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

Re: mesa-users] Semiconvection, thermohaline mixing

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

Hi Alfred,

On Oct 30, 2010, at 12:19 PM, al...@ga... wrote:

> Whom it might concern, or who might help
> 
> Going through the whole star_defaults.dek file trying to figure out  
> where I can modify parameters, I realized that apparently MESA treats  
> semiconvection and thermohaline mixing; this is great! However, as  
> these mechanisms have various recipes on how to treat them I expected  
> that at some point in star_defaults.dek one or the other parameter  
> related to the treatment of semiconvection and/or thermohaline mixing  
> would show up; I could not find anything though. Is this right? Is  
> there no user interference possible for semiconvection and  
> thermohaline mixing? How to find out what approach was adopted in MESA?

Semiconvection + thermohaline mixing were in for a time but currently are not.
But they have top priority to be (re)implemented -- so I expect to have something soon.

> 
> I think what was said above applies also to some degree to diffusion  
> of species, also apparently implemented in MESA.

We have element diffusion that works fine in non-degenerate environments
(such as solar interior).    The section star_defaults.dek is up-to-date (I hope!).


> Is there a philosophy being followed in the MESA development on how  
> "hard-wired" code parts (i.e. no modifications through namelists  
> possible)  in say numerics, microphysics, macrophysics are documented  
> and/or made accessible to the common user?

I intend to make all the lower-level functionality available at the mesa/star
level via inlist controls.  So please let me know if you discover something
that I've missed.

Cheers,
Bill

mesa-users] Semiconvection, thermohaline mixing

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

Whom it might concern, or who might help

Going through the whole star_defaults.dek file trying to figure out  
where I can modify parameters, I realized that apparently MESA treats  
semiconvection and thermohaline mixing; this is great! However, as  
these mechanisms have various recipes on how to treat them I expected  
that at some point in star_defaults.dek one or the other parameter  
related to the treatment of semiconvection and/or thermohaline mixing  
would show up; I could not find anything though. Is this right? Is  
there no user interference possible for semiconvection and  
thermohaline mixing? How to find out what approach was adopted in MESA?

I think what was said above applies also to some degree to diffusion  
of species, also apparently implemented in MESA.

Is there a philosophy being followed in the MESA development on how  
"hard-wired" code parts (i.e. no modifications through namelists  
possible)  in say numerics, microphysics, macrophysics are documented  
and/or made accessible to the common user?

With regards,
Alfred Gautschy

Re: mesa-users] (no subject)

[Aaron D. <aar...@gm...>]

Hi Duligur,

We are checking to see what the problem is.  In general, you should only
update to a number listed on the mesa webpage.

The current number there is 2734 and I see that your version is 2740.  Only
numbers reported on the webpage or by one of the developers should be
used--otherwise you may get a version that doesn't work!

If the problem you have persists with 2734, you can try reverting to 2699
(the last reported version).

svn update -r 2699

should work even if you have a newer version currently installed.  Let us
know if this doesn't solve your problem.

Aaron


On Fri, Oct 22, 2010 at 3:41 PM, Duligur Ibeling <du...@gm...> wrote:

> Hello,
>
> When installing, I get the following error: (Mac OS 10.6.4, gfortran, mesa
> rev. 2740):
>
>
>> gfortran -fno-range-check  -fopenmp  -o ../star \
>
>  run_star_support.o se_support_stub.o run_star_extras.o  run_star.o  run.o
>> -L../../make -lstar -L../../../lib -ldiffusion -lionization -lmlt -latm
>> -lother_atm -lkaro -lcolors -leos -lother_eos -lkap -lother_kap -ljina
>> -lweak -lnet -lscreen -lrates -lneu -lchem -linterp_2d -linterp_1d -lnum
>> -lutils -lalert -lconst -lmtx -framework Accelerate
>
>
>> At line 1877 of file ../private/ctrls_io.f (unit = 9, file = 'inlist')
>
> Fortran runtime error: namelist not terminated with / or &end
>
> first file is short
>
>
>> /Users/chep/mesa/star/test
>
> TEST FAILED -- compare test_output to tmp.txt
>
>
> Thanks.
>
>
> ------------------------------------------------------------------------------
> Nokia and AT&T present the 2010 Calling All Innovators-North America
> contest
> Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in
> marketing
> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
> http://p.sf.net/sfu/nokia-dev2dev
> _______________________________________________
> mesa-users mailing list
> mes...@li...
> https://lists.sourceforge.net/lists/listinfo/mesa-users
>
>

mesa-users] (no subject)

[Duligur I. <du...@gm...>]

Hello,

When installing, I get the following error: (Mac OS 10.6.4, gfortran, mesa
rev. 2740):


