AMBER Archive (2008)

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

From: Robert Duke (rduke_at_email.unc.edu)
Date: Fri Dec 05 2008 - 14:32:04 CST

Yes, seconding Ross' comments, this seems likely to be an out-of-memory
swapping situation, or a broken version of the compiler. PMEMD typically
compiles in well under a minute for intel non-itanium architectures.
Regards - Bob Duke

----- Original Message -----
From: "Hazard, E. Starr" <hazards_at_musc.edu>
To: <amber_at_scripps.edu>
Sent: Friday, December 05, 2008 3:12 PM
Subject: AMBER: compiling PMEMD spits out lots of -tp not supported and
hangs @ pmemd.f90

>
> 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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