Administering Platform LSF - SAS

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$Intel(R) Math Kernel Library for Linux* OS User's Guide$

Creating Custom echkpnt and erestart for Application-level Checkpointing Configuring LSF to recognize the custom echkpnt and erestart You can set the following parameters in lsf.conf or as environment variables. If set in lsf.conf, these parameters apply globally to the cluster and will be the default values. Parameters specified as environment variables override the parameters specified in lsf.conf. If you set parameters in lsf.conf, reconfigure your cluster with lsadmin reconfig and badmin mbdrestart so that changes take effect. 1 Set LSB_ECHKPNT_METHOD=method_name in lsf.conf or as an environment variable OR When you submit the job, specify the checkpoint and restart method. For example: % bsub -k "mydir method=myapp" job1 2 Copy your echkpnt.method_name and erestart.method_name to LSF_SERVERDIR. OR If you want to specify a different directory than LSF_SERVERDIR, in lsf.conf or as an environment variable set LSB_ECHKPNT_METHOD_DIR= absolute path to the directory in which your echkpnt.method_name and erestart.method_name are located. The checkpoint method directory should be accessible by all users who need to run the custom echkpnt and erestart programs. 3 (Optional) To save standard error and standard output messages for echkpnt. method_name and erestart.method_name set LSB_ECHKPNT_KEEP_OUTPUT=y in lsf.conf or as an environment variable. The stdout and stderr output generated by echkpnt. method_name will be redirected to: ❖ checkpoint_dir/$LSB_JOBID/echkpnt.out ❖ checkpoint_dir/$LSB_JOBID/echkpnt.err The stdout and stderr output generated by erestart.method_name will be redirected to: ❖ checkpoint_dir/$LSB_JOBID/erestart.out ❖ checkpoint_dir/$LSB_JOBID/erestart.err Otherwise, if LSB_ECHKPNT_KEEP_OUTPUT is not defined, standard error and output will be redirected to /dev/null and discarded. 312 Administering Platform LSF
Checkpointing a Job Prerequisites Chapter 23 Job Checkpoint, Restart, and Migration Before LSF can checkpoint a job, it must be made checkpointable. LSF provides automatic and manual controls to make jobs checkpointable and to checkpoint jobs. When working with checkpointable jobs, a checkpoint directory must always be specified. Optionally, a checkpoint period can be specified to enable periodic checkpointing. When a job is checkpointed, LSF performs the following actions: 1 Stops the job if its running 2 Creates the checkpoint file in the checkpoint directory 3 Restarts the job LSF can create a checkpoint for any eligible job. Review the discussion about “Approaches to Checkpointing” on page 309 to determine if your application and environment are suitable for checkpointing. In this section ◆ “The Checkpoint Directory” on page 314 ◆ “Making Jobs Checkpointable” on page 315 ◆ “Manually Checkpointing Jobs” on page 316 ◆ “Enabling Periodic Checkpointing” on page 317 ◆ “Automatically Checkpointing Jobs” on page 318 Administering Platform LSF 313
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Administering Platform LSF® Versio
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Contents Welcome . . . . . . . . .
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Contents Part II: Working with Reso
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Contents 17 Reserving Resources . .
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Contents 30 External Job Submission
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Contents 40 Non-Shared File Systems
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Welcome Contents ◆ “About This
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Welcome Command notation Notation M
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Welcome Platform LSF License Schedu
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Welcome Resource requirement specif
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Welcome Run-time enhancements Threa
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Welcome Environment variables ◆
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Welcome New files added to installa
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Technical Support Contact Platform
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C H A P T E R 1 About Platform LSF
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Chapter 1 About Platform LSF Job sl
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Chapter 1 About Platform LSF Master
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Chapter 1 About Platform LSF Master
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Chapter 1 About Platform LSF Host t
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Chapter 1 About Platform LSF Extern
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Chapter 1 About Platform LSF Job Li
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C H A P T E R 2 How the System Work
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Chapter 2 How the System Works Queu
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Chapter 2 How the System Works Disp
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Job Execution Environment Shared us
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Fault Tolerance Dynamic master host
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P A R T I Managing Your Cluster Con
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Viewing Cluster Information Viewing
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Default Directory Structures Defaul
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Default Directory Structures Window
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Controlling Daemons Controlling Dae
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Controlling mbatchd Controlling mba
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Reconfiguring Your Cluster 3 Run ba
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Host States Host States Host states
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Viewing Host Information Viewing Ho
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Viewing Host Information type Viewi
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Controlling Hosts Controlling Hosts
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Adding a Host Adding a Host Use lsf
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Removing a Host Removing a Host CAU
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Adding and Removing Hosts Dynamical
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Adding and Removing Hosts Dynamical
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Adding Host Types and Host Models t
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Registering Service Ports NIS or NI
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Host Naming Host Naming Network add
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Hosts with Multiple Addresses Examp
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Host Groups Host Groups Where to us
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Tuning CPU Factors Tuning CPU Facto
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Handling Host-level Job Exceptions
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Handling Host-level Job Exceptions
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Queue States Queue States Queue sta
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Viewing Queue Information SCHEDULIN
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Controlling Queues Controlling Queu
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Controlling Queues Dispatch Windows
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Managing Queues Managing Queues Res
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Handling Job Exceptions Configuring
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Job States Job States The bjobs com
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Job States Viewing wait status and
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Viewing Job Information Viewing exc
