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

From: Mohammad Akhlaghi
Subject: Re: [bug-gnuastro] Sorry, false alarm on make crashes
Date: Thu, 1 Dec 2016 16:40:31 +0100
User-agent: Mozilla/5.0 (X11; Linux x86_64; rv:45.0) Gecko/20100101 Thunderbird/45.5.0

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

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:


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

(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
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
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.


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

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