Welcome to HPCVL -- Fluent FAQ

Fluent FAQ

This is a short FAQ on using the computational-fluid dynamics (CFD) code "Fluent" on HPCVL clusters. This software is only licensed for academic researchers who have prior training. The software is only made available to persons who belong to a specific Unix group. See details below.

Questions:

What is Fluent ?
Where is Fluent located and how do I access it ?
How do I use Fluent interactively ?
How do I setup and execute a non-interactive Fluent batch job?
How do I setup and execute a Fluent parallel production job?
Where can I get further help?

Answers:

What is Fluent ?
Fluent is a suite of programs that model systems in computational fluid dynamics (CFD). This includes flows in two- and three-dimensional geometries, and under a variety of conditions: compressible and incompressible; inviscid, laminar and turbulent; Newtonian and non-Newtonian. The analysis can be steady-state or transient. Fluent simulates convective, coupled and radiative heat transfer, it can account for the mixing and reaction of chemical species, and for arbitrary sources of heat, mass, turbulence and momentum. Calculations employ stationary or rotating frames of reference, and a variety of meshes.
Fluent can be used interactively and supplies a graphical user interface. It can also run in batch mode, if the required time for solving a problem is too long for interactive use. The latter situation is the standard if you are using Fluent on HPCVL machines.
The Fluent package consists of several programs:
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Where is Fluent located and how do I access it?
The present version of Fluent is 6.3. The programs in the Fluent package are located in the directory /opt/fluent/Fluent.Inc/.
To use Fluent on the HPCVL Sun Fire's, you have to be a trained University User of Fluent. It is furthermore required that you read our licensing terms, and sign a statement. We will confirm your statement, and you will then be made a member of a Unix group fluent, which enables you to run the software. Contact us if you are in doubt of whether you will be able to run Fluent on our system.
The Fluent license is "seat limited" and "process limited". At present, there are 50 Fluent seats available on our system, i.e. 50 separate sessions can be run simultaneously (serial or parallel). In addition, it is possible to run up to 400 "parallel only" processes in total. This means that at best you can run a parallel Fluent job using 450 processes: one process for the job, 400 additional ones in parallel, and another 49 from the remaining seats, as Fluent substitutes seat processes for parallel-only ones when it runs out of the latter. Another scenario would be 50 users have 9-process parallel jobs running, each with one master (i.e. seat) and 8 slaves (parallel only), thus using up all available Fluent resources.
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How do I run Fluent interactively?
The following instructions assume that you are a member of the Unix group fluent. The instructions in this section are only useful if you want to use the graphical user interface of Fluent, for instance to setup a job, or pre- and post-process a production job. If you want to run a production job, please refer to to instructions on how to start a Fluent batch job (see next section).
The Fluent program is started by setting a system variables FLUENT_ARCH, FLUENT_INC, and FLUENT_LICENSE_FILE to let the system know about the computing platform employed (UltraSparc), the directory where the software resides and the license file used, respectively. It is also useful to include the directory with the Fluent executable in your path. Here is the command sequences to do all this (assuming bash):
```
export FLUENT_ARCH=ultra
export FLUENT_INC=/opt/fluent/Fluent.Inc
export FLUENT_LICENSE_FILE=$FLUENT_INC/license/license.dat
export PATH=$FLUENT_INC/bin:$PATH
```
These settings apply for the 32-bit version of Fluent, which is the default. Since our Sunfires are 64-bit machines, and Solaris 10 is a 64-bit operating system, there is also a Fluent version that uses a 64-bit address space. If you want to use the 64-bit version, you need to specify ultra_64 for FLUENT_ARCH. Everything else remains the same.
There is a simple alternative for setting up your environment for the usage of Fluent: you can leave the above commands to usepackage and simply type
```
use fluent
```
for the 32-bit version, or
```
use fluent_64bit
```
for 64 bit. This will automatically issue the above commands. You can also include the use command in your setup file (e.g. .bash_profile) if you are using fluent regularly.
Then you invoke a graphical user interface by typing
```
fluent
```
The first choice you have to make is if you are solving a two- or a three-dimensional problem, and if you want to do so in single or double precision. You can do so by typing 2d, 3d, 2ddp, or 3ddp, following the fluent command. All commands can be issued in manually or by clicking on the toolbar on the top of the GUI and selecting the appropriate sub-choices. Note that if you want to type a command yourself, and you do not know what your choices are, simply pressing the Enter key will give you a list of applicable commands.
