WSL Error: 'sh: 1: Syntax error: "(" unexpected'

[kschwede]

I'm having repeated errors when building documentation with Cmake Gninja. I don't have these issues when compiling these the classic way.

master branch, WSL2 + Ubuntu 20.04, AMD 3900x, WSL2 looks like it's using about 12 gigs of memory (out of 32).

Is something going on with the multi-threading of building documentation? Currently, the only errors I see are those at the end. I'm attaching (the not very helpful) example output errors here in a zip file.
ErrorsFromBuild.zip
Some of the example outputs simply say "Killed" at the end.

Weirdly, when I try re-running
ninja install-packages
at least the second time (and getting a different similar-looking error the first time), it completed without errors.

Finally, peridocally, in the terminal output, i also see
sh: 1: Syntax error: "(" unexpected

Is this something I should be worried about?
(they don't seem to cause the compilation to fail)

[DanGrayson]

Finally, peridocally, in the terminal output, i also see
sh: 1: Syntax error: "(" unexpected

Is this something I should be worried about?

I think that is indeed something we should be worried about.

[mahrud]

Is something going on with the multi-threading of building documentation? Currently, the only errors I see are those at the end. I'm attaching (the not very helpful) example output errors here in a zip file.
ErrorsFromBuild.zip
Some of the example outputs simply say "Killed" at the end.

I doubt it has to do with multi-threading, in particular, the errors that just say "Killed" are the same functions as in #1456, where they segfault.

Weirdly, when I try re-running
ninja install-packages
at least the second time (and getting a different similar-looking error the first time), it completed without errors.

The other error, on line clean (0.001, sosPoly sol), is calling csdp and I can reproduce that when csdp is not found, but I can't see how the second time csdp is found, unless csdp is also crashing and hence not returning anything.

Finally, peridocally, in the terminal output, i also see
sh: 1: Syntax error: "(" unexpected

Do you see this appearing in any other example files? Perhaps try:

cat usr-dist/common/share/doc/Macaulay2/Elimination/example-output/* | grep unexpected

[kschwede]

The cat command produces no output.

I'll try rebuilding again.

Should I try uninstalling csdp?

[mahrud]

Might be worth trying with both system csdp and csdp built by M2. Let's try to reproduce it without rebuilding first. Try:

ninja uninstall-SumsOfSquares uninstall-NumericalImplicitization
ninja install-SumsOfSquares install-NumericalImplicitization

Do you see any errors? What if you do:

ninja uninstall-packages
ninja install-packages

[kschwede]

Whoops, I just rebuilt from scratch now. Seeing the same errors. the cat command produces nothing.

Running

ninja uninstall-SumsOfSquares uninstall-NumericalImplicitization
ninja install-SumsOfSquares install-NumericalImplicitization

produces no errors even on the same system that just had errors. The only concerning information is the syntax error warnings.

[5/5] Installing package SumsOfSquares
sh: 1: Syntax error: "(" unexpected
sh: 1: Syntax error: "(" unexpected
 -- making example results for RoundTol
 -- making example results for SOSPoly
 -- making example results for sosPoly
 -- making example results for coefficient field
 -- making example results for sosdecTernary
 -- making example results for TraceObj
 -- making example results for clean(RR,SOSPoly)
 -- making example results for SumsOfSquares
 -- making example results for solveSOS
 -- making example results for solveSOS(RingElement,RingElement,Matrix)
 -- making example results for sosInIdeal
 -- making example results for library
 -- making example results for SDPResult
 -- making example results for recoverSolution
 -- making example results for value(SOSPoly)
 -- making example results for lowerBound
 -- info: there are 18 documentation nodes that are not listed as a subnode

I'm running the full uninstall and install of packages now, but I expect that to take a bit longer.

[kschwede]

The same errors occurred with the full uninstall + install of the packages that did not occur when just installing NumericalImplicitization.

