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

Re: mesa-users] Regarding the MESA EOS

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

Hi Ricky,

Actually, the eos module works with Pgas, see mesa/eos/public/eos_def.f for
a list of variables that it works with.

So, for example, the eos call that returns P(Rho,T) = eosDT_get actually
returns Pgas.  See also mesa/eos/public/eos_lib.f for a list of different
eos subroutines.  A function called Radiation_Pressure(T) is included in
eos_lib as a convenience.

Best wishes,
Aaron




On Mon, Feb 22, 2010 at 1:25 AM, Ricky Olivier <ol...@sa...> wrote:

> Hi,
>
> I am interested in using the MESA EOS and Opacity modules for use with
> my stellar pulsation code. As such, I have been poking around the MESA
> source files, and hacked the sample_eos.f source file to generate EOS
> tables in the format I need. However, it seems the MESA EOS routines
> automatically add the contribution due to radiation  into the
> thermodynamic variables. I could easily subtract the contribution to
> radiation out, but is there a way of switching it off inside MESA? I
> treat  radiation separately from the gas in the code I use.
>
> Can anyone help me with this?
>
> Regards,
> Ricky
>
>
>
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mesa-users] Regarding the MESA EOS

[Ricky O. <ol...@sa...>]

Hi,

I am interested in using the MESA EOS and Opacity modules for use with 
my stellar pulsation code. As such, I have been poking around the MESA 
source files, and hacked the sample_eos.f source file to generate EOS 
tables in the format I need. However, it seems the MESA EOS routines 
automatically add the contribution due to radiation  into the 
thermodynamic variables. I could easily subtract the contribution to 
radiation out, but is there a way of switching it off inside MESA? I 
treat  radiation separately from the gas in the code I use. 

Can anyone help me with this?

Regards,
Ricky

Re: mesa-users] Compiling latest MESA release - svn 1943

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

On Dec 14, 2009, at 1:00 PM, Marcin @ astrophysics wrote:

> I use ifort 11.0

I've had to upgrade to 11.1 -- 11.0 was failing for me too for some  
reason.

Could you perhaps get 11.1?

-Bill

mesa-users] Compiling latest MESA release - svn 1943

[Marcin @ a. <ast...@o2...>]

Hi Bill,

I have a problem with compiling latest mesa release.

I use ifort 11.0. Compilation stops at kap module.
To be sure I was compiling a fresh installation I deleted all subfolders 
in /mesa/data and I ran ./clean and ./install again. It did not work
Please, take a look at an attached compilation log. Test_output and 
tmp.txt files are also included.

Could you advise me what might be causing the test problem?

Best regards

Marcin Mackiewicz

Re: mesa-users] Compiling MESA EOS and OPACITY modules

[NORHASLIZA B. Y. <nor...@pe...>]

Hello,
Hi Ricky,

I suggest you download the code using svn instead of tar file. As
Bill suggested, try the new gfortran, for my case, I upgraded the
whole system, gcc and gfortran 4.3.0 (previously I used ubuntu 8.04,
then the same problem happen and I upgraded using ubuntu 9.04 where
it come with gfortran 4.3.0 I think) and it works smoothly without
any error.

Hope it helps.

Cheers,

Liza

Quoting Ricky Olivier <ol...@sa...> on Mon, 14 Dec 2009
17:42:09 +0200:

> Hi Bill,
>
> Tried that already. Even deleted the mesa root directory and
recreated
> it from the original tarball. Still no luck ...
>
> Ricky
>
>
>
> Bill Paxton wrote:
>> Hi,
>>
>> Let's try again with gfortran.
>> To ensure that everything has been
>> recompiled with the new compiler,
>> remove the old stuff and then
>> redo the entire install by doing this:
>>
>> cd mesa
>> ./clean
>> ./install
>>
>> Once you have completed a normal install,
>> the eos and kap tables will have been created
>> automatically, so let's focus on the install
>> for now.
>>
>> Bill
>>
>>
>>
>>
>>
>> On Dec 14, 2009, at 6:18 AM, Ricky Olivier wrote:
>>
>>> Dear Bill,
>>>
>>> Thanks for the info. I upgraded to gfortran 4.5.0 and still it
hangs.
>>> It seems to hang at the following compilation line:
>>>
>>> gfortran -fopenmp -o ../tester test_superlu.o test_sparskit.o
>>> test_mtx.o -L../../make -lmtx -L../../../lib  -lmesalapack
-lmesablas
>>> -lutils -lalert
>>>
>>> On another point, I looked through all the directories, and I
still
>>> don't find the eos and kap tables anywhere. Thanks to both you
and
>>> Aaron's  responses so far.
>>>
>>> Ricky
>>>
>>> Bill Paxton wrote:
>>>> Hi Ricky,
>>>>
>>>> The "infinite hang" symptom has happened in the past with
>>>> older versions of gfortran.  So, my first suggestion is to
>>>> try again with the most recent gfortran version --
>>>> for example, I'm using 4.5.0 without problems.
>>>> you can get gfortran binaries to download at
>>>> http://gcc.gnu.org/wiki/GFortran
>>>>
>>>> -Bill Paxton
>>>>
>>>>
>>
>
>
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Norhasliza Yusof
Dept of Physics
University of Malaya
50603 Kuala Lumpur
MALAYSIA
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Re: mesa-users] Compiling MESA EOS and OPACITY modules

