You are here: Home / FAQ & tutorials / Frequently Asked Questions

Frequently Asked Questions

Table of Contents


Downloading MESA


Q
: When trying to download the SDK using wget, I get the error

403: Forbidden

A: Our web server is set up to reject requests from wget. As a workaround, add the flag --user-agent="" to your wget invocation.

 

Compiling with the SDK


General Issues


Q
: I'm getting compilation errors of the form:

Fatal Error: Wrong module version '7' (expected '5')

A: Such errors typically arise because you have upgraded the gfortran compiler since you last built MESA. To fix, run ./clean in the MESA directory, and then try building again.


Q: I'm getting compilation errors of the form:

/usr/bin/ld: cannot find -lX11
/usr/bin/ld: cannot find -lz

A: Have you properly installed the X windows and Z compression libraries, as specified in the SDK pre-requisites (see here for Linux, and here for Mac OS X)?

 

Q: I'm getting compilation errors of the form:

libpng warning: Application built with libpng-1.2.10 but running with 1.5.6
PGPLOT /png: error in libpng while writing file...

A: This is a known problem, caused by the pgplot library being compiled with the wrong libpng headers. It was fixed in the 20120727 release of the SDK; if you are using an older release, please upgrade.

 

Q: I'm getting compilation errors of the form:

../private/utils_isnan_okay.f:43.36:

        is_real_inf = (2*x==x .and. x /= 0)
                                   1
Warning: Inequality comparison for REAL(4) at (1)

A: This is a known issue with the 20130320 (and later) releases of the SDK, caused by the upgrade to gfortran 4.8.0.  To fix, add the flags '-Wno-compare-reals' to the end of the definition of the FCwarn variable in mesa/utils/makefile_header.

 

Q: I'm getting compilation errors of the form:

../private/utils_dict.f:429.41:

        integer, parameter :: multiplier = 31
                                        1
Warning: Unused parameter 'multiplier' declared at (1)

A: This is a known issue with the 20130320 (and later) releases of the SDK, caused by the upgrade to gfortran 4.8.0.  To fix, add the flags '-Wno-unused-parameter' to the end of the definition of the FCwarn variable in mesa/utils/makefile_header.

 

Platform-Specific Issues - Ubuntu Linux


Q
: On Ubuntu Linux I encounter these errors during compilation:

/usr/bin/ld: cannot find crt1.o: No such file or directory
/usr/bin/ld: cannot find crti.o: No such file or directory
collect2: error: ld returned 1 exit status

A: This is a known problem, caused by Ubuntu's use of non-standard installation locations. It was fixed in the 20120727 release of the SDK; if you are using an older release, please upgrade.

 

Q: On Ubuntu linux I encounter the error that 

/opt/mesasdk/lib/gcc/i686-pc-linux-gnu/4.7.0/include-fixed/features.h:338:25: fatal error: sys/cdefs.h: No such file or directory compilation terminated.
make: *** [btf_order.o] Error 1

A: This is a known problem, caused by Ubuntu's use of non-standard installation locations. It was fixed in the 20120727 release of the SDK; if you are using an older release, please upgrade.

 

Platform-Specific Issues - Red Hat Enterprise Linux


Q
: On Red Hat Enterprise Linux (RHEL) I encounter this error during compilation:

gfortran: /lib/libc.so.6: version `GLIBC_2.11' not found (required by gfortran)

A: This is a known problem, caused by the SDK being compiled with a more-recent version of the GNU C Library (GLIBC) than is installed on RHEL systems. It was fixed in the 20120120 release of the SDK; if you are using an older release, please upgrade.

 

Platform-Specific Issues - Mac OS X


Q
: On OS X I encounter this error during compilation:

Re: dyld: unknown required load command 0x80000022

A: This problem likely stems from trying to use the SDK on an older version of OS X (10.4 Tiger or 10.5 Leopard), as these have difficulty running 64-bit executables. Please contact Rich Townsend for further support.


Q: On OS X 10.8 I find an error such as

dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address

  Referenced from: /usr/local/lib/libgomp.1.dylib

  Expected in: /usr/lib/libSystem.B.dylib

This is a run-time error.  It shows up, for example, in the output of a module test such as const/test/tmp.txt.

A: It has been found that it may be necessary to add both the mesasdk/lib directory (i.e., $MESASDK_ROOT/lib) and /usr/local/lib to your DYLD_LIBRARY_PATH.

Empirical evidence suggests that these should appear first and second, respectively, in that path.

 

Q: How do I install the command-line tools needed by the SDK for OS X 10.9?

A: After installing the Xcode app, you need to open a terminal window and type

  xcode-select —install

A dialog box, asking if you would like to install the tools, should appear.

 

Q: I tried to compile MESA on OS X 10.9, and I got the following error

/usr/bin/awk: can't open file ../ndiff/share/lib/ndiff/ndiff-2.00/ndiff.awk
source line number 1 source file ../ndiff/share/lib/ndiff/ndiff-2.00/ndiff.awk

A: This means ndiff didn't compile correctly, most likely because the command-line tools weren't installed.  See the previous question.


PGPlot and MESA

 

Q: I'm not seeing any PGPLOT output when I run MESA.

