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-
> lonepeak/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 - 14:00:02 PST