[Ricky O. <ol...@sa...>]

I got the file from the original sourceforge page 
http://sourceforge.net/projects/mesa/

I'll try svn now. Probably need to install svn first

Thanks for all the help! Hope this sorts it out.

R.

Bill Paxton wrote:
>
> On Dec 14, 2009, at 7:42 AM, Ricky Olivier wrote:
>
>> recreated it from the original tarball
>
> Did you start from a current svn checkout?
> svn co -r 1943 https://mesa.svn.sourceforge.net/svnroot/mesa/trunk mesa
>
> -B
>
>
>
>
>
>
>
>

Re: mesa-users] Compiling MESA EOS and OPACITY modules

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

On Dec 14, 2009, at 7:42 AM, Ricky Olivier wrote:

> recreated it from the original tarball

Did you start from a current svn checkout?
svn co -r 1943 https://mesa.svn.sourceforge.net/svnroot/mesa/trunk mesa

-B

Re: mesa-users] Compiling MESA EOS and OPACITY modules

[Ricky O. <ol...@sa...>]

Hi Bill,

Tried that already. Even deleted the mesa root directory and recreated 
it from the original tarball. Still no luck ...

Ricky



Bill Paxton wrote:
> Hi,
>
> Let's try again with gfortran.
> To ensure that everything has been
> recompiled with the new compiler,
> remove the old stuff and then
> redo the entire install by doing this:
>
> cd mesa
> ./clean
> ./install
>
> Once you have completed a normal install,
> the eos and kap tables will have been created
> automatically, so let's focus on the install
> for now.
>
> Bill
>
>
>
>
>
> On Dec 14, 2009, at 6:18 AM, Ricky Olivier wrote:
>
>> Dear Bill,
>>
>> Thanks for the info. I upgraded to gfortran 4.5.0 and still it hangs. 
>> It seems to hang at the following compilation line:
>>
>> gfortran -fopenmp -o ../tester test_superlu.o test_sparskit.o 
>> test_mtx.o -L../../make -lmtx -L../../../lib  -lmesalapack -lmesablas 
>> -lutils -lalert
>>
>> On another point, I looked through all the directories, and I still 
>> don't find the eos and kap tables anywhere. Thanks to both you and 
>> Aaron's  responses so far.
>>
>> Ricky
>>
>> Bill Paxton wrote:
>>> Hi Ricky,
>>>
>>> The "infinite hang" symptom has happened in the past with
>>> older versions of gfortran.  So, my first suggestion is to
>>> try again with the most recent gfortran version --
>>> for example, I'm using 4.5.0 without problems.
>>> you can get gfortran binaries to download at
>>> http://gcc.gnu.org/wiki/GFortran
>>>
>>> -Bill Paxton
>>>
>>>
>

Re: mesa-users] Compiling MESA EOS and OPACITY modules

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

Hi,

Let's try again with gfortran.
To ensure that everything has been
recompiled with the new compiler,
remove the old stuff and then
redo the entire install by doing this:

cd mesa
./clean
./install

Once you have completed a normal install,
the eos and kap tables will have been created
automatically, so let's focus on the install
for now.

