[R] Irreproducible exception in R extension

Simon Zehnder szehnder at uni-bonn.de
Fri Dec 28 11:54:05 CET 2012


Dear R-Users,

I am having some trouble running an R extension on our cluster (linux). I call C++ code in which I use a) the Scythe Statistical Library and b) OpenMP. Most of the jobs run without a problem, but some arbitrary jobs throw an exception of the kind printed below while running in a parallel loop. The behavior is to me not reproducible, although at every run of 729 Jobs it at least happens once. I already tried to enforce the error by using the Intel Compiler instead of the GCC 4.7.2 and using the Options '-checkinit' for possibly uninitialized values and '-ftrapuv' for initialization of stack variables to unusual values to aid error detection. But I cannot enforce the exception, which makes it impossible to debug. I already googled this error,  but there only 2-3 small forum discussions about it, and so I hope I find some suggestions here. 

1. What do you think this error comes from? 
2. What do you advice me to do to detect the error?

I am excited for your answers.

Simon




*** glibc detected *** /home/simo_109//opt/R/lib64/R/bin/exec/R: double free or corruption (!prev): 0x0000000001355610 ***
======= Backtrace: =========
/lib64/libc.so.6[0x3845a75916]
/lib64/libc.so.6[0x3845a78443]
/rwthfs/rz/cluster/home/simo_109/opt/R/lib64/R/library/MCpkg/libs/MCpkg.so(_ZN6scythe9DataBlockIdE10deallocateEv+0x7b)[0x7f4645d5d6db]
/rwthfs/rz/cluster/home/simo_109/opt/R/lib64/R/library/MCpkg/libs/MCpkg.so(_ZN6scythe9DataBlockIdED1Ev+0x47)[0x7f4645d5d5bb]
/rwthfs/rz/cluster/home/simo_109/opt/R/lib64/R/library/MCpkg/libs/MCpkg.so(_ZN6scythe18DataBlockReferenceIdE17withdrawReferenceEv+0xaa)[0x7f4645d83442]
/rwthfs/rz/cluster/home/simo_109/opt/R/lib64/R/library/MCpkg/libs/MCpkg.so(_ZN6scythe18DataBlockReferenceIdED1Ev+0x94)[0x7f4645d82cc8]
/rwthfs/rz/cluster/home/simo_109/opt/R/lib64/R/library/MCpkg/libs/MCpkg.so(_ZN6scythe18DataBlockReferenceIdED2Ev+0x47)[0x7f4645d82d9f]
/rwthfs/rz/cluster/home/simo_109/opt/R/lib64/R/library/MCpkg/libs/MCpkg.so(_ZN6scythe6MatrixIdLNS_12matrix_orderE0ELNS_12matrix_styleE1EED1Ev+0x5d)[0x7f4645d8b26d]
/rwthfs/rz/cluster/home/simo_109/opt/R/lib64/R/library/MCpkg/libs/MCpkg.so(_Z11MCgmmS_implIN6scythe8mersenneEEvRNS0_3rngIT_EERP7SEXPRECS8_jjRNS0_6MatrixIdLNS0_12matrix_orderE0ELNS0_12matrix_styleE0EEERKSC_jS8_S8_+0x478f)[0x7f4645d6d6af]
/opt/intel/Compiler/12.1/6.361/rwthlnk/compiler/lib/intel64/libiomp5.so(__kmp_invoke_microtask+0x93)[0x7f4645aabee3]
======= Memory map: ========
00400000-00401000 r-xp 00000000 00:21 32550383                           /rwthfs/rz/cluster/home/simo_109/opt/R/lib64/R/bin/exec/R
00600000-00601000 rw-p 00000000 00:21 32550383                           /rwthfs/rz/cluster/home/simo_109/opt/R/lib64/R/bin/exec/R
00601000-029cc000 rw-p 00000000 00:00 0                                  [heap]
