[Developers] Developers Digest, Vol 52, Issue 9
John Sibert
sibert at hawaii.edu
Thu Jun 27 12:37:32 PDT 2013
Hi Matthew,
Arni's emacs ide is great, especially for newbies. Netbeans might be
useful in several ways. It may be better front end for gdb than ddd (but
it still also has problems displaying admb and autodif types). I'm
interested in using Netbeans to manage admb projects with multiple
files, ie projects where FUNCTIONs have been removed from the tpl and
place in separate files. I really like that Netbeans uses make files,
something that I already have for everything I do.
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/
On 06/26/2013 02:26 PM, Matthew Supernaw - NOAA Federal wrote:
> 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
> <mailto:developers-request at admb-project.org>> wrote:
>
> Send Developers mailing list submissions to
> developers at admb-project.org <mailto:developers at admb-project.org>
>
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> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Developers digest..."
>
>
> 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 <mailto:mmaunder at iattc.org>>
> To: John Sibert <sibert at hawaii.edu <mailto:sibert at hawaii.edu>>,
> ADMB Developers
> <developers at admb-project.org
> <mailto:developers at admb-project.org>>
> Cc: "Cristian Canales \(cristian.canales at ifop.cl
> <mailto:cristian.canales at ifop.cl>\)"
> <cristian.canales at ifop.cl <mailto:cristian.canales at ifop.cl>>
> Subject: Re: [Developers] init_number_matrix
> Message-ID:
>
> <339913E1960AE142A9373DFCD849F3DA333A25CD at mail1.lajolla.iattc.org
> <mailto: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
> <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
> <mailto: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 <tel: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 <tel:%28858%29%20546-7027>
> >
> > Fax: (858) 546-7133 <tel:%28858%29%20546-7133>
> >
> > mmaunder at iattc.org <mailto:mmaunder at iattc.org>
> <mailto: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 <mailto: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 <mailto:mmaunder at iattc.org>>
> To: John Sibert <sibert at hawaii.edu <mailto:sibert at hawaii.edu>>,
> ADMB Developers
> <developers at admb-project.org
> <mailto:developers at admb-project.org>>
> Cc: "Cristian Canales \(cristian.canales at ifop.cl
> <mailto:cristian.canales at ifop.cl>\)"
> <cristian.canales at ifop.cl <mailto:cristian.canales at ifop.cl>>
> Subject: Re: [Developers] init_number_matrix
> Message-ID:
>
> <339913E1960AE142A9373DFCD849F3DA333A25E4 at mail1.lajolla.iattc.org
> <mailto: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
> <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
> <mailto: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 <tel: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 <tel:%28858%29%20546-7027>
> >
> > Fax: (858) 546-7133 <tel:%28858%29%20546-7133>
> >
> > mmaunder at iattc.org <mailto:mmaunder at iattc.org>
> <mailto: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 <mailto: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 <mailto:johnoel at hawaii.edu>>
> To: Arni Magnusson <arnima at hafro.is <mailto:arnima at hafro.is>>
> Cc: developers at admb-project.org <mailto: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 <mailto:ML1asOo_LcyP%2BmKjsnKuoxOYsp1LabTKx0O6pt39w 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
> <mailto: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 <mailto: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 <mailto:sibert at hawaii.edu>>
> To: ADMB Developers <developers at admb-project.org
> <mailto:developers at admb-project.org>>
> Subject: [Developers] netbeans and debuggers
> Message-ID: <51CB4D12.3010803 at hawaii.edu
> <mailto: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 <tel: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 <mailto:sibert at hawaii.edu>>
> To: Mark Maunder <mmaunder at iattc.org <mailto:mmaunder at iattc.org>>
> Cc: ADMB Developers <developers at admb-project.org
> <mailto:developers at admb-project.org>>, "Cristian Canales
> \(cristian.canales at ifop.cl
> <mailto:cristian.canales at ifop.cl>\)" <cristian.canales at ifop.cl
> <mailto:cristian.canales at ifop.cl>>
> Subject: Re: [Developers] init_number_matrix
> Message-ID: <51CB4DB3.1040105 at hawaii.edu
> <mailto: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 <tel: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
> <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
> <mailto: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 <tel: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 <tel:%28858%29%20546-7027>
> >>
> >> Fax: (858) 546-7133 <tel:%28858%29%20546-7133>
> >>
> >> mmaunder at iattc.org <mailto:mmaunder at iattc.org>
> <mailto: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 <mailto: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 <mailto:johnoel at hawaii.edu>>
> To: Allan Hicks - NOAA Federal <allan.hicks at noaa.gov
> <mailto:allan.hicks at noaa.gov>>, John Sibert
> <sibert at hawaii.edu <mailto:sibert at hawaii.edu>>,
> "developers at admb-project.org <mailto:developers at admb-project.org>"
> <developers at admb-project.org
> <mailto:developers at admb-project.org>>
> Cc: Juan Valero <juanlvalero at gmail.com
> <mailto:juanlvalero at gmail.com>>, "Grandin, Chris"
> <Chris.Grandin at dfo-mpo.gc.ca
> <mailto:Chris.Grandin at dfo-mpo.gc.ca>>, Athol Whitten
> <whittena at uw.edu <mailto:whittena at uw.edu>>
> Subject: Re: [Developers] MinGW 64 and GDB
> Message-ID:
>
> <CAJMx2XWviV7471r+01HdP8KH3LcqT=TUsMHw5T279e3uUAoa_A at mail.gmail.com <mailto: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 <mailto: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
>
>
>
> _______________________________________________
> Developers mailing list
> Developers at admb-project.org
> http://lists.admb-project.org/mailman/listinfo/developers
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