> gfortran -fno-range-check  -fopenmp  -o ../star \

 run_star_support.o se_support_stub.o run_star_extras.o  run_star.o  run.o
> -L../../make -lstar -L../../../lib -ldiffusion -lionization -lmlt -latm
> -lother_atm -lkaro -lcolors -leos -lother_eos -lkap -lother_kap -ljina
> -lweak -lnet -lscreen -lrates -lneu -lchem -linterp_2d -linterp_1d -lnum
> -lutils -lalert -lconst -lmtx -framework Accelerate


> At line 1877 of file ../private/ctrls_io.f (unit = 9, file = 'inlist')

Fortran runtime error: namelist not terminated with / or &end

first file is short


> /Users/chep/mesa/star/test

TEST FAILED -- compare test_output to tmp.txt


Thanks.

mesa-users] Fwd: alert_lib.mod

[Duligur I. <du...@gm...>]

Oops, I sent to the wrong list...

---------- Forwarded message ----------
From: Duligur Ibeling <du...@gm...>
Date: Thu, Oct 21, 2010 at 10:49 PM
Subject: alert_lib.mod
To: mes...@li...


Hello,

I get the following error in installing MESA (under Mac OS X 10.6.4,
gfortran, Accelerate framework):

gfortran -fno-range-check  -fopenmp  -I../public -I../private
> -I../../include -Wunused-value -Werror -W -fimplicit-none   -fbounds-check
> -O2 -g -c -ffree-form   ../public/utils_lib.f

../public/utils_lib.f:29.19:


>       use alert_lib

                   1

Fatal Error: Can't open module file 'alert_lib.mod' for reading at (1): No
> such file or directory

make: *** [utils_lib.o] Error 1


Where is the alert_lib.mod file?

Thanks.

Re: mesa-users] Installing MESA on a Mac cluster

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

hi nathan,

perhaps slightly off topic, version 10.0.016 of ifort is dated. 
could you invoke one the more modern 11.x versions of ifort?

fxt



On Oct 21, 2010, at 1:25 PM, Nathan Thompson wrote:

> Hello,
> 
> Nathan Thompson of Wichita State University. I'm attempting to get MESA installed on a Mac cluster so that I can take advantage of ifort. I tried to install MESA to my user account and received the following error:
> 
> 
> /home/thompson/mesa/chem
> building chem package.
> 
> ifort  -vec-report0 -traceback -error-limit 6 -openmp -threads  -I../public -I..
> /private -I../../include -warn all -warn nounused -implicitnone  -check uninit -
> check pointers -check bounds -check all -O2 -g -c -fixed -132 ../public/chem_def
> .f
> fortcom: Error: ../public/chem_def.f, line 46: Syntax error, found '::' when exp
> ecting one of: ] /) , : (/ [
>       character(len=iso_name_length), dimension(0:max_el_z) :: el_name = [charac
> ter(len=iso_name_length) ::
> --------------------------------------------------------------------------------
> -------------------------^
> fortcom: Error: ../public/chem_def.f, line 57: Syntax error, found '::' when exp
> ecting one of: ] /) , : (/ [
>       character(len=long_name_length), dimension(0:max_el_z) :: el_long_name = [
> character(len=long_name_length) ::
> --------------------------------------------------------------------------------
> --------------------------------^
> fortcom: Error: ../public/chem_def.f, line 69: Syntax error, found '::' when exp
> ecting one of: ] /) , : (/ [
>       character(len=iso_name_length), dimension(2:3) :: al_isomers = [character(
> len=iso_name_length) ::
> --------------------------------------------------------------------------------
> ---------------------^
> fortcom: Error: ../public/chem_def.f, line 71: Syntax error, found '::' when exp
> ecting one of: ] /) , : (/ [
>       character(len=long_name_length), dimension(2:3) :: long_al_isomers = [char
> acter(len=long_name_length) ::
> --------------------------------------------------------------------------------
> ----------------------------^
> fortcom: Error: ../public/chem_def.f, line 46: This array or function or substri
> ng is invalid in constant expressions.   [CHARACTER]
>       character(len=iso_name_length), dimension(0:max_el_z) :: el_name = [charac
> ter(len=iso_name_length) ::
> --------------------------------------------------------------------------^
> fortcom: Error: ../public/chem_def.f, line 46: This is not a valid initializatio
> n expression.
>       character(len=iso_name_length), dimension(0:max_el_z) :: el_name = [charac
> ter(len=iso_name_length) ::
> --------------------------------------------------------------------------------
> -------------------------^
> fortcom: Severe: Too many errors, exiting
> compilation aborted for ../public/chem_def.f (code 1)
> make: *** [chem_def.o] Error 1
> 
> /home/thompson/mesa/chem/make
> FAILED
> 
> portal:~/mesa thompson$
> 
> Here is the version information about the architecture of the computer and the ifort version info:
> 
> Darwin portal.cluster 8.11.1 Darwin Kernel Version 8.11.1: Wed Oct 10 18:23:38 PDT 2007; root:xnu-792.25.20~1_RELEASEI386 i386 i386
> 
> Intel(R) Fortran Compiler for applications running on Intel(R) 64, Version 10.0
> Build 20070426 Package ID: m_fc_p_10.0.016
> 
> Thank you,
> Nathan ------------------------------------------------------------------------------
> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
> Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store 
> http://p.sf.net/sfu/nokia-dev2dev_______________________________________________
> mesa-users mailing list
> mes...@li...
> https://lists.sourceforge.net/lists/listinfo/mesa-users

