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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Received on Tue Jan 11 2011 - 12:00:02 PST