Bill





On Dec 14, 2009, at 6:18 AM, Ricky Olivier wrote:

> Dear Bill,
>
> Thanks for the info. I upgraded to gfortran 4.5.0 and still it  
> hangs. It seems to hang at the following compilation line:
>
> gfortran -fopenmp -o ../tester test_superlu.o test_sparskit.o  
> test_mtx.o -L../../make -lmtx -L../../../lib  -lmesalapack - 
> lmesablas -lutils -lalert
>
> On another point, I looked through all the directories, and I still  
> don't find the eos and kap tables anywhere. Thanks to both you and  
> Aaron's  responses so far.
>
> Ricky
>
> Bill Paxton wrote:
>> Hi Ricky,
>>
>> The "infinite hang" symptom has happened in the past with
>> older versions of gfortran.  So, my first suggestion is to
>> try again with the most recent gfortran version --
>> for example, I'm using 4.5.0 without problems.
>> you can get gfortran binaries to download at
>> http://gcc.gnu.org/wiki/GFortran
>>
>> -Bill Paxton
>>
>>

Re: mesa-users] Compiling MESA EOS and OPACITY modules

[Ricky O. <ol...@sa...>]

Dear Bill,

Thanks for the info. I upgraded to gfortran 4.5.0 and still it hangs. It 
seems to hang at the following compilation line:

gfortran -fopenmp -o ../tester test_superlu.o test_sparskit.o test_mtx.o 
-L../../make -lmtx -L../../../lib  -lmesalapack -lmesablas -lutils -lalert

On another point, I looked through all the directories, and I still 
don't find the eos and kap tables anywhere. Thanks to both you and 
Aaron's  responses so far.

Ricky

Bill Paxton wrote:
> Hi Ricky,
>
> The "infinite hang" symptom has happened in the past with
> older versions of gfortran.  So, my first suggestion is to
> try again with the most recent gfortran version --
> for example, I'm using 4.5.0 without problems.
> you can get gfortran binaries to download at
> http://gcc.gnu.org/wiki/GFortran
>
> -Bill Paxton
>
>

Re: mesa-users] Compiling MESA EOS and OPACITY modules

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

Hi Ricky,

The "infinite hang" symptom has happened in the past with
older versions of gfortran.  So, my first suggestion is to
try again with the most recent gfortran version --
for example, I'm using 4.5.0 without problems.
you can get gfortran binaries to download at
http://gcc.gnu.org/wiki/GFortran

-Bill Paxton

Re: mesa-users] Compiling MESA EOS and OPACITY modules

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

Hi Enrico,

The MESA physics modules, like eos and kap, require the numerics,
interpolation, and some other basic modules.

To compile the eos and kap modules, you first need to run the
'install_numerics_only' script, then compile the chem module.

In general, you can check which modules are required by either checking the
order in which the modules are compiled in the main install script or
grepping for 'use' in the source files in the module you want to compile.

When you checkout MESA for the first time, the data files are stored in the
module to which they belong.  For example, the opacity tables are stored in
kap/kap_data.tar.bz2.  When you run the main install script, it will unpack
these files and put them where they belong.  In which case, it might make
the most sense to run the main install script even if you don't want to
compile the entire package because it sets everything up for later use.

To check what has been compiled, you can look in include/ and lib/, where
each module will have a *.mod and lib* file, respectively.

Anyway, I hope this helps!


Aaron

mesa-users] Compiling MESA EOS and OPACITY modules

[Ricky O. <ol...@sa...>]

Hi,

Thanks to those who responded to my earlier message. Aaron, I tried what 
you suggested, but now the compilation proceeds to a point where it just 
hangs. I waited over 4 hours and still not finished. Seems to get stuck 
somewhere.

Anyways I am just interested at the moment in using the EOS and OPACITY 
modules in my linear and non-linear pulsation code.I tried to compile 
these separately and just end up with the following:


ricky@rickylapvm:~/mesa_1.1.1/eos$ ./install
gfortran  -fopenmp -I../public -I../../include -Wunused-value 
-Wuninitialized -Werror -W -fimplicit-none   -O2 -c -ffixed-form 
-ffixed-line-length-132 ../private/eos_eval.f
../private/eos_eval.f:1096.132:

                                                                          
                                                                          
1                                                        
Fatal Error: Can't open module file 'num_lib.mod' for reading at (1): No 
such file or directory
make: *** [eos_eval.o] Error 1

/home/ricky/mesa_1.1.1/eos/make
FAILED


Any ideas? Where is num_lib.mod located? By the way, I don't think I got 
the actual data tables either. Where can I find these? I just downloaded 
the tarball of the SourceForge.net site.

