Hi, Scott
I think I know what's going on with the partition error in shake. For a
multi-molecule system, sander assumes/requires that atoms of the same
molecule are in the same block of the PDB file (I don't remember if this
is documented anywhere). But my PDB file has a metal ion bonded to one
of the monomer, but this metal ion is not located in the same block as
the monomer. This created the partition error in shake. Reordering this
atom solved the problem.
Regards,
Guanglei
Scott Brozell wrote:
> Hi Guanglei,
>
> This indicates that a constrained pair of atoms are on different
> processors.
> I have slightly cleaned up the amber9/src/sander/shake.f and
> added a more detailed error message. If this is really a bug
> then you will probably have to trace back to the creation of the
> ib and jb arguments.
>
> The ./Run.ubiquitin test fails in amber9 using an identical config.h
> to that in amber8 where the test passes.
> This occurs on several linux machines using ifc 7.1.
>
> Tail of amber9 mdout:
> | TOTAL SIZE OF NONBOND LIST = 3971390
> vlimit exceeded for step 0 ; vmax = 807276600744896.
>
> NSTEP = 1 TIME(PS) = 1000.001 TEMP(K) =????????? PRESS
=********
> Etot = ?????????????? EKtot = ?????????????? EPtot =
**************
> BOND = 220.7117 ANGLE = 637.0885 DIHED =
738.4775
> 1-4 NB = 275.3945 1-4 EEL = 3165.3009 VDWAALS =
**************
> EELEC = -15813.8927 EHBOND = 0.0000 RESTRAINT =
0.0000
> EKCMT = 4180.1500 VIRIAL = ************** VOLUME =
167676.3480
> EPOLZ = -391.0542 E3BODY = 0.0000
>
> Diff with amber8:
> ...
> < Box X = 65.656 Box Y = 51.770 Box Z = 49.331
> ---
>
>> Box X = 63.571 Box Y = 50.126 Box Z = 47.764
>
> 135c135
> < NFFT1 = 72 NFFT2 = 54 NFFT3 = 50
> ---
>
>> NFFT1 = 64 NFFT2 = 50 NFFT3 = 48
>
> 181,183c181,182
> < | Local SIZE OF NONBOND LIST = 3971390
> < | TOTAL SIZE OF NONBOND LIST = 3971390
> < vlimit exceeded for step 0 ; vmax = 807276600744896.
> ---
>
>>| Local SIZE OF NONBOND LIST = 4374419
>>| TOTAL SIZE OF NONBOND LIST = 4374419
>
> 185,186c184,185
> < NSTEP = 1 TIME(PS) = 1000.001 TEMP(K) =????????? PRESS
=********
> < Etot = ?????????????? EKtot = ?????????????? EPtot =
**************
> ---
>
>> NSTEP = 1 TIME(PS) = 1000.001 TEMP(K) = 298.34 PRESS =
-15.2
>> Etot = -38796.4732 EKtot = 9246.2358 EPtot =
-48042.7090
>
>
> ...
>
> Scott
>
> ---------- Forwarded message ----------
> Date: Fri, 23 Apr 2004 11:18:19 -0400
> From: Guanglei Cui <cuigl.csb.sunysb.edu>
> Reply-To: amber.scripps.edu
> To: amber.scripps.edu
> Subject: AMBER: partition error in shake
>
> Dear all,
>
> After I managed to get SCALI to work with AMBER8, I found I can't use
> more than 4 CPUs for one of my systems (80,000 atoms), but it worked
> fine with a regular DNA test case (10 base pairs). It failed because of
> "partition error in shake". Before I dive into shake.f, I wonder if
> anyone has a quick guess what might be the problem. Thanks in advance.
Received on Wed Apr 05 2006 - 23:50:03 PDT
