mesa-users — open list for mesa comments, questions, & answers

[mesa-users] MESA summer school and MESA education

[david a. <wda...@gm...>]

Hi Frank,
Why not make a MESA "intro manual" as a spin-off of the exercises in the
summer school? With such  a base it could become a community project. That
might be feasible if the work was shared with new and eager MESAns.
Dave

-- 
David Arnett
Regents Professor
Steward Observatory
University of Arizona

Re: [mesa-users] bad CPU in executable

[andres s. <asu...@uc...>]

Sorry, I did mean Tiger...

uname -m
i386

____________________
a.


On Fri, Jan 13, 2012 at 9:10 PM, Richard Townsend
<tow...@as...>wrote:

> Hi Andres -
>
> Do you mean OS X Tiger? Because Lion is 10.7, not 10.4.
>
> In any case, can you send me the output from 'uname -m'
>
> Cheers,
>
> Rich
>
>
> On Jan 13, 2012, at 10:55 PM, andres suarez <asu...@uc...> wrote:
>
> Hi,
> I am trying to install mesa on a MacPro 1.1 running MAC OS 10.4.11
> When I try to use the mesasdk package for Darwin, the gfortran and gcc
> compilers provided seem to not be supported by my system, as I get the
> errors:
>
>        -bash ./gfortran: Bad CPU type in executable
>        -bash: ./gcc: Bad CPU type in executable
>
> I tried getting the gfortran appropriate to my system, but I cannot find
> anything beyond gfortran4.2 that runs with Lion Mac OS (10.4), and when
> trying to install without mesasdk, I noticed that mesa explicitly requires
> a gfortran equal or higher to 4.5.
>
> so, anyone can tell me if there is a gfortran4.5 that runs in Mac OS 10.4
> and where to find it?
> Is there a workaround?
>
> Thank you.
> a.
>
>
> ------------------------------------------------------------------------------
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> Mar 27 - Feb 2
> Save $400 by Jan. 27
> Register now!
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>
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> mes...@li...
> https://lists.sourceforge.net/lists/listinfo/mesa-users
>
>

Re: [mesa-users] bad CPU in executable

[Richard T. <tow...@as...>]

Hi Andres -

Do you mean OS X Tiger? Because Lion is 10.7, not 10.4.

In any case, can you send me the output from 'uname -m'

Cheers,

Rich

On Jan 13, 2012, at 10:55 PM, andres suarez <asu...@uc...> wrote:

>> Hi,
>> I am trying to install mesa on a MacPro 1.1 running MAC OS 10.4.11
>> When I try to use the mesasdk package for Darwin, the gfortran and gcc compilers provided seem to not be supported by my system, as I get the errors:
>> 
>>        -bash ./gfortran: Bad CPU type in executable
>>        -bash: ./gcc: Bad CPU type in executable
>> 
>> I tried getting the gfortran appropriate to my system, but I cannot find anything beyond gfortran4.2 that runs with Lion Mac OS (10.4), and when trying to install without mesasdk, I noticed that mesa explicitly requires a gfortran equal or higher to 4.5.
>> 
>> so, anyone can tell me if there is a gfortran4.5 that runs in Mac OS 10.4 and where to find it?
>> Is there a workaround?
>> 
>> Thank you.
>> a.
> ------------------------------------------------------------------------------
> RSA(R) Conference 2012
> Mar 27 - Feb 2
> Save $400 by Jan. 27
> Register now!
> http://p.sf.net/sfu/rsa-sfdev2dev2
> _______________________________________________
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> mes...@li...
> https://lists.sourceforge.net/lists/listinfo/mesa-users

[mesa-users] bad CPU in executable

[andres s. <asu...@uc...>]

Hi,
I am trying to install mesa on a MacPro 1.1 running MAC OS 10.4.11
When I try to use the mesasdk package for Darwin, the gfortran and gcc
compilers provided seem to not be supported by my system, as I get the
errors:

       -bash ./gfortran: Bad CPU type in executable
       -bash: ./gcc: Bad CPU type in executable

I tried getting the gfortran appropriate to my system, but I cannot find
anything beyond gfortran4.2 that runs with Lion Mac OS (10.4), and when
trying to install without mesasdk, I noticed that mesa explicitly requires
a gfortran equal or higher to 4.5.

so, anyone can tell me if there is a gfortran4.5 that runs in Mac OS 10.4
and where to find it?
Is there a workaround?

Thank you.
a.

[mesa-users] 2012 MESA Summer School

[Francis T. <fx...@ma...>]

Dear MESA community,

The 2012 MESA Summer School is now accepting applications:

http://cococubed.asu.edu/mesa_school_website

This 2012 MESA Summer School is aimed at graduate students and
postdoctoral researchers who are interested in using, developing,
and sharing their research experiences with MESA. Interested faculty
should contact one of the School Directors. Themes for the 2012
MESA Summer School include pulsation, rotation, and astroseismology.

Enrollment will be limited to no more than 44 participants. 
Applications close February 1, 2012, so apply now!

The School Directors

Re: [mesa-users] MESA for Education

[Maarit K. <mj...@gm...>]

Dear all,

I recently lectured a course on stellar structure and evolution in the
University of Helsinki (undergrad level) using MESA both for demonstration
purposes during the lectures, and also for hands-on exercises for the
students. After having seen some trouble getting MESA installed and working
on the student computers, preparing some introductory material how to use
it and so forth, the students were able to use it themselves for
calculating simple stellar models. Developing further MESA for education
purposes it would be necessary to have some sort of quick reference guide
or manual, with some ready-to-run samples coming with the svn-distribution.
I am definitely interested in developing this idea further, although my own
expertise on MESA is still quite poor.

best wishes, Maarit Mantere

On 13 December 2011 01:03, Steve Kawaler <sd...@ia...> wrote:

