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 - 16:46:57 CST


The pmemd Makefile does not take targets of serial or parallel. What you
get depends on how you ran configure. So just type "make".
----- Original Message -----
From: "David Watson" <dewatson_at_olemiss.edu>
To: <amber_at_scripps.edu>
Sent: Friday, December 05, 2008 5:30 PM
Subject: Re: AMBER: compiling PMEMD spits out lots of -tp not supported and
hangs @ pmemd.f90

> On Dec 5, 2008, at 4:11 PM, Starr Hazard wrote:
>
>> 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
>
> I should have clarified that I am using Amber9.
>
> The "-xHost" option chooses the proper switches for the processor you are
> compiling on at the moment (in the ifort 11 suite).
>
>>
>>
>> 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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