Thank you.

Regards,
Enrico

Re: mesa-users] Installation Problem: "Function 'isnan' at (1) has no IMPLICIT type"

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

Hi Enrico,

You need to edit the file utils/makefile_header:

# step 2) specify whether isnan is supported or not

# pick one of the following options:

UTILS_ISNAN = utils_isnan_okay
#UTILS_ISNAN = utils_isnan_nope

# If you aren't sure, try setting UTILS_ISNAN = utils_isnan_okay
# If this works, great.  Otherwise, the compilation of the
# mesa/utils module will complain when it tries to invoke isnan.
# In case that happens, you can simply change this makefile_header
# to the UTILS_ISNAN = utils_isnan_nope setting and redo the
# ./install command for mesa.

By default, the relevant section looks like the above.  Change the
UTILS_ISNAN line by commenting out the first and uncommenting the second,
like this:


#UTILS_ISNAN = utils_isnan_okay
UTILS_ISNAN = utils_isnan_nope

This should solve your problem; please let us know if it does not.

Aaron

mesa-users] Installation Problem: "Function 'isnan' at (1) has no IMPLICIT type"

[Ricky O. <ol...@sa...>]

Hi,

I got the following problem when trying to install MESA:

/home/ricky/mesa_1.1.1/utils
building utils package.

gfortran  -fopenmp -I../public -I../../include -Wunused-value 
-Wuninitialized -Werror -W -fimplicit-none   -O2 -c -ffree-form 
../private/utils_isnan_okay.f
../private/utils_isnan_okay.f:38.29:

         check_for_bad_num = isnan(x) .or. is_inf(x)
                            1
Error: Function 'isnan' at (1) has no IMPLICIT type
make: *** [utils_isnan_okay.o] Error 1

/home/ricky/mesa_1.1.1/utils/make
FAILED

Could anyone please advise as to what the problem is maybe? I installed 
ndiff-2.00 and the latest version of MESA on sourceforge.net (as of 
today 10 Dec. 2009).

Regards,
Enrico

mesa-users] MESA test failure on installation

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

Hello Bill. I have decided to use MESA for my research, and like some 
previous first time users, I had a test failure by ndiff during 
installation. I have seen a similar message in the list with your 
response, so I'll try to provide as much more information to you.

To begin with, I had to install ndiff. I want MESA installed at one of 
the afs cells of my university, where of course I have no root 
privileges. So for the ndiff installation I did something like

./configure --prefix=(some folder where I have access)
make all
make install

Make all was successful, but make install gave me an error. However, I 
got the ndiff binary, and it seems to be working fine. After that I put 
the ndiff binary to my path.

Then I got the MESA release 1822 by doing an svn in my "MESA directory" 
as you call it in your web page (~/MESA for my case)

svn co -r 1822 https://mesa.svn.sourceforge.net/svnroot/mesa/trunk ./

I use the intel 11 compiler for fortran. I believe the "which ifort" 
result will give you all the info you need

/afs/crc.nd.edu/x86_64_linux/intel/11.0/074/bin/intel64/ifort

I put some extra options for fortran in makefile_header. Specifically,

SPECIAL_FC_FLAGS = -align all #-L/opt/crc/hdf/intel/hdf5/lib 
-lhdf5_fortran -lhdf5 -lm

I put align all just in case there are some pointless warnings regarding 
some common blocks (something I used to see in another code I use), and 
for the moment I keep the options for hdf5 commented out. I plan to make 
some changes to MESA, where I'll need to export data in hdf5 format.

Although the first time I did not do a ./clean prior to ./install, I did 
the second time I tried. The error message was the same for both cases. 
That is

eval_equ
first file is short
11c11
<  nvar /= s% nvar
--- field 7
 >        0.500000   -1.389511   -0.350759   11.088481    3.589636    
1.903144    0.907085

/afs/crc.nd.edu/user/g/gmagkots/MESA/star/test
TEST FAILED -- compare test_output to tmp.txt

 From the MESA/star/test folder, I do a diff and an ndiff. What I get is

$ diff test_output tmp.txt
11,13c11
<        0.500000   -1.389511   -0.350759   11.088481    3.589636    
1.903144    0.907085
<        1.000000   -0.136118   -0.048875   10.136118    3.752045    
1.881756    1.352341
<
---
 >  nvar /= s% nvar

and

$ ndiff test_output tmp.txt
11c11
<        0.500000   -1.389511   -0.350759   11.088481    3.589636    
1.903144    0.907085
--- field 7
 >  nvar /= s% nvar
second file is short

So the problem is that test_output has two lines of data for M/Msun etc, 
while tmp.txt has the line  "nvar /= s% nvar" instead of the data. I 
hope this description of the problem is adequate enough. Thank you in 
advance for your response.

