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Intel

About

The Intel compiler suite is the default development environment on the HPC@LSU clusters.

Versions and Availability

▶ Display Softenv Keys for Intel all clusters
Machine Version Softenv Key
eric 11.1 +intel-cc-11.1
eric 11.1 +intel-fc-11.1
eric 10.2 +intel-mkl-10.2
qb 10.1 +intel-cc-10.1
qb 11.1 +intel-cc-11.1
qb 10.1 +intel-fc-10.1
qb 11.1 +intel-fc-11.1
qb 10.2 +intel-mkl-10.2
oliver 11.1 +intel-cc-11.1
oliver 11.1 +intel-fc-11.1
oliver 10.2 +intel-mkl-10.2
louie 11.1 +intel-cc-11.1
louie 11.1 +intel-fc-11.1
louie 10.2 +intel-mkl-10.2
poseidon 11.1 +intel-cc-11.1
poseidon 11.1 +intel-fc-11.1
poseidon 10.2 +intel-mkl-10.2
painter 11.1 +intel-cc-11.1
painter 11.1 +intel-fc-11.1
painter 10.2 +intel-mkl-10.2
philip 10.1 +intel-cc-10.1
philip 10.1 +intel-fc-10.1
philip 10.1 +intel-mkl-10.1
philip 10.2 +intel-mkl-10.2
philip 11.1 +intel-cc-11.1
philip 11.1 +intel-fc-11.1
philip 12.1 +intel-12.1
philip 13.1.0 +intel-13.1.0
supermike2 12.1.4 +Intel-12.1.4
supermike2 13.0.0 +Intel-13.0.0
supermike2 13.1.3 +Intel-13.1.3
▶ 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 Intel on all clusters.
Machine Version Module
smic 13.0.0 intel/13.0.0
smic 13.1.3 intel/13.1.3
smic 14.0.2 intel/14.0.2
smic 14.0.2 INTEL/14.0.2
smic 3.1.1 INTEL-140-MPICH/3.1.1
smic 2.0 INTEL-140-MVAPICH2/2.0
qb2 13.0.0 intel/13.0.0
qb2 13.1.3 intel/13.1.3
qb2 14.0.2 intel/14.0.2
qb2 14.0.2 INTEL/14.0.2
qb2 3.1.1 INTEL-140-MPICH/3.1.1
qb2 2.0 INTEL-140-MVAPICH2/2.0
▶ 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

Select the desired compiler name (possibly including an option) from the following table under the type of code being developed:

Language Serial Codes MPI Codes OpenMP Codes Hybrid Codes
Fortran ifort mpif90 ifort -openmp mpif90 -openmp
C icc mpicc icc -openmp mpicc -openmp
C++ icpc mpiCC icpc -openmp mpiCC -openmp

If you are compiling an MPI program, make sure you use an MPI library that was built with the version of compiler you choose. The softenv key names provide that information. For example, using the MVAPICH2 version 1.9a2 library with the 13.0.0 version of the Intel compiler would be specified with keys that look something like:

+Intel-13.0.0
+mvapich2-1.9a2-Intel-13.0.0

Of course, always verify what is available on the machine you choose to use. Checking what command would be selected is as simple as:

[user@mach1 ~]$ which mpif90
/usr/local/packages/openmpi/1.6.2/Intel-13.0.0/bin/mpif90
[user@mach1 ~]$

This shows that the OpenMPI is set as the MPI library of choice, along with the 13.0.0 release of the Intel compiler.

▶ 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.

Compiler Options

The behavior of the compiler can be controlled with command line options. There are way to many to list, but a few of the more commonly used ones include:

-g Enable debugging
-O0 Inhibit optimization
-O2 Default optimization - loop unrolling, loop-invariant code movement, constant and copy propagation, dead code elimination, etc.
-O3 Aggressive optimization - -O2 plus prefetching, scalar replacement, loop transformation, etc.
-FR Fortran 90 free format input files.
-ip/ipo Enable inline function expansion within the current source file or multiple files.
-axT Automatic processor-specific optimization for Intel Core 2 Duo processor family

Resources

  • See the manpages (i.e. man ifort) for usage details.

Last modified: November 11 2014 16:58:42.