> I think that a MESA for Education effort is a terrific idea - at all
> levels of post-secondary education.  For undergraduate introductory
> non-science courses all the way through graduate courses.  Please let
> me know how I can help.
>
> Steve Kawaler
>
> > Message: 3
> > Date: Mon, 12 Dec 2011 10:52:17 -0800
> > From: Bill Paxton <pa...@ki...>
> > Subject: Re: [mesa-users] mesa release 3790 + a cool movie
> > To: mzi...@ma...
> > Cc: "mes...@li... users"
> >        <mes...@li...>,
> mes...@li...
> > Message-ID: <026...@ki...>
> > Content-Type: text/plain; charset=us-ascii
> >
> > Hi Mike,
> >
> > On Dec 12, 2011, at 9:47 AM, Mike Zingale wrote:
> >
> >> Bill/Josiah, indeed that is a nice movie, and one I am sure many of us
> will want to show in our Intro to Astronomy classes when we come upon
> stellar evolution.
> >
> > Great!   A movie like that is really a huge help to see the how the
> various things change together as the evolution goes forward.
> >
> >> On that note, is there any sort of organized effort toward MESA for
> Education, instead of research.
> >
> > Excellent suggestion.   There isn't any such organized effort yet, but
> there certainly should be.
> >
> >> Perhaps providing an archive of nice movies of stellar evolution for
> use in classes would be a good start.
> >
> > That would be a wonderful start -- I know Rich Townsend has been working
> on something like that
> > (oh!  I just got his email saying he has been working on it!!!)
> >
> > It would be wonderful if you and Rich and anyone else who is interested
> in MESA for Education would
> > work together on this.   I'd love to see it happen, but I won't be the
> one to push the effort.
> >
> > Cheers,
> > Bill
> >
> >
>
>
> ------------------------------------------------------------------------------
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> Microsoft is holding a special Learn Windows Azure training event for
> developers. It will provide a great way to learn Windows Azure and what it
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>

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

[Francis T. <fx...@ma...>]

nice! thanks for sharing this info kevin.

fxt



On Jan 10, 2012, at 12:44 PM, Kevin Moore wrote:

> Success!
> 
> I just got MESA compiled and ran through inlist_first_thing_to_try and everything looks to be working fine! It took 59s of cpu time and 13s of wall time to run.
> 
> Here's what I had to do to get it working on Triton if anyone else is interested:
> 
> Add the following lines to my .bashrc file:
> module purge
> module load intel
> module load openmpi_mx
> export MX_RCACHE=0
> export LD_LIBRARY_PATH=/opt/intel/Compiler/11.1/072/lib/intel64:$LD_LIBRARY_PATH
> 
> Comment out these lines in mesa/adipls/test/ck:
> scan-amdl.d amdl.mesa >> .list
> check_okay
> 
> For some reason, the adipls test was working fine, but there was a weird error when the script called scan-amd.d and this was dumped to the diff.txt file:
> forrtl: severe (47): write to READONLY file, unit 5, file stdin
> Image              PC                Routine            Line        Source       
> 
> scan-amdl.d.x      000000000047B8ED  Unknown               Unknown  Unknown
> scan-amdl.d.x      000000000047A3F5  Unknown               Unknown  Unknown
> scan-amdl.d.x      00000000004348C0  Unknown               Unknown  Unknown
> scan-amdl.d.x      00000000004063BF  Unknown               Unknown  Unknown
> scan-amdl.d.x      0000000000405BF2  Unknown               Unknown  Unknown
> scan-amdl.d.x      000000000042E755  Unknown               Unknown  Unknown
> scan-amdl.d.x      0000000000402B6F  Unknown               Unknown  Unknown
> scan-amdl.d.x      0000000000402ACC  Unknown               Unknown  Unknown
> libc.so.6          00000038F5C1D994  Unknown               Unknown  Unknown
> scan-amdl.d.x      00000000004029D9  Unknown               Unknown  Unknown
> 
> I couldn't track down why this was happening, but commenting out those lines in the test script fixed things.
> 
> Then just ./install in the mesa directory as usual (Triton thankfully has ifort 11.1). I haven't tried linking with Triton's MKL libraries yet so I just used the default MESA blas & lapack libraries.
> 
> -Kevin
> 
> On Jan 7, 2012, at 6:52 PM, Kevin Moore wrote:
> 
>> 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 <fx...@ma...> 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 <fx...@ma...> 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
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> 
>>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>> Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
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>>>>>>>>> _______________________________________________
>>>>>>>>> mesa-users mailing list
>>>>>>>>> mes...@li...
>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/mesa-users
>>>>>>>> 
>>>>>>>> 
>>>>>>>> 
>>>>>>>> 
>>>>>>>> ------------------------------
>>>>>>>> 
>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>> Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
>>>>>>>> infrastructure or vast IT resources to deliver seamless, secure access to
>>>>>>>> virtual desktops. With this all-in-one solution, easily deploy virtual
>>>>>>>> desktops for less than the cost of PCs and save 60% on VDI infrastructure
>>>>>>>> costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
>>>>>>>> 
>>>>>>>> ------------------------------
>>>>>>>> 
>>>>>>>> _______________________________________________
>>>>>>>> mesa-users mailing list
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>>>>>>>> 
>>>>>>>> 
>>>>>>>> End of mesa-users Digest, Vol 29, Issue 2
>>>>>>>> *****************************************
>>>>>>>> 
>>>>>>> 
>>>>>>> ------------------------------------------------------------------------------
>>>>>>> Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
>>>>>>> infrastructure or vast IT resources to deliver seamless, secure access to
>>>>>>> virtual desktops. With this all-in-one solution, easily deploy virtual 
>>>>>>> desktops for less than the cost of PCs and save 60% on VDI infrastructure 
>>>>>>> costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
>>>>>>> _______________________________________________
>>>>>>> mesa-users mailing list
>>>>>>> mes...@li...
>>>>>>> https://lists.sourceforge.net/lists/listinfo/mesa-users
>>>>>> 
>>>>>> 
>>>>>> ------------------------------------------------------------------------------
>>>>>> Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
>>>>>> infrastructure or vast IT resources to deliver seamless, secure access to
>>>>>> virtual desktops. With this all-in-one solution, easily deploy virtual 
>>>>>> desktops for less than the cost of PCs and save 60% on VDI infrastructure 
>>>>>> costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
>>>>>> _______________________________________________
>>>>>> mesa-users mailing list
>>>>>> mes...@li...
>>>>>> https://lists.sourceforge.net/lists/listinfo/mesa-users
>>> 
>>> ------------------------------------------------------------------------------
>>> Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
>>> infrastructure or vast IT resources to deliver seamless, secure access to
>>> virtual desktops. With this all-in-one solution, easily deploy virtual 
>>> desktops for less than the cost of PCs and save 60% on VDI infrastructure 
>>> costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
>>> _______________________________________________
>>> mesa-users mailing list
>>> mes...@li...
>>> https://lists.sourceforge.net/lists/listinfo/mesa-users
>> 
>> 
>> ------------------------------------------------------------------------------
>> Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
>> infrastructure or vast IT resources to deliver seamless, secure access to
>> virtual desktops. With this all-in-one solution, easily deploy virtual 
>> desktops for less than the cost of PCs and save 60% on VDI infrastructure 
>> costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
>> _______________________________________________
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> 
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[mesa-users] mesa in fedora 16

[Abhisek D. <abh...@gm...>]

Hi,

Can anyone please tell me, if MESA can be installed in Fedora 16 ?

