I don't have access to the most current Intel compilers, I think. But I
have just recompiled the serial version with both GNU 4.9 and an older
Intel compiler on different systems without problems. Dan, can you advise
me on what steps I should take, or if you don't mind looking into the
problem a bit from your end, suggest things I could do or tell you about
that might help you solve it?
On Mon, Dec 12, 2016 at 4:32 PM, David Cerutti <dscerutti.gmail.com> wrote:
> When I try to compile with intel, I am getting stuck at the configure
> stage:
>
> Here's the output:
> Checking NetCDF...
> Using bundled NetCDF library.
> NetCDF must be rebuilt.
> Configuring NetCDF C interface (may be time-consuming)...
> Compiling the NetCDF C interface (may be time-consuming)...
> Configuring NetCDF Fortran interface (may be time-consuming)...
> Compiling the NetCDF Fortran interface (may be time-consuming)...
> Error: Could not compile with NetCDF Fortran interface.
> /opt/software/ClusterStudio/2013sp1/composer_xe_2013_sp1.0.080/bin/intel64/ifort
> -fPIC -I/opt/software/ClusterStudio/2013sp1/composer_xe_2013_sp1.0.080/mkl/include/intel64/lp64
> -I/opt/software/ClusterStudio/2013sp1/composer_xe_2013_sp1.0.080/mkl/include/fftw
> -I/opt/software/ClusterStudio/2013sp1/composer_xe_2013_sp1.0.080/mkl/include
> -I/mnt/home/cerutti/amber/include -o testp testp.f90
> /mnt/home/cerutti/amber/lib/libnetcdff.a /mnt/home/cerutti/amber/lib/
> libnetcdf.a
> Compile error follows:
> /mnt/home/cerutti/amber/lib/libnetcdff.a(netcdf.o): In function
> `netcdf_mp_nf90_inq_libvers_':
> netcdf.f90:(.text+0x25): undefined reference to `nf_inq_libvers_'
>
> There is a similar thread on the Amber listserv, unanswered. I've tried
> extending LD_LIBRARY_PATH, but to no avail, and the thing configures and
> compiles just fine with GNU. If I did anything in the past six months that
> would have created this problem, I might not have seen it due to being
> limited to GNU. Does anyone have an idea of what could be the problem
> compiling with the NetCDF Fortran interface?
>
> On Mon, Dec 12, 2016 at 3:08 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
>
>> On Mon, Dec 12, 2016 at 2:55 PM, Daniel Roe <daniel.r.roe.gmail.com>
>> wrote:
>>
>> > Using current GIT master (3e7cad1d67407ab152e5faa072984f6750855a86)
>> > with Intel 17.0.0 compilers.
>> >
>> > Failure:
>> >
>> > ```
>> > building 'mdgx.mdgx' extension
>> > gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3 -Wall
>> > -Wstrict-prototypes -fPIC
>> > -I/uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-
>> > lonepeak/include
>> > -I/uufs/chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-
>> > lonepeak/miniconda/include/python2.7
>> > -c
>> > <http://chpc.utah.edu/common/home/u0827715/Amber/GIT/amber-l
>> onepeak/include%0A-I/uufs/chpc.utah.edu/common/home/u0827715
>> /Amber/GIT/amber-lonepeak/miniconda/include/python2.7%0A-c>
>> > mdgx/mdgx.c -o build/temp.linux-x86_64-2.7/mdgx/mdgx.o -O0 -ggdb
>> > mdgx/mdgx.c:461:18: fatal error: mdgx.h: No such file or directory
>> > #include "mdgx.h"
>> > ```
>> >
>> >
>>
>> > So mdgx.h is not found,
>>
>>
>> Need Dave to fix mdgx. pymdgx finds mdgx.h in $AMBERHOME/inblude
>> https://github.com/Amber-MD/pymdgx/blob/master/setup.py#L14
>>
>>
>>
>> > and also it's using gcc instead of icc.
>> >
>> >
>> You catch me. I have never used icc (since I can not test it on travis).
>> May be I just exclude pymdgx build if using icc.
>>
>> Hai
>>
>>
>>
>> > -Dan
>> >
>> > --
>> > -------------------------
>> > 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
>> >
>> > _______________________________________________
>> > AMBER-Developers mailing list
>> > AMBER-Developers.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber-developers
>> >
>> _______________________________________________
>> AMBER-Developers mailing list
>> AMBER-Developers.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber-developers
>>
>
>
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Received on Mon Dec 12 2016 - 21:00:02 PST
