Hi Ross,
Yes, sander.MPI was built without errors and runs fine as far as I can
tell (test cases and all). I'll try out your suggestions and get back
to you shortly...
Just out of curiosity, do you think bugfix 8 (
http://ambermd.org/bugfixes/11.0/bugfix.8
), which is supposed to "fix" something about compiling pmemd with the
Intel compilers, could be responsible? It's easy enough to revert to
the pre-bugfix version...in fact, I'll give that a shot while I'm at it.
Thanks,
Paul
On Sep 10, 2010, at 4:46 PM, Ross Walker 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
>>
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
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Received on Fri Sep 10 2010 - 17:30:04 PDT
