[mesa-users] MESA_INLIST and clusters

Cyrus Zalian thebigkiwi2003 at yahoo.fr
Tue Dec 15 12:46:15 EST 2015


I've done everything manually (without using MESA_INLIST) launching each
run separately and it worked.

Here is the main inlist :

&star_job

    history_columns_file
='/home/zalian/xstudy/cluster/base/history_columns.list'
    profile_columns_file
='/home/zalian/xstudy/cluster/base/profile_columns.list'

    read_extra_star_job_inlist1 = .true.
    extra_star_job_inlist1_name =
'/home/zalian/xstudy/cluster/base/inlist_1'

    read_extra_star_job_inlist2 = .true.
    extra_star_job_inlist2_name = 'inlist_cluster'



/ ! end of star_job namelist


&controls

    read_extra_controls_inlist1 = .true.
    extra_controls_inlist1_name =
'/home/zalian/xstudy/cluster/base/inlist_1'

    read_extra_controls_inlist2 = .true.
    extra_controls_inlist2_name = 'inlist_cluster'



/ ! end of controls namelist


&pgstar

    read_extra_pgstar_inlist1 = .true.
    extra_pgstar_inlist1_name = '/home/zalian/xstudy/cluster/base/inlist_1'

    read_extra_pgstar_inlist2 = .true.
    extra_pgstar_inlist2_name = 'inlist_cluster'

/ ! end of pgstar namelist



2015-12-15 11:37 GMT+01:00 Robert Farmer <rjfarmer at asu.edu>:

> Hmm, this works for me as is.
>
> Can you send the MESA_INLIST file as well?
>
> Rob
>
> On Sun, Dec 13, 2015 at 9:21 PM, Cyrus Zalian <thebigkiwi2003 at yahoo.fr>
> wrote:
>
>> Thank you very much ! It's now "working" (well not really, see below).
>> For those who will face the same problem, remember to recompile the files
>> before running it.
>>
>> Now I have the following error message :
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> * WARNING: requested initial_z does not match zams file
>> initial_z.                                    zams file initial_z
>> 2.0000000000000000D-02                                    requested
>> initial_z    1.0000000000000000D-04 failed in get_zams_model star_load_zams
>> ierr          -1 do_load1_star ierr          -1 before_evolve_loop
>> ierr          -1*
>> The problem is that, I don't ask for a zams star in my inlists :
>>
>>    - This is the inlist specific for each mass :
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> *&star_job  / ! end of star_job namelist&controls initial_mass= 5       /
>> ! end of controls namelist*
>>
>>    - Here is my main inlist in base :
>>
>> ! 1st part : creates pre main-sequence star (pre_MS)
>>
>> &star_job
>>
>>   ! begin with a pre-main sequence model
>>     create_pre_main_sequence_model = .true.
>>
>>     pre_ms_T_c = 3e5 ! use for M>= 0.2 Mo initial center temperature
>> (below 1d6)
>>
>>     eos_file_prefix = 'mesa'
>>     kappa_file_prefix = 'gs98'
>>
>>     change_net = .true. ! switch nuclear reaction network
>>     new_net_name = 'pp_extras.net'
>>
>>   ! save a model at the end of the run
>>     save_model_when_terminate = .true.
>>     save_model_filename = 'pre_MS.mod'
>>
>>   ! display on-screen plots
>>     pgstar_flag = .false.
>>
>> / !end of star_job namelist
>>
>>
>> &controls
>>
>>   ! starting specifications
>>     !initial_mass = 0.5 ! in Msun units : to be changed
>>     initial_Z = 0.0001 ! metallicity : to be changed
>>     initial_Y = 0.2499 ! supposing X = 0.75
>>
>>     mixing_length_alpha = 1.5d0
>>
>>     max_age = 100 ! years ! a bit after fully convective
>>
>> / ! end of controls namelist
>>
>> Once again, thanking everyone who could help...
>>
>> 2015-12-13 19:26 GMT+01:00 Robert Farmer <rjfarmer at asu.edu>:
>>
>>> Okay, sorry there is a bug, my mistake. A quick fix for your case is to
>>> edit $MESA_BASE/src/run.f and replace the line
>>>
>>> inlist_fname = 'inlist'
>>> with
>>> inlist_fname='' ! Empty single quotes
>>>
>>> And make sure MESA_INLIST is set to the correct file (otherwise MESA
>>> will run with the default inlist options without throwing an error)
>>>
>>> Rob
>>>
>>>
>>> On Sun, Dec 13, 2015 at 1:11 PM, Cyrus Zalian <thebigkiwi2003 at yahoo.fr>
>>> wrote:
>>>
>>>> Thank you for your answer,
>>>>
>>>> Ok, so I'm stuck, and I have no idea why it's not working. Here is the
>>>> error message :
>>>>
>>>>
>>>>
>>>> *Failed to open control namelist file inlistierr from read_star_job
>>>> inlist*
>>>> Here is the bash file used :
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> *#!/bin/bash##OAR -n mesaMass#OAR --notify  mail:cyrus.zalian at oca.eu
>>>> <mail%3Acyrus.zalian at oca.eu>echo "mon hostname : " `hostname`echo
>>>> "OAR_JOB_NAME : $OAR_JOB_NAME"echo "OAR_JOB_ID : $OAR_JOB_ID"echo
>>>> "OAR_ARRAY_ID : $OAR_ARRAY_ID"echo "OAR_ARRAY_INDEX :
>>>> $OAR_ARRAY_INDEX"export MESASDK_ROOT=/home/zalian/mesasdksource
>>>> $MESASDK_ROOT/bin/mesasdk_init.shexport
>>>> MESA_DIR=/home/zalian/mesa-r7624export OMP_NUM_THREADS=1export
>>>> GYRE_DIR=$MESA_DIR/gyre/gyreexport
>>>> PGPLOT_FONT=/home/zalian/mesasdk/pgplot/grfont.dat#$MESASDK_ROOT/pgplot/pgxwin_server&export
>>>> MESA_BASE="/home/zalian/xstudy/cluster/base"export
>>>> MESA_INLIST="/home/zalian/xstudy/cluster/base/inlist"export
>>>> MESA_RUN="/home/zalian/xstudy/cluster/Z0.0001"#CD to foldercd
>>>> $MESA_RUN/$OAR_ARRAY_INDEXecho -n processing $OAR_ARRAY_INDEX ...#Run
>>>> MESA$MESA_BASE/starecho ..done*
>>>>
>>>>
>>>> And finally here is the file directory :
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
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>>>>
>>>>
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>>>>
>>>>
>>>>
>>>> *[zalian at hal cluster]$ pwd;ls -R/home/zalian/xstudy/cluster.:base
>>>> cluster.oar  OAR.mesaMass.9029.stderr  OAR.mesaMass.9029.stdout
>>>> Z0.0001./base:clean    history_columns.list  inlist_1  inlist_project
>>>> LOGS  mk      png                   re      restart_photo  script
>>>> stargyre.in <http://gyre.in>  inlist                inlist_2
>>>> inlist_re2      make  photos  profile_columns.list  README  rn
>>>> src./base/LOGS:./base/make:makefile  run.o  run_star_extras.mod
>>>> run_star_extras.o  run_star.mod
>>>> run_star.o./base/photos:./base/png:./base/src:run.f
>>>> run_star_extras.f./Z0.0001:1  2  3  4  5  6
>>>> 7./Z0.0001/1:inlist_cluster./Z0.0001/2:inlist_cluster./Z0.0001/3:inlist_cluster./Z0.0001/4:inlist_cluster./Z0.0001/5:inlist_cluster./Z0.0001/6:inlist_cluster./Z0.0001/7:inlist_cluster*
>>>> Thanking you all in advance for your help.
>>>> Cyrus.
>>>>
>>>> 2015-12-13 12:04 GMT+01:00 Robert Farmer <rjfarmer at asu.edu>:
>>>>
>>>>> It does work as long as you have a mesa version > 6995
>>>>>
>>>>> Rob
>>>>> On Dec 13, 2015 10:27, "Cyrus Zalian" <thebigkiwi2003 at yahoo.fr> wrote:
>>>>>
>>>>>> Hello to everybody,
>>>>>>
>>>>>> I'm trying to run mesa on clusters following the instructions I've
>>>>>> found in :
>>>>>> http://mesastar.org/tools-utilities/mesa-on-clusters/structuring-inlists-for-running-many-mesa-models
>>>>>>
>>>>>> The problem is that I keep on receving a error message saying that
>>>>>> there is no inlist file. So, first of all, I was wondering if the
>>>>>> MESA_INLIST variable works.
>>>>>>
>>>>>> Thanking you in advance.
>>>>>> Cyrus.
>>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------------------------
>>>>>>
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>>>>>>
>>>>>>
>>>>
>>>>
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>>>
>>
>>
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>
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