On Mon, Jul 9, 2012 at 3:43 PM, Gustavo Seabra <gustavo.seabra.gmail.com>wrote:
> Hi there,
>
> Has anyone here tried to compile Amber12 on the Jaguar system (Cray
> XK6)? According to their User manual (here:
>
> http://www.olcf.ornl.gov/support/user-guides-policies/jaguar-xk6-user-guide/#6221
> ),
> one should try and use the compile wrappers (cc, CC, ftn). So, I tried
> to use the -crayxt5 option for the configure*. However, I get an error
> like:
>
> ----
>
> ~/local/amber> ./configure -nomtkpp -crayxt5 pgi 2>&1 | tee
> configure_crayxt5.log
> Checking for updates...
> AmberTools12 is up to date
> Amber12 is up to date
>
> Searching for python2... Found python2.6: /usr/bin/python2.6
>
> Obtaining the PGI suite version:
> pgcc -V
> The version is 12.1-0
>
> Testing the cc compiler:
> cc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c
> Error: Unable to compile a C program using cc -D_FILE_OFFSET_BITS=64
> -D_LARGEFILE_SOURCE
> Please check your compiler settings or configure flags.
> Configure failed due to the errors above!
> ~/local/amber>
>
> ---
>
> Would anyone know what I'm doing wrong here?
>
> I noticed that if I use ./configure -mpi pgi, the configure works
> fine, but I'm thinking that it may not generate the best code for this
> machine. I'd really appreciate any insights here.
>
> * NOTE: I know Jaguar is a XK6, not XT5, but the configure flag is
> only supposed to check for incompatibility with mtkpp and then use cc,
> ftn and CC, so it *should* work (is this wrong?)
>
Yes, this is wrong, because the compiler wrappers on Jaguar are hopelessly
broken :) -- I tried my hand at it myself. In my experience, the options
are either: 1) continue to bug the Jaguar support folks until the -crayxt5
flag "just works" (because it's doing the correct thing!). 2) Work around
the issue by using the compilers directly and building your own MPI (may I
suggest the configure_mpich2 included with AmberTools).
Hope Brazil is treating you well ;).
All the best,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Jul 09 2012 - 13:00:03 PDT
