Hi,
I'm getting the following error when running a minimization in sander.
| Flags: SGIFFT MEM_ALLOC MPI RLE ROWAT HAS_FTN_ERFC
| NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation
| New format PARM file beingparsed.
| Version = 1.000 Date = 10/07/02 Time = 12:55:44
NATOM = 34759 NTYPES = 16 NBONH = 18344 MBONA = 16779
NTHETH = 36099 MTHETA = 22715 NPHIH = 68670 MPHIA = 41972
NHPARM = 0 NPARM = 0 NNB = 181415 NRES = 2869
NBONA = 16779 NTHETA = 22715 NPHIA = 41972 NUMBND = 43
NUMANG = 88 NPTRA = 40 NATYP = 29 NPHB = 1
IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0
Failed to allocate memory for ipairs: 604076661
The last suggestion was to find a cluster with at least 600MB of physical
memory. I am running this job on an origin cluster with 200MB memory per
CPU. I've tried to run this job on increased number of processors from 8
to 128 but it does not seem to make any difference.
>From what I understand looking into the code is that ipairs takes values
from 1 to lastpr which is equal to MAXPR. In sizes.h there is the
following part that allocates a value to MAXPR
#ifndef MEM_ALLOC
parameter (MAXREA=2000000)
parameter (MAXINT=2000000)
parameter (MAXHOL=400000)
parameter (MAXPR=5400000)
#endif
I understand that the above value for MAXPR is only used if the
-DMEM_ALLOC flag is not set in the MACHINE file and that actually what
happens is that these sizes are determined by the code and allocated at
run-time.
My questions are:
1. Why is the program not able to allocate the right amount of memory? I
mean when I run on 128 processors the available physical memory is
25 Gbytes. Is it possible that this is still not enough?
2. Would it make any difference if I would compile the program with a
larger value for MAXPR?
I would appreciate if anyone could help me understand how this things are
related and how they work and could suggest anything to help me solve this
problem.
Thank you,
Ioana
Received on Fri Oct 18 2002 - 12:50:22 PDT
