Since NetCDF compilation fails, why not use the system NetCDF here.
That's what I do on BW.
-Dan
On Thu, Sep 21, 2017 at 6:12 PM, Timothy Schutt
<tschutt.mymail.mines.edu> wrote:
> There is a Prg environment module for gnu on the machine, but even after
> loading it and associated modules the configure reports errors immediately -
> and since it was a cray machine we struggled down the cray path first. The
> error with gnu that we abandoned was:
> ...[Many lines and some OK's]....
> Checking NetCDF...
> Using bundled NetCDF library.
> Starting NetCDF build.
> Configuring NetCDF C interface (may be time-consuming)...
> Compiling the NetCDF C interface (may be time-consuming)...
> Error: NetCDF C compile failed.
> Check
> /p/home/tschutt7/Software/Try2amber16/amber16/AmberTools/src/netcdf-4.3.0/netcdf.c.compile.log
> for errors.
> Configure failed due to the errors above!
>
>
> And the referenced netcdf.c.compile.log said:
> ....[lots of lines]...
> /bin/sh ../libtool --tag=CC --mode=link cc -fPIC -D_FILE_OFFSET_BITS=64
> -D_LARGEFILE_SOURCE -DBINTRAJ \
> -o ncgen3 main.o load.o escapes.o getfill.o init.o genlib.o ncgentab.o
> ../liblib/libnetcdf.la -lm
> libtool: link: cc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ
> -o .libs/ncgen3 main.o load.o esc\
> apes.o getfill.o init.o genlib.o ncgentab.o ../liblib/.libs/libnetcdf.so
> -lm -Wl,-rpath -Wl,/p/home/tschutt7/\
> Software/Try2amber16/amber16/lib
> /usr/bin/ld: attempted static link of dynamic object
> `../liblib/.libs/libnetcdf.so'
> collect2: error: ld returned 1 exit status
> Makefile:589: recipe for target 'ncgen3' failed
> make[1]: *** [ncgen3] Error 1
> make[1]: Leaving directory
> '/p/home/tschutt7/Software/Try2amber16/amber16/AmberTools/src/netcdf-4.3.0/ncgen3'
> Makefile:555: recipe for target 'install-recursive' failed
> make: *** [install-recursive] Error 1
>
>
> Is this an easier problem to solve potentially?
> And I verified this same result with a freshly unpacked amber and ambertools
> directory from the tar.bz2 files. Along that thought - is there a validated
> checksum somewhere I can make sure my tar.bz2 files are what they're
> supposed to be?
>
> Thanks!
>
>
> On Thu, Sep 21, 2017 at 4:34 PM, Thomas Cheatham <tec3.utah.edu> wrote:
>>
>>
>>> Sorry to be a hassle again. Still trying to get Amber to work on this
>>> Cray
>>> XC40/50 system. Is it possible to compile amber without C++ linking to
>>> fortran, perhaps without cuda or EMIL features?
>>
>>
>> Can you use the gnu compilers on the Cray? On Blue Waters they have cray,
>> intel and gnu and AMBER works easily with gnu without a major performance
>> hit (and none on the GPU).
>>
>> We were able to get AMBER to compile on the Blue Waters with the cray
>> option, right Dan?
>>
>> --tom
>>
>> \-/ Professor Thomas E. Cheatham, III
>> -/- Department of Medicinal Chemistry, College of Pharmacy
>> /-\ Director, Research Computing and CHPC, UIT, U of Utah
>> \-/
>> -/- tec3.utah.edu http://www.chpc.utah.edu/~cheatham
>> /-\ SKH-4914 (801) 587-9652; FAX: (801) 585-6208
>> \-/ INSCC-410 (801) 585-6318; FAX: (801) 585-5366
>>
>
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Thu Sep 21 2017 - 17:30:02 PDT
