20051026: 20051026: 20051005: GEMPAK 5.8.3a problem with garp

David,

Its disappointing that flavors of Linux aren't binary compatible. 
I'd certainly like to make the source distribution build as readily as possible 
so that
users of could build from source as easily as installing a binary distriution.

Aside from your local modifications, are there steps you have to go through to
build that differ from RedHat/FC?

Steve Chiswell
Unidata User Support


>From: David Ovens <address@hidden>
>Organization: UCAR/Unidata
>Keywords: 200510262214.j9QMET7s022148

>On Wed, Oct 26, 2005 at 03:49:06PM -0600, Unidata Support wrote:
>> 
>> David,
>> 
>> I suspect the problem lies in that our FC3 machine is a 2.6 SMP kernel,
>> whereas your is an older 2.4.27. That could be the difference in the libc.so
> .6
>> 
>> > uname -a
>> Linux imogene.unidata.ucar.edu 2.6.12-1.1378_FC3smp #1 SMP Wed Sep 14 04:52:
> 36 EDT 2005 i686 athlon i386 GNU/Linux
>> 
>> That FC3 is the base system I build binaries on. Our other machines are FC4,
>  gcc 4.0:
>> Linux johnny.unidata.ucar.edu 2.6.12-1.1398_FC4 #1         i686 athlon
>> Linux daffy.unidata.ucar.edu 2.6.12-1.1447_FC4smp #1 SMP   x86_64
>> 
>> I build and test under the 64 bit FC4 as well.
>> Do you run any 2.6 kernel versions of Linux?
>> The variety of kernels in Linux is getting to be problematic for providing b
> inaries
>> and maintaining current OS and system patches.
>> 
>> Steve Chiswell
>> Unidata User Support
>
>
>Steve,
>
>On freshair, we are running Debian 2.6 kernel:
>  Linux freshair2 2.6.11.12 #1 SMP Wed Oct 19 11:33:01 PDT 2005 i686 GNU/Linux
>
>and when I try to run the Unidata binaries, I still get:
>
>114 freshair2% $GEMEXE/garp
>G A R P - v2.1 starting...
>/tmp/GEMPAK5.8.3a/bin/linux/garp: relocation error:
>/tmp/GEMPAK5.8.3a/bin/linux/garp: symbol __strncpy_chk, version
>GLIBC_2.3.4 not defined in file libc.so.6 with link time reference
>
>
>I did find a machine, husky, in the department running Redhat
>enterprise and a 2.6 kernel
>  Linux husky 2.6.9-11.ELsmp #1 SMP Fri May 20 18:26:27 EDT 2005 i686
>  athlon i386 GNU/Linux
>
>and, indeed, that does work with the binaries.  Not only does it work,
>but the bug that I encountered with garp and the ETA 104 grids is
>gone.  All frames appear and all lines and contours are drawn.  I
>copied over the entire comet/garp/fdf directory to ensure that I was
>comparing apples to apples.
>
>Debianitits strikes again!!!
>
>We have a campus site license for RedHat enterprise and I will get it
>installed on my desktop machine, frosty, sometime in the next month.
>
>David
>
>> 
>> 
>> >From: David Ovens <address@hidden>
>> >Organization: UCAR/Unidata
>> >Keywords: 200510261952.j9QJq97s005538
>> 
>> >Steve,
>> >
>> >Here's what Harry has to say:
>> >
>> >On Mon, 24 Oct 2005 15:25:42 -0700, Harry Edmon wrote:
>> >----------------------------------------------------------------------
>> >What machine?
>> >frosty has gcc-lib 3.3.5
>> >
>> >1 frosty% ls /usr/lib/gcc-lib/i486-linux/
>> >3.3.5/
>> >
>> >and gcc 3.4.4
>> >
>> >4 frosty% ls /usr/lib/gcc/i486-linux/
>> >3.4.4/
>> >----------------------------------------------------------------------
>> >
>> >My machine, frsoty, is running Debian Linux:
>> >Linux frosty 2.4.27-2-686 #1 Mon May 16 17:03:22 JST 2005 i686 GNU/Linux
>> >
>> >Is that enough info?
