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


From: Jiawei Zhao Zhao <J.W.Zhao@...4429...>
Date: Fri, 30 Jun 2017 09:35:26 +0000

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?


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