AMBER Archive (2008)

Subject: AMBER: Question fot Amber 10 Benchmarks

From: sychen (u8613020_at_msg.ndhu.edu.tw)
Date: Thu Nov 27 2008 - 01:50:11 CST

Dear all,
We have compiled AMBER10 on the machines & platforms which are the same
as those described by Ross Walker in Amber 10 Benchmarks. (Dual XEON E5430 on SuperMicro X7DWA-N)
We use mpich2-1.0.8 & ifort9.1 to build sander.MPI, the benchmark of original JAC by sander.mpi seems fine
(2cpu: 161sec, 4cpu: 88sec, 8cpu: 54sec), but the result for 16cpu (on 2nodes & all 6 nodes are the same machine & platform) was very bad (83sec).
(For 16cpu computation, abnormal usage of system CPU (60~70%) was observed by top or Ganglia monitoring, while 8cpu computation was fine & system CPU < 5% & user CPU > 95%)

Command for building MPICH2 is 'export CC=gcc && export F77=ifort && export F90=ifort && ./configure -prefix=/opt/mpich2 --with-device=ch3:ssm'
I've tested mpich2 by 'mpiexec -l -machinefile mpd.hosts -n 48 hostname', and normal messages returned by 8 thread from node1~node6.
PS: Each nodes communicates with each other by one GbE switch (3COM 2924-SFPplus)

Can anyone give me some ideas to solve this problem while running parallel sander jobs across nodes?
Thank you very much.

Sincerely,
yuann

#######command for parallel sander (JAC benchmark)############
/opt/mpich2/bin/mpirun -machinefile hostlist -n 16 /opt/amber10/exe/sander.MPI -O -i mdin -c inpcrd.equil -p prmtop -o 16cpu.out

######hostlist######
node01:8
node02:8
node03:8
node04:8
node05:8
node06:8

#############################################################################################
config_amber.h for parallel sander was generated by ./configure_amber -mpich2 -p4 -mmtsb -static -verbose -nobintraj ifort
#############################################################################################
AMBERBUILDFLAGS=
LOCALFLAGS=
USE_BLASLIB=$(SOURCE_COMPILED)
USE_LAPACKLIB=$(SOURCE_COMPILED)
CC= gcc
CPLUSPLUS=g++
CFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -m64 -O2 $(AMBERBUILDFLAGS)
CPPFLAGS= -DMMTSB $(AMBERBUILDFLAGS)
FPPFLAGS= -I/opt/mpich2/include -P -DMMTSB -DMPI -DUSE_MPI_IN_PLACE $(AMBERBUILDFLAGS)
FPP= cpp -traditional $(FPPFLAGS)
FC= /opt/mpich2/bin/mpif90
FFLAGS= -w95 -sox -vec_report3 -opt_report -opt_report_level max -opt_report_phase all -V -v -Wl,-verbose,-M -mp1 -O0 $(LOCALFLAGS) $(AMBERBUILDFLAGS)
FOPTFLAGS= -w95 -sox -vec_report3 -opt_report -opt_report_level max -opt_report_phase all -V -v -Wl,-verbose,-M -mp1 -ip -O3 -axWP $(LOCALFLAGS) $(AMBERBUILDFLAGS)
FREEFORMAT_FLAG= -FR
LOAD= /opt/mpich2/bin/mpif90 -static $(LOCALFLAGS) $(AMBERBUILDFLAGS)
LOADCC= gcc -static $(LOCALFLAGS) $(AMBERBUILDFLAGS)
LOADLIB=
LM= -lm
XHOME= /usr/X11R6
XLIBS= -L/usr/X11R6/lib64 -L/usr/X11R6/lib
.SUFFIXES: .f90
EMPTY=
AR=ar rv
M4=m4
RANLIB=ranlib
SFX=
NETCDF=
NETCDFLIB=
MODULEDIR=-I
testsanderDIVCON=test.sander.DIVCON
INCDIVCON=divcon
LIBDIVCON=../dcqtp/src/qmmm/libdivcon.a
BINDIR=/home/sychen/amber10/bin
LIBDIR=/home/sychen/amber10/lib
INCDIR=/home/sychen/amber10/include
DATDIR=/home/sychen/amber10/dat
.f.o: $<
        $(FPP) $< > _$<
        $(FC) -c $(FFLAGS) -o $@ _$<
.c.o:
        $(CC) -c $(CFLAGS) $(CPPFLAGS) -o $@ $< 

-- 
sychen <u8613020_at_mail.ndhu.edu.tw>

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