Testing and feedback needed for upcoming ADMB-13.0 release #249

johnoel · 2022-05-09T23:55:21Z

johnoel
May 9, 2022
Maintainer

Hi all,

ADMB-13 will be the next major release. It is scheduled to be released at the near the end of May 2022. To ensure a smooth release, user testing is requested. Please download and build the admb-13.0 branch and test with existing models. The major release has many changes and new features included. One of the big changes is improving the program display (see issue #221). The display is more concise and provides additional diagnostics such as bounds checking. @Cole-Monnahan-NOAA and @wStockhausen lead the development. One major feature that was developed is to run the body of a for loop in parallel instead of sequentially. The forest example was modified to run the funnel function in parallel. The modified example has shown improved runtime performance compared to the original version. So, please try out the release and provide feedback and report any errors that were found.

Thank you,
Johnoel

Cole-Monnahan-NOAA · 2022-05-10T20:55:31Z

Cole-Monnahan-NOAA
May 10, 2022
Collaborator

@johnoel At least two of us can't get it to run, see this issue. Could you provide more details on how to install? Thanks!

5 replies

k-doering-NOAA May 10, 2022

Also having issues compiling locally with mingw64 on windows.

johnoel May 11, 2022
Maintainer Author

Corrected issue. Please pull updates and try again.

k-doering-NOAA May 11, 2022

Hi Johnoel, I still wasn't able to compile locally after pulling in updates. Here is what I am seeing ( I think this was different than the errors others were encountering, though):

C:\Users\Kathryn.Doering\Documents\github_repos\admb>make g++-dist DEBUG=
make g++-core
make[1]: Entering directory '/c/Users/Kathryn.Doering/Documents/github_repos/admb'
make --directory=src CC=gcc CXX=g++ all
make[2]: Entering directory '/c/Users/Kathryn.Doering/Documents/github_repos/admb/src'
make _objects
make[3]: Entering directory '/c/Users/Kathryn.Doering/Documents/github_repos/admb/src'
g++ -c -std=c++14 -O2 -Wall -Wextra -Wconversion -Wno-unused-result -Wno-unused-parameter -DOPT_LIB -D_USE_MATH_DEFINES -I../build/admb/include -o ../build/objects-mingw64-g++8/optlp-nh99-model9.obj nh99/model9.cpp
nh99/model9.cpp: In function 'int operator+(int, const data_int&)':
nh99/model9.cpp:12:14: error: 'int data_int::val' is protected within this context
   return n+v.val;
              ^~~
In file included from nh99/model9.cpp:8:
../build/admb/include/admodel.h:1484:7: note: declared protected here
   int val;
       ^~~
nh99/model9.cpp: In function 'int operator+(const data_int&, int)':
nh99/model9.cpp:17:14: error: 'int data_int::val' is protected within this context
   return n+v.val;
              ^~~
In file included from nh99/model9.cpp:8:
../build/admb/include/admodel.h:1484:7: note: declared protected here
   int val;
       ^~~
nh99/model9.cpp: In function 'int operator+(const data_int&, const data_int&)':
nh99/model9.cpp:22:12: error: 'int data_int::val' is protected within this context
   return n.val + v.val;
            ^~~
In file included from nh99/model9.cpp:8:
../build/admb/include/admodel.h:1484:7: note: declared protected here
   int val;
       ^~~
nh99/model9.cpp:22:20: error: 'int data_int::val' is protected within this context
   return n.val + v.val;
                    ^~~
In file included from nh99/model9.cpp:8:
../build/admb/include/admodel.h:1484:7: note: declared protected here
   int val;
       ^~~
make[3]: *** [GNUmakefile:630: ../build/objects-mingw64-g++8/optlp-nh99-model9.obj] Error 1
make[3]: Leaving directory '/c/Users/Kathryn.Doering/Documents/github_repos/admb/src'
make[2]: *** [GNUmakefile:551: objects] Error 2
make[2]: Leaving directory '/c/Users/Kathryn.Doering/Documents/github_repos/admb/src'
make[1]: *** [Makefile:97: g++-core] Error 2
make[1]: Leaving directory '/c/Users/Kathryn.Doering/Documents/github_repos/admb'
make: *** [Makefile:92: g++-dist] Error 2

johnoel May 11, 2022
Maintainer Author

Did you clean first?

