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
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Received on Sun Nov 23 2014 - 20:30:02 PST