See for instance:

[202/206] Installing package NumericalImplicitization                                                                                                                 
FAILED: Macaulay2/packages/CMakeFiles/install-NumericalImplicitization usr-dist/x86_64-Linux-Ubuntu-20.04/lib/x86_64-linux-gnu/Macaulay2/NumericalImplicitization/.ins
d                                                                                                                                                                     
cd /home/schwede/M2Ninja/M2/M2/BUILD/build/Macaulay2/packages && /home/schwede/M2Ninja/M2/M2/BUILD/build/usr-dist/x86_64-Linux-Ubuntu-20.04/bin/M2 -q --stop --silent 
preload --no-threads -e errorDepth=3 -e debugLevel=0 -e "installPackage(\"NumericalImplicitization\", Verbose => false, RerunExamples => false, CheckDocumentation => 
 IgnoreExampleErrors => false, RemakeAllDocumentation => false, InstallPrefix => \"/home/schwede/M2Ninja/M2/M2/BUILD/build/usr-dist/\", UserMode => false, SeparateExe
true, DebuggingMode => true)" -e "\"info-\"|\"NumericalImplicitization\" << NumericalImplicitization#\"test number\" << close" -e "exit 0" && gzip -nf9 /home/schwede/
ja/M2/M2/BUILD/build/usr-dist/common/share/info/NumericalImplicitization.info                                                                                         
 -- making example results for numericalHilbertFunction                                                                                                               
 -- making example results for ConvertToCone                                                                                                                          
 -- making example results for isOnImage                                                                                                                              
 ulimit -c unlimited; ulimit -t 700; ulimit -m 850000; ulimit -s 8192; ulimit -n 512;  cd /tmp/M2-15785-0/4-rundir/; GC_MAXIMUM_HEAP_SIZE=400M "/home/schwede/M2Ninja/
/BUILD/build/usr-dist/x86_64-Linux-Ubuntu-20.04/bin/M2-binary" -q --int --no-randomize --no-readline --silent --stop --print-width 77 -e 'needsPackage("NumericalImpli
ation", Reload => true, FileName => "/home/schwede/M2Ninja/M2/M2/Macaulay2/packages/NumericalImplicitization.m2")' <"/tmp/M2-15785-0/1_is__On__Image.m2" >>"/home/schw
2Ninja/M2/M2/BUILD/build/usr-dist/common/share/doc/Macaulay2/NumericalImplicitization/example-output/_is__On__Image.errors" 2>&1                                      
/home/schwede/M2Ninja/M2/M2/BUILD/build/usr-dist/common/share/doc/Macaulay2/NumericalImplicitization/example-output/_is__On__Image.errors:0:1: (output file) error: Ma
y2 killed by signal 9                                                                                                                                                 
/tmp/M2-15785-0/1_is__On__Image.m2:0:1: (input file)                                                                                                                  
M2: *** Error 9                                                                                                                                                       
 -- making example results for NumericalInterpolationTable                                                                                                            
 -- making example results for numericalImageDim                                                                                                                      
 -- making example results for PseudoWitnessSet                                                                                                                       
 -- making example results for pseudoWitnessSet                                                                                                                       
 ulimit -c unlimited; ulimit -t 700; ulimit -m 850000; ulimit -s 8192; ulimit -n 512;  cd /tmp/M2-15785-0/8-rundir/; GC_MAXIMUM_HEAP_SIZE=400M "/home/schwede/M2Ninja/
/BUILD/build/usr-dist/x86_64-Linux-Ubuntu-20.04/bin/M2-binary" -q --int --no-randomize --no-readline --silent --stop --print-width 77 -e 'needsPackage("NumericalImpli
ation", Reload => true, FileName => "/home/schwede/M2Ninja/M2/M2/Macaulay2/packages/NumericalImplicitization.m2")' <"/tmp/M2-15785-0/1_pseudo__Witness__Set.m2" >>"/ho
hwede/M2Ninja/M2/M2/BUILD/build/usr-dist/common/share/doc/Macaulay2/NumericalImplicitization/example-output/_pseudo__Witness__Set.errors" 2>&1                        
/home/schwede/M2Ninja/M2/M2/BUILD/build/usr-dist/common/share/doc/Macaulay2/NumericalImplicitization/example-output/_pseudo__Witness__Set.errors:0:1: (output file) er
Macaulay2 killed by signal 9                                                                                                                                          
/tmp/M2-15785-0/1_pseudo__Witness__Set.m2:0:1: (input file)                                                                                                           
M2: *** Error 9                                                                                                                                                       
 -- making example results for extractImageEquations                                                                                                                  
 -- making example results for numericalImageSample                                                                                                                   
 -- making example results for numericalSourceSample                                                                                                                  
 -- making example results for numericalImageDegree                                                                                                                   
 ulimit -c unlimited; ulimit -t 700; ulimit -m 850000; ulimit -s 8192; ulimit -n 512;  cd /tmp/M2-15785-0/12-rundir/; GC_MAXIMUM_HEAP_SIZE=400M "/home/schwede/M2Ninja
2/BUILD/build/usr-dist/x86_64-Linux-Ubuntu-20.04/bin/M2-binary" -q --int --no-randomize --no-readline --silent --stop --print-width 77 -e 'needsPackage("NumericalImpl
zation", Reload => true, FileName => "/home/schwede/M2Ninja/M2/M2/Macaulay2/packages/NumericalImplicitization.m2")' <"/tmp/M2-15785-0/1_numerical__Image__Degree.m2" >
me/schwede/M2Ninja/M2/M2/BUILD/build/usr-dist/common/share/doc/Macaulay2/NumericalImplicitization/example-output/_numerical__Image__Degree.errors" 2>&1               
/home/schwede/M2Ninja/M2/M2/BUILD/build/usr-dist/common/share/doc/Macaulay2/NumericalImplicitization/example-output/_numerical__Image__Degree.errors:0:1: (output file
or: Macaulay2 killed by signal 9                                                                                                                                      
/tmp/M2-15785-0/1_numerical__Image__Degree.m2:0:1: (input file)                                                                                                       
M2: *** Error 9                                                                                                                                                       
 -- making example results for numericalNullity                                                                                                                       
currentString:1:1:(3):[2]: error: installPackage: 3 error(s) occurred running examples for package NumericalImplicitization

