Running Fluent Using a Load Manager

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Table of Contents
I. Running Fluent Under LSF ....................................................................................................................... 1
About This Part ...................................................................................................................................... iii
1. Introduction ...................................................................................................................................... 5
1.1. Overview of Fluent and LSF Integration ....................................................................................... 6
1.1.1. Requirements .................................................................................................................... 6
1.1.2. Optional Requirements ...................................................................................................... 6
1.1.3. Integration Components .................................................................................................... 6
2. Checkpointing and Restarting .......................................................................................................... 7
2.1. Fluent Checkpoint Files ............................................................................................................... 7
2.2. Checkpoint Directories ............................................................................................................... 7
2.3. Checkpoint Trigger Files .............................................................................................................. 7
2.4. Restart Jobs ................................................................................................................................ 8
3. Configuring LSF for Fluent ................................................................................................................ 9
4. Working with Fluent Jobs ................................................................................................................ 11
4.1. Submitting a Fluent Job from the Command Line ...................................................................... 11
4.2. Submitting a Fluent Job Using Fluent Launcher ......................................................................... 11
4.3. Manually Checkpointing Fluent Jobs ......................................................................................... 13
4.4. Restarting Fluent Jobs ............................................................................................................... 13
4.5. Migrating Fluent Jobs ............................................................................................................... 13
4.6. Coupling LSF Job Submissions and ANSYS Licensing ................................................................. 14
5. Fluent and LSF Examples ................................................................................................................ 17
5.1. Examples Without Checkpointing ............................................................................................. 17
5.2. Examples with Checkpointing ................................................................................................... 17
II. Running Fluent Under PBS Professional ............................................................................................... 21
About This Document ......................................................................................................................... xxiii
1. Introduction .................................................................................................................................... 25
1.1. Overview of Running Fluent Jobs with PBS Professional ............................................................. 25
1.1.1. Requirements .................................................................................................................. 25
1.1.2. Fluent and PBS Professional Communication .................................................................... 25
2. Running Fluent Simulation under PBS Professional ....................................................................... 27
2.1. Using the Integrated PBS Professional Capability ....................................................................... 27
2.1.1. Overview ......................................................................................................................... 27
2.1.2. Usage .............................................................................................................................. 27
2.1.3. Examples ......................................................................................................................... 28
2.1.4. Limitations ....................................................................................................................... 28
2.2. Using Your Own Supplied Job Script .......................................................................................... 29
2.3. Using Altair’s Sample Script ....................................................................................................... 29
2.3.1. Configuration File Example ............................................................................................... 29
2.3.2. Altair’s Sample Script ........................................................................................................ 30
2.3.3. Submitting Altair’s Sample Script ...................................................................................... 30
2.3.4. Epilogue/Prologue ........................................................................................................... 31
2.4. Monitoring/Manipulating Jobs .................................................................................................. 31
2.4.1. Monitoring the Progress of a Job ...................................................................................... 31
2.4.2. Removing a Job from the Queue ...................................................................................... 31
III. Running Fluent Under SGE .................................................................................................................. 33
About This Document ........................................................................................................................ xxxv
1. Introduction .................................................................................................................................... 37
1.1. Overview of Fluent and SGE Integration .................................................................................... 37
1.1.1. Requirements .................................................................................................................. 37
1.1.2. Fluent and SGE Communication ....................................................................................... 38

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Running Fluent Using a Load Manager

1.1.3. Checkpointing Directories ................................................................................................ 38

1.1.4. Checkpointing Trigger Files .............................................................................................. 38
1.1.5. Default File Location ......................................................................................................... 38
2. Configuring SGE for Fluent ............................................................................................................. 39
2.1. General Configuration ............................................................................................................... 39
2.2. Checkpoint Configuration ......................................................................................................... 39
2.3. Configuring Parallel Environments ............................................................................................ 40
2.4. Default Request File .................................................................................................................. 41
3. Running a Fluent Simulation under SGE ......................................................................................... 43
3.1. Submitting a Fluent Job from the Command Line ..................................................................... 43
3.2. Submitting a Fluent Job Using Fluent Launcher ........................................................................ 44
4. Running Fluent Utility Scripts under SGE ....................................................................................... 47
4.1. Special Considerations for Running the viewfac Utility under SGE .............................................. 48

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List of Figures
4.1. The Scheduler Tab of Fluent Launcher (Linux Version) ............................................................................ 12
3.1. The Scheduler Tab of Fluent Launcher (Linux Version) ........................................................................... 45

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 Part I: Running Fluent Under LSF

About This Document (p. iii)

1. Introduction (p. 5)
2. Checkpointing and Restarting (p. 7)
3. Configuring LSF for ANSYS Fluent (p. 9)
4. Working with ANSYS Fluent Jobs (p. 11)
5. ANSYS Fluent and LSF Examples (p. 17)
About This Part
This part provides general information about running Fluent under LSF. Examples have also been included,
where available.

Information in this part is presented in the following chapters:

• Introduction (p. 5)

• Checkpointing and Restarting (p. 7)

• Configuring LSF for Fluent (p. 9)

• Working with Fluent Jobs (p. 11)

• Fluent and LSF Examples (p. 17)

This document is made available via the ANSYS, Inc. website for your convenience. Contact Platform
Computing Inc. (http://www.platform.com/) directly for support of their product.

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Chapter 1: Introduction
Platform Computing’s LSF software is a distributed computing resource management tool that you can
use with either the serial or the parallel version of ANSYS Fluent. This document provides general in-
formation about running Fluent under LSF, and is made available via the ANSYS, Inc. website for your
convenience. Contact Platform directly for support of their product.

Using LSF, Fluent simulations can take full advantage of LSF checkpointing (saving Fluent .cas and
.dat files) and migration features. LSF is also integrated with various MPI communication libraries for
distributed MPI processing, increasing the efficiency of the software and data processing.

Important

Running Fluent under LSF is not supported on Windows.

Platform’s Standard Edition is the foundation for all LSF products, it offers users load sharing and batch
scheduling across distributed Linux and Windows computing environments. Platform’s LSF Standard
Edition provides the following functionality:

• comprehensive distributed resource management

– provides dynamic load sharing services

– allows for batch scheduling and resource management policies

• flexible queues and sharing control

– prioritizes jobs

– schedules jobs with load conditions

– processes jobs with time windows

– provides limits on the number of running jobs and job resource consumption

• fair-share scheduling of limited resources

– manages shares for users and user groups

– ensures fair sharing of limited computing resources

• maximum fault tolerance

– provides batch service as long as one computer is active

– ensures that no job is lost when the entire network goes down

– restarts jobs on other compute nodes when a computer goes down

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Introduction

For more information, see the following section:

1.1. Overview of Fluent and LSF Integration

1.1. Overview of Fluent and LSF Integration

For more information, see the following sections:
1.1.1. Requirements
1.1.2. Optional Requirements
1.1.3. Integration Components

1.1.1. Requirements
• LSF 10.1, available from Platform Computing at http://www.platform.com/

• Fluent 2019 R2

1.1.2. Optional Requirements

• The echkpnt.fluent and erestart.fluent binary files

These files are available from Platform Computing or ANSYS, Inc., and permit Fluent checkpointing
and restarting from within LSF.

