High Performance Computing

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.

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.

Flat profile:

Each sample counts as 0.01 seconds.
  %   cumulative   self              self     total           
 time   seconds   seconds    calls   s/call   s/call  name    
 56.91     13.33    13.33       11     1.21     1.21  rank
 43.16     23.44    10.11                             main
  0.00     23.44     0.00        2     0.00     0.00  wtime_
  0.00     23.44     0.00        1     0.00     0.00  c_print_results
  0.00     23.44     0.00        1     0.00     0.00  timer_clear
  0.00     23.44     0.00        1     0.00     0.00  timer_read
  0.00     23.44     0.00        1     0.00     0.00  timer_start
  0.00     23.44     0.00        1     0.00     0.00  timer_stop

 %         the percentage of the total running time of the
time       program used by this function.

cumulative a running sum of the number of seconds accounted
 seconds   for by this function and those listed above it.

 self      the number of seconds accounted for by this
seconds    function alone.  This is the major sort for this
           listing.

calls      the number of times this function was invoked, if
           this function is profiled, else blank.
 
 self      the average number of milliseconds spent in this
ms/call    function per call, if this function is profiled,
           else blank.

 total     the average number of milliseconds spent in this
ms/call    function and its descendents per call, if this 
           function is profiled, else blank.

name       the name of the function.  This is the minor sort
           for this listing. The index shows the location of
           the function in the gprof listing. If the index is
           in parenthesis it shows where it would appear in
           the gprof listing if it were to be printed.


                     Call graph (explanation follows)


granularity: each sample hit covers 2 byte(s) for 0.04% of 23.44 seconds

index % time    self  children    called     name
                                                 
[1]    100.0   10.11   13.33                 main [1]
               13.33    0.00      11/11          rank [2]
                0.00    0.00       1/1           timer_clear [5]
                0.00    0.00       1/1           timer_start [7]
                0.00    0.00       1/1           timer_read [6]
                0.00    0.00       1/1           timer_stop [8]
                0.00    0.00       1/1           c_print_results [4]
-----------------------------------------------
               13.33    0.00      11/11          main [1]
[2]     56.9   13.33    0.00      11         rank [2]
-----------------------------------------------
                0.00    0.00       1/2           timer_start [7]
                0.00    0.00       1/2           timer_stop [8]
[3]      0.0    0.00    0.00       2         wtime_ [3]
-----------------------------------------------
                0.00    0.00       1/1           main [1]
[4]      0.0    0.00    0.00       1         c_print_results [4]
-----------------------------------------------
                0.00    0.00       1/1           main [1]
[5]      0.0    0.00    0.00       1         timer_clear [5]
-----------------------------------------------
                0.00    0.00       1/1           main [1]
[6]      0.0    0.00    0.00       1         timer_read [6]
-----------------------------------------------
                0.00    0.00       1/1           main [1]
[7]      0.0    0.00    0.00       1         timer_start [7]
                0.00    0.00       1/2           wtime_ [3]
-----------------------------------------------
                0.00    0.00       1/1           main [1]
[8]      0.0    0.00    0.00       1         timer_stop [8]
                0.00    0.00       1/2           wtime_ [3]
-----------------------------------------------

 This table describes the call tree of the program, and was sorted by
 the total amount of time spent in each function and its children.

 Each entry in this table consists of several lines.  The line with the
 index number at the left hand margin lists the current function.
 The lines above it list the functions that called this function,
 and the lines below it list the functions this one called.
 This line lists:
     index      A unique number given to each element of the table.
                Index numbers are sorted numerically.
                The index number is printed next to every function name so
                it is easier to look up where the function in the table.

     % time     This is the percentage of the `total' time that was spent
                in this function and its children.  Note that due to
                different viewpoints, functions excluded by options, etc,
                these numbers will NOT add up to 100%.

     self       This is the total amount of time spent in this function.

     children   This is the total amount of time propagated into this
                function by its children.

     called     This is the number of times the function was called.
                If the function called itself recursively, the number
                only includes non-recursive calls, and is followed by
                a `+' and the number of recursive calls.

     name       The name of the current function.  The index number is
                printed after it.  If the function is a member of a
                cycle, the cycle number is printed between the
                function's name and the index number.


 For the function's parents, the fields have the following meanings:

     self       This is the amount of time that was propagated directly
                from the function into this parent.

     children   This is the amount of time that was propagated from
                the function's children into this parent.

     called     This is the number of times this parent called the
                function `/' the total number of times the function
                was called.  Recursive calls to the function are not
                included in the number after the `/'.

     name       This is the name of the parent.  The parent's index
                number is printed after it.  If the parent is a
                member of a cycle, the cycle number is printed between
                the name and the index number.

 If the parents of the function cannot be determined, the word
 `' is printed in the `name' field, and all the other
 fields are blank.

 For the function's children, the fields have the following meanings:

     self       This is the amount of time that was propagated directly
                from the child into the function.

     children   This is the amount of time that was propagated from the
                child's children to the function.

     called     This is the number of times the function called
                this child `/' the total number of times the child
                was called.  Recursive calls by the child are not
                listed in the number after the `/'.

     name       This is the name of the child.  The child's index
                number is printed after it.  If the child is a
                member of a cycle, the cycle number is printed
                between the name and the index number.

 If there are any cycles (circles) in the call graph, there is an
 entry for the cycle-as-a-whole.  This entry shows who called the
 cycle (as parents) and the members of the cycle (as children.)
 The `+' recursive calls entry shows the number of function calls that
 were internal to the cycle, and the calls entry for each member shows,
 for that member, how many times it was called from other members of
 the cycle.



Index by function name

   [4] c_print_results         [5] timer_clear             [8] timer_stop
   [1] main                    [6] timer_read              [3] wtime_
   [2] rank                    [7] timer_start