build hangs without error message
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Denis Sunko
Apr 14, 2025, 10:03:25 AMApr 14
to sage-support
I have been installing Sage from source on three workstations and a laptop for ages. The last release which went without a hitch was 10.3. I skipped 10.4, but with 10.5 and 10.6 one of the workstations has a weird problem: the build simply hangs and stays that way, for as long as I let it (two days now). Below is the output of ps -xuwa | grep python and the tail of the install log. The log is 97 MB, but there seems to be nothing there save a few error messages from various packages which are the same as on the other three machines where there were no problems.
All four machines are Debian bookworm on amd64, fully up to date. The one where the build fails is only different in that I installed all the packages suggested by configure and did `make reconfigure' after that, as recommended. I can imagine that could cause some conflict, but not such silent failure of the build.
Any suggestion?
Thanks,
Denis
=========================================================================
output of ps xuwa | grep python, showing lots of defunct processes
=========================================================================
myuserid 213668 0.0 0.0 2584 916 ? S Apr12 0:00 /bin/sh /opt/Sage/sage-10.6/src/bin/sage-python /opt/Sage/sage-10.6/src/bin/sage-cleaner
myuserid 213669 0.0 0.0 17376 13008 ? S Apr12 0:01 python3 /opt/Sage/sage-10.6/src/bin/sage-cleaner
myuserid 213932 0.0 0.0 3108 2444 ? S Apr12 0:00 make doc-inventory--reference-spkg doc-inventory--reference-manifolds doc-inventory--reference-algebras doc-inventory--reference-polynomial_rings doc-inventory--reference-repl doc-inventory--reference-tensor_free_modules doc-inventory--reference-combinat doc-inventory--reference-dynamics doc-inventory--reference-plot3d doc-inventory--reference-arithgroup doc-inventory--reference-graphs doc-inventory--reference-misc doc-inventory--reference-parallel doc-inventory--reference-topology doc-inventory--reference-arithmetic_curves doc-inventory--reference-asymptotic doc-inventory--reference-calculus doc-inventory--reference-categories doc-inventory--reference-coding doc-inventory--reference-coercion doc-inventory--reference-constants doc-inventory--reference-cpython doc-inventory--reference-cryptography doc-inventory--reference-curves doc-inventory--reference-data_structures doc-inventory--reference-databases doc-inventory--reference-diophantine_approximation doc-inventory--reference-discrete_geometry doc-inventory--reference-doctest doc-inventory--reference-documentation doc-inventory--reference-drinfeld_modules doc-inventory--reference-euclidean_spaces doc-inventory--reference-finite_rings doc-inventory--reference-function_fields doc-inventory--reference-functions doc-inventory--reference-game_theory doc-inventory--reference-games doc-inventory--reference-groups doc-inventory--reference-hecke doc-inventory--reference-history_and_license doc-inventory--reference-homology doc-inventory--reference-hyperbolic_geometry doc-inventory--reference-interfaces doc-inventory--reference-knots doc-inventory--reference-lfunctions doc-inventory--reference-libs doc-inventory--reference-logic doc-inventory--reference-matrices doc-inventory--reference-matroids