Georgios

Re: mesa-users] parallel usage of MESA...

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

Hi Ehsan,

MESA supports OpenMP parallelism.

There are compiler flags for openmp;
the standard default in utils/makefile_header
is to enable OpenMP, but you might want
to double check.

For ifort, you should find:
FCopenmp = -openmp -threads

For gfortran,
FCopenmp = -fopenmp


At runtime, the openmp implementation checks
an environment variable to see how many
threads to use.   On my dual core Mac,
I set this to 2.  On a qual-core server, you might
set it to 4 or even 8.  Depending on your shell,
the command looks something like this:

setenv OMP_NUM_THREADS 2


Finally, to get the most benefit, it helps to reduce
the IO since it is a bottleneck for parallelism.
For mesa/star, this means limiting the frequency
of writing info to log files.   My default is

       photostep = 50
       profile_interval = 50
       log_cnt = 5

You can of course reduce these to increase the
frequency of log entries during interesting events.

Hope that helps!

Cheers,
Bill




On Sep 21, 2009, at 7:35 AM, Ehsan Moravveji wrote:

>
> Dear MESA users,
> Hi. I'm Ehsan, and quite new to MESA.
> I remember to read somewhere either in the manual, or the webpage  
> that it
> supports parallel computing. However, I do not remember how to  
> activate
> this option.
> Anyone to help me with that?
> Thanks.
>
> -- 
> Moravveji, Ehsan.
> Ph.D student of Astrophysics.
> Institute for Advanced Studies in Basic Sciences (IASBS).
> Gavazang Road, Zanjan, Iran. P.O. Box: 45195-1159
>
> Office: (+98)241-415 2212
> Fax:    (+98)241-415 2104
> http://iasbs.ac.ir/students/moravveji
>
>
> ------------------------------------------------------------------------------
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Re: mesa-users] parallel usage of MESA...

[Falk H. <fh...@uv...>]

Mesa is shared memory OpenMP parallel.

During compile time the parallel option is switched on by default. See  
for example

FCopenmp = -openmp -threads

in utils/makefile_header.


At runtime the environment variable OMP_NUM_THREADS is providing the  
number of threads that the OpenMP application can use. For example, add

  export OMP_NUM_THREADS=4

to you .bashrc if you run on a quad-core machine and want to use all  
cores.


On Sep 21, 2009, at 7:35 AM, Ehsan Moravveji wrote:

> I remember to read somewhere either in the manual, or the webpage  
> that it
> supports parallel computing.

--
Falk Herwig
Dept of Physics & Astronomy, U of Victoria
fh...@uv..., tel: +1 (250) 721-7743

--------------------------------------------------
I support http://www.rainforestsos.org

mesa-users] parallel usage of MESA...

[Ehsan M. <mor...@ia...>]

Dear MESA users,
Hi. I'm Ehsan, and quite new to MESA.
I remember to read somewhere either in the manual, or the webpage that it
supports parallel computing. However, I do not remember how to activate
this option.
Anyone to help me with that?
Thanks.

-- 
Moravveji, Ehsan.
Ph.D student of Astrophysics.
Institute for Advanced Studies in Basic Sciences (IASBS).
Gavazang Road, Zanjan, Iran. P.O. Box: 45195-1159

Office: (+98)241-415 2212
Fax:    (+98)241-415 2104
http://iasbs.ac.ir/students/moravveji

Re: mesa-users] test failed during compilation

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

Hi Jason,

Glad you're looking into using mesa.   Sorry that the initial build  
failed.
It seems that getting everything setup right the first time is a  
challenge
for everyone.

First question: which gfortran?  If you don't have a recent version,
that could be a problem.  I get binaries for the mac from this site:

http://gcc.gnu.org/wiki/GFortranBinaries

Second question: which mesa?  what svn version number?
The number of the most recent "approved" version can be found here:

http://mesa.sourceforge.net/getting_started.html

Third: what did you do, exactly?

The installation dance goes like this:
	cd mesa
	./clean
	./install

You do clean and install from the top-level mesa directory.

