Hi Vijay,
> The machine that I am using is SGI_ALTIX XE1300 with 4 nodes, each with
> 8 cores. So the total is 32 cores. Using intel fortran compiler
...
> Lastly I wanted to compile PMEMD and tried to do as; ./configure
> sgi_altix ifort mpi pubfft. There is no option for Xeon so I chose this
> configuration. In the config.h file I added
>
> MATH_LIBS = -L/opt/intel/mkl/10.0.010/lib/64/ -Wl,--start-group
> /opt/intel/mkl/10.0.010/lib/64/libmkl_intel_lp64.
> a /opt/intel/mkl/10.0.010/lib/64/libmkl_sequential.a
> /opt/intel/mkl/10.0.010/lib/64/libmkl_core.a -Wl,--end-group
> -lpthread
This is your problem unfortunately. At the time AMBER 9 was written an Altix
was very different to what the Altix you have today is like. It was a fully
shared memory machine using Intel Itanium processors. Your Altix on the
other hand is essentially an Intel x86_64 infiniband cluster. As such you
will have all sorts of problems using the build scripts for a traditional
Altix that shipped with AMBER 9.
I would suggest using the linux_em64t.ifort target - assuming you are using
the intel compilers and your MPI installation is configured for the intel
compilers.
Check that
mpif90 -show reports the intel compiler.
Then edit the resulting config.h file and change:
all occurrences of ifort to mpif90
all occurrences of icc or gcc to mpicc
remove all occurrences of -tpp7
Change the -xN to -xHost
You will probably then be good to go. Although you may still want to skip
using MKL so 'unset MKL_HOME'
Good luck,
All the best
Ross
/\
\/
|\oss Walker
---------------------------------------------------------
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Adjunct Assistant Professor |
| Dept. of Chemistry and Biochemistry |
| University of California San Diego |
| NVIDIA Fellow |
|
http://www.rosswalker.co.uk |
http://www.wmd-lab.org/ |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
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Received on Fri Nov 18 2011 - 10:30:07 PST