doc-inventory--reference-modabvar doc-inventory--reference-modfrm doc-inventory--reference-modsym doc-inventory--reference-modules doc-inventory--reference-monoids doc-inventory--reference-noncommutative_polynomial_rings doc-inventory--reference-number_fields doc-inventory--reference-numerical doc-inventory--reference-oremodules doc-inventory--reference-padics doc-inventory--reference-plotting doc-inventory--reference-power_series doc-inventory--reference-probability doc-inventory--reference-quadratic_forms doc-inventory--reference-quat_algebras doc-inventory--reference-quivers doc-inventory--reference-resolutions doc-inventory--reference-riemannian_geometry doc-inventory--reference-rings doc-inventory--reference-rings_numerical doc-inventory--reference-rings_standard doc-inventory--reference-sat doc-inventory--reference-schemes doc-inventory--reference-semirings doc-inventory--reference-sets doc-inventory--reference-stats doc-inventory--reference-structure doc-inventory--reference-valuations
myuserid 213939 0.0 0.0 2584 912 ? S Apr12 0:00 /bin/sh /opt/Sage/sage-10.6/src/bin/sage-python -m sage_docbuild --no-pdf-links reference/combinat inventory
myuserid 214317 0.0 1.5 5934336 514660 ? S Apr12 0:03 python3 -m sage_docbuild --no-pdf-links reference/combinat inventory
myuserid 239376 0.0 0.0 0 0 ? Z Apr12 0:00 [sage-python] <defunct>
myuserid 242472 0.0 0.0 2584 928 ? S Apr12 0:00 /bin/sh /opt/Sage/sage-10.6/src/bin/sage-python -m sage_docbuild --no-pdf-links reference/topology inventory
myuserid 242503 0.0 1.4 5896956 482552 ? S Apr12 0:02 python3 -m sage_docbuild --no-pdf-links reference/topology inventory
myuserid 245156 0.0 0.0 2584 912 ? S Apr12 0:00 /bin/sh /opt/Sage/sage-10.6/src/bin/sage-python -m sage_docbuild --no-pdf-links reference/asymptotic inventory
myuserid 245187 0.0 1.4 5897396 482376 ? S Apr12 0:02 python3 -m sage_docbuild --no-pdf-links reference/asymptotic inventory
myuserid 247309 0.0 0.0 2584 956 ? S Apr12 0:00 /bin/sh /opt/Sage/sage-10.6/src/bin/sage-python -m sage_docbuild --no-pdf-links reference/calculus inventory
myuserid 247421 0.0 1.4 5897300 482752 ? S Apr12 0:02 python3 -m sage_docbuild --no-pdf-links reference/calculus inventory
myuserid 247894 0.0 0.0 0 0 ? Z Apr12 0:00 [sage-python] <defunct>
myuserid 252785 0.0 0.0 0 0 ? Z Apr12 0:00 [sage-python] <defunct>
myuserid 253518 0.0 0.0 0 0 ? Z Apr12 0:00 [sage-python] <defunct>
myuserid 265977 0.0 0.0 2584 956 ? S Apr12 0:00 /bin/sh /opt/Sage/sage-10.6/src/bin/sage-python -m sage_docbuild --no-pdf-links reference/cryptography inventory
myuserid 266008 0.0 1.4 5898164 483948 ? S Apr12 0:02 python3 -m sage_docbuild --no-pdf-links reference/cryptography inventory
myuserid 268893 0.0 0.0 0 0 ? Z Apr12 0:00 [sage-python] <defunct>
myuserid 269896 0.0 0.0 2584 912 ? S Apr12 0:00 /bin/sh /opt/Sage/sage-10.6/src/bin/sage-python -m sage_docbuild --no-pdf-links reference/databases inventory
myuserid 269942 0.0 1.5 5902180 487812 ? S Apr12 0:02 python3 -m sage_docbuild --no-pdf-links reference/databases inventory
myuserid 276088 0.0 0.0 0 0 ? Z Apr12 0:00 [sage-python] <defunct>
myuserid 287956 0.0 0.0 2584 884 ? S Apr12 0:00 /bin/sh /opt/Sage/sage-10.6/src/bin/sage-python -m sage_docbuild --no-pdf-links reference/euclidean_spaces inventory
