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Published 20 hours ago • verified publisher icon Macaulay2

Debian M2 crash

Open maruthaman opened this issue 3 years ago • 4 comments

I am unable to run macaulay2 in debian. It gives the following error: /usr/bin/M2-binary: symbol lookup error: /usr/bin/M2-binary: undefined symbol: GC_abort_on_oom

I tried the 1.17 that comes with debian stable. I also tried the 1.20 comes with testing. Both versions gave the same error message.

I tried to compile. But getting an error

if [ -e /root/M2/M2/usr-dist/common/share/info/Style.info ]; then install-info --info-dir=/root/M2/M2/usr-dist/common/share/info /root/M2/M2/usr-dist/common/share/info/Style.info; fi : installing package SCSCP === remaking /root/M2/M2/usr-dist/x86_64-Linux-Debian-11/lib/Macaulay2/SCSCP/.installed in packages : === -rw-r--r-- 1 root root 0 Aug 19 16:12 /root/M2/M2/usr-dist/x86_64-Linux-Debian-11/lib/Macaulay2/SCSCP/.installed === -r--r--r-- 1 root root 688 Aug 29 14:09 SCSCP/docinput/Makefile /usr/bin/install -c -d SCSCP-temporary make: Entering directory /root/M2/M2/Macaulay2/packages/SCSCP-temporary' cd SCSCP-temporary && /root/M2/M2/usr-dist/x86_64-Linux-Debian-11/bin/M2 -q --stop --silent --no-preload -e errorDepth=0 -e debugLevel=0 -e "installPackage(\"SCSCP\", MakeDocumentation => true, MakeHTML => true, MakeInfo => true, MakePDF => false, RemakeAllDocumentation => false, IgnoreExampleErrors => false, RerunExamples => false, CheckDocumentation => true, UserMode => false, Verbose => false, InstallPrefix => \"/root/M2/M2/usr-dist/\", SeparateExec => true, DebuggingMode => true); exit 0" -- warning: found 6 documentation node(s) not listed as a subnode make: Leaving directory /root/M2/M2/Macaulay2/packages/SCSCP-temporary' ls -l SCSCP-temporary total 0 rm -rf SCSCP-temporary if [ -e /root/M2/M2/usr-dist/common/share/info/SCSCP.info ]; then install-info --info-dir=/root/M2/M2/usr-dist/common/share/info /root/M2/M2/usr-dist/common/share/info/SCSCP.info; fi : installing package SpecialFanoFourfolds /usr/bin/install -c -d SpecialFanoFourfolds-temporary make: Entering directory `/root/M2/M2/Macaulay2/packages/SpecialFanoFourfolds-temporary' cd SpecialFanoFourfolds-temporary && /root/M2/M2/usr-dist/x86_64-Linux-Debian-11/bin/M2 -q --stop --silent --no-preload -e errorDepth=0 -e debugLevel=0 -e "installPackage("SpecialFanoFourfolds", MakeDocumentation => true, MakeHTML => true, MakeInfo => true, MakePDF => false, RemakeAllDocumentation => false, IgnoreExampleErrors => false, RerunExamples => false, CheckDocumentation => true, UserMode => false, Verbose => false, InstallPrefix => "/root/M2/M2/usr-dist/", SeparateExec => true, DebuggingMode => true); exit 0" -- making example results for "mirrorFourfold"
ulimit -c unlimited; ulimit -t 700; ulimit -m 850000; ulimit -s 8192; ulimit -n 512; cd /tmp/M2-1486204-0/1-rundir/; GC_MAXIMUM_HEAP_SIZE=400M "/root/M2/M2/usr-dist/x86_64-Linux-Debian-11/bin/M2-binary" -q --no-randomize --no-readline --silent --stop --print-width 77 -e 'needsPackage("SpecialFanoFourfolds",Reload=>true,FileName=>"/root/M2/M2/Macaulay2/packages/SpecialFanoFourfolds.m2")' <"/tmp/M2-1486204-0/0_mirror__Fourfold.m2" >>"/root/M2/M2/usr-dist/common/share/doc/Macaulay2/SpecialFanoFourfolds/example-output/_mirror__Fourfold.errors" 2>&1 /root/M2/M2/usr-dist/common/share/doc/Macaulay2/SpecialFanoFourfolds/example-output/_mirror__Fourfold.errors:0:1: (output file) error: Macaulay2 exited with status code 1 /tmp/M2-1486204-0/0_mirror__Fourfold.m2:0:1: (input file) M2: *** Error 1 -- 1.24605 seconds elapsed -- making example results for "map(CongruenceOfCurves)"
