You are here

Memory error - double free or corruption

1 post / 0 new
Memory error - double free or corruption
#1

Hello,

I am running a design xml script and for some of my systems the run crashes with the following error:

*** Error in `/home/myasalme/Softwares/rosetta.source.release-314/main/source/bin/rosetta_scripts.mpi.linuxgccrelease': double free or corruption (!prev): 0x0000000013044c20 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x81329)[0x2b79ce247329]
/home/myasalme/Softwares/rosetta.source.release-314/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/mpi/libprotocols.7.so(_ZNSt8_Rb_treeImSt4pairIKmN7utility7vector1ImSaImEEEESt10_Select1stIS6_ESt4lessImESaIS6_EE8_M_eraseEPSt13_Rb_tree_nodeIS6_E+0x55)[0x2b79bbfbf505]
/home/myasalme/Softwares/rosetta.source.release-314/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/mpi/libcore.2.so(_ZN4core12conformation7Residue30update_connections_to_residuesEv+0x3b)[0x2b79c96fd4db]
/home/myasalme/Softwares/rosetta.source.release-314/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/mpi/libcore.2.so(_ZN4core12conformation7Residue26residue_connection_partnerEmmm+0x1f)[0x2b79c96fd78f]
/home/myasalme/Softwares/rosetta.source.release-314/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/mpi/libcore.2.so(_ZN4core12conformation12Conformation21declare_chemical_bondEmRKSsmS3_+0xfd)[0x2b79c96c576d]
/home/myasalme/Softwares/rosetta.source.release-314/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/mpi/libprotocols_a.6.so(_ZN9protocols14cyclic_peptide11DeclareBond5applyERN4core4pose4PoseE+0x120)[0x2b79bea79840]
/home/myasalme/Softwares/rosetta.source.release-314/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/mpi/libprotocols.1.so(_ZN9protocols15rosetta_scripts14ParsedProtocol11apply_moverERN4core4pose4PoseERKNS1_18ParsedProtocolStepE+0x230)[0x2b79c4cdf030]
/home/myasalme/Softwares/rosetta.source.release-314/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/mpi/libprotocols.1.so(_ZN9protocols15rosetta_scripts14ParsedProtocol10apply_stepERN4core4pose4PoseERKNS1_18ParsedProtocolStepEb+0x1f)[0x2b79c4cdf42f]
/home/myasalme/Softwares/rosetta.source.release-314/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/mpi/libprotocols.1.so(_ZN9protocols15rosetta_scripts14ParsedProtocol17sequence_protocolERN4core4pose4PoseEN9__gnu_cxx17__normal_iteratorIPKNS1_18ParsedProtocolStepESt6vectorI
S8_SaIS8_EEEE+0x3d)[0x2b79c4cdfded]
/home/myasalme/Softwares/rosetta.source.release-314/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/mpi/libprotocols.1.so(_ZN9protocols15rosetta_scripts14ParsedProtocol5applyERN4core4pose4PoseE+0x130)[0x2b79c4ce0ff0]
/home/myasalme/Softwares/rosetta.source.release-314/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/mpi/libprotocols.1.so(_ZN9protocols3jd214JobDistributor11run_one_jobERSt10shared_ptrINS_5moves5MoverEElRSsS7_RmS8_b+0xc52)[0x2b79c4e0d422]
/home/myasalme/Softwares/rosetta.source.release-314/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/mpi/libprotocols.1.so(_ZN9protocols3jd214JobDistributor7go_mainESt10shared_ptrINS_5moves5MoverEE+0xc1)[0x2b79c4e0f141]
/home/myasalme/Softwares/rosetta.source.release-314/main/source/build/src/release/linux/3.10/64/x86/gcc/4.8/mpi/libprotocols.1.so(_ZN9protocols3jd224MPIFileBufJobDistributor2goESt10shared_ptrINS_5moves5MoverEE+0xd6)[0x2b79c4e2e2b6]
/home/myasalme/Softwares/rosetta.source.release-314/main/source/bin/rosetta_scripts.mpi.linuxgccrelease[0x403d1e]
/lib64/libc.so.6(__libc_start_main+0xf5)[0x2b79ce1e8555]
/home/myasalme/Softwares/rosetta.source.release-314/main/source/bin/rosetta_scripts.mpi.linuxgccrelease[0x4040c1]

Is this a bug? Any idea will be apreciated.

Thanks in advance

 

Category: 
Post Situation: 
Thu, 2023-05-25 06:18
almeida85