Re: [AMBER] Amber 12 on OSX 10.8.4

From: Wang Chern Hoe (Dr) <"Wang>
Date: Thu, 11 Jul 2013 14:01:34 +0800

server:amber12 user$ port installed | grep netcdf
  netcdf .4.2.1.1_2+dap+netcdf4 (active)


On 11 Jul, 2013, at 12:44 PM, Jason Swails <jason.swails.gmail.com> wrote:

> What is the result of the following command:
>
> port installed | grep netcdf
>
> ?
>
>
> On Wed, Jul 10, 2013 at 10:09 PM, Wang Chern Hoe (Dr) <WangCH.ntu.edu.sg>wrote:
>
>> Hi Jason,
>>
>> I followed your instructions on your wiki, and still got a similar error
>> message.
>>
>> Undefined symbols for architecture x86_64:
>> "___netcdf_MOD_nf90_close", referenced from:
>> ___trajenemod_MOD_trajene in trajene.o
>> ___bintraj_MOD_close_binary_files in bintraj.o
>> ___binrestart_MOD_read_nc_restart in binrestart.o
>> ___binrestart_MOD_check_nc_restart in binrestart.o
>> ___binrestart_MOD_read_nc_restart_box in binrestart.o
>> ___binrestart_MOD_write_nc_restart in binrestart.o
>> ___ncsu_umbrella_MOD_umbrella_save in ncsu-umbrella.o
>> .
>>
>> ld: symbol(s) not found for architecture x86_64
>> collect2: error: ld returned 1 exit status
>> make[2]: *** [sander.MPI] Error 1
>> make[1]: *** [parallel] Error 2
>>
>>
>>
>>
>>
>> On 11 Jul, 2013, at 7:41 AM, Jason Swails <jason.swails.gmail.com> wrote:
>>
>>>
>>>
>>> On Jul 10, 2013, at 7:17 PM, "Wang Chern Hoe (Dr)" <WangCH.ntu.edu.sg>
>> wrote:
>>>
>>>> Hi,
>>>>
>>>> I got this error message while compiling using this configure setting:
>>>>
>>>> ./configure -macAccelerate -mpi gnu
>>>> make install
>>>>
>>>> ncsu-umbrella.F90:9.42:
>>>>
>>>> use netcdf, only : nf90_double, nf90_float
>>>> 1
>>>> Fatal Error: Wrong module version '10' (expected '4') for file
>> 'netcdf.mod' opened at (1)
>>>> make[2]: *** [ncsu-umbrella.o] Error 1
>>>> make[1]: *** [parallel] Error 2
>>>> make: *** [install] Error 2
>>>
>>> This indicates that a different compiler was used to build the NetCDF
>> module as you are currently using to build Amber. There is a link to my
>> wiki on the Amber website with instructions for setting up a Mac to work
>> with Amber.
>>>
>>> When everything is set up correctly, use the command "make uninstall" to
>> clean out the old files and then recompile.
>>>
>>> HTH,
>>> Jason
>>>
>>>>
>>>> Can someone help me please ? I really do not wish to use the -nobintraj
>> option.
>>>>
>>>>
>>>> Thanks
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>> --
>>> Jason M. Swails
>>> Quantum Theory Project
>>> University of Florida
>>> Ph.D. Candidate
>>> 352-392-4032
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber






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Received on Wed Jul 10 2013 - 23:30:03 PDT
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