> make clean

k-doering-NOAA May 11, 2022

Did you clean first?
> make clean

Nope, I did not! Thanks @johnoel . I compiled successfully now!

Rick-Methot-NOAA · 2022-05-11T19:09:12Z

Rick-Methot-NOAA
May 11, 2022

successful compile for me too, but the installer reports that it cannot find many files in examples/admb-re folders.
looking forward to giving it a try.

1 reply

johnoel May 11, 2022
Maintainer Author

are you using?

> make install

Can you post the errors?

Rick-Methot-NOAA · 2022-05-11T19:36:03Z

Rick-Methot-NOAA
May 11, 2022

errors looked like:
Could Not Find c:\ADMB-13.0\examples\admb-re\pheno\pheno.bar
Could Not Find c:\ADMB-13.0\examples\admb-re\pheno\pheno.bgs
Could Not Find c:\ADMB-13.0\examples\admb-re\pheno\pheno.cor
Could Not Find c:\ADMB-13.0\examples\admb-re\pheno\pheno.cpp
and many more files not found.

2 replies

johnoel May 11, 2022
Maintainer Author

What command did you use to get the errors?

johnoel May 11, 2022
Maintainer Author

Was it?

> make clean

Rick-Methot-NOAA · 2022-05-11T19:42:42Z

Rick-Methot-NOAA
May 11, 2022

make clean

1 reply

johnoel May 11, 2022
Maintainer Author

Those can be ignored. Should be better though...

Cole-Monnahan-NOAA · 2022-05-11T20:34:33Z

Cole-Monnahan-NOAA
May 11, 2022
Collaborator

I can also now compile and run locally. I found no errors or issues on my small test set.

Windows 10. g++ (Built by Jeroen for the R-project) 8.3.0

0 replies

Rick-Methot-NOAA · 2022-05-11T20:40:29Z

Rick-Methot-NOAA
May 11, 2022

When trying to compile ss3 locally, I got this error:

*** Compile: ss.cpp
g++ -c -std=c++14 -O3 -fpermissive -D_FILE_OFFSET_BITS=64 -DUSE_ADMB_CONTRIBS -D_USE_MATH_DEFINES -I. -I"C:\ADMB-13.0\include" -I"C:\ADMB-13.0\include\contrib" -o ss.obj ss.cpp
ss.cpp: In member function 'void model_parameters::write_bigoutput()':
ss.cpp:29906:27: error: 'get_ln_det_value' was not declared in this scope
temp = get_ln_det_value();
^

1 reply

johnoel May 11, 2022
Maintainer Author

I can't seem to duplicate the compile error. How did you build ss.tpl?

Rick-Methot-NOAA · 2022-05-11T21:26:27Z

Rick-Methot-NOAA
May 11, 2022

I simply ran tpl2cpp, then ran admb

1 reply

johnoel May 11, 2022
Maintainer Author

Looks like you need to clean and recompile again. I can send you a precompiled admb directory for testing.

C:\stock-synthesis-github\ss330>C:\Users\johnoel\admb-github\admb.cmd ss.tpl

*** Parse: ss.tpl
xxglobal.tmp
xxhtop.tmp
header.tmp
xxalloc.tmp
xxtopm.tmp
        1 file(s) copied.
tpl2cpp   ss

*** Compile: ss.cpp
g++ -c -std=c++14 -O2 -D_FILE_OFFSET_BITS=64 -DUSE_ADMB_CONTRIBS -D_USE_MATH_DEFINES -I. -I"C:\Users\johnoel\admb-github\build\admb\include" -I"C:\Users\johnoel\admb-github\build\admb\include\contrib" -o ss.obj ss.cpp

