[Developers] Developers Digest, Vol 52, Issue 9
Matthew Supernaw - NOAA Federal
matthew.supernaw at noaa.gov
Wed Jun 26 17:26:41 PDT 2013
John-
Netbeans is the tool I showed in Seattle(with that horrible display). It
has a lot of useful features. My method is to convert the tpls to c++ and
import them into a Netbeans project. I link, compile, debug, and run from
Netbeans. I considered writing a Netbeans plugin for tpl files last year,
but figured people were happy to use Arni's IDE.
On Wed, Jun 26, 2013 at 7:03 PM, <developers-request at admb-project.org>wrote:
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> Today's Topics:
>
> 1. Re: init_number_matrix (Mark Maunder)
> 2. Re: init_number_matrix (Mark Maunder)
> 3. Re: Serious bug in ADMB 11.1 for Windows (GCC) (Johnoel Ancheta)
> 4. netbeans and debuggers (John Sibert)
> 5. Re: init_number_matrix (John Sibert)
> 6. Re: MinGW 64 and GDB (Johnoel Ancheta)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 26 Jun 2013 20:09:34 +0000
> From: Mark Maunder <mmaunder at iattc.org>
> To: John Sibert <sibert at hawaii.edu>, ADMB Developers
> <developers at admb-project.org>
> Cc: "Cristian Canales \(cristian.canales at ifop.cl\)"
> <cristian.canales at ifop.cl>
> Subject: Re: [Developers] init_number_matrix
> Message-ID:
> <339913E1960AE142A9373DFCD849F3DA333A25CD at mail1.lajolla.iattc.org>
> Content-Type: text/plain; charset="us-ascii"
>
> John,
>
> What version of ADMB are you using?
>
> Mark
>
> -----Original Message-----
> From: John Sibert [mailto:sibert at hawaii.edu]
> Sent: Wednesday, June 26, 2013 12:51 PM
> To: ADMB Developers
> Cc: Mark Maunder; Cristian Canales (cristian.canales at ifop.cl)
> Subject: Re: [Developers] init_number_matrix
>
> I routinely use init_bounded_number_matrix
>
> But I have no idea what init_vector_matrix might be.
>
> John Sibert
> Emeritus Researcher, SOEST
> University of Hawaii at Manoa
> Honolulu HI (GMT-10)
> 808-294-3842
>
> Visit the ADMB project http://admb-project.org/
>
> On 06/26/2013 08:59 AM, Mark Maunder wrote:
> >
> > A good addition to the ADMB code would be
> >
> > Init_number_matrix so you could have a matrix of phases. I am assuming
> > that init_matrix_matrix and init_vector_vector don't do this.
> >
> > Probably need init_vector_matrix as well.
> >
> > Mark
> >
> > The CAPAM selectivity workshop report is now online
> >
> > ftp://ftp.capamresearch.org/incoming/selevtivity_workshop/CAPAM_Select
> > ivity%20Workshop_Series%20Report_June%202013.pdf
> >
> > The Stock Synthesis special issue of the journal Fisheries Research is
> > now published
> >
> > http://www.sciencedirect.com/science/journal/01657836/142
> >
> > Mark Maunder
> >
> > Head of the Stock Assessment Program
> >
> > Inter-American Tropical Tuna Commission
> >
> > 8604 La Jolla Shores Drive
> >
> > La Jolla, CA, 92037-1508, USA
> >
> > Tel: (858) 546-7027
> >
> > Fax: (858) 546-7133
> >
> > mmaunder at iattc.org <mailto:mmaunder at iattc.org>
> >
> > http://www.fisheriesstockassessment.com/TikiWiki/tiki-index.php?page=M
> > ark+Maunder
> >
> > Visit the Center for the Advancement of Population Assessment
> > Methodology at
> >
> > http://www.capamresearch.org/
> >
> > Visit the AD Model Builder project at
> >
> > http://admb-project.org/
> >
> > See the following website for information on fisheries stock
> > assessment http://www.fisheriesstockassessment.com/
> >
> >
> >
> > _______________________________________________
> > Developers mailing list
> > Developers at admb-project.org
> > http://lists.admb-project.org/mailman/listinfo/developers
>
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 26 Jun 2013 20:14:27 +0000
> From: Mark Maunder <mmaunder at iattc.org>
> To: John Sibert <sibert at hawaii.edu>, ADMB Developers
> <developers at admb-project.org>
> Cc: "Cristian Canales \(cristian.canales at ifop.cl\)"
> <cristian.canales at ifop.cl>
> Subject: Re: [Developers] init_number_matrix
> Message-ID:
> <339913E1960AE142A9373DFCD849F3DA333A25E4 at mail1.lajolla.iattc.org>
> Content-Type: text/plain; charset="us-ascii"
>
> It is not defined in version 10.0?