Abhisek datta

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

[Kevin M. <km...@ph...>]

Success!

I just got MESA compiled and ran through inlist_first_thing_to_try and everything looks to be working fine! It took 59s of cpu time and 13s of wall time to run.

Here's what I had to do to get it working on Triton if anyone else is interested:

Add the following lines to my .bashrc file:
module purge
module load intel
module load openmpi_mx
export MX_RCACHE=0
export LD_LIBRARY_PATH=/opt/intel/Compiler/11.1/072/lib/intel64:$LD_LIBRARY_PATH

Comment out these lines in mesa/adipls/test/ck:
scan-amdl.d amdl.mesa >> .list
check_okay

For some reason, the adipls test was working fine, but there was a weird error when the script called scan-amd.d and this was dumped to the diff.txt file:
forrtl: severe (47): write to READONLY file, unit 5, file stdin
Image              PC                Routine            Line        Source       
      
scan-amdl.d.x      000000000047B8ED  Unknown               Unknown  Unknown
scan-amdl.d.x      000000000047A3F5  Unknown               Unknown  Unknown
scan-amdl.d.x      00000000004348C0  Unknown               Unknown  Unknown
scan-amdl.d.x      00000000004063BF  Unknown               Unknown  Unknown
scan-amdl.d.x      0000000000405BF2  Unknown               Unknown  Unknown
scan-amdl.d.x      000000000042E755  Unknown               Unknown  Unknown
scan-amdl.d.x      0000000000402B6F  Unknown               Unknown  Unknown
scan-amdl.d.x      0000000000402ACC  Unknown               Unknown  Unknown
libc.so.6          00000038F5C1D994  Unknown               Unknown  Unknown
scan-amdl.d.x      00000000004029D9  Unknown               Unknown  Unknown

I couldn't track down why this was happening, but commenting out those lines in the test script fixed things.

Then just ./install in the mesa directory as usual (Triton thankfully has ifort 11.1). I haven't tried linking with Triton's MKL libraries yet so I just used the default MESA blas & lapack libraries.

-Kevin

On Jan 7, 2012, at 6:52 PM, Kevin Moore wrote:

> 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 <fx...@ma...> 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 <fx...@ma...> 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
>>>>>>>> 
>>>>>>>> 
>>>>>>>> 
>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>> Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
>>>>>>>> infrastructure or vast IT resources to deliver seamless, secure access to
>>>>>>>> virtual desktops. With this all-in-one solution, easily deploy virtual
>>>>>>>> desktops for less than the cost of PCs and save 60% on VDI infrastructure
>>>>>>>> costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
>>>>>>>> _______________________________________________
>>>>>>>> mesa-users mailing list
>>>>>>>> mes...@li...
>>>>>>>> https://lists.sourceforge.net/lists/listinfo/mesa-users
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> ------------------------------
>>>>>>> 
>>>>>>> ------------------------------------------------------------------------------
>>>>>>> Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
>>>>>>> infrastructure or vast IT resources to deliver seamless, secure access to
>>>>>>> virtual desktops. With this all-in-one solution, easily deploy virtual
>>>>>>> desktops for less than the cost of PCs and save 60% on VDI infrastructure
>>>>>>> costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
>>>>>>> 
>>>>>>> ------------------------------
>>>>>>> 
>>>>>>> _______________________________________________
>>>>>>> mesa-users mailing list
>>>>>>> mes...@li...
>>>>>>> https://lists.sourceforge.net/lists/listinfo/mesa-users
>>>>>>> 
>>>>>>> 
>>>>>>> End of mesa-users Digest, Vol 29, Issue 2
>>>>>>> *****************************************
>>>>>>> 
>>>>>> 
>>>>>> ------------------------------------------------------------------------------
>>>>>> Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
>>>>>> infrastructure or vast IT resources to deliver seamless, secure access to
>>>>>> virtual desktops. With this all-in-one solution, easily deploy virtual 
>>>>>> desktops for less than the cost of PCs and save 60% on VDI infrastructure 
>>>>>> costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
>>>>>> _______________________________________________
>>>>>> mesa-users mailing list
>>>>>> mes...@li...
>>>>>> https://lists.sourceforge.net/lists/listinfo/mesa-users
>>>>> 
>>>>> 
>>>>> ------------------------------------------------------------------------------
>>>>> Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
>>>>> infrastructure or vast IT resources to deliver seamless, secure access to
>>>>> virtual desktops. With this all-in-one solution, easily deploy virtual 
>>>>> desktops for less than the cost of PCs and save 60% on VDI infrastructure 
>>>>> costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
>>>>> _______________________________________________
>>>>> mesa-users mailing list
>>>>> mes...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/mesa-users
>> 
>> ------------------------------------------------------------------------------
>> Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
>> infrastructure or vast IT resources to deliver seamless, secure access to
>> virtual desktops. With this all-in-one solution, easily deploy virtual 
>> desktops for less than the cost of PCs and save 60% on VDI infrastructure 
>> costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
>> _______________________________________________
>> mesa-users mailing list
>> mes...@li...
>> https://lists.sourceforge.net/lists/listinfo/mesa-users
> 
> 
> ------------------------------------------------------------------------------
> Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
> infrastructure or vast IT resources to deliver seamless, secure access to
> virtual desktops. With this all-in-one solution, easily deploy virtual 
> desktops for less than the cost of PCs and save 60% on VDI infrastructure 
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[mesa-users] problem with mesa release 3844

[G.J. S. <gjs...@gm...>]

Thank you for installing the new version of the EOS in Mesa, that might be
very useful for astroseismology.  However, like A. Gautschy I get the
following error during installation:

ERROR:  bad header info in ../../data/eosDT_data/mesa-eosDT_00z00x.data
                         min_version > ep% versionT        50        49


first file is short
13c13
< ERROR:  bad header info in ../../data/eosDT_data/mesa-eosDT_00z00x.data
--- field 6
>                              P      6.2100730711604395E+11
14c14
<                          min_version > ep% versionT        50        49
--- field 6
>                              E      1.1185928203373142E+14
15c15
<
--- field 2
>                              S      8.9350156636595654E+08

/home/gertjan/mesa/eos/test
TEST FAILED -- compare test_output to tmp.txt

Gertjan Savonije

Re: [mesa-users] Evolving a white dwarf on the cooling sequence

[Francesca V. <val...@gm...>]

Hi Jing,

Thank you for the suggestion.
It looks like it worked!
>From a quick look at the HR diagram the WD is cooling down.
I also compared the evolution on the HR diagram with the evolution of a He
WD with the same mass provided by Deloye et al. (2007) and there is good
agreement between the two.