369ac00000-369ac3a000 r-xp 00000000 08:01 263771                         /lib64/libreadline.so.6.0
369ac3a000-369ae3a000 ---p 0003a000 08:01 263771                         /lib64/libreadline.so.6.0
369ae3a000-369ae42000 rw-p 0003a000 08:01 263771                         /lib64/libreadline.so.6.0
369ae42000-369ae43000 rw-p 00000000 00:00 0 
369bc00000-369bc16000 r-xp 00000000 08:01 263757                         /lib64/libgcc_s-4.4.6-20120305.so.1
369bc16000-369be15000 ---p 00016000 08:01 263757                         /lib64/libgcc_s-4.4.6-20120305.so.1
369be15000-369be16000 rw-p 00015000 08:01 263757                         /lib64/libgcc_s-4.4.6-20120305.so.1
369c000000-369c0e8000 r-xp 00000000 08:01 656025                         /usr/lib64/libstdc++.so.6.0.13
369c0e8000-369c2e8000 ---p 000e8000 08:01 656025                         /usr/lib64/libstdc++.so.6.0.13
369c2e8000-369c2ef000 r--p 000e8000 08:01 656025                         /usr/lib64/libstdc++.so.6.0.13
369c2ef000-369c2f1000 rw-p 000ef000 08:01 656025                         /usr/lib64/libstdc++.so.6.0.13
369c2f1000-369c306000 rw-p 00000000 00:00 0 
369d000000-369d00d000 r-xp 00000000 08:01 671072                         /usr/lib64/libgomp.so.1.0.0
369d00d000-369d20c000 ---p 0000d000 08:01 671072                         /usr/lib64/libgomp.so.1.0.0
369d20c000-369d20d000 rw-p 0000c000 08:01 671072                         /usr/lib64/libgomp.so.1.0.0
369fa00000-369faf0000 r-xp 00000000 08:01 660772                         /usr/lib64/libgfortran.so.3.0.0
369faf0000-369fcef000 ---p 000f0000 08:01 660772                         /usr/lib64/libgfortran.so.3.0.0
369fcef000-369fcf1000 rw-p 000ef000 08:01 660772                         /usr/lib64/libgfortran.so.3.0.0
369fcf1000-369fcf2000 rw-p 00000000 00:00 0 
36a3600000-36a373f000 r-xp 00000000 08:01 675210                         /usr/lib64/libicuuc.so.42.1
36a373f000-36a393f000 ---p 0013f000 08:01 675210                         /usr/lib64/libicuuc.so.42.1
36a393f000-36a3950000 rw-p 0013f000 08:01 675210                         /usr/lib64/libicuuc.so.42.1
36a3950000-36a3952000 rw-p 00000000 00:00 0 
36a3a00000-36a3b88000 r-xp 00000000 08:01 657732                         /usr/lib64/libicui18n.so.42.1
36a3b88000-36a3d88000 ---p 00188000 08:01 657732                         /usr/lib64/libicui18n.so.42.1
36a3d88000-36a3d95000 rw-p 00188000 08:01 657732                         /usr/lib64/libicui18n.so.42.1
36a3d95000-36a3d96000 rw-p 00000000 00:00 0 
3845600000-3845620000 r-xp 00000000 08:01 263850                         /lib64/ld-2.12.so
384581f000-3845820000 r--p 0001f000 08:01 263850                         /lib64/ld-2.12.so
3845820000-3845821000 rw-p 00020000 08:01 263850                         /lib64/ld-2.12.so
3845821000-3845822000 rw-p 00000000 00:00 0 
3845a00000-3845b89000 r-xp 00000000 08:01 283486                         /lib64/libc-2.12.so
3845b89000-3845d89000 ---p 00189000 08:01 283486                         /lib64/libc-2.12.so
