Dear AMBER Team,
I will be very appreciated if you can help to understand the error messages. Sandar was crashing when a MD run carried out on a supercell of rubreren crystal with periodic boundary condition. The typology and coordinates files were generated with Leap and they have been tested with NAMD package
A similar run worked well for two systems I previously worked on, benzene and pentacene but not for this bigger molecular supercell. Please find the error messages below. It takes me ages to look for the errors but I still have no idea what is wrong. I tested input file, which worked fine for other systems. What are possible reasons causing the crash? Please help me with this issue. Many thanks.
*** glibc detected *** /homes/hyang/Work/amber/amber14/bin/sander: double free or corruption (out): 0x000000002d357be0 ***
======= Backtrace: =========
/lib64/libc.so.6[0x3b5f675f4e]
/lib64/libc.so.6[0x3b5f678cf0]
/homes/hyang/Work/amber/amber14/bin/sander[0x4e304a]
/homes/hyang/Work/amber/amber14/bin/sander[0x486fac]
/homes/hyang/Work/amber/amber14/bin/sander[0x484b5b]
/homes/hyang/Work/amber/amber14/bin/sander[0xbb71fa]
/lib64/libc.so.6(__libc_start_main+0xfd)[0x3b5f61ed5d]
/homes/hyang/Work/amber/amber14/bin/sander[0x404889]
======= Memory map: ========
00400000-00c70000 r-xp 00000000 00:1a 18486 /homes/hyang/Work/amber/amber14/bin/sander
00e70000-00f83000 rw-p 00870000 00:1a 18486 /homes/hyang/Work/amber/amber14/bin/sander
00f83000-2c2d2000 rw-p 00000000 00:00 0
2d2ae000-2d3ac000 rw-p 00000000 00:00 0 [heap]
3b5f200000-3b5f220000 r-xp 00000000 fd:00 1835088 /lib64/ld-2.12.so
3b5f41f000-3b5f420000 r--p 0001f000 fd:00 1835088 /lib64/ld-2.12.so
3b5f420000-3b5f421000 rw-p 00020000 fd:00 1835088 /lib64/ld-2.12.so
3b5f421000-3b5f422000 rw-p 00000000 00:00 0
3b5f600000-3b5f78a000 r-xp 00000000 fd:00 1835092 /lib64/libc-2.12.so
3b5f78a000-3b5f98a000 ---p 0018a000 fd:00 1835092 /lib64/libc-2.12.so
3b5f98a000-3b5f98e000 r--p 0018a000 fd:00 1835092 /lib64/libc-2.12.so
3b5f98e000-3b5f98f000 rw-p 0018e000 fd:00 1835092 /lib64/libc-2.12.so
3b5f98f000-3b5f994000 rw-p 00000000 00:00 0
3b5fa00000-3b5fa83000 r-xp 00000000 fd:00 1835209 /lib64/libm-2.12.so
3b5fa83000-3b5fc82000 ---p 00083000 fd:00 1835209 /lib64/libm-2.12.so
3b5fc82000-3b5fc83000 r--p 00082000 fd:00 1835209 /lib64/libm-2.12.so
3b5fc83000-3b5fc84000 rw-p 00083000 fd:00 1835209 /lib64/libm-2.12.so
3b5fe00000-3b5fe17000 r-xp 00000000 fd:00 1835267 /lib64/libpthread-2.12.so
3b5fe17000-3b60017000 ---p 00017000 fd:00 1835267 /lib64/libpthread-2.12.so
3b60017000-3b60018000 r--p 00017000 fd:00 1835267 /lib64/libpthread-2.12.so
3b60018000-3b60019000 rw-p 00018000 fd:00 1835267 /lib64/libpthread-2.12.so
3b60019000-3b6001d000 rw-p 00000000 00:00 0
3b60a00000-3b60af8000 r-xp 00000000 fd:00 547473 /usr/lib64/libfftw3.so.3.2.3
3b60af8000-3b60cf7000 ---p 000f8000 fd:00 547473 /usr/lib64/libfftw3.so.3.2.3
3b60cf7000-3b60cfe000 rw-p 000f7000 fd:00 547473 /usr/lib64/libfftw3.so.3.2.3
3b69a00000-3b69a16000 r-xp 00000000 fd:00 1835224 /lib64/libgcc_s-4.4.7-20120601.so.1
3b69a16000-3b69c15000 ---p 00016000 fd:00 1835224 /lib64/libgcc_s-4.4.7-20120601.so.1
3b69c15000-3b69c16000 rw-p 00015000 fd:00 1835224 /lib64/libgcc_s-4.4.7-20120601.so.1
3b69e00000-3b69ee8000 r-xp 00000000 fd:00 529434 /usr/lib64/libstdc++.so.6.0.13
3b69ee8000-3b6a0e8000 ---p 000e8000 fd:00 529434 /usr/lib64/libstdc++.so.6.0.13
3b6a0e8000-3b6a0ef000 r--p 000e8000 fd:00 529434 /usr/lib64/libstdc++.so.6.0.13
3b6a0ef000-3b6a0f1000 rw-p 000ef000 fd:00 529434 /usr/lib64/libstdc++.so.6.0.13
3b6a0f1000-3b6a106000 rw-p 00000000 00:00 0
7f6104000000-7f6104021000 rw-p 00000000 00:00 0
7f6104021000-7f6108000000 ---p 00000000 00:00 0
7f6109800000-7f610ae58000 rw-p 00000000 00:00 0
7f610ae58000-7f610af48000 r-xp 00000000 fd:00 534454 /usr/lib64/libgfortran.so.3.0.0
7f610af48000-7f610b147000 ---p 000f0000 fd:00 534454 /usr/lib64/libgfortran.so.3.0.0
7f610b147000-7f610b149000 rw-p 000ef000 fd:00 534454 /usr/lib64/libgfortran.so.3.0.0
7f610b149000-7f610b14c000 rw-p 00000000 00:00 0
7ffc06751000-7ffc06766000 rw-p 00000000 00:00 0 [stack]
7ffc06769000-7ffc0676a000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
./run_md_amber.sh: line 3: 14789 Aborted (core dumped) $AMBERHOME/bin/sander -O -i rub_108_min.in -o rub_min.out -c rub_108.inpcrd -p rub_108.prmtop -r rub.rst -x rub.mdcrd
Best regards,
Hui
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Received on Thu May 05 2016 - 06:30:05 PDT
