mesa-users

[mesa-users] can't run pgplot with mesa with gfortran on mac

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

Hi,

I just tried to run pgplot with with mesa/star after recompiling both mesa and pgplot with 4.6.1 on my mac.
pgplot runs the /XWIN demo fine, but when i try to run it with star I get this as soon as it starts up:


star(64896,0x7fff70fa8cc0) malloc: *** error for object 0x10a804208: incorrect checksum for freed object - object was probably modified after being freed.
*** set a breakpoint in malloc_error_break to debug
./re: line 13: 64896 Abort trap              ./star


Any ideas?

Thanks,
Bill

Re: [mesa-users] can't run pgplot with mesa with gfortran on mac

[Max K. <ka...@rp...>]

I can confirm that I've seen a very similar issue using gfortran 4.6.1 on
Ubuntu with version 36** (it points to malloc upon crashing when pgstar is
activated, but the demos also ran fine for me), but haven't been able to
track down the problem at all.

Max Katz
Rensselaer Polytechnic Institute
M.S. Physics, 2011


On Thu, Oct 6, 2011 at 6:18 PM, Bill Paxton <pa...@ki...> wrote:

> Hi,
>
> I just tried to run pgplot with with mesa/star after recompiling both mesa
> and pgplot with 4.6.1 on my mac.
> pgplot runs the /XWIN demo fine, but when i try to run it with star I get
> this as soon as it starts up:
>
>
> star(64896,0x7fff70fa8cc0) malloc: *** error for object 0x10a804208:
> incorrect checksum for freed object - object was probably modified after
> being freed.
> *** set a breakpoint in malloc_error_break to debug
> ./re: line 13: 64896 Abort trap              ./star
>
>
> Any ideas?
>
> Thanks,
> Bill
>
>
>
>
>
> ------------------------------------------------------------------------------
> All the data continuously generated in your IT infrastructure contains a
> definitive record of customers, application performance, security
> threats, fraudulent activity and more. Splunk takes this data and makes
> sense of it. Business sense. IT sense. Common sense.
> http://p.sf.net/sfu/splunk-d2dcopy1
> _______________________________________________
> mesa-users mailing list
> mes...@li...
> https://lists.sourceforge.net/lists/listinfo/mesa-users
>

[mesa-users] Using Tioga

[Roni W. <ron...@gm...>]

Hi,

I have been using MESA for I while now, and I wanted to start plotting using
Tioga.
I installed Tioga apparently successfully. Ran ruby ts_Tioga.rb and worked
well.
I ran the sample test_suite/15M_dynamo.
I try to run e.g. ruby history_by_step.rb in the directory star_history of
the above run.
I get an output saying:
Read ../LOGS/star.log
Age 819048.300....

But, no output plot is created.

Obviously I'm doing something basically wrong.

Thanks for any help.

Roni

[mesa-users] Fwd: Using Tioga

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

Hi Roni,

Good to hear from you!

On Oct 9, 2011, at 2:19 AM, Roni Waldman wrote:

> Obviously I'm doing something basically wrong.

you need to use the "tioga" command instead of just plain "ruby"
if the install worked okay, you should be able to get a brief "help"
just by typing tioga at the command line.  It outputs the following.
Let me know if you have problems.

Cheers,
Bill




/Users/bpaxton/mesa: tioga

This program is a command line interface for the open-source tioga kernel.
The tioga kernel is for creating figures and plots using Ruby, PDF, and TeX.
Following is a brief description of the tioga command line options.
For more information, visit http://theory.kitp.ucsb.edu/~paxton/tioga.html.

Before any command line information is processed, tioga runs ~/.tiogainit if it exists.
   The primary use of this file is to set your default pdf viewer command (see below).

If there are no command line arguments, or the argument is -h, this help info is output.

Otherwise, the command line should start with a tioga file name (with extension .rb).
    Since the extension is known, you can skip typing it if you like.

