Versions and Availability
Module Names for uberftp on smic
▶ Module FAQ?
The information here is applicable to LSU HPC and LONI systems.
A user may choose between using /bin/bash and /bin/tcsh. Details about each shell follows.
System resource file: /etc/profile
When one access the shell, the following user files are read in if they exist (in order):
- ~/.bash_profile (anything sent to STDOUT or STDERR will cause things like rsync to break)
- ~/.bashrc (interactive login only)
When a user logs out of an interactive session, the file ~/.bash_logout is executed if it exists.
The default value of the environmental variable, PATH, is set automatically using Modules. See below for more information.
The file ~/.cshrc is used to customize the user's environment if his login shell is /bin/tcsh.
Modules is a utility which helps users manage the complex business of setting up their shell environment in the face of potentially conflicting application versions and libraries.
When a user logs in, the system looks for a file named .modules in their home directory. This file contains module commands to set up the initial shell environment.
Viewing Available Modules
$ module avail
displays a list of all the modules available. The list will look something like:
--- some stuff deleted --- velvet/1.2.10/INTEL-14.0.2 vmatch/2.2.2 ---------------- /usr/local/packages/Modules/modulefiles/admin ----------------- EasyBuild/1.11.1 GCC/4.9.0 INTEL-140-MPICH/3.1.1 EasyBuild/1.13.0 INTEL/14.0.2 INTEL-140-MVAPICH2/2.0 --- some stuff deleted ---
The module names take the form appname/version/compiler, providing the application name, the version, and information about how it was compiled (if needed).
Besides avail, there are other basic module commands to use for manipulating the environment. These include:
add/load mod1 mod2 ... modn . . . Add modules rm/unload mod1 mod2 ... modn . . Remove modules switch/swap mod . . . . . . . . . Switch or swap one module for another display/show . . . . . . . . . . List modules loaded in the environment avail . . . . . . . . . . . . . . List available module names whatis mod1 mod2 ... modn . . . . Describe listed modules
The -h option to module will list all available commands.
▶ Did not find the version you want to use??
If a software package you would like to use for your research is not available on a cluster, you can request it to be installed. The software requests are evaluated by the HPC staff on a case-by-case basis. Before you send in a software request, please go through the information below.
Types of request
Depending on how many users need to use the software, software requests are divided into three types, each of which corresponds to the location where the software is installed:
- The user's home directory
- Software packages installed here will be accessible only to the user.
- It is suitable for software packages that will be used by a single user.
- Python, Perl and R modules should be installed here.
- Software packages installed in /project can be accessed by a group of users.
- It is suitable for software packages that
- Need to be shared by users from the same research group, or
- are bigger than the quota on the home file syste.
- This type of request must be sent by the PI of the research group, who may be asked to apply for a storage allocation.
- Software packages installed under /usr/local/packages can be accessed by all users.
- It is suitable for software packages that will be used by users from multiple research groups.
- This type of request must be sent by the PI of a research group.
How to request
Please send an email to firstname.lastname@example.org with the following information:
- Your user name
- The name of cluster where you want to use the requested software
- The name, version and download link of the software
- Specific installation instructions if any (e.g. compiler flags, variants and flavor, etc.)
- Why the software is needed
- Where the software should be installed (locally, /project, or /usr/local/packages) and justification explaining how many users are expected.
Please note that, once the software is installed, testing and validation are users' responsibility.
About the Software
Description Path: key[@id="uberftp"]/whatis Not Found!
The following usage summary is lifted from the User's Guide:
Usage: uberftp [options] [host options] [host] uberftp [options] [host options] host cmds uberftp [options] srcurl dsturl uberftp [options] -f urlfile uberftp [options] -cmd url Note: Only the first usage creates an interactive session. host Connect to host. cmds This specifies the FTP commands to run once the control connection is establish. This list must be enclosed in quotes. Multiple commands are semicolon delimited. uberftp will execute these commands and then exit. srcurl and dsturl These denote the source URL and destination URL respectively. The accepted forms are: gsiftp://host[:port]/path ftp://[user[:pass]@]host[:port]/path file:path urlfile This file is a list of srcurl/dsturl pairs, one pair per line. Blanks lines and lines beginning with '#' are ignored. -cmd This will execute the given command using the url as the target. The supported commands and their syntax are listed below. The "host options" are: -P port Connect to port (default 2811 for GSI) -u user Specify the user to authenticate as. -p pass | X Use password 'pass' when authenticating with 'host'. If 'pass' equals 'X', read the password from STDIN with character echoing turned off. The "options" are: -active Use ACTIVE mode for data transfers. -ascii Use ASCII mode for data transfers. -binary Use BINARY mode for data transfers. -blksize n Set the internal buffer size to n. -cksum [on|off] Enable/Disable CRC checks after file transfers. -debug n Set the debug level to n. -family name Set the remote storage family to name. -glob [on|off] Enable/Disable filename globbing. -hash Enable hashing. -keepalive n Send control channel keepalive messages every n seconds during data transfers. -mode [E|S] Switch the transfer mode to extend block (E) or streams mode(S). -parallel n Use n parallel data channels during extended block transfers. -passive Use PASSIVE mode for data transfers. -pbsz n Set the data protection buffer size to n bytes. -prot [C|S|E|P|] Set the data protection level to clear (C), safe (S), confidential (E) or private (P). -retry n Retry commands that fail with transient errors n times. -resume path Retry the recursive transfer starting at path. -tcpbuf n Set the TCP read/write buffers to n bytes. -wait This will cause the client to wait for remote files to stage before attempting to transfer them. -v Print UberFTP version information and exit. Deprecated. -version Print UberFTP version information and exit. -versions Print version information about all used globus modules and exit. The supported "-cmds" are: -cat
Print to stdout the contents of the remote file. -chgrp [-r] group Set the group ownership on the remote object(s). -chmod [-r] perms Set the permissions on the remote object(s). -dir [-r] List the contents of the remote object. -ls [-r] List the contents of the remote object. -mkdir Create the remote directory. -rename Rename the remote object to the given . -rm [-r] Remove the remote object(s). -rmdir Remove the remote directory. -size Return the size of the remote object. -stage -r seconds Attempt to stage the remote object(s) over the time period given in seconds. Note: uberftp uses passive STREAMS mode by default.
Last modified: September 10 2020 11:58:50.