AMBER Archive (2009)
Subject: Re: [AMBER] Error with calculation of the potential energy
From: Per Jr. Greisen (pgreisen_at_gmail.com)
Date: Mon Apr 27 2009 - 13:57:58 CDT
The system is
SunOS newton 5.10 Generic_137111-01 sun4u sparc SUNW,Sun-Fire-15000
and I am using the fortran compiler from sun. I have written the
following config.h file for sunOS
FFT_DEFINES = -DPUBFFT
#DIRFRC_DEFINES = -DDIRFRC_EFS -DDIRFRC_NOVEC
CPP = /lib/cpp
##CPPFLAGS = -P
#F90_DEFINES = -DFFTLOADBAL_2PROC
PREPROCFLAGS = -DMPI -I/opt/SUNWhpc/include
F90 = mpf90
#MODULE_SUFFIX = mod
#F90FLAGS = -c -auto
#F90_OPT_DBG = -g -traceback
F90_OPT_LO = -c -O1 $NFLAGS
F90_OPT_MED = -c -O2 $NFLAGS
#F90_OPT_HI = -c -fast $NFLAGS
F90_OPT_HI = -g -c -fast -ftrap=%none -xlic_lib=sunperf
#F90_OPT_HI = -c -fast -xlic_lib=sunperf
F90_OPT_DFLT = $(F90_OPT_HI)
OPT_LO = "mpf90 -c -O1 $NFLAGS"
OPT_MED = "mpf90 -c -O2 $NFLAGS"
#OPT_HI = "mpf90 -c -fast $NFLAGS"
OPT_HI = "mpf90 -c -fast -xlic_lib=sunperf"
OPT_EW_PAIRLIST = "$OPT_MED"
CC = mpcc
CFLAGS = -fast $NFLAGS
LOAD = mpf90
LOADLIBS = -g -ftrap=%none -L/opt/SS12/SUNWspro/lib/ -xlic_lib=sunperf
#LOADLIBS = -g -L/opt/SS12/SUNWspro/lib/ -xlic_lib=sunperf -lmpi -fast
#LOADLIBS = "-L/opt/SS12/SUNWspro/lib/ -xlic_lib=sunperf -lmvec -fast"
Any suggestions to fix the problem appreciated - thanks in advance
With kind regards
On Mon, Apr 27, 2009 at 8:25 PM, Robert Duke <rduke_at_email.unc.edu> wrote:
> What is the chip? The compiler? The config file? This is definitely a
> config or compiler or unsupported s/w or h/w problem. - Bob Duke
> ----- Original Message ----- From: "Per Jr. Greisen" <pgreisen_at_gmail.com>
> To: "AMBER Mailing List" <amber_at_ambermd.org>
> Sent: Monday, April 27, 2009 1:11 PM
> Subject: Re: [AMBER] Error with calculation of the potential energy
> When I try to test the pmemd it seems that it has an error with
> calculating the potential energy - I put out the output from some of
> the tests.
> export TESTsander='../../exe/pmemd'; cd dhfr && ./Run.dhfr
> which returns some of the following in the TEST_FAILURES.diff
> < NSTEP = 1 TIME(PS) = 510.051 TEMP(K) = 301.29 PRESS = 0.
> < Etot = -57751.8286 EKtot = 14110.5335 EPtot =
>> NSTEP = 1 TIME(PS) = 510.051 TEMP(K) = 301.65 PRESS = 0.
>> Etot = 3706.9950 EKtot = 14127.5125 EPtot =
> < 1-4 NB = 545.9440 1-4 EEL = 6666.3920 VDWAALS =
> < EELEC = -89881.6441 EHBOND = 0. RESTRAINT = 0.
>> 1-4 NB = 545.9440 1-4 EEL = 6666.3920 VDWAALS -727.9808
>> EELEC = -19602.4294 EHBOND = 0. RESTRAINT = 0.
> so it seems that it has not been compiled correctly; here it is
> compiled with ftrap=%none - if I on the other hand compile remove
> that compiling option the pmemd ends with FPE - division by zero. If I
> write the following part out in pairs_calc_vec.i by modifying the
> ! Do the Coulomb part of the direct sum using erfc spline table:
> delr = sqrt(delr2)
> write (0,*) delr
> delr is set to zero - how to fix this and why should one compile with
> Thanks in advance
> Best regards
> On Mon, Apr 27, 2009 at 1:08 PM, Carlos Simmerling
> <carlos.simmerling_at_gmail.com> wrote:
>> please give more info- you said serial, parallel and pmemd, but only give
>> examples so we don't know where to look for the problem. also give the
>> section from the energy, not just the totals, so we can see which
>> differ. finally, did all of the test cases pass?
>> On Mon, Apr 27, 2009 at 7:03 AM, Per Jr. Greisen <pgreisen_at_gmail.com>
>>> Hi all,
>>> I have compiled a serial, parallel, and pmemd of amber but I get some
>>> strange results when I try to run the test examples it seems that the
>>> potential energy is calculated wrongly in the different test cases
>>> < NSTEP = 1 TIME(PS) = 5420.002 TEMP(K) = 301.21
>>> PRESS = -5.8
>>> < Etot = -608.3990 EKtot = 1063.0604 EPtot =
>>> > NSTEP = 1 TIME(PS) = 5420.002 TEMP(K) = 301.03 PRESS =
>>> > Etot = 1257.0312 EKtot = 1062.3997 EPtot =
>>> Any suggestions on how to fix this? Thanks in advance
>>> With kind regards
>>> AMBER mailing list
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