| • |
|
|
|
|||
|
||||
 |
Known Symptoms of a Broken netCDF Build
This is where we document some common symptoms of broken builds, and their resolution. Another place to look for fixes to problems installing netCDF on platforms not listed in the NetCDF Installation and Porting Guide is Other Builds of the netCDF Package. |
|
|
|
|||
|
||||
The fortran test fails:
make[1]: Entering directory `/home/Ed/netcdf-3/nf_test' f77 -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -I../libsrc -Df2cFortran -g -O2 -c -o test_get.o test_get.F f77 -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -I../libsrc -Df2cFortran -g -O2 -c -o test_put.o test_put.F f77 -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -I../libsrc -Df2cFortran -g -O2 -c -o nf_error.o nf_error.F f77 -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -I../libsrc -Df2cFortran -g -O2 -c -o nf_test.o nf_test.F f77 -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -I../libsrc -Df2cFortran -g -O2 -c -o test_read.o test_read.F f77 -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -I../libsrc -Df2cFortran -g -O2 -c -o test_write.o test_write.F f77 -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -I../libsrc -Df2cFortran -g -O2 -c -o util.o util.F depbase=`echo fortlib.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`; \ if cc -DHAVE_CONFIG_H -I. -I. -I.. -I../fortran -I../libsrc -Df2cFortran -g -O2 -MT fortlib.o -MD -MP -MF "$depbase.Tpo" -c -o fortlib.o fortlib.c; \ then mv -f "$depbase.Tpo" "$depbase.Po"; else rm -f "$depbase.Tpo"; exit 1; fi /bin/bash ../libtool --mode=link --tag=F77 f77 -g -O2 -L../libsrc -o nf_test.exe test_get.o test_put.o nf_error.o nf_test.o test_read.o test_write.o util.o fortlib.o -lnetcdf -lm mkdir .libs f77 -g -O2 -o nf_test.exe test_get.o test_put.o nf_error.o nf_test.o test_read.o test_write.o util.o fortlib.o -L/home/Ed/netcdf-3/libsrc /home/Ed/netcdf-3/libsrc/.libs/libnetcdf.a test_get.o(.text+0x31): In function `test_nf_get_var1_text__': /home/Ed/netcdf-3/nf_test/test_get.F:25: undefined reference to `_nf_open__' test_get.o(.text+0xc3):/home/Ed/netcdf-3/nf_test/test_get.F:34: undefined reference to `_nf_get_var1_text__' test_get.o(.text+0x10f):/home/Ed/netcdf-3/nf_test/test_get.F:37: undefined reference to `_nf_get_var1_text__' test_get.o(.text+0x193):/home/Ed/netcdf-3/nf_test/test_get.F:43: undefined reference to `_nf_get_var1_text__' test_get.o(.text+0x282):/home/Ed/netcdf-3/nf_test/test_get.F:60: undefined reference to `_nf_get_var1_text__' etc.
This happens to me on Cygwin/Windows, if I have my windows directories ahead of my cygwin directories in my path. To fix it, move the cygwin /usr/bin directory to the front of your path.
Then cd to the netcdf build directory (the src subdirectory for release 3.6.1 and earlier, and the main netcdf directory for releases 4.0 onward). Execute the following:
make distclean && ./configure && make test
On Cygwin, the libsrc build fails:
make[2]: Entering directory `/home/klindsay/netcdf-3.6.0-p1/src/libsrc' gcc -c -g -I. -Df2cFortran attr.c gcc -c -g -I. -Df2cFortran dim.c gcc -c -g -I. -Df2cFortran error.c gcc -c -g -I. -Df2cFortran -DVERSION=`cat ../VERSION` libvers.c gcc -c -g -I. -Df2cFortran nc.c gcc -c -g -I. -Df2cFortran ncio.c gcc -c -g -I. -Df2cFortran ncx.c ncx.c:1119:2: #error "ix_float implementation" ncx.c:1542:2: #error "ix_double implementation" make[2]: *** [ncx.o] Error 1 make[2]: Leaving directory `/home/klindsay/netcdf-3.6.0-p1/src/libsrc' make[1]: *** [subdir_target] Error 1 make[1]: Leaving directory `/home/klindsay/netcdf-3.6.0-p1/src' make: *** [libsrc/all] Error 2
This happens prior to 3.6.1-beta3. Get the latest beta and try again.