• (For Linux) Hardware vendor-supplied MPI environment for network computing

1.1.3. Integration Components

The LSF components used by the Fluent integration are included in all versions of LSF packages that
are able to be downloaded from the Platform ftp site (ftp.platform.com). If you are a current LSF
customers, contact Platform support personnel for downloading instructions at support@plat-
form.com. New LSF customers should contact the Platform sales department.

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Chapter 2: Checkpointing and Restarting
LSF provides utilities to save (i.e., checkpoint), and restart an application. The Fluent and LSF integration
allows Fluent to take advantage of the checkpoint and restart features of LSF. At the end of each iteration,
Fluent looks for the existence of a checkpoint or checkpoint-exit file. If Fluent detects the checkpoint
file, it writes a case and data file, removes the checkpoint file, and continues iterating. If Fluent detects
the checkpoint-exit file, it writes a case file and data file, then exits. LSF’s bchkpnt utility can be used
to create the checkpoint and checkpoint-exit files, thereby forcing Fluent to checkpoint itself, or
checkpoint and terminate itself. In addition to writing a case file and data file, Fluent also creates a
simple journal file with instructions to read the checkpointed case file and data file, and continues iter-
ating. Fluent uses that journal file when restarted with LSF’s brestart utility. For more details on
checkpointing features and options within Fluent, see the Fluent User's Guide.

The greatest benefit of the checkpoint facilities occurs when it is used on an automatic basis. By starting
jobs with a periodic checkpoint, LSF automatically restarts any jobs that are lost due to host failure from
the last checkpoint. This facility can dramatically reduce lost compute time, and also avoids the task of
manually restarting failed jobs.

For more information, see the following sections:

2.1. Fluent Checkpoint Files
2.2. Checkpoint Directories
2.3. Checkpoint Trigger Files
2.4. Restart Jobs

2.1. Fluent Checkpoint Files

In order to allow you to checkpoint Fluent jobs using LSF, LSF supplies special versions of echkpnt
and erestart. These Fluent checkpoint files are called echkpnt.fluent and erestart.fluent.

2.2. Checkpoint Directories

When you submit a checkpointing job, you specify a checkpoint directory. Before the job starts running,
LSF sets the environment variable LSB_CHKPNT_DIR. The value of LSB_CHKPNT_DIR is a subdirectory
of the checkpoint directory specified in the command line. This subdirectory is identified by the job ID
and only contains files related to the submitted job.

2.3. Checkpoint Trigger Files

When you checkpoint a Fluent job, LSF creates a checkpoint trigger file (check) in the job subdirectory,
which causes Fluent to checkpoint and continue running. A special option is used to create a different
trigger file (exit), to cause Fluent to checkpoint and exit the job. Fluent uses the LSB_CHKPNT_DIR
environment variable to determine the location of checkpoint trigger files. It checks the job subdirectory
periodically while running the job. Fluent does not perform any checkpointing unless it finds the LSF
trigger file in the job subdirectory. Fluent removes the trigger file after checkpointing the job.

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Checkpointing and Restarting

2.4. Restart Jobs

If a job is restarted, LSF attempts to restart the job with the -restart option appended to the original
fluent command. Fluent uses the checkpointed data and case files to restart the process from that
checkpoint point, rather than repeating the entire process.

Each time a job is restarted, it is assigned a new job ID, and a new job subdirectory is created in the
checkpoint directory. Files in the checkpoint directory are never deleted by LSF, but you may choose
to remove old files once the Fluent job is finished and the job history is no longer required.

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Chapter 3: Configuring LSF for Fluent
LSF provides special versions of echkpnt and erestart called echkpnt.fluent and ere-
start.fluent to allow checkpointing with Fluent. You must make sure LSF uses these files instead
of the standard versions.

To configure LSF 9.1.1 for Fluent:

• Copy the echkpnt.fluent and erestart.fluent files to the $LSF_SERVERDIR for each architecture
that is desired.

• When submitting the job from the command line, include the -a fluent parameter when specifying the
checkpoint information (see Submitting a Fluent Job from the Command Line (p. 11) for details).

Important

Note that LSF includes an email notification utility that sends email notices to users
when an LSF job has been completed. If a user submits a batch job to LSF and the email
notification utility is enabled, LSF will distribute an email containing the output for the
particular LSF job. When a Fluent job is run under LSF with the -g option, the email
will also contain information from the Fluent console.

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Chapter 4: Working with Fluent Jobs
Information in this chapter is provided in the following sections:
4.1. Submitting a Fluent Job from the Command Line
4.2. Submitting a Fluent Job Using Fluent Launcher
4.3. Manually Checkpointing Fluent Jobs
4.4. Restarting Fluent Jobs
4.5. Migrating Fluent Jobs
4.6. Coupling LSF Job Submissions and ANSYS Licensing

4.1. Submitting a Fluent Job from the Command Line

The following shows how to submit a Fluent job from the Linux line command using LSF:

fluent <solver_version> [<Fluent_options>] -scheduler=lsf [-scheduler_queue=<queue>]

[-scheduler_opt=<opt>] [-gui_machine=<hostname>]

where

• fluent is the command that launches Fluent.

• <solver_version> specifies the dimensionality of the problem and the precision of the Fluent calculation
(e.g., 3d, 2ddp).

• <Fluent_options> can be added to specify the startup option(s) for Fluent, including the options for running
Fluent in parallel. For more information, see the Fluent User's Guide.

• -scheduler=lsf is added to the Fluent command to specify that you are running under LSF. This option
causes Fluent to check for trigger files in the checkpoint directory if the environment variable LSB_CH-
KPNT_DIR is set.

• -scheduler_queue=<queue> sets the queue to <queue>.

• -scheduler_opt=<opt> enables an additional option <opt> that is relevant for LSF; see the LSF docu-
mentation for details. Note that you can include multiple instances of this option when you want to use
more than one scheduler option.

• -gui_machine=<hostname> specifies that Cortex is run on a machine named <hostname>. This option
may be necessary to avoid poor graphics performance when running Fluent under LSF.

4.2. Submitting a Fluent Job Using Fluent Launcher

Fluent Launcher has graphical user input options that allow you to submit a Fluent job using LSF. Perform
the following steps:

1. Open Fluent Launcher (Figure 4.1: The Scheduler Tab of Fluent Launcher (Linux Version) (p. 12)) by entering
fluent without any arguments in the Linux command line.

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Working with Fluent Jobs

Figure 4.1: The Scheduler Tab of Fluent Launcher (Linux Version)

2. Enable Use Job Scheduler under General Options tab.

3. Click the Show More Options button to expand Fluent Launcher.

4. Select the Scheduler tab.

a. Ensure that Use LSF is selected.

b. To specify a job queue, enable the LSF queue option and enter the queue name in the text box.

c. Enable the Use Checkpointing option to utilize LSF checkpointing. By default, the checkpointing dir-
ectory will be the current working directory; you have the option of enabling Checkpointing Directory
and specifying a different directory, either by entering the name in the text box or by browsing to it.