The remainder of the command line should consist of an optional series of control commands
   followed by a figure command.

Any control commands are done after ~/.tiogainit and before the figure file is loaded.
    -r file      runs the file (using Ruby's require method).
    -C dir       changes the working directory.
                 If there is no -C command, tioga changes the working directory to the
                 location of the figure file .
    -v           prints version information.

The figure command comes last and should be one of these:
    -l           output a list of the defined figures by number and name.
    -<num>       make and show figure with index equal <num> (0 <= num < num_figures).
    -m <figs>    make PDFs without showing them in the viewer.
    -s <figs>    make and show PDFs, each in a separate viewer window.
    -p <figs>    make PDFs and show the portfolio as a multi-page document.

If the figure command is omitted, then it defaults to -0.

If <figs> is omitted, then tioga does all the figures defined in the file
    ordered by their definition index numbers.

Otherwise, <figs> must be either
    a defined figure name (as supplied to def_figure in the tioga file), or
    a valid ruby array index number for a figure (can be negative), or
    a valid ruby range specification selecting a sequence of figures, or
    a space-less, comma-separated list of figure indices and ranges.

    For example, -s Plot1 makes and shows the pdf for the figure named Plot1,
    and -p 5,0..3,-1 makes a portfolio with the figure having index 5 on page 1,
    followed by pages showing the figures with indices 0, 1, 2, 3, and -1.

The viewer for showing PDFs is specified by the $pdf_viewer variable in tioga.
    The default value can be set by creating a .tiogainit file in your home directory.
    The .tiogainit file is run before any command line options are processed.
    Your current setting for $pdf_viewer is repreview.
    To change it, edit ~/.tiogainit to add the line $pdf_viewer = 'my viewer command'.
    The command tioga uses to show a pdf is $pdf_viewer + ' ' + full_PDF_filename.
    You can use the -e control command to try a different viewer setting
    by doing the $pdf_viewer assignment from the command line.

Re: [mesa-users] Using Tioga

[Roni W. <ron...@gm...>]

Hi Bill,
Many thanks.
So now I got an HR plot.
How do I get other types of plots, e.g. a Kippenhahn plot?
Cheers,
Roni