>
> -----Original Message-----
> From: John Sibert [mailto:sibert at hawaii.edu]
> Sent: Wednesday, June 26, 2013 12:51 PM
> To: ADMB Developers
> Cc: Mark Maunder; Cristian Canales (cristian.canales at ifop.cl)
> Subject: Re: [Developers] init_number_matrix
>
> I routinely use init_bounded_number_matrix
>
> But I have no idea what init_vector_matrix might be.
>
> John Sibert
> Emeritus Researcher, SOEST
> University of Hawaii at Manoa
> Honolulu HI (GMT-10)
> 808-294-3842
>
> Visit the ADMB project http://admb-project.org/
>
> On 06/26/2013 08:59 AM, Mark Maunder wrote:
> >
> > A good addition to the ADMB code would be
> >
> > Init_number_matrix so you could have a matrix of phases. I am assuming
> > that init_matrix_matrix and init_vector_vector don't do this.
> >
> > Probably need init_vector_matrix as well.
> >
> > Mark
> >
> > The CAPAM selectivity workshop report is now online
> >
> > ftp://ftp.capamresearch.org/incoming/selevtivity_workshop/CAPAM_Select
> > ivity%20Workshop_Series%20Report_June%202013.pdf
> >
> > The Stock Synthesis special issue of the journal Fisheries Research is
> > now published
> >
> > http://www.sciencedirect.com/science/journal/01657836/142
> >
> > Mark Maunder
> >
> > Head of the Stock Assessment Program
> >
> > Inter-American Tropical Tuna Commission
> >
> > 8604 La Jolla Shores Drive
> >
> > La Jolla, CA, 92037-1508, USA
> >
> > Tel: (858) 546-7027
> >
> > Fax: (858) 546-7133
> >
> > mmaunder at iattc.org <mailto:mmaunder at iattc.org>
> >
> > http://www.fisheriesstockassessment.com/TikiWiki/tiki-index.php?page=M
> > ark+Maunder
> >
> > Visit the Center for the Advancement of Population Assessment
> > Methodology at
> >
> > http://www.capamresearch.org/
> >
> > Visit the AD Model Builder project at
> >
> > http://admb-project.org/
> >
> > See the following website for information on fisheries stock
> > assessment http://www.fisheriesstockassessment.com/
> >
> >
> >
> > _______________________________________________
> > Developers mailing list
> > Developers at admb-project.org
> > http://lists.admb-project.org/mailman/listinfo/developers
>
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 26 Jun 2013 10:18:35 -1000
> From: Johnoel Ancheta <johnoel at hawaii.edu>
> To: Arni Magnusson <arnima at hafro.is>
> Cc: developers at admb-project.org
> Subject: Re: [Developers] Serious bug in ADMB 11.1 for Windows (GCC)
> Message-ID:
> <CAJMx2XXK=
> ML1asOo_LcyP+mKjsnKuoxOYsp1LabTKx0O6pt39w at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> Thank you for reporting it. It has been corrected in version control.
> Please test
> and provide feedback.
>
>
> On 6/25/13, Arni Magnusson <arnima at hafro.is> wrote:
> > The official ADMB release for Windows (GCC)
> >
> http://admb-project.googlecode.com/files/admb-11.1-windows-mingw-32bit.zip
> > has a serious bug. The most basic test fails spectacularly. Not only does
> >
> > tpl2cpp simple
> > adcomp simple
> > adlink simple
> >
> > fail to build an executable, but it even removes a system library
> > 'libcontribo.a' from the hard drive. Hold on, this new feature could be
> > good for our download statistics...