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 Migrating Fluent Jobs

You can specify that the checkpointing is done automatically at a set time interval by enabling
the Automatic Checkpoint with Setting of Period option and entering the period (in minutes)
in the text box; otherwise, checkpointing will not occur unless you call the bchkpnt command.

5. Set up the other aspects of your Fluent simulation using the Fluent Launcher GUI items. For more inform-
ation, see the Fluent User's Guide.

Note

If you experience poor graphics performance when running ANSYS Fluent under LSF, you
may be able to improve performance by running Cortex on a specified machine. This can
be done by launching ANSYS Fluent from the command line rather than Fluent Launcher,
through the use of the -gui_machine=<hostname> and -scheduler=lsf options. For
details, see Submitting a Fluent Job from the Command Line (p. 11).

4.3. Manually Checkpointing Fluent Jobs

You can checkpoint a batch job manually by using the bchkpnt command. Note that you can set up
automatic checkpointing using Fluent Launcher as described previously. The syntax for the bchkpnt
command is

bchkpnt [<bchkpnt_options>] [-k] <job_ID>

where

• <bchkpnt_options> are options for the job checkpointing. See the Platform LSF Reference guide for a complete
list with descriptions.

• -k is the regular option to the bchkpnt command, and specifies checkpoint and exit. The job will be killed
immediately after being checkpointed. When the job is restarted, it does not have to repeat any operations.

• <job_ID> is the job ID of the Fluent job, which is used to specify which job to checkpoint.

4.4. Restarting Fluent Jobs

Restarting a batch job requires the brestart command. The syntax for the brestart command is

brestart [<bsub_options>]<checkpoint_directory> <job_ID>

where

• <bsub_options> are options for the job restart. See the Platform LSF Reference guide for a complete list with
descriptions.

• <checkpoint_directory> specifies the checkpoint directory where the job subdirectory is located.

• <job_ID> is the job ID of the Fluent job, and specifies which job to restart. At this point, the restarted job is
assigned a new job ID, and the new job ID is used for checkpointing. The job ID changes each time the job
is restarted.

4.5. Migrating Fluent Jobs

Migrating a Fluent job requires the bmig command. The syntax for the bmig command is

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Working with Fluent Jobs

bmig [<bmig_options>] <job_ID>

where

• <bmig_options> are options for the job migration. See the Platform LSF Reference guide for a complete list
with descriptions.

• <job_ID> is the job ID of the Fluent job, and specifies which job to checkpoint and restart on the migration
target. At this point, the restarted job is assigned a new job ID, and the new job ID is used for checkpointing.
The job ID changes each time the job is restarted.

4.6. Coupling LSF Job Submissions and ANSYS Licensing

You can couple your LSF job submission with ANSYS licensing by revising the LSF configuration files.
Such a coupling will ensure that submitted jobs do not fail because licenses are not available. The jobs
will be held in the queue until licenses are available. To set up such coupling, perform the following
steps:

1. Copy the elim script from your ANSYS installation area to $LSF_SERVERDIR. The elim script is located
in the following directory:

<path>/ansys_inc/v194/fluent/fluent19.4.0/multiport/mpi_wrapper/bin/

where <path> is the directory in which you have installed Fluent (e.g., /opt/apps/).

2. Edit the copy of the elim script to add your license server and license feature details. The following is an
example where acfd_fluent, acfd_par_proc, and anshpc are ANSYS solver and parallel license
features:
$ENV{'ANSYSLMD_LICENSE_FILE'} = "1055\@deva12"
my @features = qw(acfd_fluent acfd_par_proc anshpc);

3. Set the permissions to 755 and set root as the owner for the elim script.

4. Add all of your ANSYS solver license feature names and ANSYS parallel/HPC license feature names under
Resource section in the file lsf.shared, which is located in $LSF_ENVDIR in your LSF installation
area. The following is an example in which acfd, acfd_fluent, acfd_solver, and acfd_flu-
ent_solver are the ANSYS solver license feature names and anshpc, anshpc_pack, and
acfd_par_proc are the ANSYS parallel/HPC license feature names.
acfd Numeric 20 N (available ANSYS Fluent Solver licenses)
acfd_fluent Numeric 20 N (available ANSYS Fluent Solver licenses)
acfd_solver Numeric 20 N (available ANSYS Fluent Solver licenses)
acfd_fluent_solver Numeric 20 N (available ANSYS Fluent Solver licenses)
anshpc Numeric 20 N (available ANSYS Fluent Parallel licenses)
anshpc_pack Numeric 20 N (available ANSYS Fluent Parallel licenses)
acfd_par_proc Numeric 20 N (available ANSYS Fluent Parallel licenses)

5. Add all of your ANSYS solver license feature names and ANSYS parallel/HPC license feature names in the
file lsf.cluster.<cluster_name> (where <cluster_name> is the name of the cluster), which is located
in $LSF_ENVDIR in your LSF installation area. The following is an example in which acfd, acfd_fluent,
acfd_solver, and acfd_fluent_solver are the ANSYS solver license feature names and anshpc,
anshpc_pack, and acfd_par_proc are the ANSYS parallel/HPC license feature names.
# For LSF-ANSYS Licensing Coupling
Begin ResourceMap
RESOURCENAME LOCATION

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 Coupling LSF Job Submissions and ANSYS Licensing

acfd ([all])
acfd_fluent ([all])
acfd_solver ([all])
acfd_fluent_solver ([all])
anshpc ([all])
anshpc_pack ([all])
acfd_par_proc ([all])
End ResourceMap

6. Reconfigure the LSF daemons using the following commands, to specify that they reread their configuration.
Note that you need administrator privileges to implement these changes.

lsadmin reconfig

badmin reconfig

7. Submit the Fluent job using the "select[<solver_license_feature>] rusage[<parallel_license_feature>]"

option, as described in Submitting a Fluent Job from the Command Line (p. 11). In this option, <solver_li-
cense_feature> has the following form:

<serial_lic_name>>0

where <serial_lic_name> is the name of the serial ANSYS solver license feature name. Similarly,
<parallel_license_feature> has the following form:

<parallel_lic_name>=<N>

where <parallel_lic_name> is the name of the ANSYS parallel/HPC license feature name, and <N>
is the number of processes to use.

