Re: AMBER: compiling AMBER9 with bintraj option on AMD64

From: Vlad Cojocaru <>
Date: Tue, 18 Mar 2008 10:32:13 +0100

Dear David,

Thanks a lot for the answer. We used gcc 4.1 (Debian Linux) and netcdf
was compiled with the same compiler. It seems that in the end our adm
managed to get it compiled. I am not sure though if he didn't use a
pre-compiled netcdf directly from NetCDF (this was a solution I used to
compile ptraj separately with netcdf support) ... I didnt manage to test
yet the new compilation

I will have to double check with him and test the compilation and in
case we still have problems, I will get back with more details

Best wishes

David A. Case wrote:
> On Fri, Mar 14, 2008, Vlad Cojocaru wrote:
>> Our administrator is struggling to compile AMBER9 for AMD64 architecture
>> (Debian Linux) with the bintraj option. The error he gets is below. It
>> seems to be related to the netcdf libs for f90. Has anybody seen
>> something like this ? Any idea what can be the problem?
> What compiler and OS are you using? Is there any chance that netcdf was
> compiled with a different compiler than amber was? If these are gnu-ish
> compilers (like g95 or gfortran), it is likely that the -fno-second-underscore
> flag needs to be given to the netcdf configure (if it has not been already).
> But basically, we need more information; be sure to look carefully for
> errors in the netcdf configuration step.
> ...dac
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Dr. Vlad Cojocaru
EML Research gGmbH
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EML Research gGmbH
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Received on Fri Apr 18 2008 - 21:11:57 PDT
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