ulimit -c unlimited; ulimit -t 700; ulimit -m 850000; ulimit -s 8192; ulimit -n 512; cd /tmp/M2-1486204-0/2-rundir/; GC_MAXIMUM_HEAP_SIZE=400M "/root/M2/M2/usr-dist/x86_64-Linux-Debian-11/bin/M2-binary" -q --no-randomize --no-readline --silent --stop --print-width 77 -e 'needsPackage("SpecialFanoFourfolds",Reload=>true,FileName=>"/root/M2/M2/Macaulay2/packages/SpecialFanoFourfolds.m2")' <"/tmp/M2-1486204-0/0_map_lp__Congruence__Of__Curves_rp.m2" >>"/root/M2/M2/usr-dist/common/share/doc/Macaulay2/SpecialFanoFourfolds/example-output/_map_lp__Congruence__Of__Curves_rp.errors" 2>&1 /root/M2/M2/usr-dist/common/share/doc/Macaulay2/SpecialFanoFourfolds/example-output/_map_lp__Congruence__Of__Curves_rp.errors:0:1: (output file) error: Macaulay2 exited with status code 1 /tmp/M2-1486204-0/0_map_lp__Congruence__Of__Curves_rp.m2:0:1: (input file) M2: *** Error 1 -- 5.83296 seconds elapsed -- making example results for "associatedK3surface(SpecialCubicFourfold)"
ulimit -c unlimited; ulimit -t 700; ulimit -m 850000; ulimit -s 8192; ulimit -n 512; cd /tmp/M2-1486204-0/3-rundir/; GC_MAXIMUM_HEAP_SIZE=400M "/root/M2/M2/usr-dist/x86_64-Linux-Debian-11/bin/M2-binary" -q --no-randomize --no-readline --silent --stop --print-width 77 -e 'needsPackage("SpecialFanoFourfolds",Reload=>true,FileName=>"/root/M2/M2/Macaulay2/packages/SpecialFanoFourfolds.m2")' <"/tmp/M2-1486204-0/0_associated__K3surface_lp__Special__Cubic__Fourfold_rp.m2" >>"/root/M2/M2/usr-dist/common/share/doc/Macaulay2/SpecialFanoFourfolds/example-output/_associated__K3surface_lp__Special__Cubic__Fourfold_rp.errors" 2>&1 /root/M2/M2/usr-dist/common/share/doc/Macaulay2/SpecialFanoFourfolds/example-output/_associated__K3surface_lp__Special__Cubic__Fourfold_rp.errors:0:1: (output file) error: Macaulay2 exited with status code 1 /tmp/M2-1486204-0/0_associated__K3surface_lp__Special__Cubic__Fourfold_rp.m2:0:1: (input file) M2: *** Error 1 -- 1.2548 seconds elapsed -- making example results for "associatedK3surface(SpecialGushelMukaiFourfold)" ulimit -c unlimited; ulimit -t 700; ulimit -m 850000; ulimit -s 8192; ulimit -n 512; cd /tmp/M2-1486204-0/4-rundir/; GC_MAXIMUM_HEAP_SIZE=400M "/root/M2/M2/usr-dist/x86_64-Linux-Debian-11/bin/M2-binary" -q --no-randomize --no-readline --silent --stop --print-width 77 -e 'needsPackage("SpecialFanoFourfolds",Reload=>true,FileName=>"/root/M2/M2/Macaulay2/packages/SpecialFanoFourfolds.m2")' <"/tmp/M2-1486204-0/0_associated__K3surface_lp__Special__Gushel__Mukai__Fourfold_rp.m2" >>"/root/M2/M2/usr-dist/common/share/doc/Macaulay2/SpecialFanoFourfolds/example-output/_associated__K3surface_lp__Special__Gushel__Mukai__Fourfold_rp.errors" 2>&1 /root/M2/M2/usr-dist/common/share/doc/Macaulay2/SpecialFanoFourfolds/example-output/_associated__K3surface_lp__Special__Gushel__Mukai__Fourfold_rp.errors:0:1: (output file) error: Macaulay2 exited with status code 1 /tmp/M2-1486204-0/0_associated__K3surface_lp__Special__Gushel__Mukai__Fourfold_rp.m2:0:1: (input file) M2: *** Error 1 -- 4.16648 seconds elapsed -- making example results for "parametrize(HodgeSpecialFourfold)"
ulimit -c unlimited; ulimit -t 700; ulimit -m 850000; ulimit -s 8192; ulimit -n 512; cd /tmp/M2-1486204-0/5-rundir/; GC_MAXIMUM_HEAP_SIZE=400M "/root/M2/M2/usr-dist/x86_64-Linux-Debian-11/bin/M2-binary" -q --no-randomize --no-readline --silent --stop --print-width 77 -e 'needsPackage("SpecialFanoFourfolds",Reload=>true,FileName=>"/root/M2/M2/Macaulay2/packages/SpecialFanoFourfolds.m2")' <"/tmp/M2-1486204-0/0_parametrize_lp__Hodge__Special__Fourfold_rp.m2" >>"/root/M2/M2/usr-dist/common/share/doc/Macaulay2/SpecialFanoFourfolds/example-output/_parametrize_lp__Hodge__Special__Fourfold_rp.errors" 2>&1 /root/M2/M2/usr-dist/common/share/doc/Macaulay2/SpecialFanoFourfolds/example-output/_parametrize_lp__Hodge__Special__Fourfold_rp.errors:0:1: (output file) error: Macaulay2 exited with status code 1 /tmp/M2-1486204-0/0_parametrize_lp__Hodge__Special__Fourfold_rp.m2:0:1: (input file) M2: *** Error 1 -- 1.27149 seconds elapsed ../../m2/debugging.m2:23:6:(1):[9]: error: installPackage: 5 error(s) occurred running examples for package SpecialFanoFourfolds

