[mesa-users] Problems with MESA_DIR variable

Max Katz maxpkatz at gmail.com
Mon Mar 2 11:59:52 EST 2015 

You can get rid of the reference to that inlist entirely. All it does is
include the inlist_test_suite in the test_suite directory, and all *that *does
is to again set mesa_dir, which we don't want.

Max Katz
Department of Physics and Astronomy
Vice President, Graduate Student Organization
Stony Brook University
http://astro.sunysb.edu/mkatz/

On Mon, Mar 2, 2015 at 11:54 AM, Mairan Teodoro <mairan.teodoro at gmail.com>
wrote:

> Hi, all!
>
> As an update, setting the full path for the required file in inlist does
> not solve the problem. Below is the message I'm getting now.
>
> ###########################
> argus:high_mass mairan$ pwd
> /Users/mairan/MESA/mairan_models/high_mass
> argus:high_mass mairan$ ./mk
> gfortran -fopenmp -o ../star run_star_extras.o run_star.o  run.o
>  -L/Users/mairan/MESA/mesa-r7385/lib -lstar -lionization -latm -lcolors
> -lmlt -lnse -lnet -leos -lkap -lrates -lneu -lchem -linterp_2d -linterp_1d
> -lnum -lf2crlibm -lcrlibm -lmtx -lconst -lutils -lmesaklu
> `mesasdk_lapack_link` `mesasdk_blas_link` `mesasdk_pgplot_link`
> `mesasdk_se_link`
> argus:high_mass mairan$ ./rn
> DATE: 2015-03-02
> TIME: 11:52:11
>  open failed for $MESA_DIR/data/version_number
>  please check that mesa_dir is set correctly
>  failed in stardata_init
>  star_init ierr           2
>  before_evolve_loop ierr           2
> DATE: 2015-03-02
> TIME: 11:52:11
> argus:high_mass mairan$ more inlist
>
> &star_job
>
>         mesa_dir = '/Users/mairan/MESA/mesa-r7385'
>
>       read_extra_star_job_inlist1 = .true.
>       extra_star_job_inlist1_name =
> '/Users/mairan/MESA/mesa-r7385/star/test_suite/inlist_test_suite'
>
>       read_extra_star_job_inlist2 = .true.
>       extra_star_job_inlist2_name = 'inlist_high_mass'
>
> / ! end of star_job namelist
>
> &controls
>
>       read_extra_controls_inlist2 = .true.
>       extra_controls_inlist2_name = 'inlist_high_mass'
>
> / ! end of controls namelist
>
> argus:high_mass mairan$
> ###############################
>
>
> Thanks for any help!
> m.
>
> --
> Dr. Mairan Teodoro
>
> Research Associate
> Department of Physics
> Western Michigan University
> Kalamazoo MI 49008-5252 USA
> mairan.teodoro at wmich.edu
>
> Science Collaborator
> NASA Goddard Space Flight Center
> 8800 Greenbelt Rd.
> Greenbelt, MD 20771 USA
> Bldg. 34, Rm. 321, Code 667
> 301-286-6321
> mairan.teodoro at nasa.gov
> --
>
> On Mon, Mar 2, 2015 at 11:50 AM, Mairan Teodoro <mairan.teodoro at gmail.com>
> wrote:
>
>> Hi, Ehsan and Max!
>>
>> Thanks for your suggestions! Looks like Max solved part of the problem
>> with the MESA_DIR. Now, when running the 'high_mass' case, I get this error
>> message:
>>
>> ############################
>> argus:high_mass mairan$ pwd
>> /Users/mairan/MESA/mairan_models/high_mass
>> argus:high_mass mairan$ ./mk
>> gfortran -fopenmp -o ../star run_star_extras.o run_star.o  run.o
>>  -L/Users/mairan/MESA/mesa-r7385/lib -lstar -lionization -latm -lcolors
>> -lmlt -lnse -lnet -leos -lkap -lrates -lneu -lchem -linterp_2d -linterp_1d
>> -lnum -lf2crlibm -lcrlibm -lmtx -lconst -lutils -lmesaklu
>> `mesasdk_lapack_link` `mesasdk_blas_link` `mesasdk_pgplot_link`
>> `mesasdk_se_link`
>> argus:high_mass mairan$ ./rn
>> DATE: 2015-03-02
>> TIME: 11:45:34
>>  Failed to open control namelist file ../inlist_test_suite
>>  ierr from read_star_job inlist
>> STOP 1
>> DATE: 2015-03-02
>> TIME: 11:45:34
>> argus:high_mass mairan$
>> ############################
>>
>> The requested file lies in $MESA_DIR/star/test_suite/inlist_test_suite,
>> but the local inlist file is looking for it one folder above. Do I have to
>> set it to the full path?
>>
>> Thank you!
>> m.
>>
>> --
>> Dr. Mairan Teodoro
>>
>> Research Associate
>> Department of Physics
>> Western Michigan University
