bugGNU Astronomy Utilities - Bugs: bug #61795, Make step crashes in version...

 
 

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bug #61795: Make step crashes in version 0.16.68-92ff442

Submitted by:  Raul Infante-Sainz <infantesainz>
Submitted on:  Tue 11 Jan 2022 12:19:48 PM UTC
 
Category:  Installation Severity:  3 - Normal
Item Group:  * Crash Status:  Fixed
Privacy:  Public Assigned to:  makhlaghi
Open/Closed:  Closed
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Wed 26 Jan 2022 11:29:48 PM UTC, comment #3: 

This bug was fixed in Commit 1ac084b438.

Mohammad Akhlaghi <makhlaghi>
Project Administrator
Tue 11 Jan 2022 02:38:26 PM UTC, comment #2: 

Thanks Mohammad.

My operating system is Ubuntu 20.04.3 LTS, so GNU/Linux.

That line in particular shows "no":

checking for pthread_barrier_wait in -lpthread... no

Attached you have the file 'config.log.gz'

Thanks again

(file #52645)

Raul Infante-Sainz <infantesainz>
Project Member
Tue 11 Jan 2022 02:16:43 PM UTC, comment #1: 

Thanks a lot for reporting this Raul.

The 'pthread_barrier_*' set of functions are defined for operating systems that don't have it (mostly macOS), they are described in the Implementation of pthread_barrier section of the book.

The reason for the "conflicting types" can be that during the configuration phase, Gnuastro has not been able to detect your system's 'pthread_barrier_t'.

Was this on a GNU/Linux OS?

Can you have a look in the './configure' output, and this line in particular:

checking for pthread_barrier_wait in -lpthread... yes

If my assumption is correct, you should be using a GNU/Linux OS, but this './configure' check should be a 'no'. In this case, can you also send me the 'config.log' file (while removing private directories and doing a 'gzip --best config.log' to avoid wasting space)?

With the 'config.log', we'll be able to see why this test failed, even though the function already (probably!) existed in your OS... let's see

Mohammad Akhlaghi <makhlaghi>
Project Administrator
Tue 11 Jan 2022 12:19:48 PM UTC, original submission:  

While trying to install the latest version of Gnuastro (right now it is 0.16.68-92ff442), it crashes with the output shown below. I am also attaching the output of the configure step in case it can provide some clues.

depbase=`echo arithmetic.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`;\
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I. -I..  -I\../bootstrapped/lib -I\../bootstrapped/lib -DSYSCONFIG_DIR=\"/usr/local/etc\"   -Wall -O3  -pthread -MT arithmetic.lo -MD -MP -MF $depbase.Tpo -c -o arithmetic.lo arithmetic.c &&\
mv -f $depbase.Tpo $depbase.Plo
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -I.. -I../bootstrapped/lib -I../bootstrapped/lib -DSYSCONFIG_DIR=\"/usr/local/etc\" -Wall -O3 -pthread -MT arithmetic.lo -MD -MP -MF .deps/arithmetic.Tpo -c arithmetic.c  -fPIC -DPIC -o .libs/arithmetic.o
In file included from arithmetic.c:41:
./gnuastro/threads.h:72:13: error: conflicting types for ‘pthread_barrierattr_t’
   72 | typedef int pthread_barrierattr_t;
      |             ^~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/x86_64-linux-gnu/sys/types.h:227,
                 from ../bootstrapped/lib/sys/types.h:39,
                 from ../bootstrapped/lib/stdio.h:58,
                 from ../bootstrapped/lib/error.h:23,
                 from arithmetic.c:26:
/usr/include/x86_64-linux-gnu/bits/pthreadtypes.h:118:3: note: previous declaration of ‘pthread_barrierattr_t’ was here
  118 | } pthread_barrierattr_t;
      |   ^~~~~~~~~~~~~~~~~~~~~
In file included from arithmetic.c:41:
./gnuastro/threads.h:81:3: error: conflicting types for ‘pthread_barrier_t’
   81 | } pthread_barrier_t;
      |   ^~~~~~~~~~~~~~~~~
In file included from /usr/include/x86_64-linux-gnu/sys/types.h:227,
                 from ../bootstrapped/lib/sys/types.h:39,
                 from ../bootstrapped/lib/stdio.h:58,
                 from ../bootstrapped/lib/error.h:23,
                 from arithmetic.c:26:
/usr/include/x86_64-linux-gnu/bits/pthreadtypes.h:112:3: note: previous declaration of ‘pthread_barrier_t’ was here
  112 | } pthread_barrier_t;
      |   ^~~~~~~~~~~~~~~~~
In file included from arithmetic.c:41:
./gnuastro/threads.h:84:1: error: conflicting types for ‘pthread_barrier_init’
   84 | pthread_barrier_init(pthread_barrier_t *b, pthread_barrierattr_t *attr,
      | ^~~~~~~~~~~~~~~~~~~~
In file included from ./gnuastro/threads.h:28,
                 from arithmetic.c:41:
/usr/include/pthread.h:1080:12: note: previous declaration of ‘pthread_barrier_init’ was here
 1080 | extern int pthread_barrier_init (pthread_barrier_t *__restrict __barrier,
      |            ^~~~~~~~~~~~~~~~~~~~
In file included from arithmetic.c:41:
./gnuastro/threads.h:88:1: error: conflicting types for ‘pthread_barrier_wait’
   88 | pthread_barrier_wait(pthread_barrier_t *b);
      | ^~~~~~~~~~~~~~~~~~~~
In file included from ./gnuastro/threads.h:28,
                 from arithmetic.c:41:
/usr/include/pthread.h:1090:12: note: previous declaration of ‘pthread_barrier_wait’ was here
 1090 | extern int pthread_barrier_wait (pthread_barrier_t *__barrier)
      |            ^~~~~~~~~~~~~~~~~~~~
In file included from arithmetic.c:41:
./gnuastro/threads.h:91:1: error: conflicting types for ‘pthread_barrier_destroy’
   91 | pthread_barrier_destroy(pthread_barrier_t *b);
      | ^~~~~~~~~~~~~~~~~~~~~~~
In file included from ./gnuastro/threads.h:28,
                 from arithmetic.c:41:
/usr/include/pthread.h:1086:12: note: previous declaration of ‘pthread_barrier_destroy’ was here
 1086 | extern int pthread_barrier_destroy (pthread_barrier_t *__barrier)
      |            ^~~~~~~~~~~~~~~~~~~~~~~

Raul Infante-Sainz <infantesainz>
Project Member

 

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Attached Files
file #52645:  config.log.gz added by infantesainz (56KiB - application/gzip)
file #52642:  configure.txt added by infantesainz (31KiB - text/plain)

 

Depends on the following items: None found

Items that depend on this one: None found

 

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    Follow 5 latest changes.

    Date Changed by Updated Field Previous Value => Replaced by
    2022-01-26 makhlaghi StatusNone => Fixed
        Assigned toNone => makhlaghi
        Open/ClosedOpen => Closed
    2022-01-11 infantesainz Attached File- => Added config.log.gz, #52645
    2022-01-11 infantesainz Attached File- => Added configure.txt, #52642

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