AMBER Archive (2007)

Subject: Re: AMBER: pmemd with openmpi

From: Myunggi Yi (myunggi_at_gmail.com)
Date: Mon Nov 19 2007 - 15:40:41 CST

I used Intel openmpi 1.2.4
As you see my config.h, I just used what I have (version 10.0.026).
Sorry. That's all I know.
The head node of the cluster is down. I can't access.

On Nov 19, 2007 3:31 PM, Francesco Pietra <chiendarret_at_yahoo.com> wrote:
> Great, thank you.
>
> Which version of openmpi? Any idea if icc 9.1.042 and ifort 9.1.036 are OK?
>
> francesco pietra
>
>
> --- Myunggi Yi <myunggi_at_gmail.com> wrote:
>
> > Dear Amber users,
> >
> > I compiled PMEMD with openmpi on a linux cluster.
> > Somebody may want to this.
> >
> > ./configure linux64_opteron ifort mpich bintraj
> >
> > Then replace ifort with mpif90 and comment out -lmpich
> >
> >
> > ========================================
> > MATH_DEFINES =
> > MATH_LIBS =
> > IFORT_RPATH =
> >
> /usr/mpi/intel/openmpi/lib64:/opt/intel/fce/10.0.026/lib:/opt/intel/cce/10.0.026/lib
> > FFT_DEFINES = -DPUBFFT
> > FFT_INCLUDE =
> > FFT_LIBS =
> > NETCDF_HOME = /panfs/storage.local/scs/home/myunggi/amber-openmpi/src/netcdf
> > NETCDF_DEFINES = -DBINTRAJ
> > NETCDF_MOD = netcdf.mod
> > NETCDF_LIBS = $(NETCDF_HOME)/lib/libnetcdf.a
> > MPI_HOME = /usr/mpi/intel/openmpi/
> > MPI_DEFINES = -DMPI -DSLOW_NONBLOCKING_MPI
> > MPI_INCLUDE = -I$(MPI_HOME)/include
> > MPI_LIBDIR = $(MPI_HOME)/lib
> > #MPI_LIBS = -L$(MPI_LIBDIR) -lmpich
> > DIRFRC_DEFINES = -DDIRFRC_EFS -DDIRFRC_NOVEC
> > CPP = /lib/cpp
> > CPPFLAGS = -traditional -P
> > F90_DEFINES = -DFFTLOADBAL_2PROC
> >
> > F90 = mpif90
> > MODULE_SUFFIX = mod
> > F90FLAGS = -c -auto
> > F90_OPT_DBG = -g -traceback
> > F90_OPT_LO = -tpp7 -O0
> > F90_OPT_MED = -tpp7 -O2
> > F90_OPT_HI = -tpp7 -xW -ip -O3
> > F90_OPT_DFLT = $(F90_OPT_HI)
> >
> > CC = gcc
> > CFLAGS =
> >
> > LOAD = mpif90
> > LOADFLAGS =
> > LOADLIBS = -limf -lsvml -Wl,-rpath=$(IFORT_RPATH)
> > =======================================
> >
> >
> > --
> > Best wishes,
> >
> > MYUNGGI YI
> > ==================================
> > KLB 419
> > Institute of Molecular Biophysics
> > Florida State University
> > Tallahassee, FL 32306
> >
> > Office: (850) 645-1334
> > http://www.scs.fsu.edu/~myunggi
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> >
>
>
>
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-- 
Best wishes,

MYUNGGI YI
==================================
KLB 419
Institute of Molecular Biophysics
Florida State University
Tallahassee, FL 32306

Office: (850) 645-1334
http://www.scs.fsu.edu/~myunggi
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