Re: mesa-users] svn problem resolved, but now 2734 not building

[Kent B. <kg...@la...>]

On Thu, 2010-10-21 at 16:46 -0400, Aaron Dotter wrote:
> 
> Most of us are new at this so there is no established practice.  For
> now, the MESA council are identified on the project webpage and you
> can send any contributions to them by email.  Better yet, join the
> mesa-developers mailing list and post your contributions there.
> 

Have done so. Will shift code development discussions to that mailing
list.

-- Kent G. Budge

Re: mesa-users] svn problem resolved, but now 2734 not building

[Aaron D. <aar...@gm...>]

Hi Kent,

Glad to hear that you were able to fix the inlist problem.  Sorry about
that.

I'm going to take a stab at C/C++ wrappers for some of the modules then,
> with an eye towards including some conditionally compiled Design By
> Contract checks. Will do this without touching the underlying MESA F95
> modules as far as possible. Then I can try wiring this up with Tcl/Tk.
> How does a window with a running plot of the H-R track as you calculate
> it grab you?
>

Have you tried pgstar?  It does the same with pgplot.  You can enable it in
mesa/utils/makefile_header (once you've installed pgplot) and then give it a
try.

But that's not to say another option wouldn't be welcome!


> Am anxious to learn proper project etiquette as well. What is the
> process for submitting new code or code changes?
>

Most of us are new at this so there is no established practice.  For now,
the MESA council are identified on the project webpage and you can send any
contributions to them by email.  Better yet, join the mesa-developers
mailing list and post your contributions there.

Aaron

Re: mesa-users] svn problem resolved, but now 2734 not building

[Kent B. <kg...@la...>]

On Thu, 2010-10-21 at 16:02 -0400, Aaron Dotter wrote:
> 
>         But I can't seem to build 2734 correctly under gfortran 4.5.0.
>         It
>         compiles, but there are subtle differences in the eos tests
>         and more
>         serious differences in the model tests. Any ideas?
> 
> 
> Can you provide some more system details, like OS?

uname -a yields

Linux gondolin.lanl.gov 2.6.18-194.8.1.el5 #1 SMP Wed Jun 23 10:52:51
EDT 2010 x86_64 x86_64 x86_64 GNU/Linux

> 
> 
> In general, we do expect some minor differences in the test results
> when compiled on different machines or different compilers than the
> one where the standard results were produced, especially if OpenMP is
> involved.  What do you mean by more serious differences?
> 
The eos test problem differences do look like roundoff. The star test
problem differences involve actual crashing of code.

I found one of the problems already:  The test_star_inlist file appears
to be missing the line

/ ! end of controls namelist

at the obvious location for it, as downloaded by subversion. I've added
the line and the problem now runs to completion. Don't know if it's your
repository that is missing the line or whether subversion experienced a
hickup. My sense is that it is something like a distributed CVS so the
latter seems unlikely, but I am new to this environment.

> 
> Also, we do have some reports that gfortran 4.5.0 is problematic.  On
> the Mac, 4.5.1 should work.  On linux, I'm pretty sure that 4.4.4
> works but I have no information about 4.5.*.  If you have access to
> ifort, you are encouraged to use it as it (at least version 11) has no
> known problems with the current MESA.

We are only to version 1.10 on ifort so I should probably hold off on
that until we update. Will soldier on with gfortran 4.5.0 unless I hit a
brick wall; I can then drop back to 4.4.4 if necessary. However, I may
try building with the PGI F95 compiler, which is fairly widely used
hereabouts, just to see what happens.

