Hi Xiongwu,
You seem to have version differences between your mpi and non-mpi
compilers. You will see that your mpi compiler points to gcc 3.4.6,
while your non-mpi compiler is version 4.1.2.
I'm not sure whether version 3.4.6 supports Fortran 90; the page at
http://gcc.gnu.org/onlinedocs/gcc-3.4.6/g77/News.html suggests that it
used g77, which sounds (by the name) like it supports only Fortran 77.
If that's the case, the Fortran 90 features in Amber (of which there are
many) will not be correctly built. Another possibility is to pass the
"-ff90" flag to your mpif77, though see my next point.
Mixing compiler versions between the serial and parallel code may cause
enough problems of its own for the resulting binaries, even if you could
get your code compiled.
One thing you could try is to update your LAM-MPI. You may need to get
LAM-MPI source and build it against your current (4.1.2) gcc, g++ and
gfortran compilers. Alternatively, there may be a newer LAM-MPI binary
package available for you. Much of my work has been with openMPI, so I
can't help you with specifics.
I hope that helps a bit...
Cheers,
Ben
Wu, Xiongwu (NIH/NHLBI) [E] wrote:
> Hi Ben,
>
> I did all you said and have no luck. Here are the outputs:
>
> EMstation 424: mpif77 -v
> Reading specs from /usr/lib/gcc/x86_64-redhat-linux/3.4.6/specs
> Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --disable-checking --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-languages=c,c++,f77 --disable-libgcj --host=x86_64-redhat-linux
> Thread model: posix
> gcc version 3.4.6 20060404 (Red Hat 3.4.6-4)
>
> EMstation 425: gfortran -v
> Using built-in specs.
> Target: x86_64-redhat-linux
> Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-libgcj-multifile --enable-languages=c,c++,objc,obj-c++,java,fortran,ada --enable-java-awt=gtk --disable-dssi --enable-plugin --with-java-home=/usr/lib/jvm/java-1.4.2-gcj-1.4.2.0/jre --with-cpu=generic --host=x86_64-redhat-linux
> Thread model: posix
> gcc version 4.1.2 20080704 (Red Hat 4.1.2-44)
>
> EMstation 426: make parallel
> Starting installation of Amber11 (parallel) at Thu Oct 22 12:59:19 EDT 2009.
> cd sander && make parallel
> make[1]: Entering directory `/v/bigbox6/home/wxw/ambers/amber11/src/sander'
> cpp -traditional -P -DNO_SANDER_DIVCON -DBINTRAJ -DMPI constants.f > _constants.f
> mpif77 -c -O3 -ffree-form -o constants.o _constants.f
> _constants.f:89:
> module constants
> 1 2
> Unrecognized statement name at (1) and invalid form for assignment or statement-function definition at (2)
> _constants.f: In program `MAIN__':
> _constants.f:93:
> double precision, parameter :: TEN_TO_MINUS2 = 1.0d-2
> ^
> ......
> (a lot of output)
> ......
> integer, parameter :: NO_INPUT_VALUE = 12344321 ! from Bob Duke
> ^
> Fortran 90 feature at (^) unsupported
> _constants.f:228:
> end module constants
> ^
> Invalid form for END statement at (^)
> _constants.f:93:
> double precision, parameter :: TEN_TO_MINUS2 = 1.0d-2
> ^
> End of source file before end of block started at (^)
> mpif77: No such file or directory
> make[1]: *** [constants.o] Error 1
> make[1]: Leaving directory `/v/bigbox6/home/wxw/ambers/amber11/src/sander'
> make: *** [parallel] Error 2
>
>
> there is no mpif90 $(AMBERHOME)/bin from lam-7.1.3
>
> Thanks!
>
> Xiongwu
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Received on Thu Oct 22 2009 - 11:00:02 PDT
