Is there a particular reason why you set cut to 40 ?
That is huge, and probably completely undeeded
Try cut 9 or 10 and see if this works
If it doesm then it is a memory allocation, trying to setup enough space
for a huge number of residues.
On 1/11/11 8:52 PM, Hector Chang wrote:
> Dear Amber Users,
>
> Please I want to ask about my molecular dynamics run in AMBER. I'm running a
>
> production run under constant pressure (NPT), but my simulation gets canceled or
>
> crashed after few seconds of running. My system contains around 600,000 atoms in
>
> explicit solvent. I have tried "sander.MPI" and ''pmemd", and both gave me the
>
> same problem. I ran the minimization and constant volume (NVT) where everything
>
> is fine, but once I get to run NPT the system is canceled or crashed.
>
>
> If it helps, this is my input file:
>
> &cntrl
>
> imin = 0, irest = 1, ntx = 7,
>
> ntb = 2, pres0 = 1.0, ntp = 1,
>
> taup = 2.0,
>
> cut = 40.0, ntr = 1,
>
> ntc = 2, ntf = 2,
>
> tempi = 300.0, temp0 = 300.0,
>
> ntt = 3, gamma_ln = 1.0,
> nstlim = 50000, dt = 0.002, ig = -1,
>
> ntpr = 100, ntwx = 100, ntwr = 100
>
> /
>
> Keep Struct fixed with weak restraints
> 10.0
> ATOMS 986 20185
> END
> END
>
> The following report is from amber expert in Teragrid:
>
>
> I've investigated this issue with Amber11. I've been unable to correct the
>
> issue, although reproductions of the error are bountiful. All the segmentation
>
> faults occur with the following stack trace.
>
>
>
> Program terminated with signal 11, Segmentation fault.
>
> #0 0x00000000006602d5 in free ()
>
> (gdb) bt
>
> #0 0x00000000006602d5 in free ()
>
> #1 0x000000000049d972 in mol_list_mod_setup_molecule_lists_ () at
>
> ./mol_list.f90:224
>
> #2 0x00000000004e3abd in pme_alltasks_setup_mod_pme_alltasks_setup_ () at
>
> ./pme_alltasks_setup.f90:126
>
> #3 0x00000000004ca4ce in pmemd () at ./pmemd.f90:129
>
> #4 0x0000000000400330 in main ()
>
>
>
> This is definitely a memory allocation or freeing issue within the code. These
>
> routines are the initial setup routines after all the input data is read and
>
> broadcast to all processes. These routines build module lists which is
>
> dependent on the number of atoms involved in the calculation. It is possible
>
> that there are too many atoms.
>
>
>
> However, I ran a benchmark case (Cellulose NPT) which includes 408609 atoms.
>
> This is less than what the user is trying to run (606580 atoms); however, it is
>
> not that far off. This benchmark ran successfully. I also ran an altered
>
> version of this benchmark to closely resemble this users run (via options in the
>
> input file). No option in the input file seems to be causing this problem
>
> since this run was successful.
>
>
>
> I tried running the code at various core counts 12 to 120. All runs reproduce
>
> the segmentation fault.
>
> I tried running the code using 1 core per socket. All runs reproduce the
>
> segmentation fault.
>
>
>
> I applied all known bugfixes to the code. The runs using this code still
>
> reproduce the segmentation fault.
>
>
>
> Using the sander.MPI executable instead of pmemd.MPI produces the following
>
> error (not the segmentation fault). (12 cores)
>
>
>
> NATOM = 606580 NTYPES = 23 NBONH = 586742 MBONA = 18645
>
> NTHETH = 800 MTHETA = 27640 NPHIH = 1345 MPHIA = 24420
>
> NHPARM = 0 NPARM = 0 NNB = 857864 NRES = 195911
>
> NBONA = 18645 NTHETA = 27640 NPHIA = 24420 NUMBND = 57
>
> NUMANG = 113 NPTRA = 33 NATYP = 40 NPHB = 1
>
> IFBOX = 1 NMXRS = 114 IFCAP = 0 NEXTRA = 0
>
> NCOPY = 0
>
>
>
> Unreasonably large value for MAXPR: 0.15E+11
>
>
>
> This value is too large when it is greater than or equal to 2^31 (will fit in a
>
> signed 32 bit integer). This vault is calculated via several formula, but one
>
> is [NATOM*(NATOM-1) ]/(2*MPI_processes). Once again, a possible link to the
>
> number of atoms. However, I'm unable to get this case to run by using more
>
> processors. The same error is presented.
>
>
>
> Using the pmemd executable from amber/9, I receive the following error instead
>
> of a segmentation fault. However, the format of files may have changed between
>
> version 9 and 11.
>
>
>
> | ERROR: Bad residue/molecule data in prmtop!
>
> | Residue 34(atoms 618- 684) is in multiple molecules.
>
>
>
> In conclusion, the problem is one of two things. 1) This bug occurs in the
>
> Amber11 source code and is very specific to systems with large numbers of atoms.
>
> 2) The user's input is problematic in some way and the problem is specific to
>
> the users input data.
>
>
>
> To test this -- the user could produce for us a similar case which contains less
>
> atoms (less than 408609 would be great!). If this is successful then it is most
>
> likely item (1); however, if it is not successful then item (2) may be a
>
> possibility. In either case, the user should check their input data for
>
> consistency in order to eliminate item (2). If it is item (1), then a bug
>
> report should be sent to the developers.
>
>
> I want to ask if you have any solution for this.
>
>
> Thanks,
> Hector
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Dr. Adrian E. Roitberg
Associate Professor
Quantum Theory Project, Department of Chemistry
University of Florida
Senior Editor. Journal of Physical Chemistry.
on Sabbatical in Barcelona until August 2011.
Email roitberg.ufl.edu
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Received on Tue Jan 11 2011 - 12:00:02 PST