>> >
>> >David
>> >
>> >On Mon, Oct 24, 2005 at 03:27:00PM -0600, Unidata Support wrote:
>> >> 
>> >> David,
>> >> 
>> >> I'm looking in to  the strncpy_chk error. At the time the binaries were 
>> >> compiled, the compile used under FC3 was gcc 3.4.4. We also have FC4 with
>> >> gcc 4.0. It seems that the libc.so.6 has a version incompatibility.
>> >> Can you tell me what the compiler and OS version you are using is?
>> >> 
>> >> I have not been able to duplicate the garp problem you reported. One
>> >> change a few versions back in gemlib was the ability to compute 
>> >> precipitation when accumulation grids were present (such as with the CMC 
> GEM
>> > ).
>> >> The precip grids in the ETA104 are 3 hourly, so doing a P06I is performin
> g
>> >> a calculation to sum the grids, so its possible that something is involve
> d t
>> > here,
>> >> but at this point I'm still investigating.
>> >> 
>> >> STeve Chiswell
>> >> 
>> >> >From: David Ovens <address@hidden>
>> >> >Organization: UCAR/Unidata
>> >> >Keywords: 200510051834.j95IY5G7028870
>> >> 
>> >> >Hello Unidata support,
>> >> >
>> >> >I would have tested this problem out with the Linux GEMPAK 5.8.3a
>> >> >pre-built binaries, but I cannot run them on our machines.  I get
>> >> >errors like:
>> >> >
>> >> >  GEMPAK5.8.3a/bin/linux/garp: relocation error:
>> >> >  /home/disk/frosty/ovens/GEMPAK5.8.3a/bin/linux/garp: symbol
>> >> >  __strncpy_chk, version GLIBC_2.3.4 not defined in file libc.so.6 with
>> >> >  link time reference 3
>> >> >
>> >> >If you have any suggestions on how to fix this, I'd appreciate them,
>> >> >also.
>> >> >
>> >> >So, anyhow, in garp, I load up 6-hour precipitation for the ETA104
>> > >grids for all forecast house 0-84.  That works fine, with hours 0 and
>> >> >3 being blank, of course.  Then I attempt to overlay MSLP using
>> >> >EMSL@0%NONE.  The first few frames (up to frame 12 = f33) load fine,
>> >> >then I see lots of these errors in my xterm window where garp was
>> >> >started:
>> >> >  GEMPAK: [DG -10]  Internal grid list is full; simplify function.
>> >> >  GEMPAK: [DG -10]  Internal grid list is full; simplify function.
>> >> >and from frame 13 on all of the color-filled 6-hour precipitation is
>> >> >gone, and all I see is MSLP.  Do you have any idea how I can fix this? 
