Based on the error message you posted, it looks like you do not have enough
memory to perform the calculation. PBSA calculations can be
memory-intensive if the system is of considerable size. Did the GB
calculation finish before this error message occurred? Or did the error
message occur right after execution of the command? Also, it looks like you
are performing the calculation in parallel. Have you tried running it in
serial to see if that works? It is possible that running in parallel
requires more memory than your calculation has access to.
-Bill
On Mon, Jun 24, 2013 at 4:03 AM, Changqing Yan <ycqchemical.gmail.com>wrote:
> 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.
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-846-1633
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Received on Mon Jun 24 2013 - 05:30:03 PDT