maruthaman avatar Aug 29 '22 10:08 maruthaman

Doug Torrance might be able to say something about this. @d-torrance

I've just upgraded my Debian 11 system, and M2 1.20 ( as provided at https://faculty.math.illinois.edu/Macaulay2/Downloads/GNU-Linux/Debian/index.html ) still works.

For compiling youself, you may wish to bypass those errors in package examples by adding IgnoreExampleErrors=true to the make command line ( if you're building with autoconf and not cmake ).

DanGrayson avatar Aug 29 '22 11:08 DanGrayson

How much memory does your system have? I believe the "oom" GC_abort_on_oom message means "out of memory". That likely also explains the SpecialFanoFourfolds example failures -- I've seen those errors plenty of times on lower memory systems.

I haven't seen any such issues with the Macaulay2 packages in the Debian archives. Debian runs continuous integration tests on all of its packages regularly, and the Macaulay2 tests in stable and testing have been passing without any problems. (See https://ci.debian.net/packages/m/macaulay2/).

d-torrance avatar Aug 29 '22 11:08 d-torrance

My system has 192GB ram 24core Xeon processor. I dont think this is a problem with memory. I was running M2 for a long time in this machine till I updated it to bullseye.

maruthaman avatar Aug 30 '22 02:08 maruthaman

IgnoreExampleErrors=true

This worked for the compilation. M2 is working with this compiled version. Thank you very much.

narayanan

maruthaman avatar Aug 30 '22 10:08 maruthaman