The previous descriptions are applicable when you have a single serial and/or parallel license feature.
If you have multiple serial and/or parallel license features, you must add additional <solver_license_fea-
ture> and/or <parallel_license_feature> entries, separating them with ||; additionally, you must
enclose all of the <solver_license_feature> entries in a single pair of parentheses. The following is
an example of submitting a Fluent job in which acfd and acfd_fluent are the ANSYS solver li-
cense feature names, anshpc and acfd_par_proc are the ANSYS parallel/HPC license feature
names, and the number of processes to use is 4:

fluent 3d -t4 -scheduler=lsf -scheduler_opt='-R "select[(acfd>0 ||

acfd_fluent>0)] rusage[anshpc=4 || acfd_par_proc=4]"'

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Chapter 5: Fluent and LSF Examples
This chapter provides various examples of running Fluent and LSF.
5.1. Examples Without Checkpointing
5.2. Examples with Checkpointing

5.1. Examples Without Checkpointing

• Serial 3D Fluent interactive job under LSF

fluent 3d -scheduler=lsf

• Serial 3D Fluent batch job under LSF, which reads the journal file called journal_file

fluent 3d -g -i journal_file -scheduler=lsf

• Parallel 3D Fluent interactive job under LSF, on 4 CPUs

fluent 3d -t4 -scheduler=lsf

Important

PAM is an extension of LSF that manages parallel processes by choosing the appropriate
compute nodes and launching child processes. When using Fluent on Linux, PAM is
not used to launch Fluent (so the JOB_STARTER argument of the LSF queue should
not be set). Instead, LSF will set an environment variable that contains a list of N hosts,
and Fluent will use this list to launch itself.

• Parallel 3D Fluent batch job under LSF, which uses 5 processes and reads the journal file called journ-
al_file

fluent 3d -t5 -g -i journal_file -scheduler=lsf

5.2. Examples with Checkpointing

The examples that follow apply to both interactive and batch submissions. For brevity, only batch
submissions are described. Usage of the LSF checkpoint and restart capabilities, requiring echkpnt
and erestart, are described as follows:

• Serial 3D Fluent batch job under LSF with checkpoint/restart

fluent 3d -g -i journal_file -scheduler=lsf -scheduler_opt='-k "

/home/username 60"' -scheduler_opt='-a fluent'

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Fluent and LSF Examples

– In this example, the LSF -a fluent specification identifies which echkpnt/ erestart combination
to use, /home/username is the checkpoint directory, and the duration between automatic checkpoints
is 60 minutes.

The following commands can then be used:

– bjobs -l <job_ID>

→ This command returns the job information about <job_ID> in the LSF system.

– bchkpnt <job_ID>

→ This command forces Fluent to write a case file, a data file, and a restart journal file at the end of its
current iteration.

→ The files are saved in a directory named <checkpoint_directory>/<job_ID>. The <checkpoint_dir-

ectory> is defined through the -scheduler_opt= option in the original fluent command.

→ Fluent then continues to iterate.

– bchkpnt -k <job_ID>

→ This command forces Fluent to write a case file, a data file, and a restart journal file at the end of its
current iteration.

→ The files are saved in a directory named <checkpoint_directory>/<job_ID> and then Fluent exits.
The <checkpoint_directory> is defined through the -scheduler_opt= option in the original
fluent command.

– brestart <checkpoint_directory> <job_ID>

→ This command starts a Fluent job using the latest case and data files in the <checkpoint_direct-
ory>/<job_ID> directory.

→ The restart journal file <checkpoint_directory>/<job_ID>/#restart.inp is used to instruct Fluent to

read the latest case and data files in that directory and continue iterating.

• Parallel 3D Fluent batch job under LSF with checkpoint/restart, which specifies /home/username as the
checkpoint directory, uses 4 processes, and reads a journal file called journal_file

fluent 3d -t4 -g -i journal_file -scheduler=lsf -scheduler_opt='-k "

/home/username"' -scheduler_opt='-a fluent'

The following commands can then be used:

– bjobs -l <job_ID>

→ This command returns the job information about <job_ID> in the LSF system.

– bchkpnt <job_ID>

→ This command forces parallel Fluent to write a case file, a data file, and a restart journal file at the end
of its current iteration.

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 Examples with Checkpointing

→ The files are saved in a directory named <checkpoint_directory>/<job_ID>. The <checkpoint_dir-

ectory> is defined through the -scheduler_opt= option in the original fluent command.

→ Parallel Fluent then continues to iterate.

– bchkpnt -k <job_ID>

→ This command forces parallel Fluent to write a case file, a data file, and a restart journal file at the end
of its current iteration.

→ The files are saved in a directory named <checkpoint_directory>/<job_ID>. The <checkpoint_dir-

ectory> is defined through the -scheduler_opt= option in the original fluent command.

→ Parallel Fluent then exits.

– brestart <checkpoint_directory> <job_ID>

→ This command starts a Fluent network parallel job using the latest case and data files in the <check-
point_directory>/<job_ID> directory.

→ The restart journal file <checkpoint_directory>/<job_ID>/#restart.inp is used to instruct Fluent to read

the latest case and data files in that directory and continue iterating.

→ The parallel job will be restarted using the same number of processes as that specified through
the -t<x> option in the original fluent command (4 in the previous example).

– bmig -m <host> 0

→ This command checkpoints all jobs (indicated by 0 job ID) for the current user and moves them to host
<host>.

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 Part II: Running Fluent Under PBS Professional

About This Document (p. xxiii)

1. Introduction (p. 25)
3. Running an ANSYS Fluent Simulation under PBS Professional (p. 27)
About This Document
This document provides general information about running ANSYS Fluent under PBS Professional. Ex-
amples have also been included, where available.

Information in this document is presented in the following chapters:

• Introduction (p. 25)

• Running Fluent Simulation under PBS Professional (p. 27)

This document is made available via the ANSYS, Inc. website for your convenience. Contact Altair Engin-
eering, Inc. (http://www.altair.com/) directly for support of their product.

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of ANSYS, Inc. and its subsidiaries and affiliates. xxiii
 Release 2019 R2 - © ANSYS, Inc. All rights reserved. - Contains proprietary and confidential information
xxiv of ANSYS, Inc. and its subsidiaries and affiliates.
Chapter 1: Introduction
Altair PBS Professional is an open workload management tool for local and distributed environments.
You can use PBS Professional when running Fluent simulations, and thereby control the number of jobs
running and dynamically monitor the licenses. This document provides general information about
running Fluent under PBS Professional, and is made available via the ANSYS, Inc. website for your con-
venience. Contact Altair Engineering, Inc. (http://www.altair.com/) directly for support of their product.

For more information, see the following section:

1.1. Overview of Running Fluent Jobs with PBS Professional

1.1. Overview of Running Fluent Jobs with PBS Professional

For more information, see the following sections:
1.1.1. Requirements
1.1.2. Fluent and PBS Professional Communication

1.1.1. Requirements
• Standard

– PBS Professional 18.2

– Fluent 2019 R2

Important

Running Fluent under PBS Professional is not supported on Windows.

• Optional

– Checkpoint restart scripts must be obtained/written to use the checkpoint restart functionality

1.1.2. Fluent and PBS Professional Communication

• PBS Professional has the ability to send signals to the Fluent processes inside a PBS Professional job.

• Dynamic resource functionality provides a way to monitor the availability of software licenses. Refer to the
PBS Professional Administrators Guide for more information on creating custom resources.