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Switching Jobs from One Queue to An
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Suspending and Resuming Jobs Suspen
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Sending a Signal to a Job Sending a
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Using Job Groups Creating a job gro
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Using Job Groups % bhist -l 105 You
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Viewing User and User Group Informa
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About User Groups About User Groups
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LSF User Groups LSF User Groups You
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LSF User Groups 134 Administering P
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C H A P T E R 8 Understanding Resou
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Chapter 8 Understanding Resources T
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Chapter 8 Understanding Resources S
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How LSF Uses Resources Viewing job
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Chapter 8 Understanding Resources S
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Chapter 8 Understanding Resources V
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Chapter 8 Understanding Resources A
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C H A P T E R 9 Adding Resources Co
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Adding New Resources to Your Cluste
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Chapter 9 Adding Resources Configur
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Static Shared Resource Reservation
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Chapter 9 Adding Resources Configur
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Chapter 9 Adding Resources ELIM res
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Modifying a Built-In Load Index Con
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P A R T III Scheduling Policies Con
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Specifying Time Values Specifying T
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Specifying Time Expressions Specify
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Automatic Time-based Configuration
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Deadline Constraint Scheduling Dead
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Exclusive Scheduling 176 Administer
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About Preemptive Scheduling About P
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How Preemptive Scheduling Works Job
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Configuring Preemptive Scheduling Q
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Configuring Preemptive Scheduling 1
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About Resource Requirements About R
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Queue-Level Resource Requirements V
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About Resource Requirement Strings
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Selection String Selection String S
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Order String Order String Syntax De
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Usage String Example rusage[mem=50:
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Span String Span String Syntax A sp
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Same String 200 Administering Platf
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About Fairshare Scheduling About Fa
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User Share Assignments Examples ◆
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Dynamic User Priority Default dynam
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Host Partition Fairshare Host Parti
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Queue-Level User-based Fairshare Qu
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Cross-queue Fairshare bqueues -l al
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Cross-queue Fairshare 3 In all the
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Hierarchical Fairshare Viewing hier
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Queue-based Fairshare Queue-based F
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Configuring Slot Allocation per Que
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Viewing Queue-based Fairshare Alloc
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Typical Slot Allocation Scenarios T
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Typical Slot Allocation Scenarios W
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Typical Slot Allocation Scenarios T
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Using Historical and Committed Run
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Using Historical and Committed Run
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Users Affected by Multiple Fairshar
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Ways to Configure Fairshare Ways to
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Ways to Configure Fairshare Example
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Using Goal-Oriented SLA Scheduling
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Using Goal-Oriented SLA Scheduling
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Configuring Service Classes for SLA
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Viewing Information about SLAs and
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Viewing Information about SLAs and
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Understanding Service Class Behavio
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C H A P T E R 16 Resource Allocatio
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Chapter 16 Resource Allocation Limi
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Page 275 and 276: Chapter 17 Reserving Resources View
Page 277 and 278: C H A P T E R 18 Managing Software
Page 279 and 280: Host Locked Licenses Chapter 18 Man
Page 281 and 282: Network Floating Licenses Chapter 1
Page 283 and 284: Chapter 18 Managing Software Licens
Page 285 and 286: C H A P T E R 19 Dispatch and Run W
Page 287 and 288: Run Windows Configuring run windows
Page 289 and 290: C H A P T E R 20 Job Dependencies C
Page 291 and 292: Chapter 20 Job Dependencies ◆ In
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Page 295 and 296: C H A P T E R 21 Job Priorities Con
Page 297 and 298: Chapter 21 Job Priorities Specifyin
Page 299 and 300: C H A P T E R 22 Job Requeue and Jo
Page 301 and 302: Chapter 22 Job Requeue and Job Reru
Page 307 and 308: C H A P T E R 23 Job Checkpoint, Re
Page 309 and 310: Approaches to Checkpointing Kernel-
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Page 315 and 316: Making Jobs Checkpointable Manually
Page 317 and 318: Enabling Periodic Checkpointing At
Page 319 and 320: Restarting Checkpointed Jobs Requir
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Page 323 and 324: C H A P T E R 24 Chunk Job Dispatch
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Page 327 and 328: Submitting and Controlling Chunk Jo
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Page 331 and 332: C H A P T E R Ë 25 Job Arrays LSF
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Page 341 and 342: Requeuing a Job Array Chapter 25 Jo
Page 343: P A R T V Controlling Job Execution
Page 346 and 347: About Resource Usage Limits About R
Page 348 and 349: Specifying Resource Usage Limits Sp
Page 350 and 351: Specifying Resource Usage Limits If
Page 352 and 353: Supported Resource Usage Limits and
Page 358 and 359: CPU Time and Run Time Normalization
Page 360 and 361: Automatic Job Suspension Automatic
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Suspending Conditions Suspending Co
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Suspending Conditions Viewing suspe
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About Pre-Execution and Post-Execut
