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Re: [lammps-users] Question associated with compute group/group and ave/time
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Re: [lammps-users] Question associated with compute group/group and ave/time


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Fri, 30 Jun 2017 11:29:12 -0400

On Fri, Jun 30, 2017 at 5:35 AM, Jiawei Zhao Zhao <J.W.Zhao@...4429...> wrote:
> Dear LAMMPS mailing list
>
>
> I tried to use the ave/time to output the result from compute group/group
> with following command.
>
>
> compute     PCf         CNT     group/group other
> fix dumpgg all ave/time 1 10 100  c_PCf c_PCf[1] c_PCf[2] c_PCf[3] file
> computegg2.profile
>
>
> With the latest stable version(lammps-31Mar17), I got the error massage
> below. However, it seems the code works fine in a earlier version(16Feb16).
> Both of the packages complied with g++ and mpich in a same workstation. Both
> versions works fine okay if the ave/time command was deleted.
>
>
> Could anyone please show me what was going wrong here?

can you please make a test whether this situation happens also with
the latest patch version of LAMMPS (23 Jun 2017)?
the message you receive indicates some kind of memory corruption, but
the trace information is inconclusive. however, before investing time
and effort into tracking this down, it would be extremely helpful to
know whether this is not something that is already addressed in a
newer version of LAMMPS.

thanks,
     axel.