> 
>  
>         Thanks for being patient with the tyro. I am eager to
>         contribute to the
>         project, particularly in testing out some new turbulent mixing
>         models
>         and in possibly providing C/C++ wrappers for some of the
>         modules and a
>         Tcl/Tk interface to the 1-D star code. Apologies if someone is
>         already
>         working on these or if I have just stepped in the middle of a
>         computer
>         language holy war.
> 
> 
> No language evangelism here so far.  The MESA Council is happy to look
> at anything that can broaden or improve the experience.  All of the
> things you mentioned sound great!
> 
> 
> Aaron

Excellent. I've been talking with Chris Fryer about getting funding to
compare some different turbulent mixing models; he's the one who pointed
me at MESA. I've been playing with my own C++ evolution code, which has
been great fun, but it seems unwise to reinvent so many wheels. (Though
my code does have an explicit hydrodynamics option that may be worth
preserving. Then again, perhaps not in 1-D.)

I'm going to take a stab at C/C++ wrappers for some of the modules then,
with an eye towards including some conditionally compiled Design By
Contract checks. Will do this without touching the underlying MESA F95
modules as far as possible. Then I can try wiring this up with Tcl/Tk.
How does a window with a running plot of the H-R track as you calculate
it grab you?

Am anxious to learn proper project etiquette as well. What is the
process for submitting new code or code changes?

-- Kent G. Budge

mesa-users] Installing MESA on a Mac cluster

[Nathan T. <nlt...@wi...>]

Hello,

Nathan Thompson of Wichita State University. I'm attempting to get MESA
installed on a Mac cluster so that I can take advantage of ifort. I tried to
install MESA to my user account and received the following error:


/home/thompson/mesa/chem
building chem package.

ifort  -vec-report0 -traceback -error-limit 6 -openmp -threads  -I../public
-I..
/private -I../../include -warn all -warn nounused -implicitnone  -check
uninit -
check pointers -check bounds -check all -O2 -g -c -fixed -132
../public/chem_def
.f
fortcom: Error: ../public/chem_def.f, line 46: Syntax error, found '::' when
exp
ecting one of: ] /) , : (/ [
      character(len=iso_name_length), dimension(0:max_el_z) :: el_name =
[charac
ter(len=iso_name_length) ::
--------------------------------------------------------------------------------
-------------------------^
fortcom: Error: ../public/chem_def.f, line 57: Syntax error, found '::' when
exp
ecting one of: ] /) , : (/ [
      character(len=long_name_length), dimension(0:max_el_z) :: el_long_name
= [
character(len=long_name_length) ::
--------------------------------------------------------------------------------
--------------------------------^
fortcom: Error: ../public/chem_def.f, line 69: Syntax error, found '::' when
exp
ecting one of: ] /) , : (/ [
      character(len=iso_name_length), dimension(2:3) :: al_isomers =
[character(
len=iso_name_length) ::
--------------------------------------------------------------------------------
---------------------^
fortcom: Error: ../public/chem_def.f, line 71: Syntax error, found '::' when
exp
ecting one of: ] /) , : (/ [
      character(len=long_name_length), dimension(2:3) :: long_al_isomers =
[char
acter(len=long_name_length) ::
--------------------------------------------------------------------------------
----------------------------^
fortcom: Error: ../public/chem_def.f, line 46: This array or function or
substri
ng is invalid in constant expressions.   [CHARACTER]
      character(len=iso_name_length), dimension(0:max_el_z) :: el_name =
[charac
ter(len=iso_name_length) ::
--------------------------------------------------------------------------^
fortcom: Error: ../public/chem_def.f, line 46: This is not a valid
initializatio
n expression.
      character(len=iso_name_length), dimension(0:max_el_z) :: el_name =
[charac
ter(len=iso_name_length) ::
--------------------------------------------------------------------------------
-------------------------^
fortcom: Severe: Too many errors, exiting
compilation aborted for ../public/chem_def.f (code 1)
make: *** [chem_def.o] Error 1

/home/thompson/mesa/chem/make
FAILED

portal:~/mesa thompson$

Here is the version information about the architecture of the computer and
the ifort version info:

Darwin portal.cluster 8.11.1 Darwin Kernel Version 8.11.1: Wed Oct 10
18:23:38 PDT 2007; root:xnu-792.25.20~1_RELEASEI386 i386 i386

Intel(R) Fortran Compiler for applications running on Intel(R) 64, Version
10.0
Build 20070426 Package ID: m_fc_p_10.0.016

Thank you,
Nathan

Re: mesa-users] svn problem resolved, but now 2734 not building

[Aaron D. <aar...@gm...>]

Hi Kent,

On Thu, Oct 21, 2010 at 2:34 PM, Kent Budge <kg...@la...> wrote:

> The subversion problem was fixed by my system wizard. Apparently it's a
> known gotcha in the proxy configuration, which he has now corrected.
>

Great!



> But I can't seem to build 2734 correctly under gfortran 4.5.0. It
> compiles, but there are subtle differences in the eos tests and more
> serious differences in the model tests. Any ideas?
>

Can you provide some more system details, like OS?

