Example now failing after update to R 4.1.1 and RStudio 2021.09.0 Build 351

[jjvenky]

After the update to R 4.1.1 and the necessary update of RStudio to 2021.09.0 Build 351, I had to reinstall all my R packages. This was fine (and expected) in Ubuntu 20.04.3 LTS.

Now, following the example from https://github.com/aemon-j/LakeEnsemblR/

> # 2. Run ensemble lake models
> run_ensemble(config_file = config_file, model = model)
Loading water temperature observations...[2021-11-02 14:05:21]
Finished loading water temperature observations![2021-11-02 14:05:22]
Running models... (Have you tried parallelizing?) [2021-11-02 14:05:22]
Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
  cannot open file './FLake/output/output.dat': No such file or directory

The folder './FLake/output' exists but the output.dat does not.

This looks like a workding directory problem but getwd() shows '/home/jvenkiteswaran/tmp/example/feeagh' so './FLake/output' makes sense.

[JFeldbauer]

I think this might be an issue with the shared libraries and the models not running as a consequence of this. This is described in the wiki (https://github.com/aemon-j/LakeEnsemblR/wiki/Installation-issues).

To be sure if this is the cause of the issue you can run the models on their own using the run-model() function from the model specific packages, e.g.

FLakeR::run_flake(sim_folder = "FLake", verbose = TRUE)
GLM3r::run_glm(sim_folder = "GLM", verbose = TRUE)
GOTMr::run_gotm(sim_folder = "GOTM", verbose = TRUE)
SimstratR::run_simstrat(sim_folder = "Simstrat", par_file = "simstrat.par", verbose = TRUE)

[jjvenky]

@JFeldbauer OMG I'm in GLIBC hell. I'll walk through that wiki entry.

> FLakeR::run_flake(sim_folder = "FLake", verbose = TRUE)

Program received signal SIGILL: Illegal instruction.

Backtrace for this error:
#0  0x7fd56c4bc32a
#1  0x7fd56c4bb503
#2  0x7fd56bf1420f
#3  0x7fd56c1a88d6
#4  0x55e0ac6fadac
#5  0x55e0ac6fcc51
#6  0x7fd56bef50b2
#7  0x55e0ac6f1ed9
#8  0xffffffffffffffff
Illegal instruction (core dumped)
character(0)
attr(,"status")
[1] 132
Warning message:
In system2(flake_path, wait = TRUE, stdout = TRUE, stderr = "",  :
  running command ''/home/jvenkiteswaran/R/x86_64-pc-linux-gnu-library/4.1/FLakeR/exec/nixflake' flake.nml' had status 132
  
  
  
> GLM3r::run_glm(sim_folder = "GLM", verbose = TRUE)
/home/jvenkiteswaran/R/x86_64-pc-linux-gnu-library/4.1/GLM3r/exec/nixglm: /home/jvenkiteswaran/R/x86_64-pc-linux-gnu-library/4.1/GLM3r/extbin/nixGLM/libm.so.6: version `GLIBC_2.29' not found (required by /usr/lib/x86_64-linux-gnu/libgd.so.3)
/home/jvenkiteswaran/R/x86_64-pc-linux-gnu-library/4.1/GLM3r/exec/nixglm: /home/jvenkiteswaran/R/x86_64-pc-linux-gnu-library/4.1/GLM3r/extbin/nixGLM/libm.so.6: version `GLIBC_2.29' not found (required by /usr/lib/x86_64-linux-gnu/libpng16.so.16)
/home/jvenkiteswaran/R/x86_64-pc-linux-gnu-library/4.1/GLM3r/exec/nixglm: /home/jvenkiteswaran/R/x86_64-pc-linux-gnu-library/4.1/GLM3r/extbin/nixGLM/libm.so.6: version `GLIBC_2.29' not found (required by /usr/lib/x86_64-linux-gnu/libtiff.so.5)
/home/jvenkiteswaran/R/x86_64-pc-linux-gnu-library/4.1/GLM3r/exec/nixglm: /home/jvenkiteswaran/R/x86_64-pc-linux-gnu-library/4.1/GLM3r/extbin/nixGLM/libm.so.6: version `GLIBC_2.29' not found (required by /usr/lib/x86_64-linux-gnu/libwebp.so.6)
/home/jvenkiteswaran/R/x86_64-pc-linux-gnu-library/4.1/GLM3r/exec/nixglm: /home/jvenkiteswaran/R/x86_64-pc-linux-gnu-library/4.1/GLM3r/extbin/nixGLM/libm.so.6: version `GLIBC_2.29' not found (required by /usr/lib/x86_64-linux-gnu/libsqlite3.so.0)
[1] 1