It is of course impossible to even outline how to use Fluent. In many cases, you will want to read in a case file, which has all the required information to describe the system you want to simulate. Such case files have the file extension .cas. Load them by issuing the /file/read-case command or selecting the corresponding menu-commands in the GUI. You can now check and display the grid, specify boundary conditions and material properties, initialize the flow, and perform calculations.
Results are usually saved by the /file/write-case-data command. During an interactive session, it is sometimes a good idea to keep a journal file which records all commands that you have typed in or issued via the GUI. This journal file can later be used as a template for a batch command file. Define the journal file with the /file/start-journal command.
The usage of Fluent is documented in html format on machines where Fluent is installed. On our system you can access this documentation by calling a Firefox web browser:
```
firefox file:///opt/fluent/Fluent.Inc/help/index.htm &
```
This documentation is also available in pdf format in
```
/opt/fluent/Fluent.Inc/help/pdf
```
Note that the documentation is only accessible if you are signed up as a Fluent user on our system.
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How do I set up and run a non-interactive Fluent batch job?
In most cases, you will run Fluent in batch mode. Since you have to have access to Fluent outside of the HPCVL license, most interactive work can be done elsewhere, whereas the computationally intensive runs can be executed on the Sun Fire cluster.
For this, you have to set up a batch command file that consists of a sequence of commands that are issue to Fluent. To get an idea how such a batch command file looks, you can produce a journal file during an interactive session, and edit it later to eliminate unnecessary commands. Note that this needs to be done using the command line inside Fluent, not the menu buttons of the GUI. In fact, it is best to generate journal files in sessions that have been started with the -g option, i.e. that do not use the GUI at all. You also can have a look at a simple example batch file here . The example file (let's call it "example.flin") will read in a case-file from the working directory directory, initialize the flow, and run a single iteration. It then writes out the data on a file fan_1.dat and exits. Note that every command has to be included in the batch command file, including the answer "yes" to the question if you really want to exit the program without saving the case file.
Once you have produced a working command file, you can test it by calling
```
fluent 3d -g -i example.flin
```
We have assumed you are running a three-dimensional solver in single precision. You will have to alter those entries in different cases. Make sure that the output file for the data (in this case, fan_1.dat) does not exist before you start the job, otherwise the system will query if you want to over-write it and the answer is not in your command file.
Once everything works you could submit this job into the background (using bash) by typing
```
fluent 3d -g -i example.flin > example.flout 2>&1 &
```
This would redirect standard output and standard error to example.flout.
Production jobs, especially parallel ones, are submitted on the Sun Fire systems via Grid Engine, which is the subject of the next question.
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How do I setup and execute a "Fluent" parallel production job?
To submit a production job on HPCVL clusters, you need to us the load-balancing software Grid Engine. To obtain details, read our Gridengine FAQ .
For a Fluent production job, this means that rather than issuing the above batch command directly, you wrap it into a Grid Engine script. For an example for such a batch script please click here. This script needs to be altered by replacing all the relevant items enclosed in {} by the right values.
The batch script is submitted to the GridEngine by typing
```
qsub fluent.sh
```
The advantage to submit jobs via a load balancing software is that the software will automatically find the resources required and put the job onto a set of processors that have a low load. This will help executing the job faster. Note that the usage of Gridengine for all production jobs on HPCVL clusters is mandatory. Production jobs with a running time of more than 3 hours that are submitted outside of the load balancing software will be terminated by the system administrator.
The Fluent jobs that you will want to run on the HPCVL machines are likely to be quite large. To utilize the parallel structure of the Sun Fire's, Fluent offers several options to execute the solver in a parallel environment, i.e. on several CPU's simultaneously. The default option for such runs is MPI i.e., it uses the SUN native version of the Message Passing Interface for inter-process communication.
To take advantage of the parallel capabilities of Fluent, you have to call the program with a series of commandline options that specify the details of your parallel run. Here is a short overview:
- -tn where n is the number of processors requested, e.g. if you want to run with 8 processors, you would use the option -t8
- -pvmpi specifies that the (default) vendor MPI communication system is to be used. May be omitted.
- -g specifies that the GUI should be surpressed. Required for batch jobs.
Parallel jobs should only be run in batch using the Grid Engine. The number of processors specified in our example script appears only once, after
```
#$ -pe fluent.pe
```
which is where you let the Gridengine know how many processors to allocate to run the program. The internal environment variable $NSLOTS will automatically be set to this value and can then be used in the fluent command line.
It is also necessary to source a setup file called /opt/fluent/Fluent.Inc/setup.sh for the 32-bit version. This will set various environment variables and enable the Fluent program to properly interact with Grid Engine. If you are interested, take a look. The file is readable. If you are using the 64-bit version of Fluent, you have to alter the batch script to source the /opt/fluent/Fluent.Inc/setup_64bit.sh file instead.
In the above script, the parallel environment fluent.pe is for Fluent jobs only, and is used to keep track of the available licenses. The licensing situation can also be checked interactively by typing:
```
flulic
```
Grid Engine is able to interact with the license manager of Fluent (FlexLM) to check if sufficient licenses are available for running. This will keep the scheduler from starting jobs because enough processors are available, just to be stopped again because there is not enough licenses. Grid Engine keeps an internal counter of available "license slots" which gets updated frequently. Everytime Grid Engine attempts to schedule a Fluent job and is kept from doing so because not enough licenses are available, it will "requeue" the job. Since this causes the issue of an email if notification is requested, our example script contains no #$ -m be line. Notification happens automatically when a job starts and when it is finished, and will be sent to the email specified in the line
```
#$ -M email@address
```
in the script.
All processes are allocated within a single node. This is to make communication more efficient and to avoid problems with the control by Gridengine. The effect of this is that, while still using MPI, Fluent employs a so-called shared-memory layer for communication. The disadvantage is that it takes longer until the required resources (dedicated processors) are available, i.e. you spend more time on the Grid Engine waiting queue.
Once the script has been adapted, it can be submitted to the Gridengine by
```
qsub fluent.sh
```
from the login node (which is the GridEngine submit host). Note that the job will appear as a parallel job on the GridEngine's qstat or qmon commands. Note also that submission of a parallel job in this way is only profitable for large systems that use many CPU cycles, since the overhead for assigning processes, preparing nodes, and communication between them is considerable.
There is an easier way to do this: We are supplying a small perl script called that can be called directly, and will ask a few basic questions, such as the name for the job to be submitted and the number of processes to be used in the job. Simply type
```
FluentSubmit
```
and answer the questions. The script expects a Fluent input file with "file extension" .flin to be present and will do everything else automatically. This is meant for simple Fluent job submissions. More complex job submissions are better done manually.
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Where can I get further help?
Fluent is a complex software package, and requires some practice to be used efficiently. In this FAQ we can not explain it use in any detail.
Online documentation for the programs is available on machines where Fluent is installed. On the HPCVL login node, it can be accessed through a webbrowser by typing:
```
firefox /opt/fluent/Fluent.Inc/help/index.htm
```
This should give you an index screen to the html version of the docs. You can also use the pdf documentation in
```
/opt/fluent/Fluent.Inc/help/pdf/
```
if you prefer a printable version. To look at specific pdf files, you can use acroread, for instance
```
acroread /opt/fluent/Fluent.Inc/help/pdf/ug/chp01.pdf
```
shows Chapter 1 of the User's Guide. Unfortunately, the pdf documentation is somewhat unsystematic and one has to guess from the name of the directories (e.g. "ug" for "User's Guide") what they mean.
Fluent documentation is subject to the same license terms as the software itself, i.e. you have to be signed up as a Fluent user in order to access it.
If you are experiencing trouble running a batch command script, check carefully if the sequence of commands is exactly in sync with the program. This might mean typing them in interactively as a test. If you have problems with the GridEngine, read our FAQ on that subject, and maybe consult the manual for that software which is accessible as a PDF file. HPCVL also provide user support in the case of technical problems.
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