In general, we do expect some minor differences in the test results when
compiled on different machines or different compilers than the one where the
standard results were produced, especially if OpenMP is involved.  What do
you mean by more serious differences?

Also, we do have some reports that gfortran 4.5.0 is problematic.  On the
Mac, 4.5.1 should work.  On linux, I'm pretty sure that 4.4.4 works but I
have no information about 4.5.*.  If you have access to ifort, you are
encouraged to use it as it (at least version 11) has no known problems with
the current MESA.



> Thanks for being patient with the tyro. I am eager to contribute to the
> project, particularly in testing out some new turbulent mixing models
> and in possibly providing C/C++ wrappers for some of the modules and a
> Tcl/Tk interface to the 1-D star code. Apologies if someone is already
> working on these or if I have just stepped in the middle of a computer
> language holy war.
>

No language evangelism here so far.  The MESA Council is happy to look at
anything that can broaden or improve the experience.  All of the things you
mentioned sound great!

Aaron

mesa-users] 2734 not building

[Kent B. <kg...@la...>]

And now I'm seeing:

At line 1861 of file ../private/ctrls_io.f (unit = 9, file = 'inlist')
Fortran runtime error: namelist not terminated with / or &end
first file is short

/home/kgbudge/mesa/star/test
TEST FAILED -- compare test_output to tmp.txt

mesa-users] svn problem resolved, but now 2734 not building

[Kent B. <kg...@la...>]

The subversion problem was fixed by my system wizard. Apparently it's a
known gotcha in the proxy configuration, which he has now corrected.

But I can't seem to build 2734 correctly under gfortran 4.5.0. It
compiles, but there are subtle differences in the eos tests and more
serious differences in the model tests. Any ideas?

Thanks for being patient with the tyro. I am eager to contribute to the
project, particularly in testing out some new turbulent mixing models
and in possibly providing C/C++ wrappers for some of the modules and a
Tcl/Tk interface to the 1-D star code. Apologies if someone is already
working on these or if I have just stepped in the middle of a computer
language holy war.

-- Kent G. Budge

Re: mesa-users] having trouble downloading Mesa with svn

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

hi kent,

could be a proxy issue, could be the version of svn being using 
as some svn variants seem more prone to the error than others.
see if a simple list gives an error.
svn list http://mesa.svn.sourceforge.net/svnroot/mesa/trunk

fxt


On Oct 20, 2010, at 12:12 PM, Aaron Dotter wrote:

> Hi Kent,
> 
> We are none of us subversion experts, though we do occasionally spend time trying to figure out what it's telling us.
> 
> The best I can tell, this error message has something to do with apache, possibly on the machine you're trying to do the checkout from.
> 
> Maybe there are some restrictions at LANL.  Do you have access to another computer you can try this from?
> 
> There is no plan to provide MESA as a tarball at present.  Version control is the only way we can keep up with the pace of progress.
> 
> 
> Aaron
> 
> 
> 
> 
> On Wed, Oct 20, 2010 at 2:52 PM, Kent Budge <kg...@la...> wrote:
> 
> Following the instructions on the home page ("Getting Started"), I
> entered the command:
> 
> svn co -r 2734 http://mesa.svn.sourceforge.net/svnroot/mesa/trunk mesa
> 
> And got back:
> 
> svn: PROPFIND request failed on '/svnroot/mesa/trunk'
> svn: PROPFIND of '/svnroot/mesa/trunk': 302 Found
> (http://mesa.svn.sourceforge.net)
> 
> Any suggestions welcome.
> 
> Any possibility of getting the code as a tarball?
> 
> 
> -- Kent G. Budge
> CCS-2, LANL
> 
> 
> ------------------------------------------------------------------------------
> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
> Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
> http://p.sf.net/sfu/nokia-dev2dev
> _______________________________________________
> mesa-users mailing list
> mes...@li...
> https://lists.sourceforge.net/lists/listinfo/mesa-users
> 
> ------------------------------------------------------------------------------
> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
> Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store 
> http://p.sf.net/sfu/nokia-dev2dev_______________________________________________
> mesa-users mailing list
> mes...@li...
> https://lists.sourceforge.net/lists/listinfo/mesa-users

Re: mesa-users] having trouble downloading Mesa with svn

[Aaron D. <aar...@gm...>]

Hi Kent,

We are none of us subversion experts, though we do occasionally spend time
trying to figure out what it's telling us.

The best I can tell, this error message has something to do with apache,
possibly on the machine you're trying to do the checkout from.

Maybe there are some restrictions at LANL.  Do you have access to another
computer you can try this from?

There is no plan to provide MESA as a tarball at present.  Version control
is the only way we can keep up with the pace of progress.


