Re: [bug-gnuastro] Sorry, false alarm on make crashes

[Mohammad Akhlaghi]

Hi Christopher,

On 12/01/2016 03:38 PM, Christopher Willmer wrote:
> When I run configure with
>
>  ./configure --prefix=/home/cnaw/bin LDFLAGS=-L/home/cnaw/bin/lib
> CPPFLAGS=-I/home/cnaw/bin/include
>
> make runs perfectly; I got this tip from the manual. Is this a piece of
> information that would be appropriate to add in the INSTALL file ?

I agree. It would be great if the INSTALL file could have this 
information. Currently, this file is not written by us (Gnuastro 
developers), it is imported from Autoconf (the program that generates 
the `./configure' script) during bootstrapping:

https://www.gnu.org/software/gnuastro/manual/html_node/Bootstrapping.html

So, instead of re-writing or modifying this file, I thought of fully 
describing this information in the manual instead:

https://www.gnu.org/software/gnuastro/manual/html_node/Installation-directory.html
(this is probably the page you checked, put here just as a reference.)

We can work on a generic patch to this file (and discuss `LDFLAGS' and 
`CPPFLAGS') to send to the Autoconf developers. In this way, they can 
add it to the upstream `INSTALL' file and all programs that use Autoconf 
can benefit. It is indeed strange that these two important environment 
variables aren't discussed there.

To be honest, after writing that thorough explanation in the link above, 
I don't have the time to do this now, if you can do it, or know anyone 
who can, it would be great.

> Following on, make check  passes 44 tests, skips 1 (fitstopdf.sh, because
> I am not using the latest gs) and fails 3, all with segmentation faults:
>
> FAIL: imgcrop/wcscat.sh
> =======================
>
> ./imgcrop/wcscat.sh: line 56: 12053 Segmentation fault      (core dumped)
> $execname $cat $img --suffix=_wcscat.fits --zeroisnotblank --numthreads=1
> FAIL imgcrop/wcscat.sh (exit status: 139)
>
> FAIL: imgcrop/radec.sh
> ======================
>
> ./imgcrop/radec.sh: line 52: 12150 Segmentation fault      (core dumped)
> $execname $img --ra=0.99917157 --dec=1.0008283 --wwidth=0.3
> --output=imgcrop_radec.fits
> FAIL imgcrop/radec.sh (exit status: 139)
>
> FAIL: imgcrop/wcspolygon.sh
> ===========================
>
> ./imgcrop/wcspolygon.sh: line 52: 12220 Segmentation fault      (core
> dumped) $execname $img --wcsmode --zeroisnotblank --output=wcspolygon.fits
> --polygon=0.99980497,1.0001967:0.998378,1.0012267:0.9999766,1.0013217
> FAIL imgcrop/wcspolygon.sh (exit status: 139)

These are the three tests that use WCS coordinates as inputs for 
ImageCrop (to crop regions in an image), the other tests use image 
coordinates. I guess the easiest way to pinpoint the source of the 
problem would be to use Valgrind. Could you try the following steps when 
ever you have some free time:


1. If you don't have Valgrind, could you install it? It must be 
available in the CentOS package manager.


2. Configure Gnuastro while adding the following options for no shared 
libraries, with debugging flags, and with no optimization so Valgrind 
can report the status accurately:

$ ./configure --disable-shared CFLAGS="-g -O0"
(this is also described in 
https://www.gnu.org/software/gnuastro/manual/html_node/Building-and-debugging.html 
)


3. These test scripts are located in `tests/imgcrop/XXX.sh' (from the 
top source directory), could you open them with a text editor and modify 
the last line so it starts like this (the `...' represent the rest of 
the line):

valgrind --leak-check=yes $execname ...


4. Run `make' and `make check'.


5. The `tests/test-suite.log' file should contain the detailed Valgrind 
outputs.


I am so sorry to ask for taking these steps (and taking your time). I 
have defined task #14258 to make it much more easier in the future.

https://savannah.gnu.org/task/index.php?14258

Thanks again for your patience with Gnuastro and reporting these issues,
Cheers,
Mohammad