AMBER Archive (2008)

Subject: Re: AMBER: compiling PMEMD spits out lots of -tp not supported and hangs @ pmemd.f90

From: David Watson (dewatson_at_olemiss.edu)
Date: Fri Dec 05 2008 - 14:32:45 CST

You might want to change the -tpp7 to -xHost if you are using the
ifort 11.0 compiler, although you will only be able to take advantage
of the optimizations of the hardware on the machine you are compiling
it on.
This is fine if you are compiling/running on the same architecture.

On Dec 5, 2008, at 2:12 PM, Hazard, E. Starr wrote:

>
> Here's how I set up pmemd
>
> ./configure linux_em64t ifort mpich2 pubfft nobintraj
>
>
> Here's my config.h
>
> MATH_DEFINES =
> MATH_LIBS =
> IFORT_RPATH = /share/apps/intel/lib/intel64:/share/apps/intel/lib/
> intel64:/share/apps/intel/mkl/lib/em64t:/share/apps/mpich2-
> intel_11_install/lib:/share/apps/ccp4-6.0.2/lib:/opt/openmpi/1.1.4/
> lib:/opt/lava/6.1/linux2.6-glibc2.3-ia32e/lib
> MATH_DEFINES = -DMKL
> MATH_LIBS = /share/apps/intel/mkl/lib/em64t/libmkl_intel_lp64.a /
> share/apps/intel/mkl/lib/em64t/libmkl_core.a /share/apps/intel/mkl/
> lib/em64t/libmkl_sequential.a
> FFT_DEFINES = -DPUBFFT
> FFT_INCLUDE =
> FFT_LIBS =
> NETCDF_HOME = /home/hazards/COMPILE/amber10/src/netcdf
> NETCDF_DEFINES = -DBINTRAJ
> NETCDF_MOD = netcdf.mod
> NETCDF_LIBS = $(NETCDF_HOME)/lib/libnetcdf.a
> MPI_HOME = /share/apps/mpich2-intel_11_install
> MPI_DEFINES = -DMPI -DSLOW_NONBLOCKING_MPI
> MPI_INCLUDE = -I$(MPI_HOME)/include
> MPI_LIBDIR = $(MPI_HOME)/lib
> MPI_LIBS = -L$(MPI_LIBDIR) -lmpich -lrt -luuid -lpthread
> DIRFRC_DEFINES = -DDIRFRC_EFS -DDIRFRC_COMTRANS -DDIRFRC_NOVEC
> CPP = /lib/cpp
> CPPFLAGS = -traditional -P
> F90_DEFINES = -DFFTLOADBAL_2PROC
>
> F90 = ifort
> 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 -xP -ip -O3
> F90_OPT_DFLT = $(F90_OPT_HI)
>
> CC = gcc
> CFLAGS =
>
> LOAD = ifort
> LOADFLAGS =
> LOADLIBS = -limf -lsvml -Wl,-rpath=$(IFORT_RPATH)
>
>
> make install hums along nicely up to this point and then hangs here
> for a LONG time (up to 20 minutes)
>
> /lib/cpp -traditional -P -I/share/apps/mpich2-intel_11_install/
> include -DPUBFFT -DBINTRAJ -DMPI -DSLOW_NONBLOCKING_MPI -DDIRFRC_EFS
> -DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DMKL -DFFTLOADBAL_2PROC pmemd.fpp
> pmemd.f90
> ifort -c -auto -tpp7 -xP -ip -O3 pmemd.f90
> ifort: command line remark #10148: option '-tp' not supported
>
>
> should I just keep waiting?
>
>
>
>
>
>
> Then hangs.... not for 5 minutes but up to 20.

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