>
>
> Best regards!
>
>
> Jiawei Zhao
>
> PhD student
>
> Loughborough University
>
>
> Error massage with 31Mar17
>
>
> Start of the massage:
>
>
> *** Error in `./lammps': munmap_chunk(): invalid pointer: 0x0000000062331eb0
> ***
> ======= Backtrace: =========
> /lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7f2efbe707e5]
> /lib/x86_64-linux-gnu/libc.so.6(cfree+0x1a8)[0x7f2efbe7d698]
> ./lammps[0x9111d4]
> ./lammps[0x1136ac5]
> ./lammps[0x8ef7bb]
> ./lammps[0x1101149]
> ./lammps[0x10ff35a]
> ./lammps[0x10fff97]
> ./lammps[0x40ac96]
> /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7f2efbe19830]
> ./lammps[0x40d5c9]
> ======= Memory map: ========
> 00400000-019b5000 r-xp 00000000 08:02 119801407
> /home/jiawei/Desktop/LAMMPS/LongCNT/Pull-release/Cry/lammps
> 01bb5000-01bd7000 r--p 015b5000 08:02 119801407
> /home/jiawei/Desktop/LAMMPS/LongCNT/Pull-release/Cry/lammps
> 01bd7000-01bda000 rw-p 015d7000 08:02 119801407
> /home/jiawei/Desktop/LAMMPS/LongCNT/Pull-release/Cry/lammps
> 01bda000-61d78000 rw-p 00000000 00:00 0
> 6219f000-6289c000 rw-p 00000000 00:00 0
> [heap]
> 7f2ef211f000-7f2ef2aee000 rw-p 00000000 00:00 0
> 7f2ef2aee000-7f2ef2b2f000 rw-s 00000000 00:15 83
> /dev/shm/mpich_shar_tmplanr08 (deleted)
> 7f2ef2b2f000-7f2ef2b70000 rw-s 00000000 00:15 62
> /dev/shm/mpich_shar_tmpcyhqCc (deleted)
> 7f2ef2b70000-7f2ef2f40000 rw-p 00000000 00:00 0
> 7f2ef2f40000-7f2ef2f81000 rw-s 00000000 00:15 20
> /dev/shm/mpich_shar_tmpvh6SBB (deleted)
> 7f2ef2f81000-7f2ef2fc2000 rw-s 00000000 00:15 41
> /dev/shm/mpich_shar_tmpEjVUBB (deleted)
> 7f2ef2fc2000-7f2ef3029000 rw-p 00000000 00:00 0
> 7f2ef3029000-7f2ef306a000 rw-s 00000000 00:15 61
> /dev/shm/mpich_shar_tmpJ0E5in (deleted)
> 7f2ef306a000-7f2ef330b000 rw-p 00000000 00:00 0
> 7f2ef330b000-7f2ef3316000 r-xp 00000000 08:02 6947064
> /lib/x86_64-linux-gnu/libnss_files-2.23.so
> 7f2ef3316000-7f2ef3515000 ---p 0000b000 08:02 6947064
> /lib/x86_64-linux-gnu/libnss_files-2.23.so
> 7f2ef3515000-7f2ef3516000 r--p 0000a000 08:02 6947064
> /lib/x86_64-linux-gnu/libnss_files-2.23.so
> 7f2ef3516000-7f2ef3517000 rw-p 0000b000 08:02 6947064
> /lib/x86_64-linux-gnu/libnss_files-2.23.so
> 7f2ef3517000-7f2ef351d000 rw-p 00000000 00:00 0
> 7f2ef351d000-7f2efb7a8000 rw-s 00000000 00:15 17
> /dev/shm/mpich_shar_tmpfUY3nF (deleted)
> 7f2efb7a8000-7f2efb7af000 r-xp 00000000 08:02 6947074
> /lib/x86_64-linux-gnu/librt-2.23.so
> 7f2efb7af000-7f2efb9ae000 ---p 00007000 08:02 6947074
> /lib/x86_64-linux-gnu/librt-2.23.so
> 7f2efb9ae000-7f2efb9af000 r--p 00006000 08:02 6947074
> /lib/x86_64-linux-gnu/librt-2.23.so
> 7f2efb9af000-7f2efb9b0000 rw-p 00007000 08:02 6947074
> /lib/x86_64-linux-gnu/librt-2.23.so
> 7f2efb9b0000-7f2efb9b8000 r-xp 00000000 08:02 101713947
> /usr/lib/libcr.so.0.5.5
> 7f2efb9b8000-7f2efbbb7000 ---p 00008000 08:02 101713947
> /usr/lib/libcr.so.0.5.5
> 7f2efbbb7000-7f2efbbb8000 r--p 00007000 08:02 101713947
> /usr/lib/libcr.so.0.5.5
> 7f2efbbb8000-7f2efbbb9000 rw-p 00008000 08:02 101713947
> /usr/lib/libcr.so.0.5.5
> 7f2efbbb9000-7f2efbbba000 rw-p 00000000 00:00 0
> 7f2efbbba000-7f2efbbf8000 r-xp 00000000 08:02 101715606
> /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
> 7f2efbbf8000-7f2efbdf7000 ---p 0003e000 08:02 101715606
> /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
> 7f2efbdf7000-7f2efbdf8000 r--p 0003d000 08:02 101715606
> /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
> 7f2efbdf8000-7f2efbdf9000 rw-p 0003e000 08:02 101715606
> /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
> 7f2efbdf9000-7f2efbfb9000 r-xp 00000000 08:02 6947099
> /lib/x86_64-linux-gnu/libc-2.23.so
> 7f2efbfb9000-7f2efc1b9000 ---p 001c0000 08:02 6947099
> /lib/x86_64-linux-gnu/libc-2.23.so
> 7f2efc1b9000-7f2efc1bd000 r--p 001c0000 08:02 6947099
> /lib/x86_64-linux-gnu/libc-2.23.so
> 7f2efc1bd000-7f2efc1bf000 rw-p 001c4000 08:02 6947099
> /lib/x86_64-linux-gnu/libc-2.23.so
> 7f2efc1bf000-7f2efc1c3000 rw-p 00000000 00:00 0
> 7f2efc1c3000-7f2efc1d9000 r-xp 00000000 08:02 6951254
> /lib/x86_64-linux-gnu/libgcc_s.so.1
> 7f2efc1d9000-7f2efc3d8000 ---p 00016000 08:02 6951254
> /lib/x86_64-linux-gnu/libgcc_s.so.1
> 7f2efc3d8000-7f2efc3d9000 rw-p 00015000 08:02 6951254
> /lib/x86_64-linux-gnu/libgcc_s.so.1
> 7f2efc3d9000-7f2efc4e1000 r-xp 00000000 08:02 6947092
> /lib/x86_64-linux-gnu/libm-2.23.so
> 7f2efc4e1000-7f2efc6e0000 ---p 00108000 08:02 6947092
> /lib/x86_64-linux-gnu/libm-2.23.so
> 7f2efc6e0000-7f2efc6e1000 r--p 00107000 08:02 6947092
> /lib/x86_64-linux-gnu/libm-2.23.so
> 7f2efc6e1000-7f2efc6e2000 rw-p 00108000 08:02 6947092
> /lib/x86_64-linux-gnu/libm-2.23.so
> 7f2efc6e2000-7f2efc854000 r-xp 00000000 08:02 101713917
> /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