>> >> >
>> >> >Thanks,
>> >> >
>> >> >David
>> >> >-- 
>> >> >David Ovens               e-mail: address@hidden
>> >> >Research Meteorologist    phone: (206) 685-8108
>> >> >Dept of Atm. Sciences      plan: Real-time MM5 forecasting for the
>> >> >Box 351640                        Pacific Northwest
>> >> >University of Washington          http://www.atmos.washington.edu/mm5rt
>> >> >Seattle, WA  98195               Weather Graphics and Loops
>> >> >                                  http://www.atmos.washington.edu/~ovens
> /lo
>> > ops
>> >> >
>> >> >From address@hidden  Wed Oct  5 13:51:34 2005
>> >> >Return-Path: <address@hidden>
>> >> >Received: from dew1.atmos.washington.edu (dew1.atmos.washington.edu [128
> .95
>> > .89
>> >> > .41])
>> >> > by unidata.ucar.edu (UCAR/Unidata) with ESMTP id j95JpYG7008220
>> >> > for <address@hidden>; Wed, 5 Oct 2005 13:51:34 -0600 (MDT)
>> >> >Organization: UCAR/Unidata
>> >> >Keywords: 200510051951.j95JpYG7008220
>> >> >Received: from frosty.atmos.washington.edu (root@frosty.atmos.washington
> .ed
>> > u [
>> >> > 128.95.175.84])
>> >> > by dew1.atmos.washington.edu (8.13.4/8.13.4/Debian-3) with ESMTP id j95
>> >> > JpVAk012290
>> >> > (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT);
>> >> > Wed, 5 Oct 2005 12:51:31 -0700
>> >> >Received: from frosty.atmos.washington.edu (ovens@localhost [127.0.0.1])
>> >> > by frosty.atmos.washington.edu (8.13.4/8.13.4/Debian-3) with ESMTP id j
>> >> > 95JpVMT004343;
>> >> > Wed, 5 Oct 2005 12:51:31 -0700
>> >> >Received: (from ovens@localhost)
>> >> > by frosty.atmos.washington.edu (8.13.4/8.13.4/Submit) id j95JpVnK004340
>> >> > ;
>> >> > Wed, 5 Oct 2005 12:51:31 -0700
>> >> >From: David Ovens <address@hidden>
>> >> >Date: Wed, 5 Oct 2005 12:51:30 -0700
>> >> >To: address@hidden
>> >> >Cc: Harry Edmon <address@hidden>
>> >> >Subject: Re: GEMPAK 5.8.3a problem with garp -- I think I found answer
>> >> >Message-ID: <address@hidden>
>> >> >References: <address@hidden>
>> >> >Mime-Version: 1.0
>> >> >Content-Type: text/plain; charset=us-ascii
>> >> >Content-Disposition: inline
>> >> >In-Reply-To: <address@hidden>
>> >> >User-Agent: Mutt/1.5.9i
>> >> >X-Scanned-By: MIMEDefang 2.51 on 128.95.89.40
>> >> >X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on 
>> >> > laraine.unidata.ucar.edu
>> >> >X-Spam-Level: 
>> >> >X-Spam-Status: No, score=-2.6 required=5.0 tests=AWL,BAYES_00 autolearn=
> ham
>> >  
>> >> > version=3.0.1
>> >> >
>> >> >Hello Unidata support,
>> >> >
>> >> >I believe I found the answer to this in the email archives at:
>> >> >http://www.unidata.ucar.edu/cgi-bin/getfile?file=/content/support/help/M
> ail
>> > Arc
>> >> > hives/gempak/msg03045.html
>> >> >
>> >> >I have bumped up LLMDGG in GEMPRM.PRM and gemprm.h to 9,876,543 and
>> >> >will see what that does once it's finished being rebuilt.
>> >> >
>> >> >David
>> >> >
>> >> >On Wed, Oct 05, 2005 at 11:33:55AM -0700, ovens wrote:
>> >> >> Hello Unidata support,
>> >> >> 
>> >> >> I would have tested this problem out with the Linux GEMPAK 5.8.3a
>> >> >> pre-built binaries, but I cannot run them on our machines.  I get
>> >> >> errors like:
>> >> >> 
>> >> >>   GEMPAK5.8.3a/bin/linux/garp: relocation error:
>> >> >>   /home/disk/frosty/ovens/GEMPAK5.8.3a/bin/linux/garp: symbol
>> >> >>   __strncpy_chk, version GLIBC_2.3.4 not defined in file libc.so.6 wit
> h
>> >> >>   link time reference 3
>> >> >> 
>> >> >> If you have any suggestions on how to fix this, I'd appreciate them,
>> >> >> also.
>> >> >> 
>> >> >> So, anyhow, in garp, I load up 6-hour precipitation for the ETA104
>> >> >> grids for all forecast house 0-84.  That works fine, with hours 0 and
>> >> >> 3 being blank, of course.  Then I attempt to overlay MSLP using
>> >> >> EMSL@0%NONE.  The first few frames (up to frame 12 = f33) load fine,
>> >> >> then I see lots of these errors in my xterm window where garp was
>> >> >> started:
>> >> >>   GEMPAK: [DG -10]  Internal grid list is full; simplify function.
