On Mon, May 3, 2010 at 12:56 PM, Alan <alanwilter.gmail.com> wrote:
> Hi there,
>
> First I must say that I am very very happy with Amber11. Much easier to
> install on Mac (at least with GNU).
>
> That said, I must report some results I have so far.
>
> 1) AT 1.4 and Amber11 with GNU and OMPI
> All went fine, no failures. The only detail here is that I use FINK. And
> openmpi from Fink (v. 1.3.3), whose mpicc (/sw/bin/mpicc) instead of using
> gcc-4 from fink (/sw/bin/gcc-4) is using apple system gcc (/usr/bin/gcc),
> which is WRONG in my opinion (and I believe macports did the right thing
> here); this will lead to several issues if you're not knowing what you're
> doing. I contact Fink developers and there's a openmpi 1.4.1 for tests
> addressing this issue.
>
> That said, if you want to compile Amber package with current openmpi from
> Fink, you have to, once ran ./configure -mpi gnu, edit config.h and replace
> mpicc by:
>
Something that may make compilation go along better, and is probably a
better option if you plan on building other software packages, create a link
to gcc-4 and g++-4 named gcc and g++, respectively, in /sw/bin, and make
sure that is in your path before /usr/bin (so "gcc" and "g++" invokes the
fink gcc-4 and g++-4 rather than the xcode tools version supplied in
/usr/bin)
You can do this with the commands:
cd /sw/bin
ln -s gcc-4 gcc
ln -s g++-4 g++
And in your .bashrc file put
export PATH=/sw/bin\:$PATH
This should prevent any user from having to modify the config.h file to get
the right compilers invoked. It should also fix mpicc and mpif90/mpif77,
since those are really only wrappers calling gcc and gfortran, anyway. I
say this here because both methods result in a successfully built Amber11 I
would imagine, but this method will probably be a more universal fix for
other packages users may want to install (i.e. an older version of Amber,
another MD package, or any other package someone wishes to build from
source).
> gcc-4 -D_REENTRANT -I/sw/include -I/sw/include/openmpi -L/sw/lib/openmpi
> -lmpi -lopen-rte -lopen-pal -lutil
>
> (mpif90 is calling Fink's gfortran correctly, and couldn't be different
> since Apple doesn't provide its OSX with gfortran)
>
> 2) AT 1.4 and Amber11 with Intel Compilers (v. 11.1.088)
>
> 2.1) With Amber's OMPI 1.4.1 script:
> Apart some issues with tests in serial, the paralles versions of ptraj.MPI,
> nab, sander.MPI, sander.LES.MPI and pmemd.MPI all failed to run with
> something like:
>
> otool -L ../../bin/sander.MPI
> ../../bin/sander.MPI:
> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version
> 125.0.1)
> libsvml.dylib (compatibility version 0.0.0, current version 0.0.0)
> /Users/alan/Programmes/amber11/AmberTools/lib/libmpi_f77.0.dylib
> (compatibility version 1.0.0, current version 1.0.0)
> /Users/alan/Programmes/amber11/AmberTools/lib/libmpi.0.dylib
> (compatibility
> version 1.0.0, current version 1.1.0)
> /Users/alan/Programmes/amber11/AmberTools/lib/libopen-rte.0.dylib
> (compatibility version 1.0.0, current version 1.0.0)
> /Users/alan/Programmes/amber11/AmberTools/lib/libopen-pal.0.dylib
> (compatibility version 1.0.0, current version 1.0.0)
> /usr/lib/libutil.dylib (compatibility version 1.0.0, current version 1.0.0)
> /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version
> 438.0.0)
> /usr/lib/libmx.A.dylib (compatibility version 1.0.0, current version
> 315.0.0)
> libirc.dylib (compatibility version 1.0.0, current version 1.11.0)
>
> amber11/test/4096wat% $AMBERHOME/bin/mpirun -np 2 ../../bin/sander.MPI -O
> -i
> gbin -c eq1.x -o mdout.pure_wat
> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> Image PC Routine Line Source
>
> libmpi.0.dylib 0000000105E7C957 Unknown Unknown Unknown
> libmpi_f77.0.dyli 0000000105D70046 Unknown Unknown Unknown
> sander.MPI 00000001001183AD Unknown Unknown Unknown
> sander.MPI 000000010036C434 Unknown Unknown Unknown
> sander.MPI 00000001000EC230 Unknown Unknown Unknown
> sander.MPI 00000001000AC25E Unknown Unknown Unknown
> sander.MPI 00000001000A2339 Unknown Unknown Unknown
> sander.MPI 000000010000192C Unknown Unknown Unknown
> sander.MPI 00000001000018C4 Unknown Unknown Unknown
> --------------------------------------------------------------------------
> mpirun has exited due to process rank 1 with PID 42746 on
> node amadeus.local exiting without calling "finalize". This may
> have caused other processes in the application to be
> terminated by signals sent by mpirun (as reported here).
> --------------------------------------------------------------------------
>
I do not get these errors with MacPorts GCC 4.4 installed alongside either
OpenMPI 1.4.1 (compiled from source with a simple ./configure; make; make
install) or MPICH2 1.2.1 (built the same way).