3845d89000-3845d8d000 r--p 00189000 08:01 283486                         /lib64/libc-2.12.so
3845d8d000-3845d8e000 rw-p 0018d000 08:01 283486                         /lib64/libc-2.12.so
3845d8e000-3845d93000 rw-p 00000000 00:00 0 
3845e00000-3845e83000 r-xp 00000000 08:01 283487                         /lib64/libm-2.12.so
3845e83000-3846082000 ---p 00083000 08:01 283487                         /lib64/libm-2.12.so
3846082000-3846083000 r--p 00082000 08:01 283487                         /lib64/libm-2.12.so
3846083000-3846084000 rw-p 00083000 08:01 283487                         /lib64/libm-2.12.so
3846200000-3846202000 r-xp 00000000 08:01 283492                         /lib64/libdl-2.12.so
3846202000-3846402000 ---p 00002000 08:01 283492                         /lib64/libdl-2.12.so
3846402000-3846403000 r--p 00002000 08:01 283492                         /lib64/libdl-2.12.so
3846403000-3846404000 rw-p 00003000 08:01 283492                         /lib64/libdl-2.12.so
3846600000-3846617000 r-xp 00000000 08:01 283491                         /lib64/libpthread-2.12.so
3846617000-3846817000 ---p 00017000 08:01 283491                         /lib64/libpthread-2.12.so
3846817000-3846818000 r--p 00017000 08:01 283491                         /lib64/libpthread-2.12.so
3846818000-3846819000 rw-p 00018000 08:01 283491                         /lib64/libpthread-2.12.so
3846819000-384681d000 rw-p 00000000 00:00 0 
3846a00000-3846a15000 r-xp 00000000 08:01 283488                         /lib64/libz.so.1.2.3
3846a15000-3846c14000 ---p 00015000 08:01 283488                         /lib64/libz.so.1.2.3
3846c14000-3846c15000 r--p 00014000 08:01 283488                         /lib64/libz.so.1.2.3
3846c15000-3846c16000 rw-p 00015000 08:01 283488                         /lib64/libz.so.1.2.3
3846e00000-3846e07000 r-xp 00000000 08:01 264383                         /lib64/librt-2.12.so
3846e07000-3847006000 ---p 00007000 08:01 264383                         /lib64/librt-2.12.so
3847006000-3847007000 r--p 00006000 08:01 264383                         /lib64/librt-2.12.so
3847007000-3847008000 rw-p 00007000 08:01 264383                         /lib64/librt-2.12.so
384fa00000-384fa1d000 r-xp 00000000 08:01 283493                         /lib64/libtinfo.so.5.7
384fa1d000-384fc1d000 ---p 0001d000 08:01 283493                         /lib64/libtinfo.so.5.7
384fc1d000-384fc21000 rw-p 0001d000 08:01 283493                         /lib64/libtinfo.so.5.7
3856200000-3857145000 r-xp 00000000 08:01 659000                         /usr/lib64/libicudata.so.42.1
3857145000-3857344000 ---p 00f45000 08:01 659000                         /usr/lib64/libicudata.so.42.1
3857344000-3857345000 rw-p 00f44000 08:01 659000                         /usr/lib64/libicudata.so.42.1
7efbd0000000-7efbd2901000 rw-p 00000000 00:00 0 
7efbd2901000-7efbd4000000 ---p 00000000 00:00 0 
7efbd4000000-7efbd6901000 rw-p 00000000 00:00 0 
7efbd6901000-7efbd8000000 ---p 00000000 00:00 0 