In your case, things are probably fine for all of those items --
so let's dig into the details.   The checks are done for each
module by doing 'ndiff' of an expected output versus the
actual output.  The expected is in 'test_output'; the actual
is in "tmp.txt" -- all of this is in the module test directory of  
course.

/Users/nordhaus/Physics/Codes/mesa/utils/test
TEST FAILED -- compare test_output to tmp.txt

So, what do you find when you look at those files?
In particular, what's in tmp.txt?  That might give a clue
about what's wrong.

Let me know what you find.....

Cheers,
Bill

BTW: please sign up for the mesa-users mailing list before posting.
http://mesa.sourceforge.net/mailing_lists.html





On Sep 17, 2009, at 6:49 AM, Jason Nordhaus wrote:

> Hi,
>
> I'm trying to compile mesa on mac os 10.6 using gfortran and have
> encountered a "test failed" during compilation.  I'm not sure what is
> causing this, has anyone encountered it before?  It looks like utils/
> test/test_output is different from utils/test/tmp.txt.  Here's the
> relevant part during compilation.  Any help is much appreciated!
>
> Jason
>
> make: `libutils.a' is up to date.
> gfortran -fopenmp -o ../tester test_utils.o -L../../make -lutils -
> L../../../lib -lalert
>
> first file is short
> 35c35
> <  eof_token
> --- field 3
>> name_token           3 fin
> 36c36
> <
> --- field 1
>> eof_token
> 37c37
> <  done test_token_read
> --- field 2
>>
> 38c38
> <
> --- field 2
>> done test_token_read
>
> /Users/nordhaus/Physics/Codes/mesa/utils/test
> TEST FAILED -- compare test_output to tmp.txt
>
>
> ------------------------------------------------------------------------------
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mesa-users] test failed during compilation

[Jason N. <nor...@as...>]

Hi,

I'm trying to compile mesa on mac os 10.6 using gfortran and have  
encountered a "test failed" during compilation.  I'm not sure what is  
causing this, has anyone encountered it before?  It looks like utils/ 
test/test_output is different from utils/test/tmp.txt.  Here's the  
relevant part during compilation.  Any help is much appreciated!

Jason

make: `libutils.a' is up to date.
gfortran -fopenmp -o ../tester test_utils.o -L../../make -lutils - 
L../../../lib -lalert

first file is short
35c35
<  eof_token
--- field 3
 >  name_token           3 fin
36c36
<
--- field 1
 >  eof_token
37c37
<  done test_token_read
--- field 2
 >
38c38
<
--- field 2
 >  done test_token_read

/Users/nordhaus/Physics/Codes/mesa/utils/test
TEST FAILED -- compare test_output to tmp.txt

Re: mesa-users] problem with running MESA

[Marcin @ a. <ast...@o2...>]

Hi Miroslav,

I haven't seen such an error message before. Maybe someone else could 
help you with it.

However your Fedora 8 seems to be slightly old OS.
I use Fedora 10 with ifort 11 and latest official mesa release compiles 
and runs with no errors, so far.
If it's possible, please try Fedora 10.

Best regards

Marcin Mackiewicz





Miroslav Mocak wrote:
> Dear MESA users,
>
>   I have a problem with running the latest version of
> MESA compiled by ifort (version 11) compiler on my machine which has
> the Intel I7 processor and runs Fedora 8. After
> instalation (which went ok), I tried to run the default
> problem in the /mesa/star/test directory by ./rn, but the
> code stopped by giving me the following message 
> nvar /= s% nvar eval_equ . Could you help me to resolve
> the issue? Thanks. Below you'll find the whole text output
> which I get until the code stops.
>
> Regards
> Miro
>
> ./rn
> Wed Sep  9 15:29:15 CEST 2009
>  loading eos data
>  loading kap data
>  finished loading
>
>
>  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),
>       'lg_Teff' is log10 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 and 
> neutrinos (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 <= 0.37E+00
>       'He_poor' is the core mass where helium abundance is <= 0.47E+00
>       '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,
>       'max_avg' is the star total mass fraction of the heaviest isotope,
>       '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,
>       'jacs' is the number of jacobians created in 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.
>
>  load starting model from ../starting_models
>
>
> __________________________________________________________________________________________________________________________________________________
>
>        step    lg_Tcntr    lg_Teff    lg_LH     lg_Lnuc     Mass       
> H_rich     H_cntr     N_cntr     X_surf     X_avg     eta_cntr   pts  retry
>    lg_dt_yr    lg_Dcntr   lg_Rsurf    lg_L3a    lg_Lneu     lg_Mdot    
> H_poor     He_cntr    O_cntr     Z_surf     Y_avg     gam_cntr  jacs  bckup
>      age_yr    lg_Pcntr    lg_L       lg_LZ     lg_Psurf    lg_Dsurf   
> He_poor    C_cntr     Ne_cntr    Z_cntr     Z_avg     max_avg      dt_limit
> __________________________________________________________________________________________________________________________________________________
>
>  nvar /= s% nvar
> eval_equ
>
>
>   