Thanks,

Fra

On Mon, Jan 9, 2012 at 5:58 PM, Jing Luan <jin...@ca...> wrote:

>  On 1/9/12 1:39 PM, Francesca Valsecchi wrote:
>
> Hi all,
>
>  I would like to use MESA to create white dwarf models of different
> masses and temperatures.
>
>  I created a He white dwarf using one of the test_suite runs and I am
> trying to evolve it on the cooling sequence.
>
>  I have tried using the test_suite called wd_cool, reading in input the
> He white dwarf model created, but I did not have success.
>
>  Is there any documentations on the various test_suite that deal with
> white dwarfs? Also any paper that used MESA to study white dwarfs would be
> useful.
>
>
>  Thank you very much!
>
>
>  Francesca
>
>
> ------------------------------------------------------------------------------
> Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
> infrastructure or vast IT resources to deliver seamless, secure access to
> virtual desktops. With this all-in-one solution, easily deploy virtual
> desktops for less than the cost of PCs and save 60% on VDI infrastructure
> costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
>
>
>
> _______________________________________________
> mesa-users mailing lis...@li...https://lists.sourceforge.net/lists/listinfo/mesa-users
>
>  Hello,
>
> I remember I once used mesa to deal with wd cooling and it worked well.
> Actually you do not necessarily need to go to test_suite. Here is my
> suggestion: copy a work directory, edit the inlist_project file to let mesa
> start with the model you already created, and let mesa run. When the T and
> P are too low for further nuclear fusion, the He WD is now on its cooling
> trace. There should be a variable indicating the luminosity resulted from
> nuclear burning ( maybe called Lnuc or something, you can check the file
> mesa/star/public/star_data.dek for the variable name), as long as Lnuc<<
> the total luminosity, the He WD is cooling down. MESA will continue running
> until the equation of state of the central matter is uncertain ( I remember
> it is when lgQ>some critical value, you can also check what lgQ is in
> MESA's document, probably also in the star_data.dek file).
>
> Good luck!
>
> --
> Sincerely
> Jing
>
> Ph.D candidate at physics.caltech
> email: jin...@ca...
> address: MC350-17,Caltech,1200 E.California Blvd
>          Pasadena, CA 91125
>
>
>
> ------------------------------------------------------------------------------
> Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
> infrastructure or vast IT resources to deliver seamless, secure access to
> virtual desktops. With this all-in-one solution, easily deploy virtual
> desktops for less than the cost of PCs and save 60% on VDI infrastructure
> costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
> _______________________________________________
> mesa-users mailing list
> mes...@li...
> https://lists.sourceforge.net/lists/listinfo/mesa-users
>
>

Re: [mesa-users] MESA for Education

[david a. <wda...@gm...>]

Hi all,
We have been doing this with TYCHO for some years now, and most students
seem to find it empowering. Thanks to Bill, MESA is even more user
friendly, so I expect you will have a lot of success. We tended to have a
2-mode response: the utter enthusiasts and those who had other heavy
commitments. To deal with this we used a "case study" approach, which was
flexible, and we allowed work in teams. It was always obvious who did the
work.
Good luck,
Dave

-- 
David Arnett
Regents Professor
Steward Observatory
University of Arizona

Re: [mesa-users] Evolving a white dwarf on the cooling sequence

[Jing L. <jin...@ca...>]

On 1/9/12 1:39 PM, Francesca Valsecchi wrote:
> Hi all,
>
> I would like to use MESA to create white dwarf models of different 
> masses and temperatures.
>
> I created a He white dwarf using one of the test_suite runs and I am 
> trying to evolve it on the cooling sequence.
>
> I have tried using the test_suite called wd_cool, reading in input the 
> He white dwarf model created, but I did not have success.
>
> Is there any documentations on the various test_suite that deal with 
> white dwarfs? Also any paper that used MESA to study white dwarfs 
> would be useful.
>
>
> Thank you very much!
>
>
> Francesca
>
>
> ------------------------------------------------------------------------------
> Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
> infrastructure or vast IT resources to deliver seamless, secure access to
> virtual desktops. With this all-in-one solution, easily deploy virtual
> desktops for less than the cost of PCs and save 60% on VDI infrastructure
> costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
>
>
> _______________________________________________
> mesa-users mailing list
> mes...@li...
> https://lists.sourceforge.net/lists/listinfo/mesa-users
Hello,

I remember I once used mesa to deal with wd cooling and it worked well. 
Actually you do not necessarily need to go to test_suite. Here is my 
suggestion: copy a work directory, edit the inlist_project file to let 
mesa start with the model you already created, and let mesa run. When 
the T and P are too low for further nuclear fusion, the He WD is now on 
its cooling trace. There should be a variable indicating the luminosity 
resulted from nuclear burning ( maybe called Lnuc or something, you can 
check the file mesa/star/public/star_data.dek for the variable name), as 
long as Lnuc<< the total luminosity, the He WD is cooling down. MESA 
will continue running until the equation of state of the central matter 
is uncertain ( I remember it is when lgQ>some critical value, you can 
also check what lgQ is in MESA's document, probably also in the 
star_data.dek file).

Good luck!

-- 
Sincerely
Jing

Ph.D candidate at physics.caltech
email: jin...@ca...
address: MC350-17,Caltech,1200 E.California Blvd
          Pasadena, CA 91125

[mesa-users] Evolving a white dwarf on the cooling sequence

[Francesca V. <val...@gm...>]

Hi all,

I would like to use MESA to create white dwarf models of different masses
and temperatures.

I created a He white dwarf using one of the test_suite runs and I am trying
to evolve it on the cooling sequence.

I have tried using the test_suite called wd_cool, reading in input the He
white dwarf model created, but I did not have success.

Is there any documentations on the various test_suite that deal with white
dwarfs? Also any paper that used MESA to study white dwarfs would be useful.


Thank you very much!


