[CIG-SHORT] NetCDF error when attempting to build git version
Eric Lindsey
elindsey at ucsd.edu
Fri Oct 17 14:43:25 PDT 2014
Ok, I tried that (should have been doing this originally!). However, I
still get the same error. I found this discussion:
http://www.unidata.ucar.edu/support/help/MailArchives/netcdf/msg11612.html
which I don't completely follow. The solution suggested there is: "When
building NetCDF fortran libraries I had to add mpif77 and mpif90 to every
line in configure script containing 'ifort'"...
I tried this and get a different error:
make[2]: Entering directory
`/home/class239/software/pylith-git/build/netcdf-4.1.3/libsrc4'
/bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I..
-I../fortran -I../include -g -O2 -MT libnetcdf4_la-nc4file.lo -MD -MP
-MF .deps/libnetcdf4_la-nc4file.Tpo -c -o libnetcdf4_la-nc4file.lo `test -f
'nc4file.c' || echo './'`nc4file.c
libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I../fortran -I../include
-g -O2 -MT libnetcdf4_la-nc4file.lo -MD -MP -MF
.deps/libnetcdf4_la-nc4file.Tpo -c nc4file.c -fPIC -DPIC -o
.libs/libnetcdf4_la-nc4file.o
nc4file.c: In function 'nc4_create_file':
nc4file.c:272: error: 'H5F_LIBVER_18' undeclared (first use in this
function)
nc4file.c:272: error: (Each undeclared identifier is reported only once
nc4file.c:272: error: for each function it appears in.)
make[2]: *** [libnetcdf4_la-nc4file.lo] Error 1
So, I'm not sure if I am going in the right direction or not.
Alternately, is it possible that Pylith version 2.0.4 will be released as a
binary for linux relatively soon? That would also solve my immediate
problem...
Eric
On Fri, Oct 17, 2014 at 10:13 AM, Brad Aagaard <baagaard at usgs.gov> wrote:
> Eric,
>
> You need to rebuild all the Fortran object files after adding the PIC
> flags. Do a "make clean" and then "make" in the NetCDF build directory.
>
> Brad
>
>
> On 10/17/14, 10:04 AM, Eric Lindsey wrote:
>
>> Ok, I looked through the INSTALL file and see the options it is telling
>> me to add (pic_flag=-fPIC and wl=-Wl,). These variables are defined
>> several times in libtool; I found that the section labeled # ### BEGIN
>> LIBTOOL TAG CONFIG: FC was missing the pic_flag=-fPIC option, but adding
>> it there had no effect on the error I'm getting. Maybe I did not
>> understand those instructions correctly. Here is a larger context for
>> the error:
>>
>> /bin/sh ../libtool --tag=FC --mode=link mpif90 -version-number
>> 5:1:0 -L/home/class239/software/pylith-git/pylith/lib -o libnetcdff.la
>> <http://libnetcdff.la> -rpath
>> /home/class239/software/pylith-git/pylith/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 fort-nc4.lo
>> ../liblib/libnetcdf.la <http://libnetcdf.la> ../f90/libnetcdff90.la
>> <http://libnetcdff90.la> -lhdf5_hl -lhdf5 -lm -lz
>>
>> libtool: link: mpif90 -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
>> .libs/fort-nc4.o --whole-archive ../f90/.libs/libnetcdff90.a
>> --no-whole-archive -rpath
>> /home/class239/software/pylith-git/build/netcdf-build/liblib/.libs
>> -rpath /home/class239/software/pylith-git/pylith/lib -rpath
>> /home/class239/software/pylith-git/pylith/lib
>> -L/home/class239/software/pylith-git/pylith/lib
>> ../liblib/.libs/libnetcdf.so
>> /home/class239/software/pylith-git/pylith/lib/libhdf5_hl.so
>> /home/class239/software/pylith-git/pylith/lib/libhdf5.so -lrt -lz
>> -L/opt/intel/composer_xe_2013.0.079/compiler/lib/intel64
>> -L/opt/intel/composer_xe_2013.0.079/ipp/../compiler/lib/intel64
>> -L/opt/intel/composer_xe_2013.0.079/ipp/lib/intel64
>> -L/opt/intel/composer_xe_2013.0.079/tbb/lib/intel64
>> -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/
>> -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64
>> -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../../lib64/
>> -L/lib/../lib64 -L/lib/../lib64/ -L/usr/lib/../lib64
>> -L/usr/lib/../lib64/
>> -L/opt/intel/composer_xe_2013.0.079/compiler/lib/intel64/
>> -L/opt/intel/composer_xe_2013.0.079/ipp/../compiler/lib/intel64/
>> -L/opt/intel/composer_xe_2013.0.079/ipp/lib/intel64/
