[ADMB Users] Build ADMB 11.1
Johnoel Ancheta
johnoel at hawaii.edu
Tue Mar 4 10:37:39 PST 2014
Thanks Mark for pointing those out. Committed
http://www.admb-project.org/redmine/projects/issues/repository/revisions/1731
What permission problem are you having? I can't seem to duplicate those
issues.
On Mon, Mar 3, 2014 at 10:02 PM, Mark Payne <mpa at aqua.dtu.dk> wrote:
> Hi,
>
> Thanks for the tips. It works now following these instructions, although
> with mods. However, there are a couple of things that I would point out
> * there is a tilde missing in the source directory to copy from in step 6.
> It should read:
> [~]$ sudo cp -Rvf ~/admb/build/dist /usr/local/admb
> Although the prompt indicates that this command is being run from the home
> directory there is no suggestion in the text that you need to change
> accordingly.
> * there is a permissions problem created for me (at least) when copying
> admb/ to /usr/local/admb. By copying as root ie via sudo, all new
> directories are owned by root, which means that they can't be run by the
> user. Adding the -p flag to the copy solves this problem
> sudo cp -Rvfp ~/admb/build/dist /usr/local/admb
> but may not be the cleanest solution ie having files owned by my local
> user in /usr/local...
> * Most importantly, these new build instructions are not reflected in
> INSTALL.txt!
>
> Mark
> ________________________________________
> Fra: John Sibert [sibert at hawaii.edu]
> Sendt: 4. marts 2014 07:12
> Til: bigA
> Cc: Johnoel Ancheta; Mark Payne; users at admb-project.org
> Emne: Re: [ADMB Users] Build ADMB 11.1
>
> I'm not convinced that symbolic links are really simpler (because I have
> trouble remembering the syntax), so I prefer the environment variable in
> most cases. Anyhow it is nice to have the option to do it either way.
>
> Thanks, Aaron, for preparing the man page. I'm not sure it is consistent
> with `admb --help` though. A couple of options seem to be missing.
> > $ admb --help
> >
> > Builds AD Model Builder executable or library.
> >
> > Usage: admb [-c] [-d] [-g] [-r] [-f] model [src(s)]
> >
> > Options:
> > -c Build only object file(s) (.obj).
> > -d Build a shared library (.so).
> > -g Build with debug symbols.
> > -r Build with Random effects library (ADMB-RE).
> > -f Build with Fast optimized mode library (no bounds checking).
> > By default, admb script builds with bounds checking.
> > model TPL file (ie simple.tpl or the filename simple with no .tpl
> > extension)
> > src(s) C/C++ Source file(s) containing classes, methods and variables
> > that
> > are used in model.
>
>
> 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 03/03/2014 03:48 PM, bigA wrote:
> > In general, fixing the paths and making necessary (or convenient)
> > symbolic links is better than asking people to edit their .bashrc .
> > Many bash users use their bashrc to configure their working
> > environment; admb is just one of countless things I use a shell for.
> >
> > Once again, I have assembled the extant man page; do people think more
> > content is needed?
> >
> > http://www.admb-project.org/developers/packaging/debian/man.pdf/view
> > Cheers!
> > Aaron
> >
> >
> > On Mon, Mar 3, 2014 at 5:27 PM, John Sibert <sibert at hawaii.edu> wrote:
> >> Why is it preferable to set a symbolic link than to set an environment
> >> variable in a .basrc file?
> >>
> >> 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 03/03/2014 08:07 AM, Johnoel Ancheta wrote:
> >>> Try
> >>>
> >>> http://www.admb-project.org/buildbot/documentation/QuickStartUnix.html
> >>>
> >>>
> >>>
> >>> On Mon, Mar 3, 2014 at 7:18 AM, Mark Payne <mpa at aqua.dtu.dk
> >>> <mailto:mpa at aqua.dtu.dk>> wrote:
> >>>
> >>> Hi,
> >>>
> >>> I am having problems installingADMB 11.1 from the source on the
> >>> website ie
> >>>
> >>> http://admb-project.googlecode.com/files/admb-11.1.zip
> >>>
> >>> The source appears to build correctly, but fails when trying to
> >>> run the simple example. I have RTFM'd to the letter but it seems
> >>> that the instructions are incomplete and various items are not
> >>> getting picked up in the path.... (see below) What directories
> >>> does ADMB need to be in the path?
> >>>
> >>> Mark
> >>>
> >>> admb simple.