>> >> >>   GEMPAK: [DG -10]  Internal grid list is full; simplify function.
>> >> >> and from frame 13 on all of the color-filled 6-hour precipitation is
>> >> >> gone, and all I see is MSLP.  Do you have any idea how I can fix this?
>  
>> >> >> 
>> >> >> Thanks,
>> >> >> 
>> >> >> David
>> >> >> -- 
>> >> >> David Ovens             e-mail: address@hidden
>> >> >> Research Meteorologist    phone: (206) 685-8108
> >> >> Dept of Atm. Sciences      plan: Real-time MM5 forecasting for the
>> >> >> Box 351640                        Pacific Northwest
>> >> >> University of Washington          http://www.atmos.washington.edu/mm5r
> t
>> >> >> Seattle, WA  98195               Weather Graphics and Loops
>> >> >>                                   http://www.atmos.washington.edu/~ove
> ns/
>> > loo
>> >> > ps
>> >> >
>> >> >-- 
>> >> >David Ovens               e-mail: address@hidden
>> >> >Research Meteorologist    phone: (206) 685-8108
>> >> >Dept of Atm. Sciences      plan: Real-time MM5 forecasting for the
>> >> >Box 351640                        Pacific Northwest
>> >> >University of Washington          http://www.atmos.washington.edu/mm5rt
>> >> >Seattle, WA  98195               Weather Graphics and Loops
>> >> >                                  http://www.atmos.washington.edu/~ovens
> /lo
>> > ops
>> >> >
>> >> >From address@hidden  Wed Oct  5 14:34:41 2005
>> >> >Return-Path: <address@hidden>
>> >> >Received: from dew1.atmos.washington.edu (dew1.atmos.washington.edu [128
> .95
>> > .89
>> >> > .41])
>> >> > by unidata.ucar.edu (UCAR/Unidata) with ESMTP id j95KYfG7013324
>> >> > for <address@hidden>; Wed, 5 Oct 2005 14:34:41 -0600 (MDT)
>> >> >Organization: UCAR/Unidata
>> >> >Keywords: 200510052034.j95KYfG7013324
>> >> >Received: from frosty.atmos.washington.edu (root@frosty.atmos.washington
> .ed
>> > u [
>> >> > 128.95.175.84])
>> >> > by dew1.atmos.washington.edu (8.13.4/8.13.4/Debian-3) with ESMTP id j95
>> >> > KYbVs020469
>> >> > (version=TLSv1/SSLv3 cipher=DHE-RSA-AES256-SHA bits=256 verify=NOT);
>> >> > Wed, 5 Oct 2005 13:34:37 -0700
>> >> >Received: from frosty.atmos.washington.edu (ovens@localhost [127.0.0.1])
>> >> > by frosty.atmos.washington.edu (8.13.4/8.13.4/Debian-3) with ESMTP id j
>> >> > 95KYbMX012051;
>> >> > Wed, 5 Oct 2005 13:34:37 -0700
>> >> >Received: (from ovens@localhost)
>> >> > by frosty.atmos.washington.edu (8.13.4/8.13.4/Submit) id j95KYbmU012048
>> >> > ;
>> >> > Wed, 5 Oct 2005 13:34:37 -0700
>> >> >From: David Ovens <address@hidden>
>> >> >Date: Wed, 5 Oct 2005 13:34:37 -0700
>> >> >To: address@hidden
>> >> >Cc: Harry Edmon <address@hidden>
>> >> >Subject: Re: GEMPAK 5.8.3a problem with garp -- I think I found answer
>> >> >Message-ID: <address@hidden>
>> >> >References: <address@hidden> <2005100
> 519
>> > 513
>> >> > address@hidden>
>> >> >Mime-Version: 1.0
>> >> >Content-Type: text/plain; charset=us-ascii
>> >> >Content-Disposition: inline
>> >> >In-Reply-To: <address@hidden>
>> >> >User-Agent: Mutt/1.5.9i
>> >> >X-Scanned-By: MIMEDefang 2.51 on 128.95.89.40
>> >> >X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on 
>> >> > laraine.unidata.ucar.edu
>> >> >X-Spam-Level: 
>> >> >X-Spam-Status: No, score=-2.6 required=5.0 tests=AWL,BAYES_00 autolearn=
> ham
>> >  
>> >> > version=3.0.1
>> >> >
>> >> >Hello again,
>> >> >
>> >> >Well, I ended up bumping up LLMDGG to 98,765,432 and I still see the
>> >> >exact same behavior in garp at the exact same place.  I have tracked
>> >> >the problem down to the Hi/Low symbol display for the MSLP
>> >> >(PMSL@0%NONE or EMSL@0%NONE).  When I uncheck the Hi/Low display
>> >> >(after clicking "More>>"), I can display/overlay both these fields
>> >> >without a problem for all hours 0-84.  
