I did nothing specific, because I did not track down the problem. I
started "from scratch", which means starting all over from the beginning.
Just create a clean/fresh directory tree, extract AmberTools to this
directory and proceed correspondingly.
Jan-Philip
On 11/07/2011 03:38 PM, Qinghua Liao wrote:
> Dear Jan-Philip,
>
> Thanks so much for your explanations, could you please be more detailed on
> how did you do to solve the problem? Thanks!
>
> Best Regards,
>
> Qinghua
>
> On Mon, Nov 7, 2011 at 2:55 PM, Jan-Philip Gehrcke
> <jgehrcke.googlemail.com>wrote:
>
>> On 11/07/2011 02:37 PM, Jason Swails wrote:
>>
>>>> ../libsrc/.libs/libnetcdf.a(v1hpg.o): In function `nc_get_NC':
>>>> v1hpg.c:(.text+0x1d81): undefined reference to `ncx_getn_schar_schar'
>>>> v1hpg.c:(.text+0x1e14): undefined reference to `ncx_get_size_t'
>>>> collect2: ld returned 1 exit status
>>>> make[3]: *** [ncgen] Error 1
>>>> make[3]: Leaving directory
>>>> `/home/qinghua/amber11/AmberTools/src/netcdf/src/ncgen'
>>>> make[2]: *** [install-recursive] Error 1
>>>> make[2]: Leaving directory
>>>> `/home/qinghua/amber11/AmberTools/src/netcdf/src'
>>>> make[1]: *** [/home/qinghua/amber11/lib/libnetcdf.a] Error 2
>>>> make[1]: Leaving directory `/home/qinghua/amber11/AmberTools/src/ptraj'
>>>> make: *** [serial] Error 2
>>>>
>>>
>>> This looks like NetCDF failed during the build process for some reason.
>>
>> Undefined symbols during compilation of ncgen is exactly the same error
>> I also experienced during AmberTools 1.5 make. At least two others
>> reported this to the list, too. I was not able to track down the cause
>> of this issue so far. It looks like some combination of
>> 1) linux distribution
>> 2) package manager, configure, make commands
>> lead to an invalid build environment for libnetcdf.
>>
>> For me this was resolved by starting from scratch, i.e. with extraction
>> of the source tarballs.
>>
>> Jan-Philip
>>
>>
>> _______________________________________________
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Mon Nov 07 2011 - 08:00:03 PST
