AMBER Archive (2009)

Subject: [AMBER] amber10 parallel compiling error

From: nam kim (namkkim_at_gmail.com)
Date: Sat Jul 18 2009 - 12:19:39 CDT

Ross,

I will try when I get back to the office.

Thanks
-Nam

Hi Nam,

> I have successfully compiled amber10 with g95 in serial, but for the
> parallel mode, I failed with the error message:
> /share/apps/openmpi/bin/mpif90 -c -O3 -fno-second-underscore
> -ffree-form -o ncsu-umbrella.o _
>
> ncsu-umbrella.f
>
> Fatal Error: Reading module netcdf at line 3 column 1: Expected left
> parenthesis
>
> make[1]: *** [ncsu-umbrella.o] Error 1
>
> make[1]: Leaving directory `/share/apps/amber10/src/sander'
>
> make: *** [parallel] Error 2

I have not seen this error before but a couple of things to try.

1) As a work around you could compile without NetCDF support:

  ../configure_amber -mpich2 -nobintraj g95

2) If you want to keep the netcdf support try doing a full clean of both
amber and ambertools before configuring for parallel. E.g.

cd $AMBERHOME/src/
make -f Makefile_at clean
make clean
./configure_amber -mpich2 g95
make parallel

Obviously adjusting the options (mpich2) above for the MPI version you are
using.

Good luck,
Ross

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|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
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