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Chapter 2: Running Fluent Simulation under PBS Professional
For more information, see the following sections:
2.1. Using the Integrated PBS Professional Capability
2.2. Using Your Own Supplied Job Script
2.3. Using Altair’s Sample Script
2.4. Monitoring/Manipulating Jobs

2.1. Using the Integrated PBS Professional Capability

For more information, see the following sections:
2.1.1. Overview
2.1.2. Usage
2.1.3. Examples
2.1.4. Limitations

2.1.1. Overview
One option of using PBS Professional with Fluent is to use the PBS Professional launching capability
integrated directly into Fluent. In this mode, Fluent is started from the command line with the additional
-scheduler=pbs argument. Fluent then takes responsibility for relaunching itself under PBS Profes-
sional. This has the following advantages:

• The command line usage is very similar to the non-RMS (resource management system) usage.

• You do not need to write a separate script.

The integrated PBS Professional capability is intended to simplify usage for the most common situations.
If you desire more control over the PBS Professional qsub options for more complex situations or systems
(or if you are using an older version of Fluent), you can always write or adapt a PBS Professional script
that starts Fluent in the desired manner (see Using Your Own Supplied Job Script (p. 29) and Using
Altair’s Sample Script (p. 29) for details).

2.1.2. Usage
The integrated PBS Professional capability is activated by simply adding the -scheduler=pbs option
to the Fluent line command:

fluent <solver_version> [<Fluent_options>] -i <journal_file> -scheduler=pbs [-sched-

uler_queue=<queue>] [-scheduler_opt=<opt>] [-gui_machine=<hostname>]

This syntax will start the Fluent job under PBS Professional using the qsub command in a batch manner.
When resources are available, PBS Professional will start the job and return a job ID, usually in the form
of <job_ID>.<hostname>. This job ID can then be used to query, control, or stop the job using standard

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Running Fluent Simulation under PBS Professional

PBS Professional commands, such as qstat or qdel. The job will be run out of the current working
directory, and all output will be written to the file fluent.<job_ID>.o.

Note

If you experience poor graphics performance when running Fluent under PBS Professional,
you may be able to improve it by running Cortex on a specified machine through the use
of the -gui_machine=<hostname> option.

2.1.3. Examples
• Submit a parallel, 4-process job using a journal file fl5s3.jou:
> fluent 3d -t4 -i fl5s3.jou -scheduler=pbs
Relaunching fluent under PBSPro
134.les29

In the previous example, note that 134.les29 is returned from qsub. 134 is the job ID, while les29
is the hostname on which the job was started.

• Check the status of the job:

> qstat -s

les29:
Req’d Req’d Elap
Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time
------------- -------- -------- --------- ------ --- --- ------ ----- - -----
134.les29 user1 workq fluent 11958 4 4 -- -- R 00:00
Job run at Thu Jan 04 at 14:48

> qstat -f 134

Job Id: 134.les29
Job_Name = fluent
Job_Owner = user1@les29
<... additional status of jobID 134>

The first command in the previous example lists all of the jobs in the queue. The second command lists
the detailed status about the given job.

After the job is complete, the job will no longer show up in the output of the qstat command. The
results of the run will then be available in the file fluent.134.o.

2.1.4. Limitations
The integrated PBS Professional capability in Fluent 2019 R2 has the following limitations:

• The PBS Professional commands (such as qsub) must be in the users path.

• The output is directed to the file fluent.<job_ID>.o.

• The error is directed to the file fluent.<job_ID>.e.

• For parallel jobs, Fluent processes are placed on available compute resources using the qsub options -l
select=<N>. (Optionally, for better control over the placement of processes, you can set the environment
variable SET_PBS_PPN to a value of <M>, where <M> is the number of processes per node. Setting this
variable will place Fluent processes using the option -l nodes=<total_processes_reques-
ted>/<M>:ppn=<M>. The value used for <M> has to be same for all nodes. If you desire more sophisticated

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 Using Altair’s Sample Script

placement, you may write separate PBS Professional scripts as described in Using Your Own Supplied Job
Script (p. 29).)

• RMS-specific checkpointing is not available. PBS Professional only supports checkpointing via mechanisms
that are specific to the operating system on SGI and Cray systems. The integrated PBS Professional capability
is based on saving the process state, and is not based on the standard application restart files (for example,
Fluent case and data files) on which the LSF and SGE checkpointing is based. Thus, if you need to checkpoint,
you should checkpoint your jobs by periodically saving the Fluent data file via the journal file.

2.2. Using Your Own Supplied Job Script

PBS Professional can accept any custom shell script for running Fluent that you may already use. Note
that this shell script may require modification to move files between machines in the cluster. The shell
script should also endeavor to clean up after itself when execution completes/fails.

2.3. Using Altair’s Sample Script

Altair provides a short sample script for running Fluent inside of PBS Professional. This script uses a
configuration file to tell it several pieces of information that it needs (outlined in the section that follows).
Optionally, these pieces of information can be specified on the command line. The fluent_args
option does not need to be used for specifying the number of CPUs in the default script. The script will
address this for the user, based on their PBS Professional resource requests.

For more information, see the following sections:

2.3.1. Configuration File Example
2.3.2. Altair’s Sample Script
2.3.3. Submitting Altair’s Sample Script
2.3.4. Epilogue/Prologue

2.3.1. Configuration File Example

The sample script uses a configuration file called pbs_fluent.conf if no command line arguments
are present. This configuration file should be present in the directory from which the jobs are submitted
(which is also the directory in which the jobs are executed). The following is an example of what the
content of pbs_fluent.conf can be:
input="example_small.flin"
case="Small-1.65m.cas"
fluent_args="3d -pinfiniband"
outfile="fluent_test.out"
mpp="true"

The following is an explanation of the parameters:

input
is the name of the input file.

case
is the name of the .cas file that the input file will utilize.

fluent_args
are extra Fluent arguments. As shown in the previous example, you can specify the interconnect by using
the -p<interconnect> command. The available interconnects include ethernet (the default), infiniband,
and crayx. The MPI is selected automatically, based on the specified interconnect.

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Running Fluent Simulation under PBS Professional

outfile
is the name of the file to which the standard output will be sent.

mpp="true"
will tell the job script to execute the job across multiple processors.

2.3.2. Altair’s Sample Script

Altair’s Sample script is not intended to be a full solution for running Fluent jobs in PBS Professional,
but rather a simple starting point. It runs the jobs out of the directory from which they are submitted
(PBS_O_WORKDIR). Care should be taken to submit jobs from locations that are going to be available
on any node (perhaps via NFS).
#!/bin/sh
cd $PBS_O_WORKDIR

#We assume that if they didn’t specify arguments then they should use the
#config file if [ "xx${input}${case}${mpp}${fluent_args}zz" = "xxzz" ]; then
if [ -f pbs_fluent.conf ]; then
. pbs_fluent.conf
else
printf "No command line arguments specified, "
printf "and no configuration file found. Exiting \n"
fi
fi

#Set up the license information (Note: you need to substitute your own
#port and server in this command)
export ANSYSLMD_License_FILE