7efbd8000000-7efbda901000 rw-p 00000000 00:00 0 
7efbda901000-7efbdc000000 ---p 00000000 00:00 0 
7efbdc000000-7efbde901000 rw-p 00000000 00:00 0 
7efbde901000-7efbe0000000 ---p 00000000 00:00 0 
7efbe0000000-7efbe2901000 rw-p 00000000 00:00 0 
7efbe2901000-7efbe4000000 ---p 00000000 00:00 0 
7efbe4000000-7efbe6901000 rw-p 00000000 00:00 0 
7efbe6901000-7efbe8000000 ---p 00000000 00:00 0 
7efbe8000000-7efbea901000 rw-p 00000000 00:00 0 
7efbea901000-7efbec000000 ---p 00000000 00:00 0 
7efbec000000-7efbee901000 rw-p 00000000 00:00 0 
7efbee901000-7efbf0000000 ---p 00000000 00:00 0 
7efbf0000000-7efbf2901000 rw-p 00000000 00:00 0 
7efbf2901000-7efbf4000000 ---p 00000000 00:00 0 
7efbf4000000-7efbf6901000 rw-p 00000000 00:00 0 
7efbf6901000-7efbf8000000 ---p 00000000 00:00 0 
7efbf8000000-7efbfa901000 rw-p 00000000 00:00 0 
7efbfa901000-7efbfc000000 ---p 00000000 00:00 0 
7efbfc000000-7efbfe901000 rw-p 00000000 00:00 0 
7efbfe901000-7efc00000000 ---p 00000000 00:00 0 
7efc00000000-7efc02901000 rw-p 00000000 00:00 0 
7efc02901000-7efc04000000 ---p 00000000 00:00 0 
7efc04000000-7efc06901000 rw-p 00000000 00:00 0 
7efc06901000-7efc08000000 ---p 00000000 00:00 0 
7efc08000000-7efc0a901000 rw-p 00000000 00:00 0 
7efc0a901000-7efc0c000000 ---p 00000000 00:00 0 
7efc0c000000-7efc0e901000 rw-p 00000000 00:00 0 
7efc0e901000-7efc10000000 ---p 00000000 00:00 0 
7efc10000000-7efc12901000 rw-p 00000000 00:00 0 
7efc12901000-7efc14000000 ---p 00000000 00:00 0 
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7f3cab4bf000-7f3f0da5f000 rw-p 00000000 00:00 0 
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7f3f0da60000-7f4170000000 rw-p 00000000 00:00 0 
7f4170000000-7f4172901000 rw-p 00000000 00:00 0 
7f4172901000-7f4174000000 ---p 00000000 00:00 0 
7f4174000000-7f4176901000 rw-p 00000000 00:00 0 
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7f4178000000-7f4178021000 rw-p 00000000 00:00 0 
7f4178021000-7f417c000000 ---p 00000000 00:00 0 
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7f417f967000-7f43e1f07000 rw-p 00000000 00:00 0 
7f43e1f07000-7f43e1f08000 ---p 00000000 00:00 0 
7f43e1f08000-7f46444a8000 rw-p 00000000 00:00 0 
7f46444a8000-7f46444a9000 ---p 00000000 00:00 0 
7f46444a9000-7f4644eec000 rw-p 00000000 00:00 0 
7f4644eec000-7f4645564000 r-xp 00000000 00:16 24113546                   /rwthfs/rz/SW/intel/Compiler/12.1/6.361/composer_xe_2011_sp1.12.361/compiler/lib/intel64/libsvml.so
7f4645564000-7f4645664000 ---p 00678000 00:16 24113546                   /rwthfs/rz/SW/intel/Compiler/12.1/6.361/composer_xe_2011_sp1.12.361/compiler/lib/intel64/libsvml.so
7f4645664000-7f4645666000 rw-p 00678000 00:16 24113546                   /rwthfs/rz/SW/intel/Compiler/12.1/6.361/composer_xe_2011_sp1.12.361/compiler/lib/intel64/libsvml.so
7f4645666000-7f46458ee000 r-xp 00000000 00:16 15103936                   /rwthfs/rz/SW/intel/Compiler/12.1/6.361/composer_xe_2011_sp1.12.361/compiler/lib/intel64/libimf.so