mesa-users] problem with running MESA

[Miroslav M. <mm...@ul...>]

Dear MESA users,

  I have a problem with running the latest version of
MESA compiled by ifort (version 11) compiler on my machine which has
the Intel I7 processor and runs Fedora 8. After
instalation (which went ok), I tried to run the default
problem in the /mesa/star/test directory by ./rn, but the
code stopped by giving me the following message 
nvar /= s% nvar eval_equ . Could you help me to resolve
the issue? Thanks. Below you'll find the whole text output
which I get until the code stops.

Regards
Miro

./rn
Wed Sep  9 15:29:15 CEST 2009
 loading eos data
 loading kap data
 finished loading


 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),
      'lg_Teff' is log10 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 and 
neutrinos (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 <= 0.37E+00
      'He_poor' is the core mass where helium abundance is <= 0.47E+00
      '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,
      'max_avg' is the star total mass fraction of the heaviest isotope,
      '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,
      'jacs' is the number of jacobians created in 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.

 load starting model from ../starting_models


__________________________________________________________________________________________________________________________________________________

       step    lg_Tcntr    lg_Teff    lg_LH     lg_Lnuc     Mass       
H_rich     H_cntr     N_cntr     X_surf     X_avg     eta_cntr   pts  retry
   lg_dt_yr    lg_Dcntr   lg_Rsurf    lg_L3a    lg_Lneu     lg_Mdot    
H_poor     He_cntr    O_cntr     Z_surf     Y_avg     gam_cntr  jacs  bckup
     age_yr    lg_Pcntr    lg_L       lg_LZ     lg_Psurf    lg_Dsurf   
He_poor    C_cntr     Ne_cntr    Z_cntr     Z_avg     max_avg      dt_limit
__________________________________________________________________________________________________________________________________________________

 nvar /= s% nvar
eval_equ


-- 

----------------------------------------------------------------------------------------------------

      Miroslav Mocak

      Institut d'Astronomie et d'Astrophysique
      Université Libre de Bruxelles
      Campus De La Plaine
      CP 226 - Boulevard Du Triomphe
      B-1050 Bruxelles - BELGIUM

      -- -- -- --  -- -- -- -- -- -- -- -- --  -- -- -- -- -- -- -- --

       http://www-astro.ulb.ac.be/~mocak/

      -- -- -- --  -- -- -- -- -- -- -- -- --  -- -- -- -- -- -- -- --

       Understanding is, after all, what science is all about - and science
      is a great deal more than mere mindless computation (Roger Penrose)

----------------------------------------------------------------------------------------------------

Re: mesa-users] "bad composition in setup for kap builder"

[Petar T. <pet...@ob...>]

Hello again,

a similar problem (with a similar resolution :) ) is appearing one more
time in kap_support.f, but this time in the Get_Results subroutine: right
at the beginning, just after the declaration block, you test Y for being
negative:

     Y = 1 - (X+Zbase+XC+XO)
     if (Y < 0) then ! adjust XC and XO

But sometimes the line before the 'if' test was giving to Y the value of
~-1e-17. So am I wrong changing the condition in this way:

          if (Y < -1d-9) then ! adjust XC and XO

Regards,
--Petar

Re: mesa-users] "bad composition in setup for kap builder"

[Petar T. <pet...@ob...>]

Hello Bill,

Thank you for your fast reply! That was exactly the problem: Zbase+X+XC+XO
is getting some training ones at some iterations.

> BTW: what system & compiler are you using?

I'm using gfortran 4.3 on Ubuntu 9.04 (jaunty), with Intel Celeron 1.5 GHz
and 512MB of RAM (I needed a 1GB swap partition in order to have memory to
create EOS tables)

Regards,
Petar