#Augment the Fluent command line arguments case "$mpp" in

true)
#MPI job execution scenario
num_nodes=‘cat $PBS_NODEFILE | sort -u | wc -l‘
cpus=‘expr $num_nodes \* $NCPUS‘
#Default arguments for mpp jobs, these should be changed to suit your
#needs.
fluent_args="-t${cpus} $fluent_args -cnf=$PBS_NODEFILE"
;;
*)
#SMP case
#Default arguments for smp jobs, should be adjusted to suit your
#needs.
fluent_args="-t$NCPUS $fluent_args"
;;
esac
#Default arguments for all jobs
fluent_args="-ssh -g -i $input $fluent_args"

echo "---------- Going to start a fluent job with the following settings:
Input: $input
Case: $case
Output: $outfile
Fluent arguments: $fluent_args"

#run the solver

/ansys_inc/v194/fluent/bin/fluent $fluent_args > $outfile

Note that for versions of Fluent prior to 12.0, the final line of the sample script should be changed to
the following:
usr/apps/Fluent.Inc/bin/fluent $fluent_args > $outfile

2.3.3. Submitting Altair’s Sample Script

• To submit the script with command line arguments:

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 Monitoring/Manipulating Jobs

– qsub -l <resource_requests> -v input=<input_file>,case=<case_file>,fluent_args= <fluent_ar-

guments>,outfile=<output_file>[,mpp="true"] fluent-job.sh

• To submit the script without command line arguments:

– Edit fluent_pbs.conf to suit your needs

– qsub -l <resource_requests> fluent-job.sh

Note that the resources necessary for the job (that is, <resource_requests>) should be entered with the
proper syntax. For more information about requesting resources, see the PBS Professional 7.1 Users
Guide Section 4.3.

2.3.4. Epilogue/Prologue
PBS Professional provides the ability to script some actions immediately before the job starts and im-
mediately after it ends (even if it is removed). The epilogue is a good place to put any best effort cleanup
and stray process functionality that might be necessary to clean up after a job. For instance, one could
include functionality to clean up the working/scratch area for a job if is deleted before its completion.
Fluent provides a way to get rid of job-related processes in the form of a shell script in the work directory
(cleanup-fluent-<host-pid>). It could be useful to have the epilogue call this script to ensure all
errant processes are cleaned up after a job completes.

2.4. Monitoring/Manipulating Jobs

For more information, see the following sections:
2.4.1. Monitoring the Progress of a Job
2.4.2. Removing a Job from the Queue

2.4.1. Monitoring the Progress of a Job

The qstat command is used to monitor the status of jobs in a PBS Professional queue. When no job
ID is specified, the qstat command will display all jobs. If you use qstat -an job_ID you will receive
information about a specific job. This information includes the location at which the job is executing,
which will be listed under the Job ID column.
% qstat -an

server:
Req’d Req’d Elap
Job ID Username Queue Jobname SessID NDS TSK Memory Time S Time
------------- -------- ------- ---------- ------ --- --- ------ ----- - -----
32.server user workq fluent-job 15886 -- 1 -- -- R 01:07
server/0

There are several job states to be aware of when using qstat, which are listed under the S column.
The two main states you will see are Q and R. Q indicates that the job is waiting in the queue to run.
At this point the scheduler has not found a suitable node or nodes to run the job. Once the scheduler
has found a suitable area to run the job and has sent the job to run, its state will be set to R. Full details
on the different job statuses reported by qstat can be found in the PBS Professional 7.1 Users Guide
Section 6.1.1.

2.4.2. Removing a Job from the Queue

The qdel <job_ID> command will delete the job indicated by <job_ID>.

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 Part III: Running Fluent Under SGE

About This Document (p. xxxv)

1. Introduction (p. 37)
2. Configuring SGE for ANSYS Fluent (p. 39)
3. Running an ANSYS Fluent Simulation under SGE (p. 43)
4. Running an ANSYS Fluent Utility Scripts under SGE (p. 47)
About This Document
This document provides general information about running Fluent under Univa Grid Engine (UGE) and
Sun Grid Engine software (SGE). Throughout this manual SGE is used to denote the Grid Engine software
whether UGE or SGE. Examples are included, where available.

Information in this document is presented in the following chapters:

• Introduction (p. 37)

• Configuring SGE for Fluent (p. 39)

• Running a Fluent Simulation under SGE (p. 43)

• Running Fluent Utility Scripts under SGE (p. 47)

This document is made available via the ANSYS, Inc. website for your convenience. Contact Oracle, Inc.
(http://www.oracle.com/) directly for support of their product.

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of ANSYS, Inc. and its subsidiaries and affiliates. xxxv
 Release 2019 R2 - © ANSYS, Inc. All rights reserved. - Contains proprietary and confidential information
xxxvi of ANSYS, Inc. and its subsidiaries and affiliates.
Chapter 1: Introduction
Univa (formerly Sun) Grid Engine (UGE/SGE) software is a distributed computing resource management
tool that you can use with either the serial or the parallel version of Fluent. Throughout this manual
SGE is used to denote the Grid Engine software whether UGE or SGE. This document provides general
information about running Fluent under SGE, and is made available via the ANSYS, Inc. website for your
convenience. Contact Univa (http://www.univa.com/) directly for support of their product.

Fluent submits a process to the SGE software, then SGE selects the most suitable machine to process
the Fluent simulation. You can configure SGE and select the criteria by which SGE determines the most
suitable machine for the Fluent simulation.

Among many other features, running a Fluent simulation using SGE enables you to:

• Save the current status of the job (this is also known as checkpointing when the Fluent .cas and .dat
files are saved)

• Migrate the simulation to another machine

• Restart the simulation on the same or another machine.

For more information, see the following section:

1.1. Overview of Fluent and SGE Integration

1.1. Overview of Fluent and SGE Integration

For more information, see the following sections:
1.1.1. Requirements
1.1.2. Fluent and SGE Communication
1.1.3. Checkpointing Directories
1.1.4. Checkpointing Trigger Files
1.1.5. Default File Location

1.1.1. Requirements
• Univa (Sun) Grid Engine software version 8.6, which is available online at http://www.univa.com/

• Fluent 2019 R2

Important

Running Fluent under SGE is not supported on Windows.

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Introduction

1.1.2. Fluent and SGE Communication

Fluent and SGE communicate with each other through checkpointing and migration commands. To
checkpoint, or save, Fluent simulations, SGE uses an executable file called ckpt_command.fluent.
To migrate Fluent simulations to another machine, SGE uses another executable file called migr_com-
mand.fluent.

1.1.3. Checkpointing Directories

Fluent creates a checkpointing subdirectory, identified by the job ID. The checkpointing directory contains
files related only to the submitted job.

1.1.4. Checkpointing Trigger Files

When a Fluent simulation must be checkpointed, SGE calls a command that creates a checkpoint trigger
file (check) in the job subdirectory, which causes Fluent to checkpoint and continue running. If the
job must be migrated, because of a machine crash or for some other reason, a different trigger file
(exit) is created which causes Fluent to checkpoint and exit.

1.1.5. Default File Location

For Fluent 2019 R2, SGE-related files are installed by default in path/ansys_inc/v194/fluent/flu-
ent19.4.0/addons/sge, where path is the Fluent installation directory. The files include the fol-
lowing:

• ckpt_command.fluent

• migr_command.fluent

• sge_request

• kill-fluent

• sample_ckpt_obj

• sample_pe

These files are described in the sections that follow.

