Re: [AMBER] problem (re)compiling pmemd.cuda_SPFP: Reading module netcdf at line 23 column 34: Expected integer

From: Marc van der Kamp <>
Date: Fri, 12 Jul 2013 14:53:47 +0100

Many thanks for the quick response (as always!)
Removing $AMBERHOME/include/netcdf.mod (manually) indeed did the trick.

BTW, Jason's suggestion that would allow ./configure bypass the NetCDF
configure altogether if the existing NetCDF 'works', sounds great.
My incompatible netcdf.mod was indeed likely due to using different
compilers previously, but I think there may be good reasons to use
different compilers for different executables, e.g. sander.MPI and


On 12 July 2013 14:02, David A Case <> wrote:
> On Fri, Jul 12, 2013, Marc van der Kamp wrote:
>> On a (linux) system where I previously successfully compiled
>> pmemd.cuda_SPFP (from amber12), I cannot re-compile it (after
>> updates).
>> I'm using cuda-4.2.9 (this is for Tesla M2090's).
>> "configure -cuda gnu" is successful, but when I "make install", I'm
>> running into the following error:
>> -I/gpfs/cluster/chem/chmwvdk/amber12/include -c binrestart.F90
>> Fatal Error: Reading module netcdf at line 23 column 34: Expected integer
> It sounds like the netcdf module was earlier compiled with a different
> compiler (or different compiler version). In any event, remove
> $AMBERHOME/include/netcdf.mod, than try the compilation again.
> [Developers, esp. Jason: is there any reason that "make clean" (run
> automagically by configure) should not be doing this?]
> ...hope this helps...dac
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Received on Fri Jul 12 2013 - 07:00:03 PDT
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