Francesca

Re: [mesa-users] [mesa-news] mesa release 3844

[Francis T. <fx...@ma...>]

hi bill,

i missed that new file. thanks!

fxt


On Jan 8, 2012, at 5:49 PM, Bill Paxton wrote:

> 
> On Jan 8, 2012, at 1:35 PM, Francis Timmes wrote:
> 
>> the new simpler makefile_header has removed all explicit support for ifort.
>> 
> 
> Hi,
> 
> I forgot to mention in the release message that the default makefile_header is now
> the one for the mesasdk.   For folks who want to use ifort, makefile_header_non_mesasdk
> is in utills as a template.     I'll add a comment to the default makefile_header
> explaining the setup.   Does this look okay?
> 
> 
> # NOTE: this default version of makefile_header
> # assumes you will be using the mesasdk.
> # if you do not want that, you can use the
> # makefile_header_non_mesasdk file as a template.
> 
> 
> 
> -Bill
> 
> 
> 
> 

Re: [mesa-users] [mesa-news] mesa release 3844

[Bill P. <pa...@ki...>]

On Jan 8, 2012, at 1:35 PM, Francis Timmes wrote:

> the new simpler makefile_header has removed all explicit support for ifort.
> 

Hi,

I forgot to mention in the release message that the default makefile_header is now
the one for the mesasdk.   For folks who want to use ifort, makefile_header_non_mesasdk
is in utills as a template.     I'll add a comment to the default makefile_header
explaining the setup.   Does this look okay?


# NOTE: this default version of makefile_header
# assumes you will be using the mesasdk.
# if you do not want that, you can use the
# makefile_header_non_mesasdk file as a template.



-Bill

Re: [mesa-users] MESA for Education

[Richard T. <tow...@as...>]

Hi Kevin --

I haven't used MESA as a 'student tool' --- i.e., something that I get students to run themselves --- but I've certainly used it to generate movie sequences of the evolving stellar structure, which I then show in class and discuss with my students.

I'm sure you're already familiar with EZ-Web (I know Lars is), which is a simple web interface to Bill's earlier EZ code:

http://www.astro.wisc.edu/~townsend/static.php?ref=ez-web

I've found this very useful at both undergrad and grad levels, for assigning homeworks that involve hands-on investigation of various aspects of stellar structure and evolution. I was hoping eventually to develop a similar interface to MESA, but the problem right now is that the code runs too slowly (much slower than EZ, because the physics is much more sophisticated).

cheers,

Rich

On Jan 8, 2012, at 10:05 AM, Kevin Moore wrote:

> Hi all, 
> 
> I'm just letting the mailing list know that Lars and I are planning on using MESA in our grad stellar structure class this quarter. If anyone has used MESA (or any other code) in this capacity, we'd appreciate any relevant advice or resources you may have.
> 
> In keeping with the open source spirit of MESA, I'd like to have some way to make available what we come up with so others may benefit. I'm not sure the best way to do this, ideas?
> 
> -Kevin
> 
> 
> On Dec 12, 2011, at 5:03 PM, Steve Kawaler wrote:
> 
>> I think that a MESA for Education effort is a terrific idea - at all
>> levels of post-secondary education.  For undergraduate introductory
>> non-science courses all the way through graduate courses.  Please let
>> me know how I can help.
>> 
>> Steve Kawaler
>> 
>>> Message: 3
>>> Date: Mon, 12 Dec 2011 10:52:17 -0800
>>> From: Bill Paxton <pa...@ki...>
>>> Subject: Re: [mesa-users] mesa release 3790 + a cool movie
>>> To: mzi...@ma...
>>> Cc: "mes...@li... users"
>>>       <mes...@li...>, mes...@li...
>>> Message-ID: <026...@ki...>
>>> Content-Type: text/plain; charset=us-ascii
>>> 
>>> Hi Mike,
>>> 
>>> On Dec 12, 2011, at 9:47 AM, Mike Zingale wrote:
>>> 
>>>> Bill/Josiah, indeed that is a nice movie, and one I am sure many of us will want to show in our Intro to Astronomy classes when we come upon stellar evolution.
>>> 
>>> Great!   A movie like that is really a huge help to see the how the various things change together as the evolution goes forward.
>>> 
>>>> On that note, is there any sort of organized effort toward MESA for Education, instead of research.
>>> 
>>> Excellent suggestion.   There isn't any such organized effort yet, but there certainly should be.
>>> 
>>>> Perhaps providing an archive of nice movies of stellar evolution for use in classes would be a good start.
>>> 
>>> That would be a wonderful start -- I know Rich Townsend has been working on something like that
>>> (oh!  I just got his email saying he has been working on it!!!)
>>> 
>>> It would be wonderful if you and Rich and anyone else who is interested in MESA for Education would
>>> work together on this.   I'd love to see it happen, but I won't be the one to push the effort.
>>> 
>>> Cheers,
>>> Bill
>>> 
>>> 
>> 
>> ------------------------------------------------------------------------------
>> Learn Windows Azure Live!  Tuesday, Dec 13, 2011
>> Microsoft is holding a special Learn Windows Azure training event for 
>> developers. It will provide a great way to learn Windows Azure and what it 
>> provides. You can attend the event by watching it streamed LIVE online.  
>> Learn more at http://p.sf.net/sfu/ms-windowsazure
>> _______________________________________________
>> mesa-users mailing list
>> mes...@li...
>> https://lists.sourceforge.net/lists/listinfo/mesa-users
>> 
> 
> 
> ------------------------------------------------------------------------------
> Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
> infrastructure or vast IT resources to deliver seamless, secure access to
> virtual desktops. With this all-in-one solution, easily deploy virtual 
> desktops for less than the cost of PCs and save 60% on VDI infrastructure 
> costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
> _______________________________________________
> mesa-users mailing list
> mes...@li...
> https://lists.sourceforge.net/lists/listinfo/mesa-users

Re: [mesa-users] MESA for Education

[Kevin M. <km...@ph...>]

Hi all, 

I'm just letting the mailing list know that Lars and I are planning on using MESA in our grad stellar structure class this quarter. If anyone has used MESA (or any other code) in this capacity, we'd appreciate any relevant advice or resources you may have.

In keeping with the open source spirit of MESA, I'd like to have some way to make available what we come up with so others may benefit. I'm not sure the best way to do this, ideas?