7f46458ee000-7f46459ee000 ---p 00288000 00:16 15103936                   /rwthfs/rz/SW/intel/Compiler/12.1/6.361/composer_xe_2011_sp1.12.361/compiler/lib/intel64/libimf.so
7f46459ee000-7f4645a32000 rw-p 00288000 00:16 15103936                   /rwthfs/rz/SW/intel/Compiler/12.1/6.361/composer_xe_2011_sp1.12.361/compiler/lib/intel64/libimf.so
7f4645a32000-7f4645b08000 r-xp 00000000 00:16 8598722                    /rwthfs/rz/SW/intel/Compiler/12.1/6.361/composer_xe_2011_sp1.12.361/compiler/lib/intel64/libiomp5.so
7f4645b08000-7f4645d07000 ---p 000d6000 00:16 8598722                    /rwthfs/rz/SW/intel/Compiler/12.1/6.361/composer_xe_2011_sp1.12.361/compiler/lib/intel64/libiomp5.so
7f4645d07000-7f4645d12000 rw-p 000d5000 00:16 8598722                    /rwthfs/rz/SW/intel/Compiler/12.1/6.361/composer_xe_2011_sp1.12.361/compiler/lib/intel64/libiomp5.so
7f4645d12000-7f4645d33000 rw-p 00000000 00:00 0 
7f4645d33000-7f4645dd3000 r-xp 00000000 00:21 26923045                   /rwthfs/rz/cluster/home/simo_109/opt/R/lib64/R/library/MCpkg/libs/MCpkg.so
7f4645dd3000-7f4645fd2000 ---p 000a0000 00:21 26923045                   /rwthfs/rz/cluster/home/simo_109/opt/R/lib64/R/library/MCpkg/libs/MCpkg.so
7f4645fd2000-7f4645fd9000 rw-p 0009f000 00:21 26923045                   /rwthfs/rz/cluster/home/simo_109/opt/R/lib64/R/library/MCpkg/libs/MCpkg.so
7f4645fd9000-7f4646055000 r-xp 00000000 00:21 7162351                    /rwthfs/rz/cluster/home/simo_109/opt/R/lib64/R/library/Rcpp/libs/Rcpp.so
7f4646055000-7f4646254000 ---p 0007c000 00:21 7162351                    /rwthfs/rz/cluster/home/simo_109/opt/R/lib64/R/library/Rcpp/libs/Rcpp.so
7f4646254000-7f464625a000 rw-p 0007b000 00:21 7162351                    /rwthfs/rz/cluster/home/simo_109/opt/R/lib64/R/library/Rcpp/libs/Rcpp.so
7f464625a000-7f464625e000 rw-p 00000000 00:00 0 
7f464625e000-7f4646412000 r-xp 00000000 00:21 31510233                   /rwthfs/rz/cluster/home/simo_109/opt/R/lib64/R/lib/libRlapack.so
7f4646412000-7f4646611000 ---p 001b4000 00:21 31510233                   /rwthfs/rz/cluster/home/simo_109/opt/R/lib64/R/lib/libRlapack.so
7f4646611000-7f4646613000 rw-p 001b3000 00:21 31510233                   /rwthfs/rz/cluster/home/simo_109/opt/R/lib64/R/lib/libRlapack.so
7f4646613000-7f4646681000 r-xp 00000000 00:21 17041228                   /rwthfs/rz/cluster/home/simo_109/opt/R/lib64/R/library/stats/libs/stats.so
7f4646681000-7f4646880000 ---p 0006e000 00:21 17041228                   /rwthfs/rz/cluster/home/simo_109/opt/R/lib64/R/library/stats/libs/stats.so
7f4646880000-7f4646883000 rw-p 0006d000 00:21 17041228                   /rwthfs/rz/cluster/home/simo_109/opt/R/lib64/R/library/stats/libs/stats.so
7f4646883000-7f46469f1000 rw-p 00000000 00:00 0 
7f46469f1000-7f4646a13000 r-xp 00000000 00:21 18948952                   /rwthfs/rz/cluster/home/simo_109/opt/R/lib64/R/library/grDevices/libs/grDevices.so