>> >> >
>> >> >Is LLMDGG really the parameter to modify here? or does garp use
>> >> >something different than the rest of GEMPAK?
>> >> >
>> >> >David
>> >> >-- 
>> >> >David Ovens               e-mail: address@hidden
>> >> >Research Meteorologist    phone: (206) 685-8108
>> >> >Dept of Atm. Sciences      plan: Real-time MM5 forecasting for the
>> >> >Box 351640                        Pacific Northwest
>> >> >University of Washington          http://www.atmos.washington.edu/mm5rt
>> >> >Seattle, WA  98195               Weather Graphics and Loops
>> >> >                                  http://www.atmos.washington.edu/~ovens
> /lo
>> > ops
>> >> >
>> >> >On Wed, Oct 05, 2005 at 12:51:30PM -0700, ovens wrote:
>> >> >> Hello Unidata support,
>> >> >> 
>> >> >> I believe I found the answer to this in the email archives at:
>> >> >> http://www.unidata.ucar.edu/cgi-bin/getfile?file=/content/support/help
> /Ma
>> > ilA
>> >> > rchives/gempak/msg03045.html
>> >> >> 
>> >> >> I have bumped up LLMDGG in GEMPRM.PRM and gemprm.h to 9,876,543 and
>> >> >> will see what that does once it's finished being rebuilt.
>> >> >> 
>> >> >> David
>> >> >> 
>> >> >> On Wed, Oct 05, 2005 at 11:33:55AM -0700, ovens wrote:
>> >> >> > Hello Unidata support,
>> >> >> > 
>> >> >> > I would have tested this problem out with the Linux GEMPAK 5.8.3a
>> >> >> > pre-built binaries, but I cannot run them on our machines.  I get
>> >> >> > errors like:
>> >> >> > 
>> >> >> >   GEMPAK5.8.3a/bin/linux/garp: relocation error:
>> >> >> >   /home/disk/frosty/ovens/GEMPAK5.8.3a/bin/linux/garp: symbol
>> >> >> >   __strncpy_chk, version GLIBC_2.3.4 not defined in file libc.so.6 w
> ith
>> >> >> >   link time reference 3
>> >> >> > 
>> >> >> > If you have any suggestions on how to fix this, I'd appreciate them,
>> >> >> > also.
>> >> >> > 
>> >> >> > So, anyhow, in garp, I load up 6-hour precipitation for the ETA104
>> >> >> > grids for all forecast house 0-84.  That works fine, with hours 0 an
> d
>> >> >> > 3 being blank, of course.  Then I attempt to overlay MSLP using
>> >> >> > EMSL@0%NONE.  The first few frames (up to frame 12 = f33) load fine,
>> >> >> > then I see lots of these errors in my xterm window where garp was
>> >> >> > started:
>> >> >> >   GEMPAK: [DG -10]  Internal grid list is full; simplify function.
>> >> >> >   GEMPAK: [DG -10]  Internal grid list is full; simplify function.