[mahrud]

Could you attach the log, at least after [180/206] or so and until the end? I'm wondering if this has to do with which packages must be installed before SumsOfSquares and NumericalImplicitization.

Also, could you try doing:

ninja uninstall-SumsOfSquares uninstall-NumericalImplicitization uninstall-NumericalAlgebraicGeometry
ninja install-SumsOfSquares install-NumericalImplicitization

[kschwede]

What's the best way to grab the log? (Sorry for the dumb question).

Anyways, removing NumericalAlgebraicGeometry and installing SumsOfSquare and NumericalImplicitization worked with no errors.

[mahrud]

What's the best way to grab the log? (Sorry for the dumb question).

Not a dumb question, because I don't think there's a great way other than just copy and pasting from the terminal. I guess it would be easier to paste it as a gist: https://gist.github.com/ instead of right here.

Anyways, removing NumericalAlgebraicGeometry and installing SumsOfSquare and NumericalImplicitization worked with no errors.

Hmm, this is such a Heisenbug.

[kschwede]

BuildPackages-Output.zip
That file is the complete output of a clean ninja install-packages.

[mahrud]

Thanks! I'll look into this more, though I have no idea right now.

[kschwede]

So I tried uninstalling all packages and then running
ninja install-SumsOfSquares install-NumericalImplicitization
No errors either...

I suppose we could modify the packages in question to produce more debugging output?

Is there any chance that there's some issue interacting with these third party programs simultaneously?

I'm not sure how the multi-threading package installation works. How do I reduce the number of threads it uses? (Although i guess I can control resources shared to WSL2).