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problems using install from admb-13.0-linux.zip #272

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iantaylor-NOAA opened this issue Sep 2, 2022 · 4 comments
Closed

problems using install from admb-13.0-linux.zip #272

iantaylor-NOAA opened this issue Sep 2, 2022 · 4 comments
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@iantaylor-NOAA
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I'm revising some GitHub Actions to compile Stock Synthesis with ADMB 13.0 instead of 12.3 and ran into some problems with the Linux setup.

Using the "ubuntu-20.04" runner image (listed in https://github.com/actions/runner-images#available-environments), I got these errors

tpl2cpp: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by tpl2cpp)
tpl2rem: /lib/x86_64-linux-gnu/libc.so.6: version `GLIBC_2.34' not found (required by tpl2rem)

I got that same message on a local Linux server running "gcc version 4.8.5 20150623 (Red Hat 4.8.5-44)".

Switching the GitHub Action to the newer "ubuntu-22.04" runner produced this error:

Error: Error: Unable to find libadmb-contrib-x86_64-linux-g++11.a

see context of the error at https://github.com/nmfs-stock-synthesis/stock-synthesis/runs/8126396737?check_suite_focus=true#step:21:22.

The workflow I've modified (from something that @k-doering-NOAA had working well for ADMB 12.3) is here: https://github.com/nmfs-stock-synthesis/workflows/blob/admb13/.github/workflows/build-ss3.yml.
It now works for both Windows and Mac with ADMB 13.0. I could set up the Linux compile to build from source, which is what the Mac is doing, but that takes about 40 minutes vs 6 minutes for Windows (using admb-13.0-windows.zip).

@johnoel, any advice on what might be going wrong?

Also, FYI, when unzipping the admb-13.0-src.zip release on Windows without admin privileges I get the following messages:

Cannot create symbolic link : A required privilege is not held by the client. : C:\Users\ian.taylor\Downloads\admb-13.0-src\admb-13.0\src\df1b2-separable\remod10
Cannot create symbolic link : A required privilege is not held by the client. : C:\Users\ian.taylor\Downloads\admb-13.0-src\admb-13.0\tests\pella_t\pella_t.dat
@johnoel
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johnoel commented Sep 3, 2022

Bummer...

  • Fix build files to avoid incompatible shared library linking
  • Add support for gcc-11, then update existing release
  • Fix soft links in source zip file

@iantaylor-NOAA
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Thanks @johnoel, thanks for working on this.
I'm find working around the issue by building from source on linux for now.

iantaylor-NOAA added a commit to nmfs-ost/ss3-workflows that referenced this issue Sep 6, 2022
johnoel added a commit that referenced this issue Sep 6, 2022
johnoel added a commit that referenced this issue Sep 6, 2022
Fixes for Issue #272 - avoid soft links.
@johnoel
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johnoel commented Sep 9, 2022

Okay @iantaylor-NOAA, I updated the admb-13.0-linux.zip file which should correct the errors. Please give it a try...

@iantaylor-NOAA
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Works great in the GitHub actions. Thank you @johnoel!

On my local linux server I still get some errors about missing stuff (pasted below just in case it helps someone else searching for an error), but I don't expect to ever be compiling there now that the github action is working. And if I do need to do so, I just use ADMB 13.0 built from source which worked fine.

*** Linking: ss.obj
g++ --static -std=c++11 -O3 -oss ss.obj "/home/itaylor/h_itaylor/admb/admb-13.0/lib/libadmb-contrib-x86_64-linux-g++4.a"

/usr/bin/ld: cannot find -lstdc++
/usr/bin/ld: cannot find -lm
/usr/bin/ld: cannot find -lc
collect2: error: ld returned 1 exit status
Error: Could not build ss

iantaylor-NOAA added a commit to nmfs-ost/ss3-workflows that referenced this issue Sep 9, 2022
* change to lower warning count

To use after fixing error msgs in ss3

* change workflow from admb 12.3 to 13.0
- requires now compiling admb from source for Mac OS

* fix filename error

* fix workflow for mac (checkout instead of unzip)

* increase timeout limit (cancelled mac build)

* increase timeout limit even further

* switch to newer ubuntu
-hoping to fix "'GLIBC_2.34' not found"

* newer version of r-lib action

* build linux from source
- admb-project/admb#272

* switch run with est action to Windows
- linux build is much slower right now

* fix issues with switch from linux to windows

* Revert "fix issues with switch from linux to windows"

This reverts commit d6f0725.

* Revert "switch run with est action to Windows"

This reverts commit 6a6a996.

* switch run action to build linux from source

* update more workflows for admb 13.0

* fix ADMB 13.0 build for warnings workflow

* fix admb location for warnings workflow

* attempt fix for warnings build

* another attempt to fix build with warnings

* attempt another fix for warnings build

* add diagnostics to debug failing build

* yet another try

* use revised linux distribution

* fix extra line caused fail

* another try for warnings build

* add display of warnings to console

* fix filter for warnings

* restore simpler linux install

Co-authored-by: Kathryn Doering <kathryn.doering@noaa.gov>
e-perl-NOAA pushed a commit to nmfs-ost/ss3-doc that referenced this issue May 25, 2023
* change to lower warning count

To use after fixing error msgs in ss3

* change workflow from admb 12.3 to 13.0
- requires now compiling admb from source for Mac OS

* fix filename error

* fix workflow for mac (checkout instead of unzip)

* increase timeout limit (cancelled mac build)

* increase timeout limit even further

* switch to newer ubuntu
-hoping to fix "'GLIBC_2.34' not found"

* newer version of r-lib action

* build linux from source
- admb-project/admb#272

* switch run with est action to Windows
- linux build is much slower right now

* fix issues with switch from linux to windows

* Revert "fix issues with switch from linux to windows"

This reverts commit d6f0725415cbb3a7463b68c6ae9f02a981ae0137.

* Revert "switch run with est action to Windows"

This reverts commit 6a6a99676dc4f90541f6cd08e99f0748355e2ea5.

* switch run action to build linux from source

* update more workflows for admb 13.0

* fix ADMB 13.0 build for warnings workflow

* fix admb location for warnings workflow

* attempt fix for warnings build

* another attempt to fix build with warnings

* attempt another fix for warnings build

* add diagnostics to debug failing build

* yet another try

* use revised linux distribution

* fix extra line caused fail

* another try for warnings build

* add display of warnings to console

* fix filter for warnings

* restore simpler linux install

Co-authored-by: Kathryn Doering <kathryn.doering@noaa.gov>
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