AMBER Archive (2008)

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

From: Starr Hazard (hazards_at_musc.edu)
Date: Fri Dec 05 2008 - 16:11:58 CST

Well I did get to compiling pmemd after successfully compiling amber
serial and then amber parallel. So in that sense 11.0.074 works for me too

When I try "make serial" in the $AMBERHOME/src/pmemd

I see a complaint that it has no rule for target serial

Thanks for the suggestion.

Its good to know that 11.0.074 works in your system. At least its not a
complete Amber-lemon yet :-)

Starr

David Watson wrote:
> 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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