The fortran build fails:
make[1]: Entering directory `/home/ed/n3_temp/fortran'
depbase=`echo fort-attio.lo | sed 's|[^/]*$|.deps/&|;s|\.lo$||'`; \
if /bin/sh ../libtool --tag=CC --mode=compile cc -DHAVE_CONFIG_H
-I. -I. -I.. -I. -I../libsrc -g -O2 -MT fort-attio.lo -\
MD -MP -MF "$depbase.Tpo" -c -o fort-attio.lo fort-attio.c; \
then mv -f "$depbase.Tpo" "$depbase.Plo"; else rm -f "$depbase.Tpo";
exit 1; fi
mkdir .libs
cc -DHAVE_CONFIG_H -I. -I. -I.. -I. -I../libsrc -g -O2 -MT
fort-attio.lo -MD -MP -MF .deps/fort-attio.Tpo -c fort-attio.c \
-fPIC -DPIC -o .libs/fort-attio.o
In file included from ncfortran.h:13,
from fort-attio.c:6:
cfortran.h:138:3: #error cfortran.h: Can't find your environment
among:
- MIPS cc and f77 2.0. (e.g. Silicon Graphics, DECstations, ...)
- IBM AIX XL C and FORTRAN Compiler/6000 Version 01.01.0000.0000
- VAX VMS CC 3.1 and FORTRAN 5.4.
- Alpha VMS DEC C 1.3 and DEC FORTRAN 6.0.
- Alpha OSF DEC C and DEC Fortran for OSF/1 AXP Version 1.2
- Apollo DomainOS 10.2 (sys5.3) with f77 10.7 and cc 6.7.
- CRAY
- NEC SX-4 SUPER-UX
- CONVEX
- Sun
- PowerStation Fortran with Visual C++ \
- HP9000s300/s700/s800 Latest test with: HP-UX A.08.07 A9000/730
- LynxOS: cc or gcc with f2c. \
- VAXUltrix: vcc,cc or gcc with f2c. gcc or cc with f77.
- f77 with vcc works; but missing link magic for f77 I/O.
- NO fort. None of gcc, cc or vcc generate required names
- f2c : Use #define f2cFortran, or cc -Df2cFortran
- NAG f90: Use #define NAGf90Fortran, or cc -DNAGf90Fortran
- Absoft UNIX F77: Use #define AbsoftUNIXFortran or cc -DAbsoftUNIXFortran
- Absoft Pro Fortran: Use #define AbsoftProFortran
- Portland Group Fortran: Use #define pgiFortran
- PathScale Fortran: Use #define PATHSCALE_COMPILER
make[1]: *** [fort-attio.lo] Error 1
This means that a necessary (for Fortran) C pre-processor flag is absent. The flag tells the C compiler how many underscores the Fortran compiler likes to see in function names, and other interesting name-mangling facts. Here on the one-hundred and second floor of Unidata Tower 2, dozens of programmers await some standardization of the Fortran/C interface.
If you have are using g77, try:
export CPPFLAGS=-Df2cFortran
or (for csh fans):
setenv CPPFLAGS -Df2cFortran
If you have are a Portland Group or Intel compiler, try:
export CPPFLAGS=-DpgiFortran
or (for csh fans):
setenv CPPFLAGS -DpgiFortran
If you have another type of compiler, try one of the two above choices. (pgiFortran seems to work more often than f2cFortran on a totally random selection of Fortran compilers known about here at netCDF HQ.)
