HowTo:adina
Contents
Adina
This is a short introduction about the usage of ADINA on HPCVL machines. It is intended to help HPCVL users getting started with the ADINA system, showing how to setup environment variables to use ADINA for preprocessing, processing, and postprocessing data. And how to submit large sequential and/or parallel jobs through Grid Engine. You will find also pointers to the documentation available on HPCVL machines and on ADINA web site.
General OverviewADINA(Automatic Dynamic Incremental Non-linear Analysis) is a general-purpose finite element program for advanced engineering analysis in the fields of Structural Mechanics, Fluid Mechanics, Fluid-Structure Interactions, Heat Transfer, and Themomechanical Coupling. The ADINA system consists of various programs that come with different tools and utilities that can be used independently or at once. In particular:
The present version of ADINA program in HPCVL machines is: ADINA 8.5.2 ADINA systemADINA can run indiferently from the command line in interactive or batch mode, or through the AUI graphic interface. Adina program has a large number of features and also Parallel Processing capabilities; as showed in this list of most important features: Problems Solved
For more details check the information provided at the end of this document. Solvers
For more details check the information provided at the end of this document. Parallel ProcessingADINA also allows Parallel Processing (at the solver level only for SUN)
For more details check the information provided at the end of this document. Available toolsMoreover the adina and aui binaries, the ADINA system provides a set of shell scripts and utilities that allow the user to handle all aspects of running ADINA applications (located under $ADINAHOME/tools) The most important ones are:
And, the list of applications (programs) is:
Getting started using ADINABefore starting you have to add the path to Adina binaries, scripts and libraries (namely PATH and LD_LIBRARY_PATH), to your environment variables. For instance one must add the following line into his setup file (.profile, .bashrc, .cshrc, ...)
Which takes care of all the ADINA setup, in particular the following directories:
The shared libraries are under $ADINAHOME/{ aui8.5, adfsi8.5, adina8.5, adinaf8.5, adinat8.5, adinatmc8.5, aui8.5, plugins, image, format } Once done, ADINA system can be started either with the GUI aui8.5 for interactive session, or with the adina program to run jobs from the command line. |
Running ADINALocal Usage of AdinaOn our systems, a user can only access Adina after they have filled in a Adina User statement (please fax to (613) 533-2015 or scan/email to admin@hpcvl.org. The statement is to the effect that the user will abide by the licensing terms, namely by using the software for academic research purposes only. Interactive session with ADINATo enter the ADINA Graphical environment you must be logged in to a terminal or workstation that is running X-Windows and be sure that your DISPLAY environment variable is set for the terminal from which you are running X-windows; which should be the cas if you are connecting through the portal. If you log in from a UNIX machine using ssh then type:
followed by
and then:
To start the Graphic User Interface 'AUI' type:
which gives you the ADINA graphical window consisting of three major areas:
A HELP button is present at the top right of the GUI from where you can see a list of available documents and also information about demo examples. To see all aui8.5 input options type:
The most important ones are:
Users interested in using frequently ADINA should consult the specific chapters in the ADINA User’s Guide located under directory $ADINAHOME/docs ADINA jobs from the command lineADINA programs are controlled by a shell script named adina stored in the directory $ADINAHOME/tools The shell script will submit and run your adina job, it has many input options. The minimun necessary to run a job is :
Where job_name is the name of the job which must end with a .dat suffix. Other options of interest to HPCVL users are:
fep can be one of the following letters:
-plot start in post-processor mode -cmd run in command mode -s filename command file -tools dir Directory for script to run ADINA solutions. Default is $ADINAHOME/tools -tmp dir Directory for temporary files. Default is /hpcxxxx/scratch -ma Maxsize Parameter, overrides value given in include file. The default NORMAL number is 20 Mbyte, and the maximum amount of memory MAXSIZE to allocate is 4Gbyte.
Batch ADINA jobsAs indicated above the adina utility script allow the user to run adina jobs in batch mode, which can be used without any other option in the process of developing and debugging your ADINA applications. By default adina will run the job in background and in order to avoid input verification before starting the job add the '-v no' option. For example, if the name of adina job is 'cyl2.dat' (look at the examples in one of these directories $ADINAHOME/examples or $ADINAHOME one may type:
or also, if you are using your own user defined subroutine user.f with ADINA, you can type:
Note. Once your job is ready for production, you should use instead the Grid Engine job management system to run and manage your ADINA jobs, (see next section). |
ADINA jobs with Grid EngineSubmitting sequential ADINA jobs through Grid EngineBefore starting we refer users to our HPCVL Grid Engine FAQ for more details about the usage of Grid Engine on HPCVL machines. Submitting a sequential adina job to Grid Engine queues is the same as submitting any sequential job. But users must make sure that there is no interaction between the program and them, and also note that you can not run the adina GUI program through Grid Engine. Here is some basic steps you should follow in order to submit your job:
After this, the executable line in your Grid Engine batch script should look like this:
and then you can add other Grid Engine general options like mail notification or name of the job, etc ... A full example of Adina sequential job with Grid Engine can be found here: #!/bin/sh # This is a simple example of a GE batch script for adina # request Bourne again shell as shell for job #$ -S /bin/bash # name of the job #$ -N baseline # export environment variables #$ -V # Joining standard output and error into a specified file #$ -j y #$ -cwd # run adina job adina8.5 -R 3000MB cyl2 Once your Grid Engine script for ADINA (let’s call it adina_seq.sh) is ready you can submit it to Grid Engine:
Submitting parallel adina jobs through Grid EngineADINA system has parallel processing capabilities based on domain decomposition techniques. It’s available on shared and distributed machines using multithreading for communications between the processes, while the parallel performance of the solver is done using multithreading. Note that most features of ADINA are also available within the parallel framework (to see if your adina application can run in parallel take a look at ADINA Release notes or contact HPCVL support team. For a parallel job, moreover the conditions discussed in the previous section concerning sequential adina job with Grid Engine, you need to specify the number of processors to be used. This is done with two options of the adina script
The command line in your Grid Engine batch script should look like this:
If you are interested in parallelizing the matrix solver only you can use this line:
A full example of Adina parallel job with Grid Engine can be found here: #!/bin/sh # This is a simple example of a GE batch script for adina # request Bourne again shell as shell for job #$ -S /bin/bash # name of the job #$ -N baseline # export environment variables #$ -V # Joining standard output and error into a specified file #$ -j y #$ -cwd # Request of the multithreading parallel environment #$ -pe shm.pe 4 #$ -v PARALLEL=4 #$ -v OMP_NUM_THREADS=4 # make sure <number_of_processors> is the same as above # run adina job adina8.5 -R 3000MB -t 4 cyl2 Once your Grid Engine script for Adina (let’s call it adina_par.sh) is ready you can submit is through to Grid Engine:
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Help and DocumentationA lot of ADINA specific documentation and examples can be found at http://www.adina.com/support The set of ADINA system online manuals documentation (in PDF) is under the directory $ADINAHOME/doc. HPCVL users will find the follwoing documents:
You can also access the HELP menu from the ADINA GUI, from where you get the list of all PRODUCT DOCUMENTATION and also a possibility to run DEMONSTRATION problems. HPCVL also offers user support; for questions about this FAQ and usage of ADINA software on HPCVL machines, contact us or send an email to : help@hpcvl.org |