Hi Ross,
So I compiled MPI without -static flag and as per your second suggestion I
replaced all the occurrences of "-fast" by "-ipo -O3 -no-prec-div -xHost" in
the config.h file in amber11/src. So the it looks like
---------
#PMEMD Specific build flags
PMEMD_FPP=cpp -traditional -DMPI -P -DMKL -DBINTRAJ -DDIRFRC_EFS
-DDIRFRC_COMTRANS -DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT
PMEMD_F90=mpif90
PMEMD_FOPTFLAGS=-ipo -O3 -no-prec-div -xHost
PMEMD_CC=mpicc
PMEMD_COPTFLAGS=-ipo -O3 -no-prec-div -xHost -D_FILE_OFFSET_BITS=64
-D_LARGEFILE_SOURCE -DBINTRAJ -DMPI
PMEMD_NETCDFLIB=../../netcdf/lib/libnetcdf.a
PMEMD_FLIBSF=-L/opt/intel/mkl/10.1.0.015/lib/em64t -Wl,--start-group
/opt/intel/mkl/10.1.0.015/lib/em64t/libmkl_intel_lp64.a /opt/intel/mkl/
10.1.0.015/lib/em
64t/libmkl_sequential.a
/opt/intel/mkl/10.1.0.015/lib/em64t/libmkl_core.a-Wl,--end-group
-lpthread
PMEMD_LD= mpif90
LDOUT= -o
--------
However my "make parallel" under amber11/src stops at
--------
cpp -traditional -DMPI -P -DMKL -DBINTRAJ -DDIRFRC_EFS -DDIRFRC_COMTRANS
-DDIRFRC_NOVEC -DFFTLOADBAL_2PROC -DPUBFFT pmemd.fpp pmemd.f90 mpif90 -ipo
-O3 -no-prec-div -xHost -c pmemd.f90
--------
Guidance to make successful compilation of amber11 would be highly
appreciated
Best
/Alok
On Wed, Oct 20, 2010 at 4:26 PM, Alok Juneja <junejaalok.gmail.com> wrote:
> Hi Ross,
>
> Is "./configure_openmpi -static intel" script in /AmberTools/src directory
> is not compiling the MPI statically.
>
> Best
> /Alok
>
>
> On Wed, Oct 20, 2010 at 4:12 PM, Ross Walker <ross.rosswalker.co.uk>wrote:
>
>> Hi Alok,
>>
>> The problem is that the -fast flag automatically implies static linking
>> and
>> most people don't build their MPI libraries to support this. The solution
>> is
>> either:
>>
>> 1) Rebuild your MPI to support static linking. (See your MPI manual for
>> details)
>>
>> 2) Edit the config.h file and replace -fast with all of the options -fast
>> implies "except" the -static option.
>>
>> This problem will be addressed in a bugfix shortly. Basically, giving up
>> on
>> -fast and just trying to add the multitude of different optimum options,
>> for
>> each different subversion of the compiler, individually. Got to love
>> Intel.
>> :-(
>>
>> All the best
>> Ross
>>
>> > -----Original Message-----
>> > From: Alok Juneja [mailto:junejaalok.gmail.com]
>> > Sent: Wednesday, October 20, 2010 12:42 PM
>> > To: amber.ambermd.org
>> > Subject: [AMBER] pmemd 11 (parallel) compilation error - revisiting
>> >
>> > Hi,
>> >
>> > This post is in continuation to the
>> > http://archive.ambermd.org/201009/0268.html, where Ross is suggesting
>> > two
>> > solutions to the problem.
>> >
>> > I compiled the static mpi using
>> > "./configure_openmpi -static intel" script in /AmberTools/src directory.
>> > Ideally speaking the '-fast' flag in the config.h should work for pmemd.
>> > However the compilation stops exactly at place where Paul was also
>> getting
>> > error. Please suggest the solution to the problem.
>> >
>> > Best
>> > /Alok
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> -Alok
>
--
-Alok
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Received on Wed Oct 20 2010 - 19:00:04 PDT