> >
> > As you can see below, the adlink.bat script produces a bad command that
> > asks GCC to compile nothing and then write the output to libcontribo.a.
> > Overwriting the file with a null, it dutifully shreds the library.
> >
> > Ignore the misleading error message from adlink below, but focus on the
> > g++ command that is missing the important elements 'simple' and
> > 'simple.obj':
> >
> > C:\simple>tpl2cpp simple
> > xxglobal.tmp
> > xxhtop.tmp
> > header.tmp
> > xxalloc.tmp
> > xxtopm.tmp
> > 1 file(s) copied.
> >
> > C:\simple>adcomp simple
> > g++ -c -O3 -D__GNUDOS__ -Dlinux -DOPT_LIB -DUSE_LAPLACE -fpermissive
> -I.
> > -I"c:\admb\include" -I"c:\admb\contrib\include" -o simple.obj simple.cpp
> >
> > C:\simple>adlink simple
> > g++ -s -static -o "c:\admb\contrib\lib\libcontribo.a"
> > "c:\admb\lib\libadmbo.a"
> >
> c:/gnu/gcc/bin/../lib/gcc/mingw32/4.7.2/../../..\libmingw32.a(main.o):main.c:(.text.startup+0xa7):
> >
> > undefined reference to `WinMain at 16'
> > collect2.exe: error: ld returned 1 exit status
> >
> > ---
> >
> > This will probably not be very hard to fix, but it means two things:
> >
> > 1. We should release 11.2 that passes the tpl2cpp->adcomp->adlink test.
> >
> > 2. We should add the test above as a Buildbot test, probably with more
> > variations of script calls.
> >
> > Arni
> > _______________________________________________
> > Developers mailing list
> > Developers at admb-project.org
> > http://lists.admb-project.org/mailman/listinfo/developers
> >
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 26 Jun 2013 10:20:34 -1000
> From: John Sibert <sibert at hawaii.edu>
> To: ADMB Developers <developers at admb-project.org>
> Subject: [Developers] netbeans and debuggers
> Message-ID: <51CB4D12.3010803 at hawaii.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Saw this link recently on in the G+ C++ community
> http://www.drdobbs.com/testing/13-linux-debuggers-for-c-reviewed/240156817
> reviewing front ends for gdb
>
> Netbeans came out pretty well in the comparison. I gave it try and it is
> is no worse than ddd. It doesn't really do a good job of displaying
> autodif/admb types (it depends on gdb). But is nicer to use.
>
> Also it is an ide that seems to understand make files and probably works
> on windoze. So it might be a nice way to break up large tpl files into
> more manageable pieces.
>
> So does anyone have any experience with netbeans? Perhaps a tool for
> invoking tpl2cpp or syntax highlighter for autodif/admb types?
>
> Cheers,
> John
>
>
> --
> John Sibert
> Emeritus Researcher, SOEST
> University of Hawaii at Manoa
> Honolulu HI (GMT-10)
> 808-294-3842
>
> Visit the ADMB project http://admb-project.org/
>
>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 26 Jun 2013 10:23:15 -1000
> From: John Sibert <sibert at hawaii.edu>
> To: Mark Maunder <mmaunder at iattc.org>
> Cc: ADMB Developers <developers at admb-project.org>, "Cristian Canales
> \(cristian.canales at ifop.cl\)" <cristian.canales at ifop.cl>
> Subject: Re: [Developers] init_number_matrix
> Message-ID: <51CB4DB3.1040105 at hawaii.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> It is something Johnoel developed on my request. Perhaps it hasn't found
> its way into the code base. I've been using for quite a while.
>
> John Sibert
> Emeritus Researcher, SOEST
> University of Hawaii at Manoa
> Honolulu HI (GMT-10)
> 808-294-3842
>
> Visit the ADMB project http://admb-project.org/
>
> On 06/26/2013 10:14 AM, Mark Maunder wrote:
> > It is not defined in version 10.0?
> >
> > -----Original Message-----
> > From: John Sibert [mailto:sibert at hawaii.edu]
> > Sent: Wednesday, June 26, 2013 12:51 PM
> > To: ADMB Developers
> > Cc: Mark Maunder; Cristian Canales (cristian.canales at ifop.cl)
> > Subject: Re: [Developers] init_number_matrix
> >
> > I routinely use init_bounded_number_matrix
> >
> > But I have no idea what init_vector_matrix might be.
