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Comsol on HPC server

Posted Feb 22, 2011, 9:13 a.m. EST Installation & License Management Version 4.2 7 Replies

Troy Burnett
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I have just set up Comsol on a 48 processor machine using HPC server it is one machine with no cluster. It is running extremely slow. When using all 48 processors it takes over 137 seconds to process the wrench simulation model that comes in the model library. When I limit the processors to 2 it process in about 24 seconds which is faster but still slower than it should be. I think it must be something with the configuration settings of either Comsol or HPC server or both? Can anyone help me with the configuration of Comsol and HPC server? Thanks.
7 Replies Last Post Feb 7, 2013, 12:54 p.m. EST
Christian Matyssek
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Posted: 1 decade ago Feb 22, 2011, 4:19 p.m. EST
Hi Troy!

I never tried using Comsol on so many cores, but from other parallel programming I know that you only get a speedup if the overhead of chunking the problem is much less than the solution of each problem chunk. Try monitoring the load of your server. Maybe it takes Comsol a long time to split your huge problem into chunks (which I assume is done on a single core) and then the solution of each chunk takes little time on each core. But as I said, it's just a guess.
Hi Troy! I never tried using Comsol on so many cores, but from other parallel programming I know that you only get a speedup if the overhead of chunking the problem is much less than the solution of each problem chunk. Try monitoring the load of your server. Maybe it takes Comsol a long time to split your huge problem into chunks (which I assume is done on a single core) and then the solution of each chunk takes little time on each core. But as I said, it's just a guess.
Troy Burnett
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Posted: 1 decade ago Feb 23, 2011, 8:56 a.m. EST
Thanks,

I will try monitoring the server more closely. Right now I am not running a large problem however. I am just trying to run a simple model from the model library and it seems to be taking a lot longer to solve the model than it should be even when I limit the processers.

We did learn that the math library that Comsol uses is tailored for the Intel Xeon processor and our computer uses AMD processors. We installed the AMD-speciic math library and it improved the performance of the machine, but it still seems to be slow.

The wrench model that comes with the model library has a solution time of 11 seconds. When I run it with 48 processors it takes over 70 seconds. The model seems to run fastest when using 2 processors, but it still takes over 20 seconds to solve. I am new to Comsol, but this just seems slower than it should be with this computer.
Thanks, I will try monitoring the server more closely. Right now I am not running a large problem however. I am just trying to run a simple model from the model library and it seems to be taking a lot longer to solve the model than it should be even when I limit the processers. We did learn that the math library that Comsol uses is tailored for the Intel Xeon processor and our computer uses AMD processors. We installed the AMD-speciic math library and it improved the performance of the machine, but it still seems to be slow. The wrench model that comes with the model library has a solution time of 11 seconds. When I run it with 48 processors it takes over 70 seconds. The model seems to run fastest when using 2 processors, but it still takes over 20 seconds to solve. I am new to Comsol, but this just seems slower than it should be with this computer.
Jim Freels mechanical side of nuclear engineering, multiphysics analysis, COMSOL specialist
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Posted: 1 decade ago Feb 24, 2011, 2:11 p.m. EST
What switches do you use when you start comsol ?

If you have no cluster, then you should not try to run the distributed parallel processing mode. You should only run the shared memory parallel processing mode. See the COMSOL documentation for definitions.

You should start comsol with "comsol -np 48" and do not use the "-nn" switch.

What switches do you use when you start comsol ? If you have no cluster, then you should not try to run the distributed parallel processing mode. You should only run the shared memory parallel processing mode. See the COMSOL documentation for definitions. You should start comsol with "comsol -np 48" and do not use the "-nn" switch.
Xife
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Posted: 1 decade ago Mar 26, 2011, 5:14 p.m. EDT
Troy Burnett,
I just wanted you followup on this issue. So were you able resolve the issue? if so, how?

in the near future, I hope to run comsol on a similar server. thanks.


--
merci
Troy Burnett, I just wanted you followup on this issue. So were you able resolve the issue? if so, how? in the near future, I hope to run comsol on a similar server. thanks. -- merci
Troy Burnett
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Posted: 1 decade ago Mar 28, 2011, 9:04 a.m. EDT
We were able to get the system functioning properly. Our computers use AMD processors and there is a special math library for the AMD processor. Once we obtained this math library and were able to load it the performance time was a lot better. After installing the math library you have to set the –blaspath in Comsol to read it.
We were able to get the system functioning properly. Our computers use AMD processors and there is a special math library for the AMD processor. Once we obtained this math library and were able to load it the performance time was a lot better. After installing the math library you have to set the –blaspath in Comsol to read it.
Andrea Rossi
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Posted: 1 decade ago May 16, 2012, 6:31 a.m. EDT
Hi Troy,
I have the same problem on an AMD Opteron dual socket (32 cores total) with 256 GB RAM.
The same model ran on a Intel 8 cores machine is a lot faster than on the big AMD machine.
Could you tell me more about the "special math library"? Is The ACML or something other?

Thanks!
Hi Troy, I have the same problem on an AMD Opteron dual socket (32 cores total) with 256 GB RAM. The same model ran on a Intel 8 cores machine is a lot faster than on the big AMD machine. Could you tell me more about the "special math library"? Is The ACML or something other? Thanks!
Giti Karimi
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Posted: 1 decade ago Feb 7, 2013, 12:54 p.m. EST
Hi Tory,
Would you please let me know who you set up your COMSOL fro running on HPC server? We have HPC server here at NCSU, but I could not get run on that up to now.
Thank you,
Giti
Hi Tory, Would you please let me know who you set up your COMSOL fro running on HPC server? We have HPC server here at NCSU, but I could not get run on that up to now. Thank you, Giti

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