>> >> >> > and from frame 13 on all of the color-filled 6-hour precipitation is
>> >> >> > gone, and all I see is MSLP.  Do you have any idea how I can fix thi
> s? 
>> >> >> > 
>> >> >> > Thanks,
>> >> >> > 
>> >> >> > David
>> >> >> > -- 
>> >> >> > David Ovens           e-mail: address@hidden
>> >> >> > Research Meteorologist    phone: (206) 685-8108
>> >> >> > Dept of Atm. Sciences      plan: Real-time MM5 forecasting for the
>> >> >> > Box 351640                        Pacific Northwest
>> >> >> > University of Washington          http://www.atmos.washington.edu/mm
> 5rt
>> >> >> > Seattle, WA  98195               Weather Graphics and Loops
>> >> >> >                                   http://www.atmos.washington.edu/~o
> ven
>> > s/l
>> >> > oops
>> >> >> 
>> >> >> -- 
>> >> >> David Ovens             e-mail: address@hidden
>> >> >> Research Meteorologist    phone: (206) 685-8108
>> >> >> Dept of Atm. Sciences      plan: Real-time MM5 forecasting for the
>> >> >> Box 351640                        Pacific Northwest
>> >> >> University of Washington          http://www.atmos.washington.edu/mm5r
> t
>> >> >> Seattle, WA  98195               Weather Graphics and Loops
>> >> >>                                   http://www.atmos.washington.edu/~ove
> ns/
>> > loo
>> >> > ps
>> >> >
>> >> --
>> >> *************************************************************************
> ***
>> >> Unidata User Support                                    UCAR Unidata Prog
> ram
>> >> (303)497-8643                                                  P.O. Box 3
> 000
>> >> address@hidden                                   Boulder, CO 80
> 307
>> >> -------------------------------------------------------------------------
> ---
>> >> Unidata WWW Service              http://my.unidata.ucar.edu/content/suppo
> rt 
>> >> -------------------------------------------------------------------------
> ---
>> >> NOTE: All email exchanges with Unidata User Support are recorded in the
>> >> Unidata inquiry tracking system and then made publicly available
>> >> through the web.  If you do not want to have your interactions made
>> >> available in this way, you must let us know in each email you send to us.
>> >
>> >-- 
>> >David Ovens          e-mail: address@hidden
>> >Research Meteorologist    phone: (206) 685-8108
>> >Dept of Atm. Sciences      plan: Real-time MM5 forecasting for the
>> >Box 351640                        Pacific Northwest
>> >University of Washington          http://www.atmos.washington.edu/mm5rt
>> >Seattle, WA  98195               Weather Graphics and Loops
>> >                                  http://www.atmos.washington.edu/~ovens/lo
> ops
>> >
>> --
>> ****************************************************************************
>> Unidata User Support                                    UCAR Unidata Program
>> (303)497-8643                                                  P.O. Box 3000
>> address@hidden                                   Boulder, CO 80307
>> ----------------------------------------------------------------------------
>> Unidata WWW Service              http://my.unidata.ucar.edu/content/support 
>> ----------------------------------------------------------------------------
>> NOTE: All email exchanges with Unidata User Support are recorded in the
>> Unidata inquiry tracking system and then made publicly available
>> through the web.  If you do not want to have your interactions made
>> available in this way, you must let us know in each email you send to us.
>
>-- 
>David Ovens             e-mail: address@hidden
>Research Meteorologist    phone: (206) 685-8108
>Dept of Atm. Sciences      plan: Real-time MM5 forecasting for the
>Box 351640                        Pacific Northwest
>University of Washington          http://www.atmos.washington.edu/mm5rt
>Seattle, WA  98195               Weather Graphics and Loops
>                                  http://www.atmos.washington.edu/~ovens/loops
>
--
NOTE: All email exchanges with Unidata User Support are recorded in the
Unidata inquiry tracking system and then made publicly available
through the web.  If you do not want to have your interactions made
available in this way, you must let us know in each email you send to us.