myuserid 287987 0.0 1.5 5934592 518824 ? S Apr12 0:02 python3 -m sage_docbuild --no-pdf-links reference/euclidean_spaces inventory
myuserid 292050 0.0 0.0 0 0 ? Z Apr12 0:00 [sage-python] <defunct>
myuserid 294517 0.0 0.0 2584 928 ? S Apr12 0:00 /bin/sh /opt/Sage/sage-10.6/src/bin/sage-python -m sage_docbuild --no-pdf-links reference/game_theory inventory
myuserid 294558 0.0 1.4 5897080 481316 ? S Apr12 0:01 python3 -m sage_docbuild --no-pdf-links reference/game_theory inventory
myuserid 301601 0.0 0.0 0 0 ? Z Apr12 0:00 [sage-python] <defunct>
myuserid 311825 0.0 0.0 2584 912 ? S Apr12 0:00 /bin/sh /opt/Sage/sage-10.6/src/bin/sage-python -m sage_docbuild --no-pdf-links reference/homology inventory
myuserid 311856 0.0 1.4 5896912 481720 ? S Apr12 0:01 python3 -m sage_docbuild --no-pdf-links reference/homology inventory
myuserid 314197 0.0 0.0 0 0 ? Z Apr12 0:00 [sage-python] <defunct>
myuserid 318834 0.0 0.0 2584 912 ? S Apr12 0:00 /bin/sh /opt/Sage/sage-10.6/src/bin/sage-python -m sage_docbuild --no-pdf-links reference/knots inventory
myuserid 318865 0.0 1.4 5896756 482660 ? S Apr12 0:01 python3 -m sage_docbuild --no-pdf-links reference/knots inventory
myuserid 321105 0.0 0.0 0 0 ? Z Apr12 0:00 [sage-python] <defunct>
myuserid 325926 0.0 0.0 2584 908 ? S Apr12 0:00 /bin/sh /opt/Sage/sage-10.6/src/bin/sage-python -m sage_docbuild --no-pdf-links reference/logic inventory
myuserid 325957 0.0 1.4 5895320 480732 ? S Apr12 0:01 python3 -m sage_docbuild --no-pdf-links reference/logic inventory
myuserid 328112 0.0 0.0 0 0 ? Z Apr12 0:00 [sage-python] <defunct>
myuserid 347301 0.0 0.0 2584 904 ? S Apr12 0:00 /bin/sh /opt/Sage/sage-10.6/src/bin/sage-python -m sage_docbuild --no-pdf-links reference/number_fields inventory
myuserid 347332 0.0 1.4 5897268 482656 ? S Apr12 0:01 python3 -m sage_docbuild --no-pdf-links reference/number_fields inventory
myuserid 349380 0.0 0.0 0 0 ? Z Apr12 0:00 [sage-python] <defunct>
myuserid 356077 0.0 0.0 9212 2280 pts/2 S+ 10:17 0:00 grep python
myuserid 213669 0.0 0.0 17376 13008 ? S Apr12 0:01 python3 /opt/Sage/sage-10.6/src/bin/sage-cleaner
myuserid 213932 0.0 0.0 3108 2444 ? S Apr12 0:00 make doc-inventory--reference-spkg doc-inventory--reference-manifolds doc-inventory--reference-algebras doc-inventory--reference-polynomial_rings doc-inventory--reference-repl doc-inventory--reference-tensor_free_modules doc-inventory--reference-combinat doc-inventory--reference-dynamics doc-inventory--reference-plot3d doc-inventory--reference-arithgroup doc-inventory--reference-graphs doc-inventory--reference-misc doc-inventory--reference-parallel doc-inventory--reference-topology doc-inventory--reference-arithmetic_curves doc-inventory--reference-asymptotic doc-inventory--reference-calculus doc-inventory--reference-categories doc-inventory--reference-coding doc-inventory--reference-coercion doc-inventory--reference-constants doc-inventory--reference-cpython doc-inventory--reference-cryptography doc-inventory--reference-curves doc-inventory--reference-data_structures doc-inventory--reference-databases doc-inventory--reference-diophantine_approximation doc-inventory--reference-discrete_geometry doc-inventory--reference-doctest doc-inventory--reference-documentation doc-inventory--reference-drinfeld_modules doc-inventory--reference-euclidean_spaces doc-inventory--reference-finite_rings