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 - 15:53:15 CST

We are running Xeon L5420 dual quads fine with ifort 11.0.074.

You might try backing up your config.h and performing a "make clean",
regenerate the config.h, and then try to "make serial".

On Dec 5, 2008, at 3:15 PM, Robert Duke wrote:

> I would be looking at getting either an updated or downlevel (10,
> known good release) of the compiler...
> Regards - Bob Duke
> ----- Original Message ----- From: "Starr Hazard" <hazards_at_musc.edu>
> To: <amber_at_scripps.edu>
> Sent: Friday, December 05, 2008 4:10 PM
> Subject: Re: AMBER: compiling PMEMD spits out lots of -tp not
> supported and hangs @ pmemd.f90
>
>
>> I tried replacing -tpp7 with -xHost in all three cases. It whined
>> about overriding xHost with xP and stopped at the same place.
>>
>> Then I changed in the third instance
>>
>> F90_OPT_HI = -tpp7 -xP -ip -O3 to F90_OPT_HI = -xP -ip -O3
>>
>> And it stopped at the same place.
>>
>> Starr
>>
>> David Watson wrote:
>>> 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.
>>>>
>>>
>>> 

--
David Watson • Graduate Student • Medicinal Chemistry • 425 Faser Hall  
• University MS  38677 • 1.662.915.1663

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