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uberftp

About

UberFTP is the first interactive, GridFTP-enabled ftp client. It supports GSI authentication, parallel data channels and third party transfers.

Versions and Availability

▶ Display Softenv Keys for uberftp on all clusters
Machine Version Softenv Key
▶ Softenv FAQ?

The information here is applicable to LSU HPC and LONI systems.

Shells

A user may choose between using /bin/bash and /bin/tcsh. Details about each shell follows.

/bin/bash

System resource file: /etc/profile

When one access the shell, the following user files are read in if they exist (in order):

  1. ~/.bash_profile (anything sent to STDOUT or STDERR will cause things like rsync to break)
  2. ~/.bashrc (interactive login only)
  3. ~/.profile

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 SoftEnv. See below for more information.

/bin/tcsh

The file ~/.cshrc is used to customize the user's environment if his login shell is /bin/tcsh.

Softenv

SoftEnv is a utility that is supposed to help users manage complex user environments with potentially conflicting application versions and libraries.

System Default Path

When a user logs in, the system /etc/profile or /etc/csh.cshrc (depending on login shell, and mirrored from csm:/cfmroot/etc/profile) calls /usr/local/packages/softenv-1.6.2/bin/use.softenv.sh to set up the default path via the SoftEnv database.

SoftEnv looks for a user's ~/.soft file and updates the variables and paths accordingly.

Viewing Available Packages

The command softenv will provide a list of available packages. The listing will look something like:

$ softenv
These are the macros available:
*   @default
These are the keywords explicitly available:
+amber-8                       Applications: 'Amber', version: 8 Amber is a
+apache-ant-1.6.5              Ant, Java based XML make system version: 1.6.
+charm-5.9                     Applications: 'Charm++', version: 5.9 Charm++
+default                       this is the default environment...nukes /etc/
+essl-4.2                      Libraries: 'ESSL', version: 4.2 ESSL is a sta
+gaussian-03                   Applications: 'Gaussian', version: 03 Gaussia
... some stuff deleted ...
Managing SoftEnv

The file ~/.soft in the user's home directory is where the different packages are managed. Add the +keyword into your .soft file. For instance, ff one wants to add the Amber Molecular Dynamics package into their environment, the end of the .soft file should look like this:

+amber-8

@default

To update the environment after modifying this file, one simply uses the resoft command:

% resoft

The command soft can be used to manipulate the environment from the command line. It takes the form:

$ soft add/delete +keyword

Using this method of adding or removing keywords requires the user to pay attention to possible order dependencies. That is, best results require the user to remove keywords in the reverse order in which they were added. It is handy to test out individual keys, but can lead to trouble if changing multiple keys. Changing the .soft file and issuing the resoft is the recommended way of dealing with multiple changes.

▶ Display Module Names for uberftp on all clusters.
Machine Version Module
smic 2.6 uberftp/2.6
▶ Module FAQ?

The information here is applicable to LSU HPC and LONI systems.

Shells

A user may choose between using /bin/bash and /bin/tcsh. Details about each shell follows.

/bin/bash

System resource file: /etc/profile

When one access the shell, the following user files are read in if they exist (in order):

  1. ~/.bash_profile (anything sent to STDOUT or STDERR will cause things like rsync to break)
  2. ~/.bashrc (interactive login only)
  3. ~/.profile

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 SoftEnv. See below for more information.

/bin/tcsh

The file ~/.cshrc is used to customize the user's environment if his login shell is /bin/tcsh.

Modules

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.

Default Setup

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

The command

$ 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).

Managing Modules

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.

Module is currently available only on SuperMIC.

Usage

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.
    

Resources

Last modified: November 12 2014 10:07:50.