A: Make sure you have the option pgstar_flag = .TRUE. in the &star_job section of your input file. Also, if you're not using the SDK, make sure you enabled PGPLOT in your utils/makefile_header file (when using the SDK, PGPLOT is enabled by default).

 

Using the MESA User Forum

 

Q: What is the MESA User Forum intended to be used for?

A: The main goal of the MESA User Forum is to offer a place for MESA users to share

The MESA User Forum is semi-moderated, in the sense that MESA councils plans to keep an eye on the evolution of this resource and may provide the guidance needed to ensure usefulness to a wide range of users.

As we are in the formative phase of this web source we appreciate any feedback, via e-mail to Edward Brown [ebrown at pa.msu.edu] or Falk Herwig [fherwig at uvic.ca]

 

Q: How do I add my refereed results to the mesastar.org forum?

A: Sharing knowledge in the form of inlists and technical details of your refereed published results is part of the requirements of fair use set out in the manifesto: open knowledge to match open source. You can find a Template folder in the Published results & inlists directory. Use the menu 'Actions' to copy the entire folder, and go to a suitable sub-directory. If your results absolutely do not fit into any of the categories already provided, consider creating a new one. Then edit the copy of the Template folder. One paper per folder, that means put all results into that one folder. We would like to As you can see from the Template folder we would like to get as a minimum the following information:

  • inlist and version of MESA
  • if additional modules were used, consider publishing them
  • if applicable: short statement on any technical peculiarities, for example extra modules, how and why multiply inlist were required
  • link to preprint or refereed paper

 Use 'categories' (see 2nd level menu at top) to help other people find your results. When you are done change the state (top right menu) to 'Submit for publication' and the colour will change to orange. We will have a quick check to make sure the entry technically works. There is no editorial work done on the content. We will then release the entry and the state will change to "Published".

If you have a question mail to the mesa user list mail, Edward Brown [ebrown at pa.msu.edu] or Falk Herwig [fherwig at uvic.ca].

Once your entry is published consider letting the other mesa users know by sending a message to mesa-users at lists.sourceforge.net.


Q: I have an idea for a project but I need some help and I would like to find a collaborator? Is the forum the right place to do that?

A: Absolutely yes. In fact, the forum is the place to go. There you find a category 'Ideas & marketplace'. Either you find already a forum in there that covers your idea thematically, then you just start a new conversation in there. If not, propse to add a new Forum for your theme in "Proposing/discussing new forums" in the "Organisation of this site" Forum.

 

The SourceForge repository change of March 2013

 

SourceForge.net switched to a new platform in late 2012 and required all projects to migrate to it.  MESA migrated in March 2013.

The most significant change for typical users will be that the MESA svn repository has a new URL.  The MESA project webpage "getting started" section has been updated to reflect the change.

The simplest way to keep up to date with MESA is to check out a new copy from the new repository; it's as simple as that.

If you maintain a working copy of MESA under version control for development purposes, you'll need to do something akin to "svn relocate" from the old repository to the new.  If you have svn version 1.6 or lower, then use "svn switch --relocate" instead.  See 'svn help relocate' (v1.7 and up) or 'svn help switch' (v1.6 and lower).

Don't just copy/paste the below commands.  First, run 'svn info' in your MESA directory to make sure that you have the correct URL for the old repository.

(svn 1.7 and above) svn relocate http://mesa.svn.sourceforge.net/svnroot/mesa/trunk svn://svn.code.sf.net/p/mesa/code/trunk

(svn 1.6 and below) svn switch --relocate http://mesa.svn.sourceforge.net/svnroot/mesa/trunk svn://svn.code.sf.net/p/mesa/code/trunk

Finally, if you use a version control program other than svn, see the sourceforge advice page here:

http://sourceforge.net/p/forge/community-docs/Repository%20Upgrade%20FAQ/

That should be all you need to know.  If you have any questions about this process, please send an email to mesa-users.

 

Running MESA on a 32-bit OS, such as ubuntu 12.04

 
If a computer you intend to run MESA on was made in the 5 years or so (maybe more), then chances are it has a 64-bit processor.  64-bit processors generally are able to run either a 32- or a 64-bit OS.
 
A 32-bit OS has a physical address space of 2^32 = 4 GB.  It's not too difficult to run afoul of this limit with MESA, even if your computer has more than 4 GB of RAM installed (because of the OS limitation).  There is something built into many 32-bit OSes, called physical address extension (PAE), that allows it to see more than 4 GB of RAM.  (See http://en.wikipedia.org/wiki/Physical_Address_Extension for more info.)  But your OS has to be running a kernel with PAE enabled.
 
Up to and including ubuntu 12.04, which is a very common version in use today, Canonical recommended the 32-bit version (without PAE).  Canoncal has some information about this on their webpage (https://help.ubuntu.com/community/EnablingPAE).  Starting with their most recent release, 12.10, their recommendation is the 64-bit version.  Most other linux distros have been offering the 64-bit version right alongside the 32-bit version for the last few years.  Mac OS X has been 64-bit since about 2008, near as I can tell.
 
A 64-bit OS has physical address space of 2^64 = 16 exabytes.  Try filling that up with EOS tables!
 
In summary, running MESA on a 32-bit OS without PAE will likely lead to problems going forward.  Running a 64-bit OS will eliminate any such problems and make full use of your processor.