-Kevin


On Dec 12, 2011, at 5:03 PM, Steve Kawaler wrote:

> I think that a MESA for Education effort is a terrific idea - at all
> levels of post-secondary education.  For undergraduate introductory
> non-science courses all the way through graduate courses.  Please let
> me know how I can help.
> 
> Steve Kawaler
> 
>> Message: 3
>> Date: Mon, 12 Dec 2011 10:52:17 -0800
>> From: Bill Paxton <pa...@ki...>
>> Subject: Re: [mesa-users] mesa release 3790 + a cool movie
>> To: mzi...@ma...
>> Cc: "mes...@li... users"
>>        <mes...@li...>, mes...@li...
>> Message-ID: <026...@ki...>
>> Content-Type: text/plain; charset=us-ascii
>> 
>> Hi Mike,
>> 
>> On Dec 12, 2011, at 9:47 AM, Mike Zingale wrote:
>> 
>>> Bill/Josiah, indeed that is a nice movie, and one I am sure many of us will want to show in our Intro to Astronomy classes when we come upon stellar evolution.
>> 
>> Great!   A movie like that is really a huge help to see the how the various things change together as the evolution goes forward.
>> 
>>> On that note, is there any sort of organized effort toward MESA for Education, instead of research.
>> 
>> Excellent suggestion.   There isn't any such organized effort yet, but there certainly should be.
>> 
>>> Perhaps providing an archive of nice movies of stellar evolution for use in classes would be a good start.
>> 
>> That would be a wonderful start -- I know Rich Townsend has been working on something like that
>> (oh!  I just got his email saying he has been working on it!!!)
>> 
>> It would be wonderful if you and Rich and anyone else who is interested in MESA for Education would
>> work together on this.   I'd love to see it happen, but I won't be the one to push the effort.
>> 
>> Cheers,
>> Bill
>> 
>> 
> 
> ------------------------------------------------------------------------------
> Learn Windows Azure Live!  Tuesday, Dec 13, 2011
> Microsoft is holding a special Learn Windows Azure training event for 
> developers. It will provide a great way to learn Windows Azure and what it 
> provides. You can attend the event by watching it streamed LIVE online.  
> Learn more at http://p.sf.net/sfu/ms-windowsazure
> _______________________________________________
> mesa-users mailing list
> mes...@li...
> https://lists.sourceforge.net/lists/listinfo/mesa-users
> 

[mesa-users] Problem with installing version 3844

[Alfred G. <al...@ga...>]

Thanks for all the new items implemented in MESA! I just tried to
upgrade to version 3844. The process fails with: 

gfortran -fopenmp -o ../sample sample_eos.o -L../../make -leos
-L../../../lib -lchem -lnum -lmtx -lmesaklu `mesasdk_lapack_link`
`mesasdk_blas_link` -lalert -linterp_2d -linterp_1d -lutils -lconst

 read  ../../data/eosDT_data/helm_table.dat
 write  ../../data/eosDT_data/cache/helm_table.bin

ERROR:  bad header info in ../../data/eosDT_data/mesa-eosDT_00z00x.data
                         min_version > ep% versionT        50        49

first file is short
13c13
< ERROR:  bad header info
in ../../data/eosDT_data/mesa-eosDT_00z00x.data
--- field 6
>                              P      6.2100730711604395E+11
14c14
<                          min_version > ep% versionT        50
49
--- field 6
>                              E      1.1185928203373142E+14
15c15
< 
--- field 2
>                              S      8.9350156636595654E+08


as of now, I still think that it is not a local problem of mine.
eosDT_data was apparently downloaded freshly with the upgrade. 


Alfred Gautschy

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

[Kevin M. <km...@ph...>]

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 <fx...@ma...> 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 <fx...@ma...> 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
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> ------------------------------------------------------------------------------
>>>>>>> Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
>>>>>>> infrastructure or vast IT resources to deliver seamless, secure access to
>>>>>>> virtual desktops. With this all-in-one solution, easily deploy virtual
>>>>>>> desktops for less than the cost of PCs and save 60% on VDI infrastructure
>>>>>>> costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
>>>>>>> _______________________________________________
>>>>>>> mesa-users mailing list
>>>>>>> mes...@li...
>>>>>>> https://lists.sourceforge.net/lists/listinfo/mesa-users
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> ------------------------------
>>>>>> 
>>>>>> ------------------------------------------------------------------------------
>>>>>> Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
>>>>>> infrastructure or vast IT resources to deliver seamless, secure access to
>>>>>> virtual desktops. With this all-in-one solution, easily deploy virtual
>>>>>> desktops for less than the cost of PCs and save 60% on VDI infrastructure
>>>>>> costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
>>>>>> 
>>>>>> ------------------------------
>>>>>> 
>>>>>> _______________________________________________
>>>>>> mesa-users mailing list
>>>>>> mes...@li...
>>>>>> https://lists.sourceforge.net/lists/listinfo/mesa-users
>>>>>> 
>>>>>> 
>>>>>> End of mesa-users Digest, Vol 29, Issue 2
>>>>>> *****************************************
>>>>>> 
>>>>> 
>>>>> ------------------------------------------------------------------------------
>>>>> Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
>>>>> infrastructure or vast IT resources to deliver seamless, secure access to
>>>>> virtual desktops. With this all-in-one solution, easily deploy virtual 
>>>>> desktops for less than the cost of PCs and save 60% on VDI infrastructure 
>>>>> costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
>>>>> _______________________________________________
>>>>> mesa-users mailing list
>>>>> mes...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/mesa-users
>>>> 
>>>> 
>>>> ------------------------------------------------------------------------------
>>>> Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
>>>> infrastructure or vast IT resources to deliver seamless, secure access to
>>>> virtual desktops. With this all-in-one solution, easily deploy virtual 
>>>> desktops for less than the cost of PCs and save 60% on VDI infrastructure 
>>>> costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
>>>> _______________________________________________
>>>> mesa-users mailing list
>>>> mes...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/mesa-users
> 
> ------------------------------------------------------------------------------
> Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
> infrastructure or vast IT resources to deliver seamless, secure access to
> virtual desktops. With this all-in-one solution, easily deploy virtual 
> desktops for less than the cost of PCs and save 60% on VDI infrastructure 
> costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
> _______________________________________________
> mesa-users mailing list
> mes...@li...
> https://lists.sourceforge.net/lists/listinfo/mesa-users

[mesa-users] mesa release 3844

[Bill P. <pa...@ki...>]

Hello and Happy New Year!


The first mesa release of 2012 has some cool new features:

	-- pressure instead of density as a primary variable in star
	-- Paczynski grey atmospheres for surface BCs and in pulsation models
	-- star/test_suite/astero example
	-- Hooke-Jeeves minimization option for astero model searches

Please read on if you'd like details!