> -----Original Message-----
> From: Bill Paxton [mailto:pa...@ki...]
> Sent: יום א 09 אוקטובר 2011 16:02
> To: Roni Waldman
> Subject: Re: [mesa-users] Using Tioga
> 
> Hi Roni,
> 
> Good to hear from you!
> 
> On Oct 9, 2011, at 2:19 AM, Roni Waldman wrote:
> 
> > Obviously I'm doing something basically wrong.
> 
> you need to use the "tioga" command instead of just plain "ruby"
> if the install worked okay, you should be able to get a brief "help"
> just by typing tioga at the command line.  It outputs the following.
> Let me know if you have problems.
> 
> Cheers,
> Bill
> 
> 
> 
> 
> /Users/bpaxton/mesa: tioga
> 
> This program is a command line interface for the open-source tioga
> kernel.
> The tioga kernel is for creating figures and plots using Ruby, PDF, and
> TeX.
> Following is a brief description of the tioga command line options.
> For more information, visit
> http://theory.kitp.ucsb.edu/~paxton/tioga.html.
> 
> Before any command line information is processed, tioga runs
> ~/.tiogainit if it exists.
>     The primary use of this file is to set your default pdf viewer
> command (see below).
> 
> If there are no command line arguments, or the argument is -h, this
> help info is output.
> 
> Otherwise, the command line should start with a tioga file name (with
> extension .rb).
>      Since the extension is known, you can skip typing it if you like.
> 
> The remainder of the command line should consist of an optional series
> of control commands
>     followed by a figure command.
> 
> Any control commands are done after ~/.tiogainit and before the figure
> file is loaded.
>      -r file      runs the file (using Ruby's require method).
>      -C dir       changes the working directory.
>                   If there is no -C command, tioga changes the working
> directory to the
>                   location of the figure file .
>      -v           prints version information.
> 
> The figure command comes last and should be one of these:
>      -l           output a list of the defined figures by number and
> name.
>      -<num>       make and show figure with index equal <num> (0 <= num
> < num_figures).
>      -m <figs>    make PDFs without showing them in the viewer.
>      -s <figs>    make and show PDFs, each in a separate viewer window.
>      -p <figs>    make PDFs and show the portfolio as a multi-page
> document.
> 
> If the figure command is omitted, then it defaults to -0.
> 
> If <figs> is omitted, then tioga does all the figures defined in the
> file
>      ordered by their definition index numbers.
> 
> Otherwise, <figs> must be either
>      a defined figure name (as supplied to def_figure in the tioga
> file), or
>      a valid ruby array index number for a figure (can be negative), or
>      a valid ruby range specification selecting a sequence of figures,
> or
>      a space-less, comma-separated list of figure indices and ranges.
> 
>      For example, -s Plot1 makes and shows the pdf for the figure named
> Plot1,
>      and -p 5,0..3,-1 makes a portfolio with the figure having index 5
> on page 1,
>      followed by pages showing the figures with indices 0, 1, 2, 3, and
> -1.
> 
> The viewer for showing PDFs is specified by the $pdf_viewer variable in
> tioga.
>      The default value can be set by creating a .tiogainit file in your
> home directory.
>      The .tiogainit file is run before any command line options are
> processed.
>      Your current setting for $pdf_viewer is repreview.
>      To change it, edit ~/.tiogainit to add the line $pdf_viewer = 'my
> viewer command'.
>      The command tioga uses to show a pdf is $pdf_viewer + ' ' +
> full_PDF_filename.
>      You can use the -e control command to try a different viewer
> setting
>      by doing the $pdf_viewer assignment from the command line.
> 
> 
> 

[mesa-users] can't compile sample.f

[<umb...@un...>]

Hi everyone,
I just downloaded Mesa and trying to install it. I followed all the  
instructions and I edited the makefile_header. As soon as I want to  
test all of that compiling sample.f file using Intel® Fortran Composer  
XE 2011 with Ubuntu 11.04 I have the following error:

ifort  -vec-report0 -traceback -error-limit 6 -fixed -132  
-I/home/umberto/mesa/include -c ../src/sample.f
../src/sample.f(24): error #7002: Error in opening the compiled module  
file.  Check INCLUDE paths.   [EOS_DEF]
       use eos_def
----------^
../src/sample.f(25): error #7002: Error in opening the compiled module  
file.  Check INCLUDE paths.   [EOS_LIB]
       use eos_lib
----------^
../src/sample.f(26): error #7002: Error in opening the compiled module  
file.  Check INCLUDE paths.   [CHEM_DEF]
       use chem_def
----------^
../src/sample.f(27): error #7002: Error in opening the compiled module  
file.  Check INCLUDE paths.   [CHEM_LIB]
       use chem_lib
----------^
../src/sample.f(148): error #7002: Error in opening the compiled  
module file.  Check INCLUDE paths.   [EOS_DEF]
          use eos_def
-------------^
../src/sample.f(149): error #7002: Error in opening the compiled  
module file.  Check INCLUDE paths.   [EOS_LIB]
          use eos_lib
-------------^
../src/sample.f(227): catastrophic error: Too many errors, exiting
compilation aborted for ../src/sample.f (code 1)
make: *** [sample.o] Error 1

Can anyone help me?
All the best,

  Umberto Battino

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Re: [mesa-users] can't compile sample.f

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

Hi Umberto,

What version of MESA is this?

Can you confirm that the module files exist in the place the compiler is
looking for them?

The error message is telling you that it can't find eos_def.mod and
eos_lib.mod in /home/umberto/mesa/include, which is where they should be if
the eos module compiled and exported correctly.

