[mesa-users] Installing MESA on a supercomputer (Richard Townsend)

Richard Townsend townsend at astro.wisc.edu
Thu Jan 5 15:51:02 EST 2012


Agreed - and in fact I've done these sorts of calculations myself, using Bill's earlier EZ code.

But in this context (and based on Ben's remarks about the need for specialized compilers) I was assuming 'supercomputer' means something with specialized hardware, such as a cluster linked together with Infiniband interconnects. While such systems can certainly be used for parameter surveys, a simple Ethernet-networked computer cluster can offer the same performance at a fraction of the price.

Cheers,

Rich

On Jan 5, 2012, at 7:55 AM, Francis Timmes <fxt44 at mac.com> wrote:

> hi rich,
> 
> there is lots to be gained by running multiple jobs simultaneously
> on a cluster; mesa (or any other non-mpi code) in embarrassingly parallel mode. 
> for example, a parameter survey involving a 100 stars.
> 
> fxt
> 
> 
> 
> 
> On Jan 5, 2012, at 2:41 AM, Richard Townsend wrote:
> 
>> I'm not even sure what is to be gained from running MESA on a supercomputer. Parallelism in MESA is only via OpenMP - there is no MPIA usage. As such, MESA can take advantage of shared memory architectures, but not clustered architectures.
>> 
>> Cheers,
>> 
>> Rich
>> 
>> On Jan 5, 2012, at 7:31 AM, Francis Timmes <fxt44 at mac.com> wrote:
>> 
>>> hi ben, rich, kevin (and the mesa community),
>>> 
>>> i had no luck compiling mesa under pgi on the nersc
>>> machines hopper and franklin this past summer. the issue 
>>> boiled down to certain pointer structures used in mesa
>>> not being supported in that version of the pgi compiler.
>>> 
>>> i would be interested in hearing from anyone about 
>>> successes or failures on running mesa on any supercomputer
>>> or largish parallel cluster.
>>> 
>>> fxt
>>> 
>>> 
>>> 
>>> 
>>> On Jan 4, 2012, at 3:56 PM, Ben Brown wrote:
>>> 
>>>> Kevin,
>>>>  To follow up on Rich's note: you are almost certainly not going to be 
>>>> able to use the MESA SDK on a supercomputer.  From my experiences with 
>>>> those systems (using a very different code), they tend to require highly 
>>>> specialized libraries and compilers.  A general purpose tool like the SDK 
>>>> won't work, because often the libraries being referenced need to be 
>>>> compiled against very specific hardware.
>>>> 
>>>> Put differently, the login nodes and the compute nodes tend to run very 
>>>> different operating systems and codes targeting the compute nodes need to 
>>>> be compiled using the specific compilers supported by UCSD for Triton. 
>>>> Which means you'll need to come up with a specialized solution for this 
>>>> system.  I don't have access to Triton myself, so I can't be much more 
>>>> specific than that.  Looking over the Triton webpages it looks like both 
>>>> PGI and Intel compilers are available on the system:
>>>> 
>>>>   http://tritonresource.sdsc.edu/compile_jobs.php
>>>> 
>>>> If you run into problems, you might try contacting Theodore Sande 
>>>> (formerly at MIT) for help in getting a version of MESA to compile, as he 
>>>> has had the code running on large-scale systems in the past.
>>>> 
>>>> Otherwise I could take a look at Ranger or Kraken (supercomputers at TACC 
>>>> and NICS; both have Intel and PGI compilers) later this week or next week.
>>>> They won't be a perfect match, but they may get you started.
>>>> --Ben
>>>> 
>>>> 
>>>>> 
>>>>> Hi Kevin --
>>>>> 
>>>>> This is a common problem with systems using 'older' (pre-2.11) versions of the GNU C library (glibc), which is a standard (and significant) part of all Linux distributions. At the moment, I have no plans to support pre-2.11 glibc versions, since 2.11 has been out for over two years. So, the only workaround would be to upgrade to 2.11 or later.
>>>>> 
>>>>> cheers,
>>>>> 
>>>>> Rich
>>>>> 
>>>>> On Jan 4, 2012, at 7:23 PM, Kevin Moore wrote:
>>>>> 
>>>>>> Hi all,
>>>>>> 
>>>>>> I'm trying to install MESA on the Triton computing cluster at UCSD and am getting some weird errors. I know next to nothing about this so am just following the instructions on Rich's website for using the MESA SDK (which has worked fine for my macbook many times). uname -m returns "x86_64" so I'm using the 64-bit linux version of the SDK. All the setup steps seem to work fine (no errors anyway), but I run into problems during the ./install step.
>>>>>> 
>>>>>> The first error I encounter is:
>>>>>> gfortran: /lib64/libc.so.6: version `GLIBC_2.11' not found (required by gfortran)
>>>>>> make: *** [const_def.o] Error 1
>>>>>> 
>>>>>> Perhaps tellingly, there is not a file named libc.so.6 in my mesa/utils/mesasdk/lib64.
>>>>>> 
>>>>>> In addition, now whenever I try and use the man command I get the error:
>>>>>> /usr/bin/gtbl: error while loading shared libraries: /home/kmoore-ucsb/mesa_3794/utils/mesasdk/lib64/libstdc++.so.6: ELF file OS ABI invalid
>>>>>> 
>>>>>> Any ideas what's going on from someone who may have done this before?
>>>>>> 
>>>>>> Thanks,
>>>>>> Kevin
>>>>>> 
>>>>>> 
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