Grads on Slackware 11 - segmentation faults due to a severe case of versionitis

Fri Oct 27 14:58:40 EDT 2006

On Oct 27, 2006, at 10:35 AM, Jean Pierre Arabonis wrote:

> Hi Jennifer
>     I'm back at the problem and it appears that there are others
> also now onto/in it.
>     I looked into installing the older version and have a suspicion
> that it may in the long run lead to more problems.
>     I tried to build dods version 3.2 with no success (will not
> compile) and the folk at opendap are not keen on supporting the old
> version.
Right. We're moving on to later versions too...

>     Now I expect that Patrice's -enable-dynamic-supplibs will only
> work with dods 3.2. so building Opendap 3.4 won't help.
I don't believe that is correct, but Patrice will have to answer for
sure.

>     This leads me to come to the conclusion that the mucky-muck
> solution is the way forward ?
In my experience, mucky-muck is the only way when building GrADS from
source.

>     Am I on the right track in believing that with an effective
> build of opendap 3.4 I should then have the drivers, or the updated
> version thereof that are presently packaged in supplib tar file,
> from that I should be able to create an updated supplib and then
> work through the changes required in the .configure.
Looks like when you ran configure, it told you everything was okay to
build gradsdods. That's good, that makes it simpler. All you have to
do is change dods_libs in the Makefile. In my version it looks like
this (old dods_libs commented out on the 2nd line -- note that you'll
have to change paths here and there)

dods_libs= -lgadods -lnc-dods -ldap++ -lxml2 -L/var/adm/grads/
supplib_builds/DODS/lib -lz -lpthread -lm \
-L/var/adm/grads/supplib_builds/DODS/lib -lcurl -L/usr/kerberos/lib -
lssl -lcrypto -ldl -lssl -lcrypto -lgssapi_krb5 \
-lkrb5 -lcom_err -lk5crypto -lresolv -ldl -lz -lz  -lpthread -lz $
(supp_lib_dir)/libudunits.a
#dods_libs = -lgadods -lnc-dods -ldap++ -lgadods -lnc-dods -ldap++  $
(supp_lib_dir)/libudunits.a \
$(supp_lib_dir)/libwww.a $(supp_lib_dir)/librx.a $(supp_lib_dir)/libz.a

Once you build DODS 3.4, there's a handy program called opendap-
config (look in the DODS/bin directory) that will give you the text
you need for linking. You'll have to tweak this a little to add
udunits and such, but the above example from my build should give you
some idea of what to do.

> As I am embarking on a journey of versionitis discovery any support
> you can off will be much appreciated.
I put the three required tar files for DODS 3.4 on our ftp site:
ftp://grads.iges.org/grads/Supplibs/1.9/src/
Do  the packages first, then nc-dods, then dap.