*** Linking: ss.obj
g++ -static -o ss.exe ss.obj "C:\Users\johnoel\admb-github\build\admb\lib\libadmb-contrib-mingw64-g++8.a"

Successfully built 'ss.exe'.

wStockhausen · 2022-05-11T23:24:07Z

wStockhausen
May 11, 2022

And now for some good news: I had no problems on my Mac running OSX Catalina (I hate to give up the desktop picture). Just compiled and ran my Tanner crab assessment model--no issues! *William T. Stockhausen* Research Fishery Biologist, Alaska Fisheries Science Center NOAA Fisheries | U.S. Department of Commerce Office: (206) 526-4241 www.fisheries.noaa.gov

…

On Wed, May 11, 2022 at 3:25 PM johnoel ***@***.***> wrote: Looks like you need to clean and recompile again. I can send you a precompiled admb directory for testing. C:\stock-synthesis-github\ss330>C:\Users\johnoel\admb-github\admb.cmd ss.tpl *** Parse: ss.tpl xxglobal.tmp xxhtop.tmp header.tmp xxalloc.tmp xxtopm.tmp 1 file(s) copied. tpl2cpp ss *** Compile: ss.cpp g++ -c -std=c++14 -O2 -D_FILE_OFFSET_BITS=64 -DUSE_ADMB_CONTRIBS -D_USE_MATH_DEFINES -I. -I"C:\Users\johnoel\admb-github\build\admb\include" -I"C:\Users\johnoel\admb-github\build\admb\include\contrib" -o ss.obj ss.cpp *** Linking: ss.obj g++ -static -o ss.exe ss.obj "C:\Users\johnoel\admb-github\build\admb\lib\libadmb-contrib-mingw64-g++8.a" Successfully built 'ss.exe'. — Reply to this email directly, view it on GitHub <#249 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABMAD5BIJOCMC5HOCZV5V53VJQXUZANCNFSM5VP2A5NA> . You are receiving this because you were mentioned.Message ID: ***@***.***>

0 replies

Rick-Methot-NOAA · 2022-05-12T00:19:59Z

Rick-Methot-NOAA
May 12, 2022

switched to RTools and got a
"Successfully built executable."
message from make

3 replies

johnoel May 12, 2022
Maintainer Author

Was it msys2 that did not work?

Rick-Methot-NOAA May 12, 2022

Johnoel,
even though the installation reported being successful, it still did not set up path and environment such that I could compile using admb.cmd

johnoel May 23, 2022
Maintainer Author

See Issue #260. Should make it easier to set PATH for Windows.

k-doering-NOAA · 2022-05-23T13:36:29Z

k-doering-NOAA
May 23, 2022

@johnoel wanted to report that the ADMB 13 branch works well for Stock Synthesis models! Comparable runtimes, and no change in results for the tested models. We are also able to use ADMB 13 to compile SS3 on Mac, Linux, and Windows. We also like the new console, and it has inspired us to clean up some of the console output that SS3 adds on. Thank you for the option to test in advance before releasing!

3 replies

k-doering-NOAA May 23, 2022

Sorry, one more thing: these are the compiler warnings we get with -Wall . Just reporting this in case some of them should be fixed in admb: nmfs-ost/ss3-source-code#257 (comment)

johnoel May 23, 2022
Maintainer Author

See Issue #251

k-doering-NOAA May 23, 2022

Thanks for fixing those! I was just highlighting some other compiler warnings that we see when compiling stock synthesis with either ADMB 12.3 or 13, but perhaps they are safe to ignore (as we have been doing for some time)

johnoel · 2022-06-01T01:26:00Z

johnoel
Jun 1, 2022
Maintainer Author

Sorry all, need to delay release of ADMB-13 till next month. Working on Issue #255.

0 replies

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Testing and feedback needed for upcoming ADMB-13.0 release #249

johnoel May 9, 2022 Maintainer

Replies: 11 comments · 17 replies

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