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Chapter 2: Configuring SGE for Fluent
SGE must be installed properly if checkpointing is needed or parallel Fluent is being run under SGE.
The checkpoint queues must be configured first, and they must be configured by someone with manager
or root privileges. The configuration can be performed either through the GUI qmon or the text command
qconf.

For more information, see the following sections:

2.1. General Configuration
2.2. Checkpoint Configuration
2.3. Configuring Parallel Environments
2.4. Default Request File

2.1. General Configuration

Using the SGE graphical interface, the general configuration of SGE and Fluent requires the following:

• The Shell Start Mode must be set to either unix_behavior or posix_compliant.

• Under Type, the checkpointing option must be marked as true.

When running parallel Fluent simulations, the following options are also important:

• Under Type, the parallel option must be marked as true.

• The value of slots should be set to a value greater than 1.

2.2. Checkpoint Configuration

Checkpointing can be configured using the min_cpu_interval field. This field specifies the time interval
between checkpoints. The value of min_cpu_interval should be a reasonable amount of time. Entering
a value that is too low for min_cpu_interval results in frequent checkpointing operations, and writing
.cas and .dat files can be computationally expensive.

SGE requires checkpointing objects to perform checkpointing operations. Fluent provides a sample
checkpointing object called sample_ckpt_obj.

Checkpoint configuration also requires root or manager privileges. While creating new checkpointing
objects for Fluent, keep the default values as given in the sample/default object provided by Fluent
and change only the following values:

• queue list (queue_list)

The queue list should contain the queues that are able to be used as checkpoint objects.

• checkpointing and migration commands (ckpt_command and migr_command)

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Configuring SGE for Fluent

These values should only be changed when the executable files are not in the default location, in
which case the full path should be specified. All the files (that is, ckpt_command.fluent and
migr_command.fluent) should be located in a directory that is accessible from all machines where
the Fluent simulation is running. When running Fluent 2019 R2, the default location for these files is
path/ansys_inc/v194/fluent/fluent19.4.0/addons/sge, where path is the Fluent in-
stallation directory.

• checkpointing directory (ckpt_dir)

This value dictates where the checkpointing subdirectories are created, and hence users must have
the correct permission to this directory. Also, this directory should be visible to all machines where
the Fluent simulation is running. The default value is NONE where Fluent uses the current working
directory as the checkpointing directory.

• checkpointing modes (when)

This value dictates when checkpoints are expected to be generated. Valid values of this parameter
are composed of the letters s, m, and x, in any order:

– Including s causes a job to be checkpointed, aborted, and migrated when the corresponding SGE Exceed
daemon is shut down.

– Including m results in the generation of checkpoints periodically at the min_cpu_interval interval defined
by the queue (see qconf).

– Including x causes a job to be checkpointed, aborted, and migrated when a job is suspended.

Important

The m mode must be set to permit interval checkpointing.

2.3. Configuring Parallel Environments

For submitting parallel jobs, SGE needs a parallel environment (PE) interface. Fluent provides a sample
parallel environment interface called fluent_pe.

Parallel environment configuration requires root or manager privileges. Change only the following values
when creating a new parallel environment for Fluent:

• queue list (queue_list)

This should contain all the queues where qtype has been set to PARALLEL.

• user/xuser lists (user_list and xuser_lists)

These contain the lists of users who are allowed or denied access to the parallel environment.

• Shut-down procedure invocation command (stop_proc_args)

This should be changed only if the kill-fluent executable is not in the default directory, in which
case the full path to the file should be given and the path should be accessible from every machine.

• slots (slots)

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 Default Request File

This should be set to a large numerical value, indicating the maximum of slots that can be occupied
by all the parallel environment jobs that are running.

Since Fluent uses fluent_pe as the default parallel environment, an administrator must define a
parallel environment with this name.

2.4. Default Request File

As an alternative to specifying numerous command line options or arguments when you invoke SGE,
you can provide a list of SGE options in a default request file. All default request options and arguments
for SGE that are common to all users can be placed in this file.

A default request file should be set up when using SGE with Fluent. Fluent provides a sample request
file called sge_request. To learn more about how to configure and utilize this resource, see the rel-
evant documentation available at www.oracle.com.

Individual users can set their own default arguments and options in a private general request file called
.sge_request, located in their $HOME directory. Private general request files override the options
set by the global sge_request file.

Any settings found in either the global or private default request file can be overridden by specifying
new options in the command line.

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Chapter 3: Running a Fluent Simulation under SGE
Information in this chapter is divided into the following sections:
3.1. Submitting a Fluent Job from the Command Line
3.2. Submitting a Fluent Job Using Fluent Launcher

3.1. Submitting a Fluent Job from the Command Line

When submitting a Fluent job from the Linux line command using SGE, you must include additional
options for the Fluent command syntax. The command line syntax is as follows:
fluent <solver_version> [<Fluent_options>] -scheduler=sge [-scheduler_queue=<queue>]
[-scheduler_opt=<opt>] [-scheduler_pe=<pe>] [-gui_machine=<hostname>]

where:

<solver_version>
specifies the dimensionality of the problem and the precision of the Fluent calculation (for example, 3d,
2ddp).

<Fluent_options>
specify the start-up option(s) for Fluent, including the options for running Fluent in parallel. For more in-
formation, see the Fluent User's Guide.

-scheduler=sge
(start-up option) instructs Fluent to run under SGE.

-scheduler_queue=<queue>
(start-up option) sets the queue to <queue>.

-scheduler_opt=<opt>
(start-up option) enables an additional option <opt> that is relevant for SGE; see the SGE documentation
for details. Note that you can include multiple instances of this option when you want to use more than
one scheduler option.

The following are examples of actions you might want to take through such scheduler options:

• You may want to specify the checkpointing object and override the checkpointing option specified in
the default request file. If this option is not specified in the command line and the default general request
file contains no setting, then the Fluent simulation is unable to use checkpoints.

• You may want to specify the head node machine name for SGE job submission (the default is
localhost).

-scheduler_pe=<pe>
(start-up option) sets the parallel environment to <pe> when Fluent is run in parallel. This should be used
only if the -scheduler=sge option is used.

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Running a Fluent Simulation under SGE

The specified <pe> must be defined by an administrator. For more information about creating a
parallel environment, refer to the sample_pe file that is located in the /addons/sge directory
in your Fluent installation area.

If Fluent is run in parallel under SGE and the -scheduler_pe= option is not specified, by default
it will attempt to utilize a parallel environment called fluent_pe. Note that fluent_pe must be
defined by an administrator if you are to use this default parallel environment.

-gui_machine=<hostname>
(start-up option) specifies that Cortex is run on a machine named <hostname>. This option may be necessary
to avoid poor graphics performance when running Fluent under SGE.

