Hi Amber experts,
Recently I am trying to have a PBSA calculation. However, an error
occurred. My input is :
Input file for running PB and GB
&general
startframe=393,endframe=400, keep_files=0,
receptor_mask=:1-682,688-694,
ligand_mask=:683-687,
strip_mask=:WAT:Cl-
/
&gb
igb=2, saltcon=0.105,
/
&pb
istrng=0.115,
/
And the error is:
*** glibc detected *** /opt/share/amber12/bin/mmpbsa_py_energy: malloc():
memory corruption: 0x0000000005311c20 ***
======= Backtrace: =========
/lib64/libc.so.6[0x3832871a1e]
/lib64/libc.so.6(__libc_malloc+0x6e)[0x383287374e]
/opt/share/amber12/bin/mmpbsa_py_energy[0x43cb18]
/opt/share/amber12/bin/mmpbsa_py_energy[0x486f11]
/opt/share/amber12/bin/mmpbsa_py_energy[0x4247a7]
/opt/share/amber12/bin/mmpbsa_py_energy[0x409b3e]
/lib64/libc.so.6(__libc_start_main+0xf4)[0x383281d994]
/opt/share/amber12/bin/mmpbsa_py_energy[0x408989]
======= Memory map: ========
00400000-00ae6000 r-xp 00000000 00:18 4621661487
/opt/share/amber12/bin/mmpbsa_py_energy
00ce5000-00d10000 rw-p 006e5000 00:18 4621661487
/opt/share/amber12/bin/mmpbsa_py_energy
00d10000-01254000 rw-p 00d10000 00:00 0
052f7000-05318000 rw-p 052f7000 00:00 0
[heap]
3832400000-383241c000 r-xp 00000000 08:02 14221438
/lib64/ld-2.5.so
383261c000-383261d000 r--p 0001c000 08:02 14221438
/lib64/ld-2.5.so
383261d000-383261e000 rw-p 0001d000 08:02 14221438
/lib64/ld-2.5.so
3832800000-383294d000 r-xp 00000000 08:02 14221559
/lib64/libc-2.5.so
383294d000-3832b4d000 ---p 0014d000 08:02 14221559
/lib64/libc-2.5.so
3832b4d000-3832b51000 r--p 0014d000 08:02 14221559
/lib64/libc-2.5.so
3832b51000-3832b52000 rw-p 00151000 08:02 14221559
/lib64/libc-2.5.so
3832b52000-3832b57000 rw-p 3832b52000 00:00 0
3832c00000-3832c82000 r-xp 00000000 08:02 14221571
/lib64/libm-2.5.so
3832c82000-3832e81000 ---p 00082000 08:02 14221571
/lib64/libm-2.5.so
3832e81000-3832e82000 r--p 00081000 08:02 14221571
/lib64/libm-2.5.so
3832e82000-3832e83000 rw-p 00082000 08:02 14221571
/lib64/libm-2.5.so
3833000000-3833002000 r-xp 00000000 08:02 14221599
/lib64/libdl-2.5.so
3833002000-3833202000 ---p 00002000 08:02 14221599
/lib64/libdl-2.5.so
3833202000-3833203000 r--p 00002000 08:02 14221599
/lib64/libdl-2.5.so
3833203000-3833204000 rw-p 00003000 08:02 14221599
/lib64/libdl-2.5.so
3843200000-384320d000 r-xp 00000000 08:02 14221642
/lib64/libgcc_s-4.1.2-20080825.so.1
384320d000-384340d000 ---p 0000d000 08:02 14221642
/lib64/libgcc_s-4.1.2-20080825.so.1
384340d000-384340e000 rw-p 0000d000 08:02 14221642
/lib64/libgcc_s-4.1.2-20080825.so.1
2b2a989af000-2b2a989b1000 rw-p 2b2a989af000 00:00 0
2b2a989b1000-2b2a989de000 r-xp 00000000 00:18 4314775985
/opt/share/intel/composer_xe_2011_sp1.9.293/compiler/lib/intel64/libifport.so.5