>> Kalamazoo MI 49008-5252 USA
>> mairan.teodoro at wmich.edu
>>
>> Science Collaborator
>> NASA Goddard Space Flight Center
>> 8800 Greenbelt Rd.
>> Greenbelt, MD 20771 USA
>> Bldg. 34, Rm. 321, Code 667
>> 301-286-6321
>> mairan.teodoro at nasa.gov
>> --
>>
>> On Mon, Mar 2, 2015 at 11:40 AM, Max Katz <maxpkatz at gmail.com> wrote:
>>
>>> I recently ran into an issue when using a recent version of MESA that
>>> the test_suite problems now include the line
>>>
>>> include ../../test_suite_makefile_prefix
>>>
>>>
>>> in the make/makefile. The sole effect of this source is to set
>>>
>>> MESA_DIR = ../../../..
>>>
>>>
>>> So I needed to comment out the reference to this include to get things
>>> working as expected when you copy a problem outside the MESA hierarchy.
>>>
>>> Max Katz
>>> Department of Physics and Astronomy
>>> Vice President, Graduate Student Organization
>>> Stony Brook University
>>> http://astro.sunysb.edu/mkatz/
>>>
>>> On Mon, Mar 2, 2015 at 11:09 AM, Ehsan Moravveji <e.moravveji at gmail.com>
>>> wrote:
>>>
>>>> Dear Mairan,
>>>> It is always advised not to run the test_suit examples from within your
>>>> source directory. Instead, you can copy them to wherever on your machine,
>>>> compile and run it.
>>>> A full instruction is given in part 1.2 of the following documentation
>>>> http://mesa.sourceforge.net/starting.html#toc-1-9
>>>>
>>>> Having successfully done that, you can set your MESA_DIR in three
>>>> different ways:
>>>> 1. to add to the first line in your /make/makefile file, e.g.
>>>>     MESA_DIR = /Users/me/somewhere/mesa-r7385
>>>> 2. the first control variable in the &star_job part of inlist is
>>>> "mesa_dir". You can find it in <mesa-root>/star/defalts/star_job.defaults
>>>>     then, in your local inlist, you can explicitly set it to wherever
>>>> path your root mesa directory sits, e.g.
>>>>     mesa_dir = /Users/me/somewhere/mesa-r7385
>>>> 3. the third is through setting it up in your ~/.bash_profile, followed
>>>> by sourcing it.
>>>>
>>>> I hope any of these (or a combo) helps you out.
>>>>
>>>> Best
>>>> Ehsan.
>>>>
>>>>
>>>> On Mon, Mar 2, 2015 at 4:48 PM, Mairan Teodoro <
>>>> mairan.teodoro at gmail.com> wrote:
>>>>
>>>>> Hi, all!
>>>>>
>>>>> I've just installed MESA on a Macbook Pro (OS X 10.10.2; I've got the
>>>>> successfully installed message at the end), and I'm trying to run some test
>>>>> suites. I have successfully ran the tutorial model and everything worked
>>>>> perfectly fine.
>>>>>
>>>>> However, when I try to run the 'high_mass' or the 'massive_rotating'
>>>>> test suites, I get error messages related (I believe) to the MESA_DIR
>>>>> variable. I have this variable set in my $HOME/.profile file but it seems
>>>>> that the code cannot find the files. For example, when trying to run the
>>>>> 'massive_rotating' test case, this is what I get:
>>>>>
>>>>> ##############################
>>>>> pcp072011pcs: mairan$ cd
>>>>> MESA/mesa-r7385/star/test_suite/massive_rotating/
>>>>> pcp072011pcs:massive_rotating mairan$ ./mk
>>>>> gfortran -fopenmp -o ../star run_star_extras.o run_star.o  run.o
>>>>>  -L../../../../lib -lstar -lionization -latm -lcolors -lmlt -lnse -lnet
>>>>> -leos -lkap -lrates -lneu -lchem -linterp_2d -linterp_1d -lnum -lf2crlibm
>>>>> -lcrlibm -lmtx -lconst -lutils -lmesaklu `mesasdk_lapack_link`
>>>>> `mesasdk_blas_link` `mesasdk_pgplot_link` `mesasdk_se_link`
>>>>> pcp072011pcs:massive_rotating mairan$ ./rn
>>>>> DATE: 2015-03-02
>>>>> TIME: 10:31:38
>>>>>  open failed for $MESA_DIR/data/version_number
>>>>>  please check that mesa_dir is set correctly
>>>>>  failed in stardata_init
>>>>>  star_init ierr           2
>>>>>  before_evolve_loop ierr           2
>>>>> DATE: 2015-03-02
>>>>> TIME: 10:31:38
>>>>> pcp072011pcs:massive_rotating mairan$ echo $MESA_DIR
>>>>> /Users/mairan/MESA/mesa-r7385
