IBM Spectrum LSF 10.1 436041 Fix  Readme File

Abstract

P102016. This solution allows LSF to run jobs in Singularity or Shifter containers on demand. LSF manages the entire life cycle of jobs running in these containers as common jobs.

Description

Readme documentation for IBM Spectrum LSF 10.1 Fix 436041 including installation-related instructions, prerequisites and co-requisites, and list of fixes.

This solution enables LSF to run and manage jobs in Singularity or Shifter containers.

  - The LSF server hosts must have either of the following software installed:
          - Singularity, Version 2.2, or later
          - Shifter, built from code later than 3 August 2016

  - Add the file path to the Shifter or Singularity executable file to $PATH before submitting jobs, and ensure that the executable file can be accessed on each execution host.

  - The required images must be prepared before running LSF jobs in containers. Ensure that these images are accessible to each execution host.

  - If you use mounted file systems for LSF, other software installations, or for input/output directories, you must also bind required directories into containers to ensure that LSF works properly. Configure the file systems as follows:
          1. For Singularity, add "mount hostfs = yes" to the singularity.conf file, which binds all mounted file systems to the container.
          2. For Shifter, add the pre-mount hook script "sitePreMountHook" to the udiRoot.conf file. You can define which directories to bind to the container in your script.

This solution uses the parameter CONTAINER in the lsb.applications file for configuring the Singularity and Shifter job application profile.

Syntax
CONTAINER= shifter[image(image-name) options(container-options)]

CONTAINER= singularity[image(image-name) options(container-options)]

Description
image: Required. This keyword configures the Singularity or Shifter image name that is used when running jobs.
options: Optional. This keyword configures the Singularity or Shifter job run options, which are passed to the job container with the "singularity exec" or "shifter" commands in LSF.

Note
1. Singularity / Shifter options can refer to the result by using "singularity exec --help" / "shifter --help" in command line.

2. The $LD_LIBRARY_PATH directory is cleaned per the setuid bit that Shifter or Singularity uses to work. Therefore, for some programs that depend on LD_LIBRARY_PATH to work, such as openmpi, ensure that the setuid bit can be set properly inside the container, as follows:

- For Singularity, modify related image to add $LD_LIBRARY_PATH to the ld.so.conf file and run ldconfig.
- For Shifter, add LD_LIBRARY_PATH in the siteEnvAppend section of the udiRoot.conf file.


Examples

Configure application profile in lsb.applications:

Begin Application
NAME=container
CONTAINER=singularity[image(/path/to/image/ubuntu.img)]
End Application

Begin Application
NAME=container
CONTAINER=shifter[image(ubuntu:latest)]
End Application
Jobs submitted to the singularity or shifter application profile are started in the container. For example:
bsub -app container ./myjob.sh
1. If CWD is not accessible inside the container:
    - For Singularity, the CWD is automatically set to HOME.
    - For Shifter, it is automatically set to the root directory in the container.
 
2. IBM Spectrum LSF Session Scheduler is not supported to run in Shifter or Singularity containers.

3. bsub -L login_shell  jobs and jobs where the execution user is changed by user mapping:
    - To run these two types of jobs, you must install singularity and shifter in /usr/bin or add a symbolic link under /usr/bin to the installation path of singularity or shifter.

Readme file for: IBM® Spectrum LSF

Product/Component Release: 10.1

Update Name: Fix 436041

Fix ID: LSF-10.1-build436041

Publication date: 10 January 2017

Last modified date: 10 January 2017

Contents:

1.     List of fixes

2.     Download location

3.     Products or components affected

4.     System requirements

5.     Installation and configuration

6.     List of files

7.     Product notifications

8.     Copyright and trademark information

 

1.   List of fixes

P102016.

2.   Download Location

Download Fix 436041 from the following location: http://www.ibm.com/eserver/support/fixes/

3.   Products or components affected

Affected components include: LSF/mbatchd, LSF/sbatchd, LSF/res, LSF/nios, LSF/bapp, LSF/blaunch, LSF/lsadmin, LSF/badmin

 

4.   System requirements

Linux2.6-glibc2.3-x86_64

Linux3.10-glibc2.17-x86_64

 

5.   Installation and configuration

 

5.1          Before installation

 

 (LSF_TOP=Full path to the top-level installation directory of LSF.)

1)    Log on to the LSF master host as root

2)    Set your environment:

-      For csh or tcsh: % source LSF_TOP/conf/cshrc.lsf

-      For sh, ksh, or bash: $ . LSF_TOP/conf/profile.lsf

 

5.2          Installation steps

 

1)    Go to the patch install directory: cd $LSF_ENVDIR/../10.1/install/

2)    Copy the patch file to the install directory $LSF_ENVDIR/../10.1/install/

3)    Run patchinstall: ./patchinstall <patch>

 

5.3          After installation

 

1)    Log on to the LSF master host as root

2)    Run lsfrestart

 

5.4          Uninstallation

 

To roll back a patch:

1)    Log on to the LSF master host as root

2)    Run ./patchinstall -r <patch>

3)    Run lsfrestart

6.   List of files

 
mbatchd
sbatchd
res

nios

bapp

blaunch

badmin

lsadmin

 

7.   Product notifications

To receive information about product solution and patch updates automatically, subscribe to product notifications on the My notifications page (www.ibm.com/support/mynotifications) on the IBM Support website (support.ibm.com). You can edit your subscription settings to choose the types of information you want to get notification about, for example, security bulletins, fixes, troubleshooting, and product enhancements or documentation changes.


8.   Copyright and trademark information

© Copyright IBM Corporation 2017

U.S. Government Users Restricted Rights - Use, duplication or disclosure restricted by GSA ADP Schedule Contract with IBM Corp.

IBM®, the IBM logo and ibm.com® are trademarks of International Business Machines Corp., registered in many jurisdictions worldwide. Other product and service names might be trademarks of IBM or other companies. A current list of IBM trademarks is available on the Web at "Copyright and trademark information" at www.ibm.com/legal/copytrade.shtml.