> 7f2efc854000-7f2efca54000 ---p 00172000 08:02 101713917
> /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
> 7f2efca54000-7f2efca5e000 r--p 00172000 08:02 101713917
> /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
> 7f2efca5e000-7f2efca60000 rw-p 0017c000 08:02 101713917
> /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
> 7f2efca60000-7f2efca64000 rw-p 00000000 00:00 0
> 7f2efca64000-7f2efcca6000 r-xp 00000000 08:02 101713993
> /usr/lib/x86_64-linux-gnu/libmpich.so.12.1.0
> 7f2efcca6000-7f2efcea6000 ---p 00242000 08:02 101713993
> /usr/lib/x86_64-linux-gnu/libmpich.so.12.1.0
> 7f2efcea6000-7f2efceb3000 r--p 00242000 08:02 101713993
> /usr/lib/x86_64-linux-gnu/libmpich.so.12.1.0
> 7f2efceb3000-7f2efceb5000 rw-p 0024f000 08:02 101713993
> /usr/lib/x86_64-linux-gnu/libmpich.so.12.1.0
> 7f2efceb5000-7f2efceef000 rw-p 00000000 00:00 0
> 7f2efceef000-7f2efcf07000 r-xp 00000000 08:02 6947068
> /lib/x86_64-linux-gnu/libpthread-2.23.so
> 7f2efcf07000-7f2efd106000 ---p 00018000 08:02 6947068
> /lib/x86_64-linux-gnu/libpthread-2.23.so
> 7f2efd106000-7f2efd107000 r--p 00017000 08:02 6947068
> /lib/x86_64-linux-gnu/libpthread-2.23.so
> 7f2efd107000-7f2efd108000 rw-p 00018000 08:02 6947068
> /lib/x86_64-linux-gnu/libpthread-2.23.so
> 7f2efd108000-7f2efd10c000 rw-p 00000000 00:00 0
> 7f2efd10c000-7f2efd125000 r-xp 00000000 08:02 6951407
> /lib/x86_64-linux-gnu/libz.so.1.2.8
> 7f2efd125000-7f2efd324000 ---p 00019000 08:02 6951407
> /lib/x86_64-linux-gnu/libz.so.1.2.8
> 7f2efd324000-7f2efd325000 r--p 00018000 08:02 6951407
> /lib/x86_64-linux-gnu/libz.so.1.2.8
> 7f2efd325000-7f2efd326000 rw-p 00019000 08:02 6951407
> /lib/x86_64-linux-gnu/libz.so.1.2.8
> 7f2efd326000-7f2efd44f000 r-xp 00000000 08:02 101713919
> /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
> 7f2efd44f000-7f2efd64e000 ---p 00129000 08:02 101713919
> /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
> 7f2efd64e000-7f2efd64f000 r--p 00128000 08:02 101713919
> /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
> 7f2efd64f000-7f2efd651000 rw-p 00129000 08:02 101713919
> /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
> 7f2efd651000-7f2efd654000 r-xp 00000000 08:02 6947080
> /lib/x86_64-linux-gnu/libdl-2.23.so
> 7f2efd654000-7f2efd853000 ---p 00003000 08:02 6947080
> /lib/x86_64-linux-gnu/libdl-2.23.so
> 7f2efd853000-7f2efd854000 r--p 00002000 08:02 6947080
> /lib/x86_64-linux-gnu/libdl-2.23.so
> 7f2efd854000-7f2efd855000 rw-p 00003000 08:02 6947080
> /lib/x86_64-linux-gnu/libdl-2.23.so
> 7f2efd855000-7f2efde49000 r-xp 00000000 08:02 101722644
> /usr/lib/lapack/liblapack.so.3.6.0
> 7f2efde49000-7f2efe048000 ---p 005f4000 08:02 101722644
> /usr/lib/lapack/liblapack.so.3.6.0
> 7f2efe048000-7f2efe049000 r--p 005f3000 08:02 101722644
> /usr/lib/lapack/liblapack.so.3.6.0
> 7f2efe049000-7f2efe04d000 rw-p 005f4000 08:02 101722644
> /usr/lib/lapack/liblapack.so.3.6.0
> 7f2efe04d000-7f2efe0bb000 r-xp 00000000 08:02 101722635
> /usr/lib/libblas/libblas.so.3.6.0
> 7f2efe0bb000-7f2efe2ba000 ---p 0006e000 08:02 101722635
> /usr/lib/libblas/libblas.so.3.6.0
> 7f2efe2ba000-7f2efe2bb000 r--p 0006d000 08:02 101722635
> /usr/lib/libblas/libblas.so.3.6.0
> 7f2efe2bb000-7f2efe2bc000 rw-p 0006e000 08:02 101722635
> /usr/lib/libblas/libblas.so.3.6.0
> 7f2efe2bc000-7f2efe2e2000 r-xp 00000000 08:02 6947058
> /lib/x86_64-linux-gnu/ld-2.23.so
> 7f2efe320000-7f2efe4bf000 rw-p 00000000 00:00 0
> 7f2efe4de000-7f2efe4e1000 rw-p 00000000 00:00 0
> 7f2efe4e1000-7f2efe4e2000 r--p 00025000 08:02 6947058
> /lib/x86_64-linux-gnu/ld-2.23.so
> 7f2efe4e2000-7f2efe4e3000 rw-p 00026000 08:02 6947058
> /lib/x86_64-linux-gnu/ld-2.23.so
> 7f2efe4e3000-7f2efe4e4000 rw-p 00000000 00:00 0
> 7ffc90f3b000-7ffc90f5c000 rw-p 00000000 00:00 0
> [stack]
> 7ffc90fbb000-7ffc90fbd000 r--p 00000000 00:00 0
> [vvar]
> 7ffc90fbd000-7ffc90fbf000 r-xp 00000000 00:00 0
> [vdso]
> ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0
> [vsyscall]
>
> ===================================================================================
> =   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
> =   PID 118987 RUNNING AT jiawei-HP-Z840-Workstation
> =   EXIT CODE: 134
> =   CLEANING UP REMAINING PROCESSES
> =   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
> ===================================================================================
> YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Aborted (signal 6)
> This typically refers to a problem with your application.
> Please see the FAQ page for debugging suggestions
>
> End of the massage
>
>
>
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-- 
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.