Hello,
In addition to what Ross said, is either of those files he mentioned (
libmpi_f90.so/libmpi_f90.a) in any of the library files specified by -L in
mpif90 -show? Namely, check
/global/software/centos-5.x86_64/modules/openmpi/1.4.2-intel/lib to see if
either of those files are present. If not, where are they? In any case, it
seems to be more a problem with your MPI than amber itself (or perhaps, like
Ross suggested, only dynamic or static linking is supported by this
installation of MPI and you unluckily chose the wrong one).
Good luck!
Jason
On Fri, Sep 10, 2010 at 7:46 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
> Hi Paul,
>
> This looks strange since the library is actually included by your mpif90
> script. Did this successfully build sander.MPI correctly?
>
> Take a look and see if libmpi_f90.so exists in
> /global/software/centos-5.x86_64/modules/openmpi/1.4.2-intel/lib. You may
> need to be looking in lib64 instead of lib if you are using the INTEL64
> version of the compilers (x86_64). The other possibility that would cause
> this is if you tried to link statically and only had dynamic '.so' versions
> of the library or vice versa, tried to link dynamically but only had static
> '.a' versions of the library.
>
> Try repeating the build with the -static flag given to configure and see if
> that makes any difference.
>
> Alternatively try running the link step manually using the command line
> mpif90 -show gives you in place of mpif90. Then give it the explicit path
> to
> the libmpi_f90.so library.
>
> All the best
> Ross
>
> > -----Original Message-----
> > From: Paul S. Nerenberg [mailto:psn.berkeley.edu]
> > Sent: Friday, September 10, 2010 4:27 PM
> > To: AMBER Mailing List
> > Subject: [AMBER] pmemd 11 (parallel) compilation error
> >
> > Hi all,
> >
> > I'm compiling AMBER 11 on a new system (using the Intel compilers) and
> > running into some trouble at more or less the last step of "make
> > parallel" -- compiling pmemd.MPI. The serial versions of sander and
> > pmemd both compile without a problem on this system, and the parallel
> > version of sander also compiles correctly (*and* passes the parallel
> > test cases). Here is the error that I get when compiling pmemd.MPI:
> >
> > mpif90 -fast -o pmemd.MPI gbl_constants.o ...bunch of object files...
> > charmm_gold.o ../../netcdf/lib/libnetcdf.a -L/global/software/
> > centos-5.x86_64/modules/intel/Compiler/11.1/072/mkl/lib/em64t -Wl,--
> > start-group /global/software/centos-5.x86_64/modules/intel/Compiler/
> > 11.1/072/mkl/lib/em64t/libmkl_intel_lp64.a /global/software/
> > centos-5.x86_64/modules/intel/Compiler/11.1/072/mkl/lib/em64t/
> > libmkl_sequential.a /global/software/centos-5.x86_64/modules/intel/
> > Compiler/11.1/072/mkl/lib/em64t/libmkl_core.a -Wl,--end-group -lpthread
> > ipo: remark #11000: performing multi-file optimizations
> > ipo: remark #11005: generating object file /tmp/ipo_ifortx3AcWQ.o
> > ld: cannot find -lmpi_f90
> > make[2]: *** [pmemd.MPI] Error 1
> > make[2]: Leaving directory `/global/home/users/psn/amber11/src/pmemd/
> > src'
> > make[1]: *** [parallel] Error 2
> > make[1]: Leaving directory `/global/home/users/psn/amber11/src/pmemd'
> > make: *** [parallel] Error 2
> >
> > Here is the output of "mpif90 -show":
> > [psn.ln000 bin]$ mpif90 -show
> > ifort -I/global/software/centos-5.x86_64/modules/openmpi/1.4.2-intel/
> > include -I/global/software/centos-5.x86_64/modules/openmpi/1.4.2-intel/
> > lib -L/global/software/centos-5.x86_64/modules/openmpi/1.4.2-intel/lib
> > -lmpi_f90 -lmpi_f77 -lmpi -lopen-rte -lopen-pal -ldl -Wl,--export-
> > dynamic -lnsl -lutil
> >
> > And finally, here are relevant details of the system configuration:
> > * OS: CentOS 5.5
> > * Compilers: Intel v11.1.072
> > * Math library: Intel MKL (also v11.1.072)
> > * OpenMPI 1.4.2
> > * AMBER was configured using ./configure -mpi -noX11 intel
> >
> > Any suggestions? This seems similar to an error that I saw in the
> > archive for compiling pmemd in AMBER 9, but the resolution to the
> > problem was never posted (as far as I can tell)...and it's been my
> > experience that pmemd in AMBER11 is so much more straightforward to
> > configure that I'm actually quite surprised I ran into any trouble.
> >
> > Best,
> >
> > Paul
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Fri Sep 10 2010 - 17:30:03 PDT