--Jennifer

>
>
>
>
> Jennifer M. Adams wrote:
>> Jean Pierre --
>> Current public builds of GrADS use DODS version 3.2 and were built
>> with gcc version 2.9. These versions of the libraries and the
>> complier are now in retirement, and in many operating systems are
>> dead and gone. If you can find or install the old version of gcc
>> on your box, then you can probably build 1.9b4 from source with
>> the linux supplib tar file we provide.
>>
>> If you do not have gcc version 2.9, then you must build a more
>> recent version of DODS (OPenDAP) and then you have to fiddle with
>> the configure script and/or the Makefile in order to get a build
>> of gradsdods. I have used DODS 3.4 successfully on linux, but it
>> does require a bit of mucky-muck. If you can build DODS 3.2, then
>> I would use Patrice's -enable-dynamic-supplibs mods and I bet it
>> would find the new version of dods and create a usable makefile.
>>
>> Jennifer
>>
>>
>>
>>
>>
>> On Oct 18, 2006, at 11:46 AM, Jean Pierre Arabonis wrote:
>>
>>> Thanks Patrice for the suggestions, I tried your tarball without
>>> success, same errors came up as before.
>>>
>>> I have brought across the following:
>>>
>>> grads-1.9b3-src.tar.gz
>>> grads-1.9b3-supplibs-linuxRH9.tar.gz
>>>
>>> put them in a directory and tried:
>>>
>>> >./configure --with-dods --libdir=/data/source/Grads19b3work/
>>> grads-1.9b3/supplibs/lib
>>>
>>> and I have success with everything in order, then all falls over
>>> when I try make:
>>>
>>> >make
>>>
>>> arabonis at baltic:/data/source/Grads19b3work/grads-1.9b3> make
>>> Making all in src
>>> make[1]: Entering directory `/data/source/Grads19b3work/
>>> grads-1.9b3/src'
>>> make  all-am
>>> make[2]: Entering directory `/data/source/Grads19b3work/
>>> grads-1.9b3/src'
>>> gcc -DHAVE_CONFIG_H -I. -I. -I. -I.././supplibs/include -I/usr/
>>> X11R6/include    -g -O -c `test -f 'gxdxwd.c' || echo './'`gxdxwd.c
>>> gxdxwd.c:25: error: conflicting types for 'calloc'
>>> gxdxwd.c:25: error: conflicting types for 'calloc'
>>> make[2]: *** [gxdxwd.o] Error 1
>>> make[2]: Leaving directory `/data/source/Grads19b3work/
>>> grads-1.9b3/src'
>>> make[1]: *** [all] Error 2
>>> make[1]: Leaving directory `/data/source/Grads19b3work/
>>> grads-1.9b3/src'
>>> make: *** [all-recursive] Error 1
>>>
>>> This is now well over my head, anyone out there can tell me what
>>> is going on and if/how to solve it.
>>>
>>> On the side track I tried the fedora core 1.8 compilation again
>>> through gdb, maybe someone can tell me what is going on as it
>>> seems to be the common problem with all the versions of grads:
>>>
>>> arabonis at baltic:/data/source/Gradsfedoracore> gdb --quiet gradsdods
>>> Using host libthread_db library "/lib/libthread_db.so.1".
>>> (gdb) run
>>> Starting program: /data/source/Gradsfedoracore/gradsdods
>>> warning: Cannot initialize thread debugging library: unknown
>>> thread_db error '22'
>>>
>>> Grid Analysis and Display System (GrADS) Version 1.8SL11
>>> Copyright (c) 1988-2001 by Brian Doty
>>> Center for Ocean-Land-Atmosphere Studies
>>> Institute for Global Environment and Society
>>> All Rights Reserved
>>>
>>> Config: v1.8SL11 32-bit little-endian readline sdf/xdf netcdf
>>> DODS-enabled lats printim
>>>
>>> Issue 'q config' command for more information.
>>>
>>> Landscape mode? (no for portrait):  p
>>> GX Package Initialization: Size = 11 8.5
>>> ga-> sdfopen http://monsoondata.org:9090/dods/gfs/gfs.2006101800i
>>> Scanning self-describing file:  http://monsoondata.org:9090/dods/
>>> gfs/gfs.2006101800i
>>>
>>> Program received signal SIGSEGV, Segmentation fault.
>>> 0x083a16e5 in get_cie_encoding ()
>>> (gdb)
>>>
>>>
>>> Many Thanks
>>>     Jean Pierre
>>>
>>>
>>>
>>>
>>>
>>> Patrice Dumas wrote:
>>>> On Tue, Oct 17, 2006 at 07:23:37PM +0200, Jean Pierre Arabonis
>>>> wrote:
>>>>
>>>>>    My question is is it likely that I will have success in
>>>>> compiling
>>>>> grads if I trawl the net and find these libraries and install
>>>>> them, or
>>>>> can someone point me in the right direction to solve this problem.
>>>>>
>>>> Since all the grads prerequisites are packaged for fedora, I
>>>> can't see
>>>> why it shouldn't be possible to install them on slackware,
>>>> either using
>>>> the packaging system or by recompiling (even though I don't know
>>>> anything
>>>> about slackware). In case you want to build against 'system'
>>>> libraries
>>>> (libraries not in the supplib directory) you may be interested
>>>> in the
>>>> grads tarball I distribute here (with only changes in configure
>>>> with
>>>> --dyn-supplib given):
>>>> http://www.environnement.ens.fr/perso/dumas/fc-srpms/
>>>> grads-1.9b4.1.tar.gz
>>>>
>>>>
>>>> --
>>>> Pat
>>>>
>>>>
>>>
>>>
>>> --
>>> Jean Pierre Arabonis
>>> arabonis at egs.uct.ac.za
>>> Tel 021 780 1021 cell 084 401 1365
>>> This email is 100% Microsoft Free
>>>
>>
>> Jennifer M. Adams
>> IGES/COLA
>> 4041 Powder Mill Road, Suite 302
>> Beltsville, MD 20705
>> jma at cola.iges.org
>>
>>
>>
>
>
> --
> Jean Pierre Arabonis
> arabonis at egs.uct.ac.za
> Tel 021 780 1021 cell 084 401 1365
> This email is 100% Microsoft Free

Jennifer M. Adams
IGES/COLA
4041 Powder Mill Road, Suite 302
Beltsville, MD 20705
jma at cola.iges.org

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