> >
> > John Sibert
> > Emeritus Researcher, SOEST
> > University of Hawaii at Manoa
> > Honolulu HI (GMT-10)
> > 808-294-3842
> >
> > Visit the ADMB project http://admb-project.org/
> >
> > On 06/26/2013 08:59 AM, Mark Maunder wrote:
> >> A good addition to the ADMB code would be
> >>
> >> Init_number_matrix so you could have a matrix of phases. I am assuming
> >> that init_matrix_matrix and init_vector_vector don't do this.
> >>
> >> Probably need init_vector_matrix as well.
> >>
> >> Mark
> >>
> >> The CAPAM selectivity workshop report is now online
> >>
> >> ftp://ftp.capamresearch.org/incoming/selevtivity_workshop/CAPAM_Select
> >> ivity%20Workshop_Series%20Report_June%202013.pdf
> >>
> >> The Stock Synthesis special issue of the journal Fisheries Research is
> >> now published
> >>
> >> http://www.sciencedirect.com/science/journal/01657836/142
> >>
> >> Mark Maunder
> >>
> >> Head of the Stock Assessment Program
> >>
> >> Inter-American Tropical Tuna Commission
> >>
> >> 8604 La Jolla Shores Drive
> >>
> >> La Jolla, CA, 92037-1508, USA
> >>
> >> Tel: (858) 546-7027
> >>
> >> Fax: (858) 546-7133
> >>
> >> mmaunder at iattc.org <mailto:mmaunder at iattc.org>
> >>
> >> http://www.fisheriesstockassessment.com/TikiWiki/tiki-index.php?page=M
> >> ark+Maunder
> >>
> >> Visit the Center for the Advancement of Population Assessment
> >> Methodology at
> >>
> >> http://www.capamresearch.org/
> >>
> >> Visit the AD Model Builder project at
> >>
> >> http://admb-project.org/
> >>
> >> See the following website for information on fisheries stock
> >> assessment http://www.fisheriesstockassessment.com/
> >>
> >>
> >>
> >> _______________________________________________
> >> Developers mailing list
> >> Developers at admb-project.org
> >> http://lists.admb-project.org/mailman/listinfo/developers
> >
> >
> >
>
>
>
> ------------------------------
>
> Message: 6
> Date: Wed, 26 Jun 2013 13:01:59 -1000
> From: Johnoel Ancheta <johnoel at hawaii.edu>
> To: Allan Hicks - NOAA Federal <allan.hicks at noaa.gov>, John Sibert
> <sibert at hawaii.edu>, "developers at admb-project.org"
> <developers at admb-project.org>
> Cc: Juan Valero <juanlvalero at gmail.com>, "Grandin, Chris"
> <Chris.Grandin at dfo-mpo.gc.ca>, Athol Whitten <whittena at uw.edu>
> Subject: Re: [Developers] MinGW 64 and GDB
> Message-ID:
> <CAJMx2XWviV7471r+01HdP8KH3LcqT=
> TUsMHw5T279e3uUAoa_A at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> ADMB aims be portable to all compilers. It is tricky because everyone
> has different combinations of compilers and operating systems. Added
> to that is the differences in configuration. I've tried to improve the
> build
> system to satisfy all users. Some are happy, some are not so happy.
> If we can continue to improve everyday, it should reach a state that all
> developers and users are happy with. In order to reach that state, it is
> important to try and test out what is on the HEAD of the ADMB trunk by
> as much developers and users. Having a lot of extra eyes to spot errors
> before a release improves the quality of the software. I apologize for any
> issues that was not caught by me or the automated build server.
>
> Johnoel
>
>
> ------------------------------
>
> _______________________________________________
> Developers mailing list
> Developers at admb-project.org
> http://lists.admb-project.org/mailman/listinfo/developers
>
>
> End of Developers Digest, Vol 52, Issue 9
> *****************************************
>
--
Matthew Supernaw
Scientific Programmer
*National Oceanic and Atmospheric Administration*
National Marine Fisheries Service
Sustainable Fisheries Division
St. Petersburg, FL, 33701
Phone 727-551-5606
Fax 727-824-5300
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