Aaron




On Wed, Oct 20, 2010 at 2:52 PM, Kent Budge <kg...@la...> wrote:

>
> Following the instructions on the home page ("Getting Started"), I
> entered the command:
>
> svn co -r 2734 http://mesa.svn.sourceforge.net/svnroot/mesa/trunk mesa
>
> And got back:
>
> svn: PROPFIND request failed on '/svnroot/mesa/trunk'
> svn: PROPFIND of '/svnroot/mesa/trunk': 302 Found
> (http://mesa.svn.sourceforge.net)
>
> Any suggestions welcome.
>
> Any possibility of getting the code as a tarball?
>
>
> -- Kent G. Budge
> CCS-2, LANL
>
>
>
> ------------------------------------------------------------------------------
> Nokia and AT&T present the 2010 Calling All Innovators-North America
> contest
> Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in
> marketing
> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
> http://p.sf.net/sfu/nokia-dev2dev
> _______________________________________________
> mesa-users mailing list
> mes...@li...
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mesa-users] having trouble downloading Mesa with svn

[Kent B. <kg...@la...>]

Following the instructions on the home page ("Getting Started"), I
entered the command:

svn co -r 2734 http://mesa.svn.sourceforge.net/svnroot/mesa/trunk mesa

And got back:

svn: PROPFIND request failed on '/svnroot/mesa/trunk'
svn: PROPFIND of '/svnroot/mesa/trunk': 302 Found
(http://mesa.svn.sourceforge.net)

Any suggestions welcome.

Any possibility of getting the code as a tarball?


-- Kent G. Budge
CCS-2, LANL

mesa-users] weird seg.fault

[Tuguldur S. <tug...@em...>]

Hi there,

I have been using MESA for the past 3 months with no problems at all. But
since yesterday I start seeing a weird segmentation fault error. This error
comes in suddenly not allowing me to run any models, and it disappear as
sudden as it appeared. I don't think the problem is with the code, but I was
just wondering if anybody has any ideas of why its happening?

The error:

tuguldur@tuxedo:~/data1/mesa/star/s2bx3m2$ ./rn
Revision: 2653
Wed Oct 20 01:13:09 MST 2010


 The terminal output contains the following information

      'step' is the number of steps since the start of the run,
      'lg_dt_yr' is log10 timestep in years,
      'age_yr' is the simulated years since the start run,
      'lg_Tcntr' is log10 center temperature (K),
      'lg_Dcntr' is log10 center density (g/cm^3),
      'lg_Pcntr' is log10 center pressure (ergs/cm^3),
      'Teff' is the surface temperature (K),
      'lg_R' is log10 surface radius (Rsun),
      'lg_L' is log10 surface luminosity (Lsun),
      'lg_LH' is log10 total PP and CNO hydrogen burning power (Lsun),
      'lg_L3a' is log10 total triple-alpha helium burning power (Lsun),
      'lg_LZ' is log10 total burning power excluding LH and L3a and
photodisintegrations (Lsun),
      'lg_LNuc' is log10 nuclear power excluding photodisintegration (Lsun),
      'lg_LNeu' is log10 total neutrino power (Lsun),
      'lg_Psurf' is log10 surface pressure (gas + radiation),
      'Mass' is the total stellar mass (Msun),
      'lg_Mdot' is log10 magnitude of rate of change of mass (Msun/year),
      'lg_Dsurf' is log10 surface density (g/cm^3),
      'H_rich' is the remaining mass outside of the hydrogen poor core,
      'H_poor' is the core mass where hydrogen abundance is <= 0.10E-03
      'He_poor' is the core mass where helium abundance is <= 0.10E-03
      'H_cntr' is the center H1 mass fraction,
      'He_cntr' is the center He4 mass fraction,
      'C_cntr' is the center C12 mass fraction,
      'N_cntr' is the center N14 mass fraction,
      'O_cntr' is the center O16 mass fraction,
      'Ne_cntr' is the center Ne20 mass fraction,
      'X_avg' is the star average hydrogen mass fraction,
      'Y_avg' is the star average helium mass fraction,
      'Z_avg' is the star average metallicity,
      'gam_cntr' is the center plasma interaction parameter,
      'eta_cntr' is the center electron degeneracy parameter,
      'pts' is the number of grid points in the current model,
      'iters' is the number of newton iterations for the current step,
      'retry' is the number of step retries required during the run,
      'bckup' is the number of step backups required during the run,
      'dt_limit' is an indication of what limited the timestep.

