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help to run CFX simulation via HPC, please

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Old   February 23, 2012, 04:57
Default help to run CFX simulation via HPC, please
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Hi anyone,,,
I'm now trying to conduct my simulation faster via HPC at my Uni. the probles is that my script file give me the results in .out file not .res file. Actually, I took the csript file from website and I have no idea how I can make my outlet as .res file. Here you are my script file.
#!/bin/bash -l
#
##### Job Name #####
#PBS -N 3cm
##### Select resources ####
#PBS -l nodes=1pn=4
#PBS -l walltime=01:00:00
##### Goto the directory from which you submitted the job
cd $PBS_O_WORKDIR
##### Request that regular output (stdout) and terminal output (stderr) go to the same file
PBS -o /home/eng/0000000/Gap_width=3cm.out
#PBS -wd
##### Mail Options #####
#PBS -m abe
#PBS -M 0000000@gmail.000.edu.au
##### Queue #####
#PBS -q standard
##### Add ansys_module
module load ansys
##### Specifies the version of ANSYS CFX
version=3d
# The following line would start the simulation from a
# previous results file, Gap_width=3cm_001.res
cfx5solve -double -def Gap_width=3cm.def -initial Gap_width=3cm_001.res -part 4 $nprocs -par-local
I appretiate any advise.
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Old   February 23, 2012, 05:45
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Did you get the script from a random webpage or was it given to you by the IT-guys and girls at your uni? Anyway, they should be able to help you with your batch script. Are you sure you are supposed to use PBS?

Also, this is a bit odd:
##### Specifies the version of ANSYS CFX
version=3d

I doubt you need to specify 3D, as CFX always solve in 3D (unlike Fluent, which can be 2D)
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Old   February 23, 2012, 07:18
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CFX has a demo script file for running CFX under PBS in the documentation and the script file is at <CFX_ROOT>/extras/qcfx5solve.pl
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Old   February 23, 2012, 20:12
Exclamation thanks for your input and further question& help me
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Thanks guys
For Glenn, yes,, U R right.
Our ICT devition do not want to help me to write my script file because as I understand they feel it is not their job and they get mad quickly. that is why I'm email you to help me.
I got this error however It produce my out file but it also give the messgae:

Capability CFX_SOLVER_BASIC_MP_LIMIT does not exist in the ANSYS licensing pool.
None of the products enabling this capability are available in the specified license path:
ANSYSLI_SERVERS: 2325@139.86.160.180
FLEXlm Servers: 1055@139.86.160.180
=>> PBS: job killed: walltime 92 exceeded limit 50
A fatal error has occurred in cfx5solve:
cfx5solve was killed by the user.For general information, the ansys should be work in batch mode.
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Old   February 23, 2012, 23:58
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Quote:
Originally Posted by happy View Post
Thanks guys
For Glenn, yes,, U R right.
Our ICT devition do not want to help me to write my script file because as I understand they feel it is not their job and they get mad quickly. that is why I'm email you to help me.
I got this error however It produce my out file but it also give the messgae:

Capability CFX_SOLVER_BASIC_MP_LIMIT does not exist in the ANSYS licensing pool.
None of the products enabling this capability are available in the specified license path:
ANSYSLI_SERVERS: 2325@139.86.160.180
FLEXlm Servers: 1055@139.86.160.180
=>> PBS: job killed: walltime 92 exceeded limit 50
A fatal error has occurred in cfx5solve:
cfx5solve was killed by the user.For general information, the ansys should be work in batch mode.
my out file is here and the solver stop due to error; hwever, my out file is standards file nor in .res form!!!!how I can load .out file to cfxpost. I tried but give me an error!!!By the way, in my home directory there is many files created by solver due to calculation but interstingly without extention. help me ASAP
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Old   February 24, 2012, 03:47
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Quote:
Originally Posted by happy View Post
None of the products enabling this capability are available in the specified license path:
ANSYSLI_SERVERS: 2325@139.86.160.180
FLEXlm Servers: 1055@139.86.160.180
=>> PBS: job killed: walltime 92 exceeded limit 50
Lower your time to less than 50 wall clock hours. Also, check that your license settings are correct.
I couldnt check your out file, post the error messages here instead.
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Old   February 24, 2012, 07:15
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Also, do you need to use PBS? If you are not familiar with batch scheduling software it is just making things hard for you. You can run the solver from the command line, and you can queue up a bunch of jobs if you like. If that is all you want then forget about PBS.

But if you need the power of a batch scheduling system or the HPC submits all jobs with PBS and you cannot go with the command line then you better stick with it.
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Old   February 25, 2012, 02:35
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Hi all
I would like to thank Lance for his/her input and would like to tell Glenn that my simulation now are running by PBS in perfect way
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Old   February 25, 2012, 06:54
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Good to hear.

I have wondered why CFX includes such a complex PBS script when much simpler scripts (like the one you have) work. PBS is a bit tricky to set up, especially if you want it to queue based on license availability rather than just CPU availability.
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Old   February 25, 2012, 23:05
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Hi Glenn,,
please could you please give me more explaination for 'based on license availability rather than just CPU availability'. I mean which sort of mode can work based on the CPU availability?
Actually, I did not have HPC license.
Best Regards
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Old   February 26, 2012, 05:13
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The normal mode of operation of PBS is to queue jobs based on the availability of CPUs. This is fine for unlicensed software, but for licensed software often the limitation is how many licenses you have. To make PBS also queue based on license availability we had to add a custom routine to PBS. From memory it checks the license availability on the license server every minute or so and picks up available licenses that way. We talked to PBS support to help develop this. But I remain a little surprise about this because I would have thought there would be lots of customers out there who are license limited so there should be strong demand for this.
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Old   February 26, 2012, 20:59
Thumbs up error with the time
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Thanks Glenn for your input.
I read your thesis and you looks ANSYS-CFX exprtise. First, could you please tell me the cause of this error when I conduct my running via HPC(PBS).
PBS: job killed: walltime 43238 exceeded limit 43200
However, when I reduce the no. of iteration from 1000 to 300, the .res file produced. I tried to set the walltime but without any benefit. does this error come from the limitation mem on my home directory???By the way, I did not set the required memory for my job into my script file.
I appreciate any input.
Regards
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Old   February 27, 2012, 00:05
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Firstly, PBS is not part of CFX. PBS is a third party commercial software from Altair http://www.pbsworks.com/. If you want help with PBS you are best to ask your Altair support person.

But to my reading your error message is pretty obvious - you have set a maximum wall time limit and that was exceeded so it stopped the job. If you want to run longer you need to define a longer wall time limit, or no limit at all.
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Old   February 29, 2012, 08:47
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Hi Happy!
Just as a hint: When you get an error and CFX "crashes" or stops prematurely without finishing the run correctly you will NEVER get a .res file, only an .out file.
The .res File can only be produced if CFX finishes successfully. If it doesn't you will be provided with the .out file to be able to retrace the Problem that caused the premature stop!
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Old   February 29, 2012, 09:54
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And just if you can't change the max wall time then split your job. Let's say do 300 Iterations and get a .res file. Then start your second calculation with the old .res file and continue with another 300 iterations.
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Old   March 2, 2012, 01:31
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hi again
thanks for your advices. That what I did, the perfect way is spilt my tasks to many depending on the no. of iterations. once again, thanks
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