Cheers,
Bill




pressure instead of density as a primary variable in star

Ideally it wouldn't matter whether you used density or pressure as a primary variable
in the stellar structure solutions -- for a given temperature and composition you always
can go back and forth from a density to a gas pressure, so it seems you can pick which you
use for reasons such as performance.  Since the microphysics packages tend to use
density, we use have used it in star as well.  In other words, the solver for star treats
density as a primary variable and pressure is indirectly determined as a function of
density, temperature, and composition.   If the equations were solved precisely,
then this extra level in the calculation of pressure would be harmless.  But the equations
are only solved approximately, so the indirection means that approximately correct values
for density and temperature can lead to anomalous pressure profiles -- i.e., cases
that show (tiny) violations of the expected hydrostatic balance.  The violations only
seem to show up near extreme jumps in density (such as at a sharp H/He boundary),
and the size of the violations seem to be negligible, so previously we haven't done anything 
about them.  But now the asteroseimologists have entered the scene!  They'd like to
have a perfect pressure profile as a starting model for their pulsation codes, and the
violations of hydrostatic balance, however small, are a cause for concern.

So now we have the option to replace density by gas pressure as a primary variable.
The good news it that it does seem to fix the problems with the pressure profiles.
Here's an example: this is a 25 Msun star crossing the gap at a time when Teff = 1e4.
There is no overshooting or semiconvection, so it has an extremely sharp H/He boundary;
in fact, we have single cell step function transitions in both abundances and in density;
as expected, logT is smooth across the transition.

the transition region is very thin in both mass and radius



pressure near H/He boundary is smooth when using lnPgas as primary variable (left);
however pressure is ragged when using lnd as primary variable instead of lnPgas (right).


note that the magnitude of the irregularities in P are tiny -- they are probably negligible for most applications.
but for asteroseismology, they might matter -- I don't know yet if the smoother pressure profile actually helps.
Please let me know if you find evidence that it does!

BTW: thanks to Aldo Serenelli for alerting me to the potential importance of using
pressure in place of density as a primary variable.   I fought his suggestion at first,
perhaps because I unconsciously anticipated the hard work that was going to be
required to make the necessary changes to mesa!

in star/public/run_star_defaults

   ! lnPgas variables
      
      ! lnPgas_flag is true if we are using lnPgas variables in place of lnd
      change_lnPgas_flag = .true.
      new_lnPgas_flag = .true.


Note that the default is to use gas pressure in place of density.
To go back to using density, edit your inlist to say
      change_lnPgas_flag = .true.
      new_lnPgas_flag = .false.





Paczynski grey atmospheres

Certain asteroseismology cases require a detailed stellar model out to very small optical depths (tau = 10^-4 or so).
There are even cases with small but significant convection zones out in those optically thin regions (e.g., white dwarfs).
Now, with prompting from Mike MacDonald and Hideyuki Saio, mesa can supply these models by using a scheme
described by Paczynski in this 1969 paper:


Key features are that this takes into account radiation dilution when tau < 2/3,
and calls the MLT package to get gradT allowing for convection.


To use it as the atmosphere boundary condition in star, set 
         which_atm_option = 'Paczynski_grey'   
               ! create an atmosphere for given base conditions.
               ! inspired by B. Paczynski, 1969, Acta Astr., vol. 19, 1.

The atmosphere integration is repeated until it gives a matching radius;
the tolerance for the match is given by this parameter:
            Paczynski_atm_R_surf_errtol = 3d-4

The steps for the integration are in units of log tau.  This sets the max step size:
         create_atm_max_step_size = 0.1 ! in units of log10_tau

That takes care of using Paczynski grey atmospheres for the surface boundary condition.
Next step is to include the details of the atmosphere in the input stellar model
for the pulsation code.  To do that, set one of these (from run_star_defaults):
   add_atmosphere_for_fgong = .false.
   add_atmosphere_for_osc = .false.
Alternatively, to get pulsation output created whenever a profile is written,
set these (from star_defaults)
         write_pulse_info_with_profile = .false. ! if true, write pulse info file when write profile
         pulse_info_format = 'FGONG'
         add_atmosphere_to_pulse_info = .false. 

Here are some plots showing a model output including a Paczynski atmosphere
This is the same model as shown above: a 25 Msun star crossing the gap at a time when Teff = 1e4.
The interior-atm boundary for this case is set at the photosphere (tau = 2/3, log10(tau) = -0.176).
Note that the profiles are smooth out to tau = 10^-4 and density of 10^-12







star/test_suite/astero example


We are making progress with getting mesa in shape to do asteroseismology.
The recent program at KITP had a big impact!  I've added an example case to
the star test_suite showing a typical setup for using mesa to search for a
model that matches given data from observations.  Take a look here:

	mesa/star/test_suite/astero

In addition to the usual inlists (inlist and inlist_astero), you'll find 2 more:
inlist_model_search_controls and inlist_oscillation_controls.  As you might
guess, the 1st sets the search parameters and the 2nd has information
about the data to be matched.  The adipls package is used for doing the
frequencies, so there are control files for it as well.    There are also minor
changes to make/makefile and src/run.f.  The change to run is to call
the main driver routine in mesa/astero/run_star_adipls.
	
My hope is that this will be a useful starter-kit for users who'd like to try
using mesa to search for models to match the great data coming from
KEPLER and CoRot.  Let me know if you'd like to give it a try.

BTW: the example is for HD49385 -- take a look at this lovely paper:




Hooke-Jeeves minimization option for astero model searches


Searching for a best-fit model for a set of asteroseismic data is a minimization problem
for a function f of multiple parameters (e.g., chi^2 using mass, mixing length, Y, and Z/X).
Modern algorithms for minimization can get improved performance by using the values
of previous evaluations of f to estimate the shape of the search domain to decide where
to look next.  The BOBYQA algorithm is a state-of-the-art example of such routines.
This works great for "smooth" search domains but can get lost with domains that
include "rough" spots  such as invalid parameter combinations inside the allowed
search hypercube.  In such cases, it can be better to give up the possible improved
performance to get a more robust routine.  The old (1961) Hooke-Jeeves algorithm
is just such an option.  It only uses the function values to make better-or-worse
decisions; it doesn't use the values to estimate slopes in the search domain.
So occasional "invalid" parameter combinations don't cause it problems -- 
they can simply be given a very large artificial value causing them to be rejected.