 All this and more are saved in 'LOGS/star.log' during the run.

 create pre-main-sequence model
./rn: line 4:  8924 Segmentation fault      ./star
Wed Oct 20 01:13:11 MST 2010

Again, this happens and goes away without my interference at all. The models
which run without any problems before simply wouldn't run again. Even the
example model of the handbook in "star/test/" doesn't work, giving the same
error.

thanks,
Tuguldur

mesa-users] Problem installing release 2724

[Michael P. <mpa...@gm...>]

I was trying to install MESA yesterday (with gfortran if that matters)
and it failed the net_19_to_ni56 test. It seems like it was somehow
deleted in the new release. I switched to release 2699 and everything
worked out fine.

-- 
Michael

mesa-users] post-processing mesa models

[Georgios M. <gma...@nd...>]

  Dear mesa users,

I am interested in post-processing mesa models which have been evolved 
from ZAMS to pre-collapse with a network such as approx21.net. I am not 
sure yet to what detail I want to follow the trajectories, so I thought 
starting with a couple of test runs to see what kind of results I get.

I have a one-zone burner which I intend to use for the post-processing. 
I was wondering if any user has already been involved in post-processing 
mesa trajectories, and could recommend a method employed. I understand 
that possible critical information regarding mixing will be lost, which 
is something hard to avoid when post-processing. I am particularly 
interested to figure out a way to deal with the zone refinement from 
model to model. Your feedback is mostly appreciated. Thank you.

Georgios Magkotsios

Re: mesa-users] Using the Opacity Preprocessor

[Aaron D. <aar...@gm...>]

Hello Nathan,

Depending on the version of gfortran you're using, you may find that it is
unwilling to pass the name of a function as an argument.  I compiled it
successfully using gcc version 4.4.4 20100630 (Red Hat 4.4.4-10).  My read
of the gfortran specs is that this will not work with version 4.4 or earlier
but should work with 4.5 or later.

The easiest way to get around this issue--assuming you don't want or need to
use the plot program--is to remove or comment out references to "PLOTTER" in
kap/preprocessor/make/makefile.

Aaron


On Thu, Oct 7, 2010 at 12:46 AM, Nathan Lee Thompson <
nlt...@wi...> wrote:

>
> Hello,
>
> My name is Nathan Thompson. I am a graduate student at Wichita State
> University. When I was trying to use the opacity preprocessor to generate
> kappa tables for MESA to use, I received a complier error:
>
> Error: Internal procedure 'f_for_logrho' is not allowed as an actual
> argument at (1)
> ../src/plot.f:377.12:
>
>            f_for_logRho, x1, x3, y1, y3, imax, epsx, epsy, lrpar, rpar,
> lipar,
>            1
> Error: Internal procedure 'f_for_logrho' is not allowed as an actual
> argument at (1)
> make: *** [plot.o] Error 1
>
> I am running kubuntu and using gfortran to compile MESA. I attempted to
> find the relevant lines in the makefile script to comment out to subvert the
> issue, but to no avail. Some detailed instructions on getting this to work
> would be very helpful.
>
> Thanks,
> Nathan
>
>
>
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mesa-users] Using the Opacity Preprocessor

[Nathan L. T. <nlt...@wi...>]

Hello,

My name is Nathan Thompson. I am a graduate student at Wichita State University. When I was trying to use the opacity preprocessor to generate kappa tables for MESA to use, I received a complier error:

Error: Internal procedure 'f_for_logrho' is not allowed as an actual argument at (1)
../src/plot.f:377.12:

            f_for_logRho, x1, x3, y1, y3, imax, epsx, epsy, lrpar, rpar, lipar,
            1
Error: Internal procedure 'f_for_logrho' is not allowed as an actual argument at (1)
make: *** [plot.o] Error 1

I am running kubuntu and using gfortran to compile MESA. I attempted to find the relevant lines in the makefile script to comment out to subvert the issue, but to no avail. Some detailed instructions on getting this to work would be very helpful.

Thanks,
Nathan

mesa-users] On getting pgplot to work

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

For those with problems getting PGPLOT compiled and the demos run:

I compiled pgplot with ifort in order to be compatible with compiler I
used for the mesa modules. When using ifort, make sure that
ifortvars.sh is sourced; i.e. that the machine knows where to find the
ifort libraries:

source /opt/intel/Compiler/11.1/073/bin/ifortvars.sh ia32

(or whereever your compiler is located (to find out, try "whereis
ifortvars.sh")

after having successfully compiled and linked the pgplot package in
/usr/local/pgplot in my case and having placed the libraries of pgplot
in /usr/local/lib I tried to run pgplot with mkxwin:

the contents of my mkxwin was:

ifort pgdemo_xwin.f -o demo -L/usr/local/lib -lpgplot -L/usr/X11R6/lib -lX11

then doing the following:

pgplot > ./mkxwin
pgplot > ./demo

resulted in:

./demo: error while loading shared libraries: libpgplot.so.0: cannot
open shared object file: No such file or directory

even though:

pgplot > whereis libpgplot.so.0
libpgplot.so: /usr/local/lib/libpgplot.so.0 /usr/local/lib/libpgplot.so


To remedy the above problem, proceed as described in the README file in
mesa/utils/pglot: set the following environment variables in the
appropriate ...rc file (in my case, I placed it in .bashrc)

export DISPLAY=":0"
export PGPLOT_DEV=/xwin
export PGPLOT_DIR=/usr/local/lib
export PGPLOT_FONT=/usr/local/bin/grfont.dat

*in addition* to what is written in the README file, I also set

export LD_LIBRARY_PATH=/usr/local/lib

(this is explained e.g. at the website:
  http://www.astro.caltech.edu/~tjp/pgplot/faq.html)

the last line, referring to LD_LIBRARY_PATH, must point correctly
to the place where libpg.so is stored (in my case /usr/local/lib).

So, after that you might enjoy playing with stars and seeing  
"real-time" plots.
The Mesa idea is really great! Thanks!

mesa-users] mesa 2691 is current as of 2010-10-02

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

This is just FYI.   No need to update if things are working fine for you at present.
But if you have been waiting for me to change something for you, give 2691 a try.

-Bill

mesa-users] weird performance collapse for mesa with gfortran on mac

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

Just for a change, I'll ask a question on mesa-users rather than try to give an answer.

I've run into a mystery with gfortran on my mac.  My usual compiler is ifort,
but once in a while I run something using gfortran just to check.  Up until recently
there was a small difference in performance -- gfortran was perhaps 25% slower
on average.   But yesterday, I ran a small test, and the runtime for gfortran mesa
was bizarre -- more than 20 times slower!   I checked the Activity Monitor and
discovered that with gfortran, mesa was spending almost all of its time in system
calls -- whereas with ifort and in the old days with gfortran the system time is tiny.

This is a mac problem -- I did the same comparision of ifort and gfortran on a linux
machine and found only a small difference in performance (same as I used to 
see on the mac).

I'm running the gfortran 4.5.1 release, and I upgraded to Xcode 3.2.3 recently.
Perhaps the new Xcode is the problem?

If anyone has seen a similar degradation in performance, I'd like to know.
And if you've figured out a solution, I'd really like to know.

If you are a student and run into this, you might want to switch to ifort.
Intel offers a "Intel® Software Development Suite Student Edition for Mac OS"
for only $49 -- it includes ifort.

http://software.intel.com/en-us/articles/intel-academic-developer-program/#compilers

Thanks,
Bill

Re: mesa-users] a question about MESA

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

Hi,

One small item to add concerning overshooting in MESA star
There is an option not mentioned in the paper to do a step function instead of the usual exponential.

Here are the relevant lines from star_defaults.dek

         
         ! optional step function for overshooting to be used in place of exponential
         overshoot_step_fraction = 0 ! use this if > 0
         
            ! as above, f0*Hp determines r0 where switch from convection to overshooting.
            ! D0 = diffusion coefficient D at point r0
            ! Hp0 = the scale height at r0.
            ! overshooting extends a distance f*Hp0 from r0
            ! with constant diffusion coef D = overshoot_step_fraction*D0
         


-Bill





On Sep 16, 2010, at 6:33 AM, Aaron Dotter wrote:

> Dear Masanobu,
> 
> Thanks for your question.  
> 
> Today I am writing to ask about adequate parameters of Overshooting like " overshoot_f_..." and "mass_for_overshoot_...".  I'm using version 2258 of MESA, but I don't know and couldn't find the parameters I should use.  Would you tell me generally adequate parameters for Overshooting?
> 
> My first suggestion would be that you read the MESA "instrument paper" that recently appeared on astro-ph!  
> 
> http://arxiv.org/abs/1009.1622
> 
> It contains a description of the overshoot mixing in MESA/star and plenty of references on how the method is implemented and what values of the overshoot_f_* are recommended for different boundaries (and evolutionary phases).
>  
> Moreover, I want to use same treatment for Overshooting with Girardi. If you know the parameters to do so, would you tell me also those?
> 
> There isn't a simple answer to this question.  MESA/star treats overshoot mixing in a very different manner from the Padova group in a couple of ways: (1) MESA/star treats convective mixing as a time-dependent, diffusive process and (2) the overshoot diffusion coefficient is modeled as an exponential decay of the diffusion coefficient at the convective boundary.  Many (but not all) other codes treat convective regions as instantaneously mixed and overshoot as an "all or nothing" approach, where the extent of the overshoot region is fully mixed with the adjoining convective region.
> 
> Best wishes,
> Aaron
> 
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