Hi,
I am trying to get sander_classic of AMBER 6 to run on a dual
processor machine (trying to get AMBER to utilize both processors) with
MPICH version 1.2.5.2, running on Linux (Red Hat version 7.1).
Everything appeared to compile properly using the -DMPI flag, and the
CPP and LOADLIB variables pointing to the appropriate include and
library files for MPICH in the MACHINE file. However, when I try to run
sander_classic with the command "mpirun -np 2
$AMBERHOME/exe/sander_classic -i md.in etc.", sander_classic starts up
on multiple processors, and starts writing to the output file, but after
a short period of time (~20 seconds) it only runs on one processor, and
does not write to any of the output files, so I can't tell if the
calculation is proceeding. The same calculation using the command
"mpirun -np 1 $AMBERHOME/exe/sander_classic -i md.in etc." runs just
fine, and finishes before the two processor job. Below is the MACHINE
file and input file for the mdrun.
Unfortunately I don't get any error messages from either
sander_classic or MPICH.
Here are the settings of the MACHINE file:
#
setenv MACHINE "linux/FreeBSD/Windows PC"
setenv MACH Linux
setenv MACHINEFLAGS "-DREGNML -DMPI"
# CPP is the cpp for this machine
setenv CPP "/lib/cpp -traditional -I/users/MPICH/mpich-1.2.5.2/include"
setenv CC gcc
# SYSDIR is the name of the system-specific source directory relative to
src/*/
setenv SYSDIR Machines/g77
# COMPILER ALIASES:
# LOADER/LINKER:
setenv LOAD "g77"
setenv LOADLIB "-lm -L/users/MPICH/mpich-1.2.5.2/lib -lmpich"
setenv G77_COMPAT " "
#
# following seems to actually slow down code, though it works well on
CHARMM:
#setenv G77_OPT "-O6 -m486 -malign-double -ffast-math
-fomit-frame-pointer -funroll-loops -funroll-all-loops -mcpu=pentiumpro
-march=pentiumpro -ffloat-store -fforce-mem -frerun-cse-after-loop -fex
pensive-optimizations -fugly-complex"
# following appears to be the best we have found so far:
setenv G77_OPT " "
# little or no optimization:
setenv L0 "g77 -c -g"
# modest optimization (local scalar):
setenv L1 "g77 -c $G77_OPT $G77_COMPAT"
# high scalar optimization (but not vectorization):
setenv L2 "g77 -c $G77_OPT $G77_COMPAT"
# high optimization (may be vectorization, not parallelization):
setenv L3 "g77 -c $G77_OPT $G77_COMPAT"
# ranlib, if it exists
setenv RANLIB ranlib
Here is a copy of the input file:
temperature ramping input file
&cntrl
NTX = 1,
IREST = 0,
INIT = 3,
SCEE = 1.2,
NTB = 1,
NTC = 2,
NTF = 2,
CUT = 12.0,
NSNB = 30,
NSTLIM = 10000,
DT = 0.001,
NDFMIN = 6,
TEMPI = 10,
TEMP0 = 70,
HEAT = 2.6457513,
NTT = 1,
TAUP = 0.2,
NTP = 0,
NTWR = 500,
NTWE = 500,
NTWX = 500,
NTWXM = 0,
NTWEM = 0,
NTWVM = 0,
JFASTW = 0,
NTCM = 1,
IBEllY = 0,
&end
Thank you for any assistance you may provide.
Richard Smith
Graduate Student
University of Michigan
Department of Biophysics
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Received on Tue Oct 14 2003 - 14:53:01 PDT