2b2a989de000-2b2a98add000 ---p 0002d000 00:18 4314775985
/opt/share/intel/composer_xe_2011_sp1.9.293/compiler/lib/intel64/libifport.so.5
2b2a98add000-2b2a98ae0000 rw-p 0002c000 00:18 4314775985
/opt/share/intel/composer_xe_2011_sp1.9.293/compiler/lib/intel64/libifport.so.5
2b2a98ae0000-2b2a98ae7000 rw-p 2b2a98ae0000 00:00 0
2b2a98ae7000-2b2a98c13000 r-xp 00000000 00:18 4314620746
/opt/share/intel/composer_xe_2011_sp1.9.293/compiler/lib/intel64/libifcore.so.5
2b2a98c13000-2b2a98d12000 ---p 0012c000 00:18 4314620746
/opt/share/intel/composer_xe_2011_sp1.9.293/compiler/lib/intel64/libifcore.so.5
2b2a98d12000-2b2a98d23000 rw-p 0012b000 00:18 4314620746
/opt/share/intel/composer_xe_2011_sp1.9.293/compiler/lib/intel64/libifcore.so.5
2b2a98d23000-2b2a98d2a000 rw-p 2b2a98d23000 00:00 0
2b2a98d2a000-2b2a9939b000 r-xp 00000000 00:18 4313499716
/opt/share/intel/composer_xe_2011_sp1.9.293/compiler/lib/intel64/libsvml.so
2b2a9939b000-2b2a9949b000 ---p 00671000 00:18 4313499716
/opt/share/intel/composer_xe_2011_sp1.9.293/compiler/lib/intel64/libsvml.so
2b2a9949b000-2b2a9949d000 rw-p 00671000 00:18 4313499716
/opt/share/intel/composer_xe_2011_sp1.9.293/compiler/lib/intel64/libsvml.so
2b2a994b4000-2b2a994b6000 rw-p 2b2a994b4000 00:00 0
2b2a994b6000-2b2a9973d000 r-xp 00000000 00:18 4314418120
/opt/share/intel/composer_xe_2011_sp1.9.293/compiler/lib/intel64/libimf.so
2b2a9973d000-2b2a9983d000 ---p 00287000 00:18 4314418120
/opt/share/intel/composer_xe_2011_sp1.9.293/compiler/lib/intel64/libimf.so
2b2a9983d000-2b2a99881000 rw-p 00287000 00:18 4314418120
/opt/share/intel/composer_xe_2011_sp1.9.293/compiler/lib/intel64/libimf.so
2b2a99881000-2b2a998ca000 r-xp 00000000 00:18 4314531783
/opt/share/intel/composer_xe_2011_sp1.9.293/compiler/lib/intel64/libintlc.so.5
2b2a998ca000-2b2a999c9000 ---p 00049000 00:18 4314531783
/opt/share/intel/composer_xe_2011_sp1.9.293/compiler/lib/intel64/libintlc.so.5
2b2a999c9000-2b2a999cc000 rw-p 00048000 00:18 4314531783
/opt/share/intel/composer_xe_2011_sp1.9.293/compiler/lib/intel64/libintlc.so.5
2b2a999cc000-2b2a9a7c2000 rw-p 2b2a999cc000 00:00 0
2b2a9c000000-2b2a9c021000 rw-p 2b2a9c000000 00:00 0
2b2a9c021000-2b2aa0000000 ---p 2b2a9c021000 00:00 0
7ffffb9a7000-7ffffb9bd000 rw-p 7ffffffe8000 00:00 0
[stack]
7ffffb9fd000-7ffffba00000 r-xp 7ffffb9fd000 00:00 0
[vdso]
ffffffffff600000-ffffffffffe00000 ---p 00000000 00:00 0
[vsyscall]
CalcError: /opt/share/amber12/bin/mmpbsa_py_energy failed with prmtop
ligand.prmtop!
Error occured on rank 2.
Exiting. All files have been retained.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 2
Please advise. Thx.
Rgds,
C.Q.
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Received on Mon Jun 24 2013 - 01:30:06 PDT