doc-inventory--reference-function_fields doc-inventory--reference-functions doc-inventory--reference-game_theory doc-inventory--reference-games doc-inventory--reference-groups doc-inventory--reference-hecke doc-inventory--reference-history_and_license doc-inventory--reference-homology doc-inventory--reference-hyperbolic_geometry doc-inventory--reference-interfaces doc-inventory--reference-knots doc-inventory--reference-lfunctions doc-inventory--reference-libs doc-inventory--reference-logic doc-inventory--reference-matrices doc-inventory--reference-matroids doc-inventory--reference-modabvar doc-inventory--reference-modfrm doc-inventory--reference-modsym doc-inventory--reference-modules doc-inventory--reference-monoids doc-inventory--reference-noncommutative_polynomial_rings doc-inventory--reference-number_fields doc-inventory--reference-numerical doc-inventory--reference-oremodules doc-inventory--reference-padics doc-inventory--reference-plotting doc-inventory--reference-power_series doc-inventory--reference-probability doc-inventory--reference-quadratic_forms doc-inventory--reference-quat_algebras doc-inventory--reference-quivers doc-inventory--reference-resolutions doc-inventory--reference-riemannian_geometry doc-inventory--reference-rings doc-inventory--reference-rings_numerical doc-inventory--reference-rings_standard doc-inventory--reference-sat doc-inventory--reference-schemes doc-inventory--reference-semirings doc-inventory--reference-sets doc-inventory--reference-stats doc-inventory--reference-structure doc-inventory--reference-valuations
myuserid 213939 0.0 0.0 2584 912 ? S Apr12 0:00 /bin/sh /opt/Sage/sage-10.6/src/bin/sage-python -m sage_docbuild --no-pdf-links reference/combinat inventory
myuserid 214317 0.0 1.5 5934336 514660 ? S Apr12 0:03 python3 -m sage_docbuild --no-pdf-links reference/combinat inventory
myuserid 239376 0.0 0.0 0 0 ? Z Apr12 0:00 [sage-python] <defunct>
myuserid 242472 0.0 0.0 2584 928 ? S Apr12 0:00 /bin/sh /opt/Sage/sage-10.6/src/bin/sage-python -m sage_docbuild --no-pdf-links reference/topology inventory
myuserid 242503 0.0 1.4 5896956 482552 ? S Apr12 0:02 python3 -m sage_docbuild --no-pdf-links reference/topology inventory
myuserid 245156 0.0 0.0 2584 912 ? S Apr12 0:00 /bin/sh /opt/Sage/sage-10.6/src/bin/sage-python -m sage_docbuild --no-pdf-links reference/asymptotic inventory
myuserid 245187 0.0 1.4 5897396 482376 ? S Apr12 0:02 python3 -m sage_docbuild --no-pdf-links reference/asymptotic inventory
myuserid 247309 0.0 0.0 2584 956 ? S Apr12 0:00 /bin/sh /opt/Sage/sage-10.6/src/bin/sage-python -m sage_docbuild --no-pdf-links reference/calculus inventory
myuserid 247421 0.0 1.4 5897300 482752 ? S Apr12 0:02 python3 -m sage_docbuild --no-pdf-links reference/calculus inventory
myuserid 247894 0.0 0.0 0 0 ? Z Apr12 0:00 [sage-python] <defunct>
myuserid 252785 0.0 0.0 0 0 ? Z Apr12 0:00 [sage-python] <defunct>
myuserid 253518 0.0 0.0 0 0 ? Z Apr12 0:00 [sage-python] <defunct>
myuserid 265977 0.0 0.0 2584 956 ? S Apr12 0:00 /bin/sh /opt/Sage/sage-10.6/src/bin/sage-python -m sage_docbuild --no-pdf-links reference/cryptography inventory
myuserid 266008 0.0 1.4 5898164 483948 ? S Apr12 0:02 python3 -m sage_docbuild --no-pdf-links reference/cryptography inventory
myuserid 268893 0.0 0.0 0 0 ? Z Apr12 0:00 [sage-python] <defunct>