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Configuring Pre- and Post-Execution
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Configuring Pre- and Post-Execution
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About Job Starters About Job Starte
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Command-Level Job Starters Command-
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Queue-Level Job Starters Queue-Leve
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Controlling Execution Environment U
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Understanding External Executables
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Using esub Option LSB_SUB_EXCEPTION
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Using esub General esub logic Rejec
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Using esub # Deny userC the ability
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Working with eexec Working with eex
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Default Job Control Actions Default
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Configuring Job Control Actions Con
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Configuring Job Control Actions Exa
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Customizing Cross-Platform Signal C
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C H A P T E R 32 Interactive Jobs w
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Chapter 32 Interactive Jobs with bs
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Interactive Batch Job Messaging Lim
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Running X Applications with bsub Ch
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C H A P T E R 33 Running Interactiv
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Chapter 33 Running Interactive and
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Interactive Tasks Chapter 33 Runnin
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P A R T VII Running Parallel Jobs C
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How LSF Runs Parallel Jobs How LSF
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Submitting Parallel Jobs Submitting
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Submitting MPI Jobs Submitting MPI
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Starting Parallel Tasks with LSF Ut
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Specifying a Minimum and Maximum Nu
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Specifying a Mandatory First Execut
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Controlling Processor Allocation Ac
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Running Parallel Processes on Homog
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Using LSF Make to Run Parallel Jobs
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Limiting the Number of Processors A
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Reserving Processors Reserving Proc
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Reserving Memory for Pending Parall
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Allowing Jobs to Use Reserved Job S
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Allowing Jobs to Use Reserved Job S
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Parallel Fairshare Parallel Fairsha
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Optimized Preemption of Parallel Jo
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About Advance Reservation About Adv
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Configuring Advance Reservation ◆
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Using Advance Reservation Adding a
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Using Advance Reservation Removing
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Using Advance Reservation 6:10 0 10
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Using Advance Reservation Modifying
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Using Advance Reservation 474 Admin
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C H A P T E R 36 Event Generation C
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Chapter 36 Event Generation Events
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C H A P T E R 37 Tuning the Cluster
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Adjusting LIM Parameters RUNWINDOW
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Chapter 37 Tuning the Cluster Compa
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Changing Default LIM Behavior to Im
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Chapter 37 Tuning the Cluster Whene
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Tuning mbatchd on UNIX Operating sy
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C H A P T E R 38 Authentication Con
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Chapter 38 Authentication eauth -c
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Chapter 38 Authentication How LSF d
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Chapter 38 Authentication Correctin
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Chapter 38 Authentication About Dae
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User Account Mapping Chapter 38 Aut
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C H A P T E R 39 Job Email, and Job
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Chapter 39 Job Email, and Job File
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C H A P T E R 40 Non-Shared File Sy
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Chapter 40 Non-Shared File Systems
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Chapter 40 Non-Shared File Systems
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C H A P T E R 41 Error and Event Lo
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Chapter 41 Error and Event Logging
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System Event Log CAUTION Chapter 41
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Chapter 41 Error and Event Logging
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C H A P T E R 42 Troubleshooting an
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Common LSF Problems LIM dies quietl
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Chapter 42 Troubleshooting and Erro
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Setting Daemon Timing Levels Chapte
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P A R T IX LSF Utilities Contents
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About lstcsh About lstcsh The lstcs
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Local and Remote Modes Local and Re
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Differences from Other Shells Diffe
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Starting lstcsh Starting lstcsh Sta
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Host Redirection Host Redirection E
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Built-in Commands Built-in Commands
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Writing Shell Scripts in lstcsh Wri
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Index job migration 321 job requeue
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Index D daemons authd 496 authentic
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Index file spooling. See command fi
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Index Internet addresses, matching
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Index host locked 279 interactive j
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Index pre-42 UNIX directory structu
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Index disabling 317 job-level 317 q
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Index associating with hosts 155 Bo
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Index status closed in bhosts 70 jo
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Index 580 Administering Platform LS
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Administering Platform LSF - SAS

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