Hi,
A while ago I recieved a bugfix, which solved my problem and works
perfectly in an unparallelized environment on a linux pc. The problem
pertained to the error "fill_bonded: max13 exceeded!!".
The system is a sugar, with lone pairs on all oxygens, in a box of tip5p
water (although the same result is obtained when tip3p water is used). I
have tried to run the simulation on both a single cpu as well as
in a parallelized environment. Although the bugfix was added and the code
was recompiled the same way in both cases, I recieve the error only in the
parallelized environment, while the simulation runs fine on the single
cpu:
(the end of the NPT simulation in AMBER7 with ewald)
Cutoff= 8.000 Tol =0.100E-04
Ewald Coefficient = 0.34864
Interpolation order = 4
| PLEVEL = 1: runmd parallelization, no EKCMR
fill_bonded: max13 exceeded!!
I have tried both the SGI IRIX platform and redhat linux for the
parallelized environment, while the single cpu is under the redhat linux
OS.
I have inlcuded the bugfix below, although it can also be found in the
AMBER archive contributed by Prof. David Case.
Any help would be appreciated,
Thanks
Sarah
*** extra_pts.f 2002/01/11 17:21:17 7.25
--- extra_pts.f 2002/08/15 22:57:53
***************
*** 126,132 ****
#ifndef LES
call allocate_frames(numextra,ifrtyp,iatcen,inumep,
+ iepfr,ifrst,imid,ithrd,leploc)
! max14 = 2*(nphih+nphia+ndper)
call allocate_14nb(inb_14,max14)
#endif
c
--- 126,132 ----
#ifndef LES
call allocate_frames(numextra,ifrtyp,iatcen,inumep,
+ iepfr,ifrst,imid,ithrd,leploc)
! max14 = 3*(nphih+nphia+ndper)
call allocate_14nb(inb_14,max14)
#endif
c
***************
*** 193,201 ****
call get_istack(i_numnghbr,3*natom)
call get_istack(i_epowner,natom)
max11 = natom+numextra
! max12 = 2*(nbonh+nbona+nbper)
! max13 = 2*(ntheth+ntheta+ngper)
! max14 = 2*(nphih+nphia+ndper)
maxa = max(max11,max12,max13,max14)
call get_istack(i_11,2*max11)
call get_istack(i_12,2*max12)
--- 193,201 ----
call get_istack(i_numnghbr,3*natom)
call get_istack(i_epowner,natom)
max11 = natom+numextra
! max12 = 3*(nbonh+nbona+nbper)
! max13 = 3*(ntheth+ntheta+ngper)
! max14 = 3*(nphih+nphia+ndper)
maxa = max(max11,max12,max13,max14)
call get_istack(i_11,2*max11)
call get_istack(i_12,2*max12)
***********************************************
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Received on Fri Aug 15 2003 - 08:53:00 PDT