>>>>> pcp072011pcs:massive_rotating mairan$ pwd
>>>>> /Users/mairan/MESA/mesa-r7385/star/test_suite/massive_rotating
>>>>> pcp072011pcs:massive_rotating mairan$
>>>>> ##############################
>>>>>
>>>>> If I try to run the 'high_mass' test case, the error message is as
>>>>> follows:
>>>>>
>>>>> ##############################
>>>>> /Users/mairan/MESA/mesa-r7385/star/test_suite/high_mass
>>>>> pcp072011pcs:high_mass mairan$ ./mk
>>>>> gfortran -fno-range-check -fmax-errors=100  -fprotect-parens
>>>>> -fno-sign-zero -fopenmp -fbounds-check -Wuninitialized -Warray-bounds -g
>>>>> -ffree-form -x f95-cpp-input -I../../../../include
>>>>> -I/Applications/mesasdk/include -c ../src/run_star_extras.f
>>>>> gfortran -fno-range-check -fmax-errors=100  -fprotect-parens
>>>>> -fno-sign-zero -fopenmp -fbounds-check -Wuninitialized -Warray-bounds -g
>>>>> -ffree-form -x f95-cpp-input -I../../../../include
>>>>> -I/Applications/mesasdk/include -c ../../../../star/job/run_star.f
>>>>> gfortran -fno-range-check -fmax-errors=100  -fprotect-parens
>>>>> -fno-sign-zero -fopenmp -fbounds-check -Wuninitialized -Warray-bounds -g
>>>>> -ffree-form -x f95-cpp-input -I../../../../include
>>>>> -I/Applications/mesasdk/include -c ../src/run.f
>>>>> gfortran -fopenmp -o ../star run_star_extras.o run_star.o  run.o
>>>>>  -L../../../../lib -lstar -lionization -latm -lcolors -lmlt -lnse -lnet
>>>>> -leos -lkap -lrates -lneu -lchem -linterp_2d -linterp_1d -lnum -lf2crlibm
>>>>> -lcrlibm -lmtx -lconst -lutils -lmesaklu `mesasdk_lapack_link`
>>>>> `mesasdk_blas_link` `mesasdk_pgplot_link` `mesasdk_se_link`
>>>>> pcp072011pcs:high_mass mairan$ ./rn
>>>>> DATE: 2015-03-02
>>>>> TIME: 10:47:24
>>>>>  open failed for $MESA_DIR/data/version_number
>>>>>  please check that mesa_dir is set correctly
>>>>>  failed in stardata_init
>>>>>  star_init ierr           2
>>>>>  before_evolve_loop ierr           2
>>>>> DATE: 2015-03-02
>>>>> TIME: 10:47:24
>>>>> pcp072011pcs:high_mass mairan$
>>>>> ##############################
>>>>>
>>>>> Does anyone know how to fix this? Any help would be very appreciated.
>>>>>
>>>>> Best regards!
>>>>> m.
>>>>>
>>>>> --
>>>>> Dr. Mairan Teodoro
>>>>>
>>>>> Research Associate
>>>>> Department of Physics
>>>>> Western Michigan University
>>>>> Kalamazoo MI 49008-5252 USA
>>>>> mairan.teodoro at wmich.edu
>>>>>
>>>>> Science Collaborator
>>>>> NASA Goddard Space Flight Center
>>>>> 8800 Greenbelt Rd.
>>>>> Greenbelt, MD 20771 USA
>>>>> Bldg. 34, Rm. 321, Code 667
>>>>> 301-286-6321
>>>>> mairan.teodoro at nasa.gov
>>>>> --
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>> Dive into the World of Parallel Programming The Go Parallel Website,
>>>>> sponsored
>>>>> by Intel and developed in partnership with Slashdot Media, is your hub
>>>>> for all
>>>>> things parallel software development, from weekly thought leadership
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>>>>> mesa-users mailing list
>>>>> mesa-users at lists.sourceforge.net
>>>>> https://lists.sourceforge.net/lists/listinfo/mesa-users
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> Kind regards
>>>>
>>>> Ehsan Moravveji
>>>> http://moravveji.webs.com/
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Dive into the World of Parallel Programming The Go Parallel Website,
>>>> sponsored
>>>> by Intel and developed in partnership with Slashdot Media, is your hub
>>>> for all
>>>> things parallel software development, from weekly thought leadership
>>>> blogs to
>>>> news, videos, case studies, tutorials and more. Take a look and join the
>>>> conversation now. http://goparallel.sourceforge.net/
>>>> _______________________________________________
>>>> mesa-users mailing list
>>>> mesa-users at lists.sourceforge.net
>>>> https://lists.sourceforge.net/lists/listinfo/mesa-users
>>>>
>>>>
>>>
>>
>
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