> >>>
> >>> *** adlink -s
> >>> g++ -o "/home/mpayne/Misc/admb"/contrib/lib/libcontrib.a
> >>> "/home/mpayne/Misc/admb"/lib/libadmb.a
> >>>
> /usr/lib/gcc/x86_64-linux-gnu/4.8/../../../x86_64-linux-gnu/crt1.o: In
> >>> function `_start':
> >>> (.text+0x20): undefined reference to `main'
> >>> collect2: error: ld returned 1 exit status
> >>>
> >>> Error: Could not build
> >>>
> >>>
> >>>
> >>>
> ------------------------------------------------------------------------
> >>> *Fra:* users-bounces at admb-project.org
> >>> <mailto:users-bounces at admb-project.org>
> >>> [users-bounces at admb-project.org
> >>> <mailto:users-bounces at admb-project.org>] på vegne af Johnoel
> >>> Ancheta [johnoel at hawaii.edu <mailto:johnoel at hawaii.edu>]
> >>> *Sendt:* 21. februar 2014 21:03
> >>> *Til:* bigA
> >>> *Cc:* users at admb-project.org <mailto:users at admb-project.org>
> >>> *Emne:* Re: [ADMB Users] ADMB in standard package formats
> >>>
> >>>
> >>> The build process has changed. Check the link below.
> >>>
> >>>
> http://www.admb-project.org/buildbot/documentation/QuickStartUnix.html
> >>>
> >>> It should be simpler and easier for everyone, but may need some
> >>> fine tuning.
> >>>
> >>> Feedback from Barak Pearlmutter was used for the the changes.
> >>> Such as the
> >>> eliminating the need to set System Variables. Although, it will
> >>> still work if they
> >>> are set.
> >>>
> >>> If you would like to contribute man pages, please let me know.
> >>>
> >>> Thanks,
> >>> Johnoel
> >>>
> >>>
> >>> On Wed, Feb 19, 2014 at 3:57 AM, bigA <jaguar.smart at gmail.com
> >>> <mailto:jaguar.smart at gmail.com>> wrote:
> >>>
> >>> I can work the man page; I have thus far been responsible for
> it.
> >>> I assume we don't want to write a 5460 line beast of a man
> page;
> >>> however any content that people want included in the man page
> >>> shown in
> >>> the Debian package.
> >>> Honestly, I think that focusing on the standard Linux build
> >>> process
> >>> and including the man page in the default build process will
> make
> >>> getting admb into the standard linux pipeline.
> >>> Barak Pearlmutter is probably a critical resource for this
> >>> activity;
> >>> however he cannot work on this alone. Has anyone looked at
> the
> >>> patches he has suggested? If the build process needs to be
> >>> cleaned up,
> >>> who within admb
> >>> is willing to work with us on it?
> >>>
> >>> Aaron
> >>>
> >>> On Wed, Feb 19, 2014 at 12:47 AM, Arni Magnusson
> >>> <arnima at hafro.is <mailto:arnima at hafro.is>> wrote:
> >>> > Our priority should be to release ADMB in standard package
> >>> formats: Debian,
> >>> > Gentoo, RPM, and Mac.
> >>> >
> >>> > This will make ADMB much more visible and accessible for
> >>> scientists in all
> >>> > disciplines. Package repositories are categorized, so ADMB
> >>> would be listed
> >>> > on autogenerated lists of scientific and statistical
> >>> software for Linux, for
> >>> > example. These lists are copied to Wikipedia, blogs,
> >>> newsletters, etc.
> >>> >
> >>> > Packaging means adapting the build procedure to Linux
> >>> standards (we may be
> >>> > there already), writing a short man page, and filling out a
> >>> basic template
> >>> > file for each package format. Please consider participating
> >>> in the ongoing
> >>> > effort:
> >>> >
> >>> > http://admb-project.org/developers/packaging
> >>> >
> >>> > Arni
> >>> > _______________________________________________
> >>> > Users mailing list
> >>> > Users at admb-project.org <mailto:Users at admb-project.org>
> >>>
> >>> > http://lists.admb-project.org/mailman/listinfo/users
> >>> _______________________________________________
> >>> Users mailing list
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> >>>
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> >>>
> >>>
> >>>
> >>> _______________________________________________
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> >>>
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> >>>
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> >>>
> >>>
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> >>> Users mailing list
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> >>
> >>
> >> _______________________________________________
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> >> Users at admb-project.org
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>
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