Then cd to the netcdf build directory (the src subdirectory for release 3.6.1 and earlier, and the main netcdf directory for releases 4.0 onward). Execute the following:
make distclean && ./configure && make test
Making `all' in directory /home/ed/n3_tmp4/fortran make[2]: Entering directory `/home/ed/n3_tmp4/fortran' cc -c -g -I.. -I../libsrc -DpgiFortran fort-attio.c In file included from fort-attio.c:6: ncfortran.h:27:42: NF_INT_IS_C_... not defined: No such file or directory fort-attio.c:12: error: syntax error before "NF_INTEGER" fort-attio.c:12: error: syntax error before '*' token fort-attio.c:12: error: syntax error before numeric constant fort-attio.c:12: warning: data definition has no type or storage class fort-attio.c:12: error: syntax error before numeric constant fort-attio.c:12: error: syntax error before '!' token fort-attio.c:12: error: syntax error before numeric constant etc.
This is another symptom of the Intel compiler missing library problem. See here for the solution.
When using the ifort compiler, configure reports that ifort can't be used to build f90 programs. The file config.log contains the following:
configure:3958: ./conftest ./conftest: error while loading shared libraries: libimf.so: cannot open shared object file: No such file or directory configure:3961: $? = 127 configure:3966: result: failed to build executable program
The problem is that the system doesn't know where to find libimf.so. Find this file, and set LD_LIBRARY_PATH to the directory that contains it, and try again.
Note that you must export LD_LIBRARY_PATH, something like this:
bash-3.00$ export LD_LIBRARY_PATH=/home/ed/local/lib
On our Intel fortran compiler there is a shell script that we must run (ifortvars.sh) which sets environment variables that are needed by the intel fortran compiler. Make sure you have run this script.
bash-3.00$ autoreconf
autoreconf: `configure.ac' and `configure.in' both present.
autoreconf: proceeding with `configure.ac'.
autoconf: warning: both `configure.ac' and `configure.in' are present.
autoconf: warning: proceeding with `configure.ac'.
autoconf: warning: both `configure.ac' and `configure.in' are present.
autoconf: warning: proceeding with `configure.ac'.
configure.ac:39: error: possibly undefined macro: AM_INIT_AUTOMAKE
If this token and others are legitimate, please use
m4_pattern_allow.
See the Autoconf documentation.
configure.ac:77: error: possibly undefined macro: AM_CONDITIONAL
configure.ac:190: error: possibly undefined macro: AM_PROG_CC_C_O
configure.ac:319: error: possibly undefined macro: AM_FFLAGS
configure.ac:413: error: possibly undefined macro:
AC_LIBTOOL_WIN32_DLL
configure.ac:416: error: possibly undefined macro: AC_PROG_LIBTOOL
autoreconf: /home/ed/local/bin/autoconf failed with exit status: 1
bash-3.00$ autoreconf autoreconf: `configure.ac' and `configure.in' both present. autoreconf: proceeding with `configure.ac'. autoconf: warning: both `configure.ac' and `configure.in' are present. autoconf: warning: proceeding with `configure.ac'. autoconf: warning: both `configure.ac' and `configure.in' are present. autoconf: warning: proceeding with `configure.ac'. autoheader: `configure.ac' and `configure.in' both present. autoheader: proceeding with `configure.ac'. autoheader: warning: missing template: HAVE_FTRUNCATE autoheader: Use AC_DEFINE([HAVE_FTRUNCATE], [], [Description]) autoheader: warning: missing template: NCBYTE_T autoheader: warning: missing template: NCSHORT_T autoheader: warning: missing template: NF_INT1_T autoheader: warning: missing template: NF_INT2_T autoheader: warning: missing template: NO_IEEE_FLOAT autoheader: warning: missing template: SIZEOF_OFF_T autoheader: warning: missing template: SIZEOF_SIZE_T autoreconf: /home/ed/local/bin/autoheader failed with exit status: 1
Remove aclocal.m4 and try again.
| Contact Us • Site Map • Search • Terms and Conditions • Privacy Policy • Participation Policy | ||||||
|
||||||