Aaron



On Wed, Oct 12, 2011 at 11:42 AM, <umb...@un...> wrote:

> Hi everyone,
> I just downloaded Mesa and trying to install it. I followed all the
> instructions and I edited the makefile_header. As soon as I want to
> test all of that compiling sample.f file using Intel® Fortran Composer
> XE 2011 with Ubuntu 11.04 I have the following error:
>
> ifort  -vec-report0 -traceback -error-limit 6 -fixed -132
> -I/home/umberto/mesa/include -c ../src/sample.f
> ../src/sample.f(24): error #7002: Error in opening the compiled module
> file.  Check INCLUDE paths.   [EOS_DEF]
>       use eos_def
> ----------^
> ../src/sample.f(25): error #7002: Error in opening the compiled module
> file.  Check INCLUDE paths.   [EOS_LIB]
>       use eos_lib
> ----------^
> ../src/sample.f(26): error #7002: Error in opening the compiled module
> file.  Check INCLUDE paths.   [CHEM_DEF]
>       use chem_def
> ----------^
> ../src/sample.f(27): error #7002: Error in opening the compiled module
> file.  Check INCLUDE paths.   [CHEM_LIB]
>       use chem_lib
> ----------^
> ../src/sample.f(148): error #7002: Error in opening the compiled
> module file.  Check INCLUDE paths.   [EOS_DEF]
>          use eos_def
> -------------^
> ../src/sample.f(149): error #7002: Error in opening the compiled
> module file.  Check INCLUDE paths.   [EOS_LIB]
>          use eos_lib
> -------------^
> ../src/sample.f(227): catastrophic error: Too many errors, exiting
> compilation aborted for ../src/sample.f (code 1)
> make: *** [sample.o] Error 1
>
> Can anyone help me?
> All the best,
>
>  Umberto Battino
>
> ----------------------------------------------------------------
> This message was sent using IMP, the Internet Messaging Program.
>
>
>
>
> ------------------------------------------------------------------------------
> All the data continuously generated in your IT infrastructure contains a
> definitive record of customers, application performance, security
> threats, fraudulent activity and more. Splunk takes this data and makes
> sense of it. Business sense. IT sense. Common sense.
> http://p.sf.net/sfu/splunk-d2d-oct
> _______________________________________________
> mesa-users mailing list
> mes...@li...
> https://lists.sourceforge.net/lists/listinfo/mesa-users
>

Re: [mesa-users] can't compile sample.f

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

Hi Umberto,

Glad you are ready to go now.  What sort of problems are you planning to try?
You might look in star/test_suite to see if there is something you can use as
an initial guide.    Don't hesitate to send questions to mesa-users, and don't
hesitate to answer questions you see there when you can!

Cheers,
Bill



On Oct 13, 2011, at 7:11 AM, umb...@un... wrote:

> Dear Bill, Ehsan and Aaron,
> thanks very much! Now all works correctly.. :)
> All the best.
> 
> Umberto
> 
> Quoting Bill Paxton <pa...@ki...>:
> 
>> 
>> On Oct 12, 2011, at 8:53 AM, umb...@un... wrote:
>> 
>>> Yes, I did it. I did ./install and all seemed to work except a final message saying
>>> 
>>> /home/umberto/mtx/test
>>> FAILED
>> 
>> 
>> Hi,
>> 
>> Please set the OMP_NUM_THREADS environment variable to the number of cores on your machine.
>> 
>> Thanks,
>> Bill
>> 
>> [Ehsan,  thanks for helping with this!!!]
>> 
>> 
>>> 
>>> 
>>> /home/umberto/mesa/mtx
>>> ./build_and_test FAILED
>>> 
>>> I tried to investigate about that but I don't know if it rapresent the main problem..
>>> 
>>> Umberto
>>> 
>>> Quoting Ehsan Moravveji <mor...@ia...>:
>>> 
>>>> 
>>>> <html><div>
>>>> Hi.
>>>> Can you first make clear you successfully installed mesa or
>>>> not?
>>>> did you do ./install in your main mesa directory?
>>>> Ehsan.
>>>> 
>>>>> Hi everyone,
>>>>> I just downloaded Mesa and trying to
>>>> install it. I followed all the
>>>>> instructions and I edited the
>>>> makefile_header. As soon as I want to
>>>>> test all of that compiling
>>>> sample.f file using Intel� Fortran Composer
>>>>> XE 2011 with
>>>> Ubuntu 11.04 I have the following error:
>>>>> 
>>>>> ifort
>>>> -vec-report0 -traceback -error-limit 6 -fixed -132
>>>>> 
>>>> -I/home/umberto/mesa/include -c ../src/sample.f
>>>>> 
>>>> ../src/sample.f(24): error #7002: Error in opening the compiled module
>>>>> file.  Check INCLUDE paths.   [EOS_DEF]
>>>>>      use
>>>> eos_def
>>>>> ----------^
>>>>> ../src/sample.f(25): error #7002:
>>>> Error in opening the compiled module
>>>>> file.  Check INCLUDE paths.
>>>> [EOS_LIB]
>>>>>      use eos_lib
>>>>> ----------^
>>>>> 
>>>> ../src/sample.f(26): error #7002: Error in opening the compiled module
>>>>> file.  Check INCLUDE paths.   [CHEM_DEF]
>>>>>      use
>>>> chem_def
>>>>> ----------^
>>>>> ../src/sample.f(27): error #7002:
>>>> Error in opening the compiled module
>>>>> file.  Check INCLUDE paths.
>>>> [CHEM_LIB]
>>>>>      use chem_lib
>>>>> ----------^
>>>>> 
>>>> ../src/sample.f(148): error #7002: Error in opening the compiled
>>>>> 
>>>> module file.  Check INCLUDE paths.   [EOS_DEF]
>>>>>         use
>>>> eos_def
>>>>> -------------^
>>>>> ../src/sample.f(149): error
>>>> #7002: Error in opening the compiled
>>>>> module file.  Check INCLUDE
>>>> paths.   [EOS_LIB]
>>>>>         use eos_lib
>>>>> 
>>>> -------------^
>>>>> ../src/sample.f(227): catastrophic error: Too
>>>> many errors, exiting
>>>>> compilation aborted for ../src/sample.f
>>>> (code 1)
>>>>> make: *** [sample.o] Error 1
>>>>> 
>>>>> Can
>>>> anyone help me?
>>>>> All the best,
>>>>> 
>>>>> Umberto
>>>> Battino
>>>>> 
>>>>> 
>>>> ----------------------------------------------------------------
>>>>> 
>>>> This message was sent using IMP, the Internet Messaging Program.
>>>>> 
>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>> ------------------------------------------------------------------------------
>>>>> All the data continuously generated in your IT infrastructure
>>>> contains a
>>>>> definitive record of customers, application
>>>> performance, security
>>>>> threats, fraudulent activity and more.
>>>> Splunk takes this data and makes
>>>>> sense of it. Business sense. IT
>>>> sense. Common sense.
>>>>> http://p.sf.net/sfu/splunk-d2d-oct
>>>>> _______________________________________________
>>>>> 
>>>> mesa-users mailing list
>>>>> mes...@li...
>>>>> https://lists.sourceforge.net/lists/listinfo/mesa-users
>>>>> 
>>>> 
>>>>> --
>>>>> This message has been scanned for viruses and
>>>>> dangerous content by MailScanner, and is
>>>>> believed to be
>>>> clean.
>>>>> 
>>>>> 
>>>> 
>>>> --
>>>> This message has been scanned for viruses and
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>>>> believed to be clean.
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>>>> 
>>> 
>>> 
>>> 
>>> ----------------------------------------------------------------
>>> This message was sent using IMP, the Internet Messaging Program.
>>> 
>>> 
>> 
>> 
> 
> 
> 
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> 
>