myuserid 269896 0.0 0.0 2584 912 ? S Apr12 0:00 /bin/sh /opt/Sage/sage-10.6/src/bin/sage-python -m sage_docbuild --no-pdf-links reference/databases inventory
myuserid 269942 0.0 1.5 5902180 487812 ? S Apr12 0:02 python3 -m sage_docbuild --no-pdf-links reference/databases inventory
myuserid 276088 0.0 0.0 0 0 ? Z Apr12 0:00 [sage-python] <defunct>
myuserid 287956 0.0 0.0 2584 884 ? S Apr12 0:00 /bin/sh /opt/Sage/sage-10.6/src/bin/sage-python -m sage_docbuild --no-pdf-links reference/euclidean_spaces inventory
myuserid 287987 0.0 1.5 5934592 518824 ? S Apr12 0:02 python3 -m sage_docbuild --no-pdf-links reference/euclidean_spaces inventory
myuserid 292050 0.0 0.0 0 0 ? Z Apr12 0:00 [sage-python] <defunct>
myuserid 294517 0.0 0.0 2584 928 ? S Apr12 0:00 /bin/sh /opt/Sage/sage-10.6/src/bin/sage-python -m sage_docbuild --no-pdf-links reference/game_theory inventory
myuserid 294558 0.0 1.4 5897080 481316 ? S Apr12 0:01 python3 -m sage_docbuild --no-pdf-links reference/game_theory inventory
myuserid 301601 0.0 0.0 0 0 ? Z Apr12 0:00 [sage-python] <defunct>
myuserid 311825 0.0 0.0 2584 912 ? S Apr12 0:00 /bin/sh /opt/Sage/sage-10.6/src/bin/sage-python -m sage_docbuild --no-pdf-links reference/homology inventory
myuserid 311856 0.0 1.4 5896912 481720 ? S Apr12 0:01 python3 -m sage_docbuild --no-pdf-links reference/homology inventory
myuserid 314197 0.0 0.0 0 0 ? Z Apr12 0:00 [sage-python] <defunct>
myuserid 318834 0.0 0.0 2584 912 ? S Apr12 0:00 /bin/sh /opt/Sage/sage-10.6/src/bin/sage-python -m sage_docbuild --no-pdf-links reference/knots inventory
myuserid 318865 0.0 1.4 5896756 482660 ? S Apr12 0:01 python3 -m sage_docbuild --no-pdf-links reference/knots inventory
myuserid 321105 0.0 0.0 0 0 ? Z Apr12 0:00 [sage-python] <defunct>
myuserid 325926 0.0 0.0 2584 908 ? S Apr12 0:00 /bin/sh /opt/Sage/sage-10.6/src/bin/sage-python -m sage_docbuild --no-pdf-links reference/logic inventory
myuserid 325957 0.0 1.4 5895320 480732 ? S Apr12 0:01 python3 -m sage_docbuild --no-pdf-links reference/logic inventory
myuserid 328112 0.0 0.0 0 0 ? Z Apr12 0:00 [sage-python] <defunct>
myuserid 347301 0.0 0.0 2584 904 ? S Apr12 0:00 /bin/sh /opt/Sage/sage-10.6/src/bin/sage-python -m sage_docbuild --no-pdf-links reference/number_fields inventory
myuserid 347332 0.0 1.4 5897268 482656 ? S Apr12 0:01 python3 -m sage_docbuild --no-pdf-links reference/number_fields inventory
myuserid 349380 0.0 0.0 0 0 ? Z Apr12 0:00 [sage-python] <defunct>
myuserid 356077 0.0 0.0 9212 2280 pts/2 S+ 10:17 0:00 grep python
======================================================================
output of tail install.log, showing build stopped in mid-air
======================================================================
[sagemath_doc_html-none] [spkg-install] [modules ] The inventory file is in ../../local/share/doc/sage/inventory/en/reference/modules.
[sagemath_doc_html-none] [spkg-install] sage --docbuild --no-pdf-links reference/monoids inventory
[sagemath_doc_html-none] [spkg-install] [monoids ] building [inventory]: targets for 13 source files that are out of date
[sagemath_doc_html-none] [spkg-install] [monoids ] updating environment: [new config] 13 added, 0 changed, 0 removed
[sagemath_doc_html-none] [spkg-install] [monoids ] The inventory file is in ../../local/share/doc/sage/inventory/en/reference/monoids.
