Thank you very much for the advice. I got the problem solved by
removing openmpi and using the configure_mpich2 script to recompile
Amber.
2011/7/2 case <case.biomaps.rutgers.edu>:
> On Sat, Jul 02, 2011, Fabrício Bracht wrote:
>
>> Hi. Thank you for all the advice. The error given by make
>> cuda_parallel was exactly the one I have written in my first email.
>> There are no more lines after that,
>
> We needed the lines *before* the ones that were posted...that is, the actual
> command that failed. (I understand that for many people, reading error
> messages from "make" is very hard.)
>
>> I have taken your advice and set MPI_HOME=/usr/lib/openmpi
>
> My understanding (from the Amber GPU web page) was that openmpi would not
> work for parallel cuda compiles, and that one needed an MPI implementation
> that implements MPI2 commands. However, Ross didn't complain about your
> use of openmpi, so maybe that is now OK.
>
> Even in openmpi is OK, we don't know that the compiler used to
> install whatever is in /usr/lib/openmpi is the same as you are using to
> compile Amber -- be sure that this is the case
>
>> ./cuda/cuda.a(gpu.o): In function `MPI::Cartcomm::Clone() const':
>> gpu.cpp:(.text._ZNK3MPI8Cartcomm5CloneEv[MPI::Cartcomm::Clone()
>> const]+0x24): undefined reference to `MPI::Comm::Comm()'
>
> All the errors are referring to MPI::Comm::Comm(); I'm just guessing, but
> this could arise because openmpi doesn't implement needed functions from MPI2,
> or you have a compiler mismatch.
>
> As stated earlier, the configure_mpich2 script is designed to handle such
> problems. But with infiniband, you might need MVAPICH2 for best performance.
> If so, I can't provide much help.
>
> ...dac
>
>
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Received on Sat Jul 02 2011 - 15:30:03 PDT