The following examples demonstrate some applications of the command line syntax:

• Serial 2D Fluent simulation running under SGE

fluent 2d -scheduler=sge

• Parallel 2D Fluent simulation running under SGE on 4 CPUs

fluent 2d -t4 -scheduler=sge

• Parallel 2D Fluent under SGE using the parallel environment diff_pe

fluent 2d -t4 -scheduler=sge -scheduler_pe=diff_pe

• Parallel 2D Fluent under SGE on 4 CPUs, using the parallel environment diff_pe and the queue large
fluent2d -t4 -scheduler=sge -scheduler_queue=large -scheduler_pe=diff_pe

3.2. Submitting a Fluent Job Using Fluent Launcher

Fluent Launcher has graphical user input options that allow you to submit a Fluent job using SGE.
Perform the following steps:

1. Open Fluent Launcher (Figure 3.1: The Scheduler Tab of Fluent Launcher (Linux Version) (p. 45)) by en-
tering fluent without any arguments in the Linux command line.

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 Submitting a Fluent Job Using Fluent Launcher

Figure 3.1: The Scheduler Tab of Fluent Launcher (Linux Version)

2. Enable Use Job Scheduler under Options.

3. Click Show More Options to expand Fluent Launcher.

4. Click the Scheduler tab.

a. Select Use SGE.

b. Enter the name of a node for SGE qmaster. SGE will allow this node to summon jobs. By default,

localhost is specified for SGE qmaster. Note that the button enables you to check the job status.

c. You have the option of entering the name of a queue in which you want your Fluent job submitted

for SGE queue. Note that you can use the button to contact the SGE qmaster for a list of queues.

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Running a Fluent Simulation under SGE

d. If you are running a parallel simulation, you must enter the name of the parallel environment in which
you want your Fluent job submitted for SGE pe. The parallel environment must be defined by an
administrator. For more information about creating a parallel environment, refer to the sample_pe
file that is located in the /addons/sge directory in your Fluent installation area.

e. You can specify an SGE configuration file by enabling the Use SGE settings option. Then enter the
name and location of the file in the text box or browse to the file.

5. Set up the other aspects of your Fluent simulation using the Fluent Launcher GUI items. For more inform-
ation, see the Fluent User's Guide.

Note

If you experience poor graphics performance when running ANSYS Fluent under SGE, you
may be able to improve performance by running Cortex on a specified machine. This can
be done by launching ANSYS Fluent from the command line rather than Fluent Launcher,
through the use of the -gui_machine=<hostname> and -scheduler=sge options. For
details, see Submitting a Fluent Job from the Command Line (p. 43).

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Chapter 4: Running Fluent Utility Scripts under SGE
You can run the Fluent utility scripts (for example, fe2ram, fl42seg, ic3m2ram, partition, tconv,
tmerge, viewfac, tpoly) with the SGE load management system.

The command line syntax to launch a Fluent utility script under SGE is as follows:
utility <utility_name> [<utility_opts>] -sge [-sgeq <queue_name>] [-sgepe <parallel_env> <MIN_N>-<MAX_N>] <utility_i

where

<utility_name>
is the name of the utility to be launched (for example, fe2ram, fl42seg, ic3m2ram, partition,
tconv, tmerge, viewfac, tpoly).

<utility_opts>
are the options that are part of the syntax of the utility being launched. For more information about the
options for the various utilities, see the Fluent User's Guide.

-sge
(start-up option) instructs <utility_name> to run under SGE.

-sgeq <queue_name>
(start-up option) specifies the name of the queue.

-sgepe <parallel_env> <MIN_N>-<MAX_N>

(start-up option) specifies the parallel environment to be used when <utility_name> is run in parallel. This
should be used only if the -sge option is used.

The specified <parallel_env> must be defined by an administrator. For more information about
creating a parallel environment, refer to the sample_pe file that is located in the /addons/sge
directory in your Fluent installation area.

The values for <MIN_N> and <MAX_N> specify the minimum and maximum number of compute
nodes, respectively.

If <utility_name> is run in parallel under SGE and the -sgepe parameter is not specified, by default
the utility will attempt to utilize a parallel environment called utility_pe. Note that utility_pe
must be defined by an administrator if you are to use this default parallel environment. In such a
case, <MIN_N> will be set to 1 and <MAX_N> will be set to the maximum number of requested
compute nodes specified in the <utility_opts> (for example, -t4).

For example, to run the viewfac utility on file_name in serial, the line command would be the
following:

utility viewfac -sge file_name

In parallel with 4 CPUs, without the use of -sgepe (and therefore using the parallel environment
utility_pe), the command would be:

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Running Fluent Utility Scripts under SGE

utility viewfac -t4 -sge file_name

In parallel on a range of nodes (between 1 and 2) with the use of -sgepe and the parallel environ-
ment diff_pe, the command would be:

utility viewfac -t4 -sge -sgepe diff_pe1 -2 file_name

<utility_inputs>
are the fields that are part of the syntax of the utility being launched. For more information about the ne-
cessary fields for the various utilities, see the Fluent User's Guide.

Important

Note that neither checkpointing, restarting, nor migrating are available when using the
utility scripts under SGE.

For more information, see the following section:

4.1. Special Considerations for Running the viewfac Utility under SGE

4.1. Special Considerations for Running the viewfac Utility under SGE
Given a cluster file as input, the viewfac utility is provided for the computation of viewfactors (required
in Fluent when using the S2S radiation model). Using SGE, you can create a cluster file in Fluent and
choose to compute and write viewfactors in the same Fluent session, or you can manually launch the
viewfac utility from outside Fluent and compute the viewfactors. When viewfactors are computed
from Fluent, the following must be considered:

• If Fluent is launched without the -sge option, then the viewfac utility should also be launched from
Fluent without the -sge option.

• If Fluent is launched under SGE (that is, by using the -sge option), then you should be able to launch the
viewfac utility either under SGE or without SGE. By default, the utility is launched under SGE, with the
same SGE related parameters as those used to launch Fluent under SGE.

Important

To launch a parallel version of the viewfac utility, the parallel environment util-
ity_pe must be set up and configured in a manner that is suitable for your jobs.
You may need to contact your SGE administrator for assistance.

If you do not want to launch the utility under SGE, then you may use the Scheme functions described
as follows.

The Scheme function (sge?) can be used to inquire whether the viewfac utility is enabled or
disabled under SGE. The function will return either #t (true) or #f (false).

To switch the value of the (sge?) function, use the (switch-sge) Scheme function. A message
will state the new value (for example, "SGE enabling set to #t"). Again, by default, the
viewfac utility will use the same SGE related options as Fluent. The SGE related options can also
be controlled through the (set-sge-optionsstring_arg) Scheme function. The string_arg
argument replaces the actual sge-options that you originally set (for example, (set-sge-op-
tions "-q dev-test"). Note that you should take care to set the SGE options correctly if you

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 Special Considerations for Running the viewfac Utility under SGE

use the (set-sge-options string_arg) function, because this string is simply passed to SGE
in its command and is interpreted by SGE (and not by the utility script).

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 Release 2019 R2 - © ANSYS, Inc. All rights reserved. - Contains proprietary and confidential information
50 of ANSYS, Inc. and its subsidiaries and affiliates.