Hi,
I've never seen this before, and I build GIT amber all over the place
(many systems, many compilers). You mentioned initially you see this
after a git 'clean -d -f'. Do you *only* see it after this? This is a
totally wild guess: the only thing I can think of is the '-d' flag
causes removal of some directory that is generated by netcdf during an
initial build, but for some reason is not re-created on subsequent
builds. Do you ever see this with release code?
-Dan
On Sun, Nov 23, 2014 at 9:17 PM, Andreas Goetz <agoetz.sdsc.edu> wrote:
> Hi all,
>
> I have observed compile errors of the NetCDF C and Fortran interface during configure of either fresh amber git repo clones or after git clean -d -f. I first thought this was a problem with the file system I was working on but it happened more than once during the last few weeks and now a collaborator came across the same problem. Unfortunately, it happens only sometimes and thus is not reproducible. Has anybody else observed the following:
>
> 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)...
> Configuring NetCDF Fortran interface (may be time-consuming)...
> Compiling the NetCDF Fortran interface (may be time-consuming)...
> Error: NetCDF Fortran compile failed.
> Check /home/tpirojsi/amber-clone/amber-new/AmberTools/src/netcdf-fortran-4.2/netcdf.fortran.compile.log
> for errors.
>
> When looking into /home/tpirojsi/amber-clone/amber-new/AmberTools/src/netcdf-fortran-4.2/netcdf.fortran.compile.log, I saw
>
> make[2]: Entering directory `/home/tpirojsi/amber-clone/amber-new/AmberTools/src/netcdf-fortran-4.2/fortran'
> /bin/sh ../libtool --tag=FC --mode=link gfortran -fPIC -O3 -mtune=native -version-number 5:3:1 -L/home/tpirojsi/amber-clone/amber-new/lib -olibnetcdff.la -rpath /home/tpirojsi/amber-clone/amber-new/lib fort-attio.lo fort-control.lo fort-dim.lo fort-genatt.lo fort-geninq.lo fort-genvar.lo fort-lib.lo fort-misc.lo fort-v2compat.lo fort-vario.lo fort-var1io.lo fort-varaio.lo fort-varmio.lo fort-varsio.lo ../f90/libnetcdff90.la -lnetcdf
> libtool: link: gfortran -shared .libs/fort-attio.o .libs/fort-control.o .libs/fort-dim.o .libs/fort-genatt.o .libs/fort-geninq.o .libs/fort-genvar.o .libs/fort-lib.o .libs/fort-misc.o .libs/fort-v2compat.o .libs/fort-vario.o .libs/fort-var1io.o .libs/fort-varaio.o .libs/fort-varmio.o .libs/fort-varsio.o -Wl,--whole-archive ../f90/.libs/libnetcdff90.a -Wl,--no-whole-archive -Wl,-rpath -Wl,/home/tpirojsi/amber-clone/amber-new/lib -Wl,-rpath -Wl,/home/tpirojsi/amber-clone/amber-new/lib -L/home/tpirojsi/amber-clone/amber-new/lib /home/tpirojsi/amber-clone/amber-new/lib/libnetcdf.so -lm -mtune=native -Wl,-soname -Wl,libnetcdff.so.5 -o .libs/libnetcdff.so.5.3.1
> gfortran: .libs/fort-attio.o: No such file or directory
> gfortran: .libs/fort-control.o: No such file or directory
> gfortran: .libs/fort-dim.o: No such file or directory
> gfortran: .libs/fort-genatt.o: No such file or directory
> gfortran: .libs/fort-geninq.o: No such file or directory
> gfortran: .libs/fort-genvar.o: No such file or directory
> gfortran: .libs/fort-lib.o: No such file or directory
> gfortran: .libs/fort-misc.o: No such file or directory
> gfortran: .libs/fort-v2compat.o: No such file or directory
> gfortran: .libs/fort-vario.o: No such file or directory
> gfortran: .libs/fort-var1io.o: No such file or directory
> gfortran: .libs/fort-varaio.o: No such file or directory
> gfortran: .libs/fort-varmio.o: No such file or directory
> gfortran: .libs/fort-varsio.o: No such file or directory
> gfortran: ../f90/.libs/libnetcdff90.a: No such file or directory
> make[2]: *** [libnetcdff.la] Error 1
> make[2]: Leaving directory `/home/tpirojsi/amber-clone/amber-new/AmberTools/src/netcdf-fortran-4.2/fortran'
> make[1]: *** [install] Error 2
> make[1]: Leaving directory `/home/tpirojsi/amber-clone/amber-new/AmberTools/src/netcdf-fortran-4.2/fortran'
> make: *** [install-recursive] Error 1
>
> I observed similar errors sometimes during the C and sometimes during the Fortran interface build. The .libs directory did not exist at the point the linker was trying to link. In all cases this could be resolved by repeatedly running the configure script - clearly not a good solution. I am using gnu 4.4.7-4 compilers on a RHEL 6.5 system. I have no idea what is going wrong here, comments are welcome.
>
> All the best,
> Andy
>
> --
> Dr. Andreas W. Goetz
> Assistant Project Scientist
> San Diego Supercomputer Center
> Tel : +1-858-822-4771
> Email: agoetz.sdsc.edu
> Web : www.awgoetz.de
>
>
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon Nov 24 2014 - 07:30:02 PST
