AMBER Archive (2007)

Subject: Re: AMBER: pmemd with openmpi

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Mon Nov 19 2007 - 14:31:56 CST

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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