>> -L/opt/intel/composer_xe_2013.0.079/tbb/lib/intel64/
>> -L/usr/lib/gcc/x86_64-redhat-linux/4.4.7/../../../ -L/lib64 -L/lib/
>> -L/usr/lib64 -L/usr/lib
>> /home/class239/software/pylith-git/pylith/lib/libmpi_f90.so
>> /home/class239/software/pylith-git/pylith/lib/libmpi_f77.so
>> /home/class239/software/pylith-git/pylith/lib/libmpi.so
>> /home/class239/software/pylith-git/pylith/lib/libopen-rte.so
>> /home/class239/software/pylith-git/pylith/lib/libopen-pal.so -lnsl
>> -lutil -lifport -lifcoremt -limf -lm -lipgo -lintlc -lpthread -lsvml
>> -lgcc -lgcc_s -lirc_s -ldl -lc -pthread -soname libnetcdff.so.5 -o
>> .libs/libnetcdff.so.5.1.0
>> ifort: command line warning #10006: ignoring unknown option
>> '-fwhole-archive'
>> ifort: command line warning #10006: ignoring unknown option
>> '-fno-whole-archive'
>> ifort: command line warning #10006: ignoring unknown option '-rpath'
>> ifort: command line warning #10006: ignoring unknown option '-rpath'
>> ifort: command line warning #10006: ignoring unknown option '-rpath'
>> ifort: command line remark #10010: option '-pthread' is deprecated and
>> will be removed in a future release. See '-help deprecated'
>> ifort: command line warning #10006: ignoring unknown option '-soname'
>> ifort: error #10236: File not found: 'libnetcdff.so.5'
>> ifort: command line remark #10010: option '-pthread' is deprecated and
>> will be removed in a future release. See '-help deprecated'
>> make[6]: *** [libnetcdff.la <http://libnetcdff.la>] Error 1
>> make[6]: Leaving directory
>> `/home/class239/software/pylith-git/build/netcdf-build/fortran'
>> make[5]: *** [all] Error 2
>> make[5]: Leaving directory
>> `/home/class239/software/pylith-git/build/netcdf-build/fortran'
>> make[4]: *** [all-recursive] Error 1
>> make[4]: Leaving directory
>> `/home/class239/software/pylith-git/build/netcdf-build'
>> make[3]: *** [all] Error 2
>> make[3]: Leaving directory
>> `/home/class239/software/pylith-git/build/netcdf-build'
>> make[2]: *** [netcdf] Error 2
>> make[2]: Leaving directory `/home/class239/software/pylith-git/build'
>> make[1]: *** [installed_netcdf] Error 2
>> make[1]: Leaving directory `/home/class239/software/pylith-git/build'
>> make: *** [installed_pylith] Error 2
>>
>>
>>
>> On Tue, Oct 14, 2014 at 4:05 PM, Brad Aagaard <baagaard at usgs.gov
>> <mailto:baagaard at usgs.gov>> wrote:
>>
>> Eric,
>>
>> It looks like the linker is unable to create the NetCDF shared
>> library. You need to examine the error message to see what the
>> linkiner is complaining about. Feel free to send the error message.
>>
>> At the bottom of the INSTALL file, there are some notes on manually
>> patching libtool (this will be at the top-level of the build
>> directory for NetCDF) so that the NetCDF shared library can be
>> built. The notes are a bit cryptic, so let me know if they need more
>> explanation.
>>
>> Regards,
>> Brad
>>
>>
>>
>> On 10/14/2014 03:41 PM, Eric Lindsey wrote:
>>
>> Greetings,
>>
>> I've been trying to build the latest version of Pylith from the
>> git
>> repository, but am failing on the netcdf build step. I used the
>> pylith-installer, with the configure command:
>>
>> /home/class239/software/__pylith-git/pylith-installer-2.
>> __0.3-0/configure
>> --with-pylith-git=master --with-make-threads=2
>> --prefix=/home/class239/__software/pylith-git/pylith
>> --enable-python
>> --enable-mpi=openmpi --enable-force-install
>>
>> A different version of netcdf is already installed on this
>> system, but it
>> is not an option for me to remove it (hence enable-force-install).
>>
>> The configure runs successfully, but 'make' fails with:
>>
>> ifort: error #10236: File not found: 'libnetcdff.so.5'
>> make[6]: *** [libnetcdff.la <http://libnetcdff.la>] Error 1
>> make[6]: Leaving directory
>> `/home/class239/software/__pylith-git/build/netcdf-build/
>> __fortran'
>>
>> Am I doing something wrong? Or is this a result of my having a
>> prior
>> installation of netcdf? Any hints would be appreciated.
>>
>> Thanks,
>> Eric
>>
>>
>>
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