and unrar. In case these are dynamically linked executables, it is useful to check if all required libraries are present for them to work. This is done by the ldd command, e.g.,
$ ldd rar
linux-vdso.so.1 => (0x00007ffe46f7f000)
libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00002afdb1e68000)
libm.so.6 => /lib64/libm.so.6 (0x00002afdb2170000)
libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00002afdb2472000)
libpthread.so.0 => /lib64/libpthread.so.0 (0x00002afdb2688000)
libc.so.6 => /lib64/libc.so.6 (0x00002afdb28a4000)
/lib64/ld-linux-x86-64.so.2 (0x00002afdb1c44000)No missing libraries in this case, so we are good to go! At this stage the binary is ready to be used from its working directory. You may check, for instance, the available options to be used with the executable (binary), e.g.,
$ ./rar
RAR 6.12 Copyright (c) 1993-2022 Alexander Roshal 4 May 2022
Trial version Type 'rar -?' for help
Usage: rar <command> -<switch 1> -<switch N> <archive> <files...>
<@listfiles...> <path_to_extract\>
<Commands>
a Add files to archive
c Add archive comment
ch Change archive parameters
cw Write archive comment to file
d Delete files from archive
e Extract files without archived paths
f Freshen files in archive
i[par]=<str> Find string in archives
k Lock archive
l[t[a],b] List archive contents [technical[all], bare]
m[f] Move to archive [files only]
p Print file to stdout
r Repair archive
rc Reconstruct missing volumes
rn Rename archived files
rr[N] Add data recovery record
rv[N] Create recovery volumes
s[name|-] Convert archive to or from SFX
t Test archive files
u Update files in archive
v[t[a],b] Verbosely list archive contents [technical[all],bare]
x Extract files with full path
<Switches>
- Stop switches scanning
@[+] Disable [enable] file lists
ad[1,2] Alternate destination path
ag[format] Generate archive name using the current date
ai Ignore file attributes
ap<path> Set path inside archive
as Synchronize archive contents
c- Disable comments show
cfg- Disable read configuration
cl Convert names to lower case
cu Convert names to upper case
df Delete files after archiving
dh Open shared files
ds Disable name sort for solid archive
dw Wipe files after archiving
e[+]<attr> Set file exclude and include attributes
ed Do not add empty directories
ep Exclude paths from names
ep1 Exclude base directory from names
ep3 Expand paths to full including the drive letter
ep4<path> Exclude the path prefix from names
f Freshen files
hp[password] Encrypt both file data and headers
ht[b|c] Select hash type [BLAKE2,CRC32] for file checksum
id[c,d,n,p,q] Display or disable messages
ierr Send all messages to stderr
ilog[name] Log errors to file
inul Disable all messages
isnd[-] Control notification sounds
iver Display the version number
k Lock archive
kb Keep broken extracted files
log[f][=name] Write names to log file
m<0..5> Set compression level (0-store...3-default...5-maximal)
ma[4|5] Specify a version of archiving format
mc<par> Set advanced compression parameters
md<n>[k,m,g] Dictionary size in KB, MB or GB
me[par] Set encryption parameters
ms[ext;ext] Specify file types to store
mt<threads> Set the number of threads
n<file> Additionally filter included files
n@ Read additional filter masks from stdin
n@<list> Read additional filter masks from list file
o[+|-] Set the overwrite mode
oh Save hard links as the link instead of the file
oi[0-4][:min] Save identical files as references
ol[a] Process symbolic links as the link [absolute paths]
op<path> Set the output path for extracted files
or Rename files automatically
ow Save or restore file owner and group
p[password] Set password
qo[-|+] Add quick open information [none|force]
r Recurse subdirectories
r- Disable recursion
r0 Recurse subdirectories for wildcard names only
rr[N] Add data recovery record
rv[N] Create recovery volumes
s[<N>,v[-],e] Create solid archive
s- Disable solid archiving
sc<chr>[obj] Specify the character set
sfx[name] Create SFX archive
si[name] Read data from standard input (stdin)
sl<size> Process files with size less than specified
sm<size> Process files with size more than specified
t Test files after archiving
ta[mcao]<d> Process files modified after <d> YYYYMMDDHHMMSS date
tb[mcao]<d> Process files modified before <d> YYYYMMDDHHMMSS date
tk Keep original archive time
tl Set archive time to latest file
tn[mcao]<t> Process files newer than <t> time
to[mcao]<t> Process files older than <t> time
ts[m,c,a,p] Save or restore time (modification, creation, access, preserve)
u Update files
v<size>[k,b] Create volumes with size=<size>*1000 [*1024, *1]
ver[n] File version control
vn Use the old style volume naming scheme
vp Pause before each volume
w<path> Assign work directory
x<file> Exclude specified file
x@ Read file names to exclude from stdin
x@<list> Exclude files listed in specified list file
y Assume Yes on all queries
z[file] Read archive comment from fileand also similarly for the unrar command, e.g.,
$ ./unrar
...
<omitted output>If you intend to use the binaries from the directory where they are unpacked, this would be the last step.
You can also make the executables "visible" from other locations by adding the executables' path to the PATH environment variable by:
export PATH=$HOME/Software/rar:$PATHThe above command can be also added to your .bashrc file in your home directory to make it available upon logging on to the cluster.
Finally, you are ready to use the install!
To open/extract a RAR file in the current working directory, just use the following command with unrar e option:
$ unrar e my_file.rarTo open/extract a RAR file in a specific path or destination directory, just use the unrar e option, it will extract all the files in the specified destination directory:
unrar e my_file.rar /path/to/my/directory/To open/extract a RAR file with its original directory structure, just issue the below command with unrar x option. It will extract according to their folder structure see below the output of the command:
$ unrar x example.rarAll files will be unpacked in the example/ directory.