[sagemath_doc_html-none] [spkg-install] sage --docbuild --no-pdf-links reference/noncommutative_polynomial_rings inventory
[sagemath_doc_html-none] [spkg-install] [noncommut] building [inventory]: targets for 10 source files that are out of date
[sagemath_doc_html-none] [spkg-install] [noncommut] updating environment: [new config] 10 added, 0 changed, 0 removed
[sagemath_doc_html-none] [spkg-install] [noncommut] The inventory file is in ../../local/share/doc/sage/inventory/en/reference/noncommutative_polynomial_rings.
[sagemath_doc_html-none] [spkg-install] sage --docbuild --no-pdf-links reference/number_fields inventory
[sagemath_doc_html-none] [spkg-install] sage --docbuild --no-pdf-links reference/monoids inventory
[sagemath_doc_html-none] [spkg-install] [monoids ] building [inventory]: targets for 13 source files that are out of date
[sagemath_doc_html-none] [spkg-install] [monoids ] updating environment: [new config] 13 added, 0 changed, 0 removed
[sagemath_doc_html-none] [spkg-install] [monoids ] The inventory file is in ../../local/share/doc/sage/inventory/en/reference/monoids.
[sagemath_doc_html-none] [spkg-install] sage --docbuild --no-pdf-links reference/noncommutative_polynomial_rings inventory
[sagemath_doc_html-none] [spkg-install] [noncommut] building [inventory]: targets for 10 source files that are out of date
[sagemath_doc_html-none] [spkg-install] [noncommut] updating environment: [new config] 10 added, 0 changed, 0 removed
[sagemath_doc_html-none] [spkg-install] [noncommut] The inventory file is in ../../local/share/doc/sage/inventory/en/reference/noncommutative_polynomial_rings.
[sagemath_doc_html-none] [spkg-install] sage --docbuild --no-pdf-links reference/number_fields inventory
Dima Pasechnik
Apr 14, 2025, 11:32:54 AMApr 14
to sage-s...@googlegroups.com
On Mon, Apr 14, 2025 at 9:03 AM Denis Sunko <denis...@gmail.com> wrote:
>
> I have been installing Sage from source on three workstations and a laptop for ages. The last release which went without a hitch was 10.3. I skipped 10.4, but with 10.5 and 10.6 one of the workstations has a weird problem: the build simply hangs and stays that way, for as long as I let it (two days now). Below is the output of ps -xuwa | grep python and the tail of the install log. The log is 97 MB, but there seems to be nothing there save a few error messages from various packages which are the same as on the other three machines where there were no problems.
>
> All four machines are Debian bookworm on amd64, fully up to date. The one where the build fails is only different in that I installed all the packages suggested by configure and did `make reconfigure' after that, as recommended. I can imagine that could cause some conflict, but not such silent failure of the build.
it looks like the docbuild hang, right? We see these now and then.
>
> I have been installing Sage from source on three workstations and a laptop for ages. The last release which went without a hitch was 10.3. I skipped 10.4, but with 10.5 and 10.6 one of the workstations has a weird problem: the build simply hangs and stays that way, for as long as I let it (two days now). Below is the output of ps -xuwa | grep python and the tail of the install log. The log is 97 MB, but there seems to be nothing there save a few error messages from various packages which are the same as on the other three machines where there were no problems.
>
> All four machines are Debian bookworm on amd64, fully up to date. The one where the build fails is only different in that I installed all the packages suggested by configure and did `make reconfigure' after that, as recommended. I can imagine that could cause some conflict, but not such silent failure of the build.
Often hard to reproduce.
You can try to kill the process and start "make" again, it could have
been an one-off error.
If it persists, you can try to reduce to 1 the number of parallel
processes and the number of threads used,
and restrart.
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Kevin Youren
Apr 14, 2025, 7:56:33 PMApr 14
to sage-support
Denis,
try changing the size of your SWAPFILE.
I changed mine to 10G, which was not really needed.
Try 2 or 3G.
regs, Kev
Denis Sunko
Apr 19, 2025, 4:37:12 AMApr 19
to sage-support
Thanks to everyone for their replies.
Restarting and going single-threaded did not work.
Changing the size of the swap file seemed like too much effort, or did I misunderstand something?
Finally, I did make build only, which is enough for my purposes.
Denis
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