Hello,
On Wed, Jan 27, 2010 at 12:11 PM, Sangita Kachhap <sangita.imtech.res.in> wrote:
> Hello,
>
> I am installing amber10 on linux system and in parallel I have successfully
> install it.
> But when installing PMEMD I am getting following problem.
>
>
>
> [sangita.molmod pmemd]$./configure linux64_opteron pgf90 lam pubfft bintraj
here, you claim that your computer has an AMD opteron processor. You
also claim to be using the Portland group fortran 90 compiler (pgf90),
which is not what you want it seems. Lastly, you are specifying lam
mpi, is this what you used to compile amber10 parallel?
> File config_data/fft.pubfft being used...
> configure assumes netCDF files are in /home/sangita/amber10/src/netcdf.
> File config_data/linux64_opteron.pgf90 being used...
> File config_data/interconnect.lam being used...
> Please enter directory where lam mpi files are installed:
> /home/sangita/amber10/src/pmemd/config_data
> PMEMD Configurate successfully completed.
> [sangita.molmod pmemd]$ make install
> cd src && make install
> make[1]: Entering directory `/home/sangita/amber10/src/pmemd/src'
> /lib/cpp -traditional -P -I/home/sangita/amber10/src/pmemd/config_data/include
> -DPUBFFT -DBINTRAJ -DMPI -DSLOW_NONBLOCKING_MPI -DDIRFRC_EFS -DDIRFRC_NOVEC
> -DFFTLOADBAL_2PROC gbl_constants.fpp gbl_constants.f90
> pgf90 -c -fastsse -O3 gbl_constants.f90
> make[1]: pgf90: Command not found
This tells you that it cannot find pgf90. If you have it, make sure
it's in your path, but it's more likely that you want to use a
different compiler.
> make[1]: *** [gbl_constants.o] Error 127
> make[1]: Leaving directory `/home/sangita/amber10/src/pmemd/src'
> make: *** [install] Error 2
>
>
>
> For parallel compilation i have used gfortran compiler but for PMEMD
> compillation there is no gfortran option.
> So can anybody please tell me what is wrong.
You should get a config.h file that is compatible with gfortran (some
compiler flags may be unique to the PGI fortran compiler). Moreover,
if you want to compile in parallel, you should change F90 and LOAD to
mpif90 in the config.h file (and make sure that mpif90 from the MPI
installation you want to use is the one returned by "which mpif90"!)
Also don't forget to have MPI_HOME set.
One course of action you can always take is to change these lines, and
then proceed to remove flags that the compilation complains about not
recognizing from the config.h script and retry. This may hurt code
optimization, since the compiler flags passed to gfortran will not
necessarily generate the most efficient code possible from the
compiler. However, if, as has been posted on the reflector several
times in the past, gfortran's performance is noticeably worse for
pmemd than commercial compilers such as pgf90 and ifort.
Good luck!
Jason
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Jan 28 2010 - 00:00:03 PST
