Hi,
FWIW, which probably isn't much, my routine building has been working:
make veryclean
./configure -noX11 --skip-python intel
make
icc version 15.0.3 (gcc version 4.4.7 compatibility)
I'll try a non-skipping python build.
scott
On Mon, Dec 12, 2016 at 11:54:46PM -0500, David Cerutti wrote:
> 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 - 22:00:02 PST
