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

Kevin Moore kmoore at physics.ucsb.edu
Sat Jan 7 19:52:39 EST 2012


Yes, the purpose of doing this was to do parameter surveys as well as have a centralized location where students in our stars class could run MESA. We get free time on a variety of computing centers so this is a simple solution for us.

Anyway, just an update - I actually got the people at Triton to compile a newer glibc (2.14) for me and now the installation gets all the way to the mtx module (yay?), giving the error:
/home/kmoore-ucsb/mesa_3794/utils/mesasdk/lib/liblapack.a(xerbla.o): In function `xerbla_':
xerbla.f:(.text+0x66): undefined reference to `_gfortran_transfer_character_write'
xerbla.f:(.text+0x76): undefined reference to `_gfortran_transfer_integer_write'
collect2: ld returned 1 exit status
make: *** [tester] Error 1

This is enough to convince me I should probably be compiling it from source directly so will try that and post again if it succeeds/fails.

Thanks for all the advice!

-Kevin

On Jan 5, 2012, at 2:51 PM, Richard Townsend wrote:

> 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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