>
> test/4096wat% $AMBERHOME/bin/mpirun -np 2 ../../bin/pmemd.MPI -O -i gbin -c
> eq1.x -o mdout.pure_wat
> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> Image PC Routine Line Source
>
> libmpi.0.dylib 0000000100702957 Unknown Unknown Unknown
> libmpi_f77.0.dyli 00000001005F6046 Unknown Unknown Unknown
> pmemd.MPI 0000000100050111 Unknown Unknown Unknown
> pmemd.MPI 00000001000021E8 Unknown Unknown Unknown
> pmemd.MPI 000000010000168C Unknown Unknown Unknown
> pmemd.MPI 0000000100001624 Unknown Unknown Unknown
> forrtl: severe (174): SIGSEGV, segmentation fault occurred
> Image PC Routine Line Source
>
> libmpi.0.dylib 0000000100702957 Unknown Unknown Unknown
> libmpi_f77.0.dyli 00000001005F6046 Unknown Unknown Unknown
> pmemd.MPI 0000000100050111 Unknown Unknown Unknown
> pmemd.MPI 00000001000021E8 Unknown Unknown Unknown
> pmemd.MPI 000000010000168C Unknown Unknown Unknown
> pmemd.MPI 0000000100001624 Unknown Unknown Unknown
> --------------------------------------------------------------------------
> mpirun has exited due to process rank 0 with PID 42783 on
> node amadeus.local exiting without calling "finalize". This may
> have caused other processes in the application to be
> terminated by signals sent by mpirun (as reported here).
> --------------------------------------------------------------------------
>
> For Run.lmod:
> .../amber11/AmberTools/test/nab% ../../bin/nab -o tlmod tlmod.nab
>
> otool -L tlmod
> tlmod:
> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version
> 125.0.1)
> libifport.dylib (compatibility version 1.0.0, current version 1.11.0)
> libifcore.dylib (compatibility version 1.0.0, current version 1.11.0)
> libsvml.dylib (compatibility version 0.0.0, current version 0.0.0)
> /Users/alan/Programmes/amber11/AmberTools/lib/libmpi.0.dylib (compatibility
> version 1.0.0, current version 1.1.0)
> /Users/alan/Programmes/amber11/AmberTools/lib/libopen-rte.0.dylib
> (compatibility version 1.0.0, current version 1.0.0)
> /Users/alan/Programmes/amber11/AmberTools/lib/libopen-pal.0.dylib
> (compatibility version 1.0.0, current version 1.0.0)
> /usr/lib/libutil.dylib (compatibility version 1.0.0, current version
> 1.0.0)
> /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version
> 438.0.0)
> /usr/lib/libmx.A.dylib (compatibility version 1.0.0, current version
> 315.0.0)
> libirc.dylib (compatibility version 1.0.0, current version 1.11.0)
>
> $AMBERHOME/bin/mpirun -np 2 ./tlmod
> [amadeus:06792] *** Process received signal ***
> [amadeus:06792] Signal: Segmentation fault (11)
> [amadeus:06792] Signal code: Address not mapped (1)
> [amadeus:06792] Failing at address: 0x362f62b68
> [amadeus:06792] *** End of error message ***
> [amadeus:06793] *** Process received signal ***
> [amadeus:06793] Signal: Segmentation fault (11)
> [amadeus:06793] Signal code: Address not mapped (1)
> [amadeus:06793] Failing at address: 0x362f62b68
> [amadeus:06793] *** End of error message ***
> --------------------------------------------------------------------------
> mpirun noticed that process rank 0 with PID 6792 on node amadeus.local
> exited on signal 11 (Segmentation fault).
> --------------------------------------------------------------------------
>
> 2.2) Using Fink Openmpi (1.3.3) to wrap icc and ifort:
> Using a similar approach I did to circumvent the problem I had with gcc-4
> from Fink and mpicc, I did:
>
> ./configure -mpi intel
>
> Edited config.h and replace mpicc and mpif90 by:
>
> icc -D_REENTRANT -I/sw/include -I/sw/include/openmpi -L/sw/lib/openmpi
> -lmpi
> -lopen-rte -lopen-pal -lutil
> and
> ifort -I/sw/include -I/sw/lib/openmpi -L/sw/lib/openmpi -lmpi_f90 -lmpi_f77
> -lmpi -lopen-rte -lopen-pal -lutil
>
> respectively, and compilation went very well.
>
> Doing tests in Parallel I got the issues reported with Intel compilers
> serial and all MPI version worked well (yes!) except *pmemd.MPI*, which
> gives the error:
>
> /sw/bin/om-mpirun -np 2 ../../bin/pmemd.MPI -O -i gbin -c eq1.x -o
> mdout.pure_wat
> [amadeus.local:42651] *** An error occurred in MPI_Waitany
> [amadeus.local:42651] *** on communicator MPI_COMM_WORLD
> [amadeus.local:42651] *** MPI_ERR_TRUNCATE: message truncated
> [amadeus.local:42651] *** MPI_ERRORS_ARE_FATAL (your MPI job will now
> abort)
> --------------------------------------------------------------------------
> om-mpirun has exited due to process rank 0 with PID 42651 on
> node amadeus.local exiting without calling "finalize". This may
> have caused other processes in the application to be
> terminated by signals sent by om-mpirun (as reported here).
> --------------------------------------------------------------------------
>
> And repeating, with sander.MPI, nab (MPI) etc., all test went fine or at
> least ran.
>
> I am wondering if someone else got Amber working with intel and ompi.
>
> Cheers,
>
> All
>
>
> --
> Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> Department of Biochemistry, University of Cambridge.
> 80 Tennis Court Road, Cambridge CB2 1GA, UK.
> >>http://www.bio.cam.ac.uk/~awd28 <http://www.bio.cam.ac.uk/%7Eawd28><<
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
All the best,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon May 03 2010 - 16:30:04 PDT
