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
>
>
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Received on Thu Sep 21 2017 - 15:30:02 PDT