> GOTMr::run_gotm(sim_folder = "GOTM", verbose = TRUE)
/home/jvenkiteswaran/R/x86_64-pc-linux-gnu-library/4.1/GOTMr/exec/nixgotm: /home/jvenkiteswaran/R/x86_64-pc-linux-gnu-library/4.1/GOTMr/extbin/nix/libm.so.6: version `GLIBC_2.29' not found (required by /usr/lib/x86_64-linux-gnu/libsqlite3.so.0)



> SimstratR::run_simstrat(sim_folder = "Simstrat", par_file = "simstrat.par", verbose = TRUE)

Program received signal SIGILL: Illegal instruction.

Backtrace for this error:
#0  0x7fe7275b032a
#1  0x7fe7275af503
#2  0x7fe72702320f
#3  0x7fe727294c7e
#4  0x55996ae5a860
#5  0x55996ae5e0f8
#6  0x55996ae790dc
#7  0x55996ae51b9e
#8  0x7fe7270040b2
#9  0x55996ae51bd9
#10  0xffffffffffffffff
Illegal instruction (core dumped)
[1] " Simstrat version 2.4"                                                                                 
[2] " This software has been developed at eawag - Swiss Federal Institute of Aquatic Science and Technology"
[3] " "                                                                                                     
[4] " [OK] Configuration: simstrat.par"                                                                     
[5] " [OK] Grid file successfully read"                                                                     
[6] " [OK] Morphology file successfully read"                                                               
[7] " [OK] Initial data file successfully read"                                                             
attr(,"status")
[1] 132
Warning message:
In system2(simstrat_path, wait = TRUE, stdout = TRUE, stderr = "",  :
  running command ''/home/jvenkiteswaran/R/x86_64-pc-linux-gnu-library/4.1/SimstratR/exec/nixsimstrat' simstrat.par' had status 132

[robertladwig]

A quick fix for GLM3r would be to delete libm.so.6 inside the package, re-install it and try again

[JFeldbauer]

It should be enough to delet the libm.so.6 files in your local R installlation. This is usually located in your home dir e.g. ~/R/4.1/GLM3r/extbin/nixGLM

[jjvenky]

Wild. I remove all four libm.so.6 files and the models run.

./R/x86_64-pc-linux-gnu-library/4.1/GOTMr/extbin/nix/libm.so.6
./R/x86_64-pc-linux-gnu-library/4.1/FLakeR/extbin/nix/libm.so.6
./R/x86_64-pc-linux-gnu-library/4.1/GLM3r/extbin/nixGLM/libm.so.6
./R/x86_64-pc-linux-gnu-library/4.1/SimstratR/extbin/nix/libm.so.6

FTR the three versions of libm.so.6 installed in the /lib folder(s) all have different md5sums:

4aaad6c988fb8f356db567c0bf8f0d2d  /lib/x86_64-linux-gnu/libm.so.6
b2c721e8b382f3719927210ab5de9fd5  /lib/i386-linux-gnu/libm.so.6
a403e6f0fdcd5afa42cd6d50b0a09247  /lib32/libm.so.6

[jjvenky]

I will add (before closing this issue) a note from RStudio about R 4.1 that might be worth noting that there is a new graphics engine https://blog.rstudio.com/2021/06/09/rstudio-v1-4-update-whats-new/ and this might cause some problems.

[tpetzoldt]

Wild. I remove all four libm.so.6 files and the models run.

> ./R/x86_64-pc-linux-gnu-library/4.1/GOTMr/extbin/nix/libm.so.6

Thanks, I had the same issue with GOTM and after searching the net for + an hour, removing libm.so.6 did the job.