For applications with a smooth search space (such as solar model calibration?),
BOBYQA is still one of the best options available.  But for a search space with
potential "drop-outs" such as a preliminary parameter scan for asteroseismology,
Hooke-Jeeves seems to be a better choice.   Both are now available in the astero
package.


We are using the f90 implementation from John Burkardt's website (thanks!!!).
http://people.sc.fsu.edu/~jburkardt/f_src/toms178/toms178.html

      !    Robert Hooke, Terry Jeeves,
      !    Direct Search Solution of Numerical and Statistical Problems,
      !    Journal of the ACM,
      !    Volume 8, Number 2, April 1961, pages 212-229.

[mesa-users] Mesa in scientific linux 6.1

[Abhisek D. <abh...@gm...>]

Hey,

I have successfully installed MESA in Scientific Linux 6.1

Abhisek Datta

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

[Richard T. <tow...@as...>]

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 <fx...@ma...> 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 <fx...@ma...> 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
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> ------------------------------------------------------------------------------
>>>>>> Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
>>>>>> infrastructure or vast IT resources to deliver seamless, secure access to
>>>>>> virtual desktops. With this all-in-one solution, easily deploy virtual
>>>>>> desktops for less than the cost of PCs and save 60% on VDI infrastructure
>>>>>> costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
>>>>>> _______________________________________________
>>>>>> mesa-users mailing list
>>>>>> mes...@li...
>>>>>> https://lists.sourceforge.net/lists/listinfo/mesa-users
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> ------------------------------
>>>>> 
>>>>> ------------------------------------------------------------------------------
>>>>> Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
>>>>> infrastructure or vast IT resources to deliver seamless, secure access to
>>>>> virtual desktops. With this all-in-one solution, easily deploy virtual
>>>>> desktops for less than the cost of PCs and save 60% on VDI infrastructure
>>>>> costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
>>>>> 
>>>>> ------------------------------
>>>>> 
>>>>> _______________________________________________
>>>>> mesa-users mailing list
>>>>> mes...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/mesa-users
>>>>> 
>>>>> 
>>>>> End of mesa-users Digest, Vol 29, Issue 2
>>>>> *****************************************
>>>>> 
>>>> 
>>>> ------------------------------------------------------------------------------
>>>> Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
>>>> infrastructure or vast IT resources to deliver seamless, secure access to
>>>> virtual desktops. With this all-in-one solution, easily deploy virtual 
>>>> desktops for less than the cost of PCs and save 60% on VDI infrastructure 
>>>> costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
>>>> _______________________________________________
>>>> mesa-users mailing list
>>>> mes...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/mesa-users
>>> 
>>> 
>>> ------------------------------------------------------------------------------
>>> Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
>>> infrastructure or vast IT resources to deliver seamless, secure access to
>>> virtual desktops. With this all-in-one solution, easily deploy virtual 
>>> desktops for less than the cost of PCs and save 60% on VDI infrastructure 
>>> costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
>>> _______________________________________________
>>> mesa-users mailing list
>>> mes...@li...
>>> https://lists.sourceforge.net/lists/listinfo/mesa-users

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

[david a. <wda...@gm...>]

Hi rich,

Casey Meakin and I have been doing an example of what Frank mentioned: an
extensive parameter survey.

You are quite correct of course about the lack of advantage of a
supercomputer for a single evolutionary sequence.

Dave

-- 
David Arnett
Regents Professor
Steward Observatory
University of Arizona

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

[Bill P. <pa...@ki...>]

Hi,

Saul Rappaport and Lorne Nelson and collaborators have used Lorne's cluster to run mesa.
e.g., in this recent paper http://adsabs.harvard.edu/abs/2011ApJ...732...70L
they report results of 42,000 binary evolution runs with mesa -- too many
even for my 12 core mac!  Although I'm a coauthor I don't know the details
of running on the cluster -- but perhaps Saul or Lorne can enlighten us.

Bill



On Jan 5, 2012, at 5:55 AM, Francis Timmes 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 <fx...@ma...> 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
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> ------------------------------------------------------------------------------
>>>>>> Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
>>>>>> infrastructure or vast IT resources to deliver seamless, secure access to
>>>>>> virtual desktops. With this all-in-one solution, easily deploy virtual
>>>>>> desktops for less than the cost of PCs and save 60% on VDI infrastructure
>>>>>> costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
>>>>>> _______________________________________________
>>>>>> mesa-users mailing list
>>>>>> mes...@li...
>>>>>> https://lists.sourceforge.net/lists/listinfo/mesa-users
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> ------------------------------
>>>>> 
>>>>> ------------------------------------------------------------------------------
>>>>> Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
>>>>> infrastructure or vast IT resources to deliver seamless, secure access to
>>>>> virtual desktops. With this all-in-one solution, easily deploy virtual
>>>>> desktops for less than the cost of PCs and save 60% on VDI infrastructure
>>>>> costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
>>>>> 
>>>>> ------------------------------
>>>>> 
>>>>> _______________________________________________
>>>>> mesa-users mailing list
>>>>> mes...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/mesa-users
>>>>> 
>>>>> 
>>>>> End of mesa-users Digest, Vol 29, Issue 2
>>>>> *****************************************
>>>>> 
>>>> 
>>>> ------------------------------------------------------------------------------
>>>> Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
>>>> infrastructure or vast IT resources to deliver seamless, secure access to
>>>> virtual desktops. With this all-in-one solution, easily deploy virtual 
>>>> desktops for less than the cost of PCs and save 60% on VDI infrastructure 
>>>> costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
>>>> _______________________________________________
>>>> mesa-users mailing list
>>>> mes...@li...
>>>> https://lists.sourceforge.net/lists/listinfo/mesa-users
>>> 
>>> 
>>> ------------------------------------------------------------------------------
>>> Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
>>> infrastructure or vast IT resources to deliver seamless, secure access to
>>> virtual desktops. With this all-in-one solution, easily deploy virtual 
>>> desktops for less than the cost of PCs and save 60% on VDI infrastructure 
>>> costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
>>> _______________________________________________
>>> mesa-users mailing list
>>> mes...@li...
>>> https://lists.sourceforge.net/lists/listinfo/mesa-users
> 
> 
> ------------------------------------------------------------------------------
> Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex
> infrastructure or vast IT resources to deliver seamless, secure access to
> virtual desktops. With this all-in-one solution, easily deploy virtual 
> desktops for less than the cost of PCs and save 60% on VDI infrastructure 
> costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox
> _______________________________________________
> mesa-users mailing list
> mes...@li...
> https://lists.sourceforge.net/lists/listinfo/mesa-users