[R] Irreproducible exception in R extension
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): 0x01355610 *** === 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: 0040-00401000 r-xp 00:21 32550383 /rwthfs/rz/cluster/home/simo_109/opt/R/lib64/R/bin/exec/R 0060-00601000 rw-p 00:21 32550383 /rwthfs/rz/cluster/home/simo_109/opt/R/lib64/R/bin/exec/R 00601000-029cc000 rw-p 00:00 0 [heap] 369ac0-369ac3a000 r-xp 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 00:00 0 369bc0-369bc16000 r-xp 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 369c00-369c0e8000 r-xp 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 00:00 0 369d00-369d00d000 r-xp 08:01 671072 /usr/lib64/libgomp.so.1.0.0 369d00d000-369d20c000 ---p d000 08:01 671072 /usr/lib64/libgomp.so.1.0.0 369d20c000-369d20d000 rw-p c000 08:01 671072 /usr/lib64/libgomp.so.1.0.0 369fa0-369faf r-xp 08:01 660772 /usr/lib64/libgfortran.so.3.0.0 369faf-369fcef000 ---p 000f 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 00:00 0 36a360-36a373f000 r-xp 08:01 675210 /usr/lib64/libicuuc.so.42.1 36a373f000-36a393f000 ---p 0013f000 08:01 675210 /usr/lib64/libicuuc.so.42.1 36a393f000-36a395 rw-p 0013f000 08:01 675210 /usr/lib64/libicuuc.so.42.1 36a395-36a3952000 rw-p 00:00 0 36a3a0-36a3b88000 r-xp
[R] Irreproducible exception in R extension
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): 0x01355610 *** === 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: 0040-00401000 r-xp 00:21 32550383 /rwthfs/rz/cluster/home/simo_109/opt/R/lib64/R/bin/exec/R 0060-00601000 rw-p 00:21 32550383 /rwthfs/rz/cluster/home/simo_109/opt/R/lib64/R/bin/exec/R 00601000-029cc000 rw-p 00:00 0 [heap] 369ac0-369ac3a000 r-xp 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 00:00 0 369bc0-369bc16000 r-xp 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 369c00-369c0e8000 r-xp 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 00:00 0 369d00-369d00d000 r-xp 08:01 671072 /usr/lib64/libgomp.so.1.0.0 369d00d000-369d20c000 ---p d000 08:01 671072 /usr/lib64/libgomp.so.1.0.0 369d20c000-369d20d000 rw-p c000 08:01 671072 /usr/lib64/libgomp.so.1.0.0 369fa0-369faf r-xp 08:01 660772 /usr/lib64/libgfortran.so.3.0.0 369faf-369fcef000 ---p 000f 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 00:00 0 36a360-36a373f000 r-xp 08:01 675210 /usr/lib64/libicuuc.so.42.1 36a373f000-36a393f000 ---p 0013f000 08:01 675210 /usr/lib64/libicuuc.so.42.1 36a393f000-36a395 rw-p 0013f000 08:01 675210 /usr/lib64/libicuuc.so.42.1 36a395-36a3952000 rw-p 00:00 0 36a3a0-36a3b88000 r-xp
