[CIG-SHORT] NetCDF error when attempting to build git version
Matthew Knepley
knepley at mcs.anl.gov
Fri Oct 17 16:51:44 PDT 2014
On Fri, Oct 17, 2014 at 4:43 PM, Eric Lindsey <elindsey at ucsd.edu> wrote:
> 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.
>
This means that the HDF5 that is installed is not 1.8. Do you have another
HDF5
covering up the one that PyLith tries to install?
Thanks,
Matt
> 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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