7f4646a13000-7f4646c13000 ---p 00022000 00:21 18948952                   /rwthfs/rz/cluster/home/simo_109/opt/R/lib64/R/library/grDevices/libs/grDevices.so
7f4646c13000-7f4646c14000 rw-p 00022000 00:21 18948952                   /rwthfs/rz/cluster/home/simo_109/opt/R/lib64/R/library/grDevices/libs/grDevices.so
7f4646d25000-7f4646d71000 r-xp 00000000 00:16 8598705                    /rwthfs/rz/SW/intel/Compiler/12.1/6.361/composer_xe_2011_sp1.12.361/compiler/lib/intel64/libintlc.so.5
7f4646d71000-7f4646e70000 ---p 0004c000 00:16 8598705                    /rwthfs/rz/SW/intel/Compiler/12.1/6.361/composer_xe_2011_sp1.12.361/compiler/lib/intel64/libintlc.so.5
7f4646e70000-7f4646e73000 rw-p 0004b000 00:16 8598705                    /rwthfs/rz/SW/intel/Compiler/12.1/6.361/composer_xe_2011_sp1.12.361/compiler/lib/intel64/libintlc.so.5
7f4646e73000-7f4646fa1000 rw-p 00000000 00:00 0 
7f4646fa1000-7f4646fa8000 r-xp 00000000 00:21 28286392                   /rwthfs/rz/cluster/home/simo_109/opt/R/lib64/R/library/methods/libs/methods.so
7f4646fa8000-7f46471a7000 ---p 00007000 00:21 28286392                   /rwthfs/rz/cluster/home/simo_109/opt/R/lib64/R/library/methods/libs/methods.so
7f46471a7000-7f46471a8000 rw-p 00006000 00:21 28286392                   /rwthfs/rz/cluster/home/simo_109/opt/R/lib64/R/library/methods/libs/methods.so
7f46471a8000-7f464723f000 rw-p 00000000 00:00 0 
7f464723f000-7f464724b000 r-xp 00000000 08:01 263827                     /lib64/libnss_files-2.12.so
7f464724b000-7f464744b000 ---p 0000c000 08:01 263827                     /lib64/libnss_files-2.12.so
7f464744b000-7f464744c000 r--p 0000c000 08:01 263827                     /lib64/libnss_files-2.12.so
7f464744c000-7f464744d000 rw-p 0000d000 08:01 263827                     /lib64/libnss_files-2.12.so
7f4647471000-7f46476d6000 rw-p 00000000 00:00 0 
7f46476e9000-7f46476fa000 rw-p 00000000 00:00 0 
7f46476fa000-7f4647725000 r-xp 00000000 00:21 31510228                   /rwthfs/rz/cluster/home/simo_109/opt/R/lib64/R/lib/libRblas.so
7f4647725000-7f4647924000 ---p 0002b000 00:21 31510228                   /rwthfs/rz/cluster/home/simo_109/opt/R/lib64/R/lib/libRblas.so
7f4647924000-7f4647925000 rw-p 0002a000 00:21 31510228                   /rwthfs/rz/cluster/home/simo_109/opt/R/lib64/R/lib/libRblas.so
7f4647925000-7f4647c2d000 r-xp 00000000 00:21 31510229                   /rwthfs/rz/cluster/home/simo_109/opt/R/lib64/R/lib/libR.so
7f4647c2d000-7f4647e2d000 ---p 00308000 00:21 31510229                   /rwthfs/rz/cluster/home/simo_109/opt/R/lib64/R/lib/libR.so
7f4647e2d000-7f4647e44000 rw-p 00308000 00:21 31510229                   /rwthfs/rz/cluster/home/simo_109/opt/R/lib64/R/lib/libR.so
7f4647e44000-7f4647f30000 rw-p 00000000 00:00 0 
7fffcb9ab000-7fffcb9df000 rw-p 00000000 00:00 0                          [stack]
7fffcb9ff000-7fffcba00000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]


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