[netCDF #EPQ-640599]: make check failed

Greetings Ben,

Try adding a linking flag to your second gfortran command, like this:

gfortran -g -O2 -L/lib/lib -o simple_xy_wr simple_xy_wr.o

Then,try running simple_xy_wr. If you get an error like this,

"cannot open shared object file: No such file or directory"

then do the following and run again:

export LD_LIBRARY_PATH=/lib/lib
./simple_xy_wr

Cheers!

Sean

> Hi Sean,
> 
> Thanks again for all your help. I'm still getting the same error message.
> 
> To give a precise description of what I'm doing, I started from square one
> using these commands (and attached the new .out files to this email):
> 
> sudo make distclean
> export CFLAGS="-arch x86_64"
> export FFLAGS=-m64
> sudo ./configure --prefix=/lib --disable-netcdf-4 --enable-shared
> sudo make &> make.out
> sudo make check &> make_check.out
> gfortran -c -g -O2 -I/lib/include simple_xy_wr.f
> gfortran -g -O2 -I/lib/include -o simple_xy_wr simple_xy_wr.o
> Undefined symbols for architecture x86_64:
> "_nf_strerror_", referenced from:
> _handle_err_ in simple_xy_wr.o
> "_nf_create_", referenced from:
> _MAIN__ in simple_xy_wr.o
> "_nf_def_dim_", referenced from:
> _MAIN__ in simple_xy_wr.o
> "_nf_def_var_", referenced from:
> _MAIN__ in simple_xy_wr.o
> "_nf_enddef_", referenced from:
> _MAIN__ in simple_xy_wr.o
> "_nf_put_var_int_", referenced from:
> _MAIN__ in simple_xy_wr.o
> "_nf_close_", referenced from:
> _MAIN__ in simple_xy_wr.o
> ld: symbol(s) not found for architecture x86_64
> collect2: ld returned 1 exit status
> 
> Sorry again for all this trouble.
> 
> Ben
> 
> address@hidden> wrote:
> 
> > Hi Ben,
> >
> > It looks like you used the wrong compile variables:
> >
> > export CFLAG=-m64
> > export FFLAG=-m64
> >
> > It should be CFLAGS and FFLAGS. For the CFLAGS, use -arch x86_64. Try
> > rebuilding, but this time use this:
> >
> > export CFLAGS="-arch x86_64"
> > export FFLAGS=-m64
> >
> > Let me know how that works.
> >
> > Sean
> >
> > > Hi Sean,
> > >
> > > Thanks again for your prompt response. I'm not sure if I'm using the
> > > gfortran compiler correctly. When I downloaded one of the simple test
> > codes
> > > from the website and attempted to run it, I got this response (here I
> > link
> > > the directory that contains the libraries, just in case):
> > >
> > > gfortran -I /usr/bin/include -o simple_xy_wr.exe simple_xy_wr.f
> > > Undefined symbols for architecture x86_64:
> > > "_nf_create_", referenced from:
> > > _MAIN__ in ccVJvzkh.o
> > > "_nf_def_dim_", referenced from:
> > > _MAIN__ in ccVJvzkh.o
> > > "_nf_def_var_", referenced from:
> > > _MAIN__ in ccVJvzkh.o
> > > "_nf_enddef_", referenced from:
> > > _MAIN__ in ccVJvzkh.o
> > > "_nf_put_var_int_", referenced from:
> > > _MAIN__ in ccVJvzkh.o
> > > "_nf_close_", referenced from:
> > > _MAIN__ in ccVJvzkh.o
> > > "_nf_strerror_", referenced from:
> > > _handle_err_ in ccVJvzkh.o
> > > ld: symbol(s) not found for architecture x86_64
> > > collect2: ld returned 1 exit statu
> > >
> > > Is this related to the same error?
> > >
> > > Hope you're well,
> > >
> > > Ben
> > >
> > > address@hidden> wrote:
> > >
> > > > Hi Ben,
> > > >
> > > > From the looks of you make_check.out file, everything compiled
> > correctly
> > > > and is good. Now I see what happened. So you did a make check install
> > first,
> > > > which will compile netCDF, check it for errors, and install it. When
> > you ran
> > > > make check the second time, the code behind make check could not find
> > the
> > > > compiled libraries under your source directories because they had
> > already
> > > > been moved out of there to some other location on your disk (make check
> > > > specifically looks in some temporary folders for the compiled libraries
> > -
> > > > once you make install, those libraries are taken out of the temp
> > folders,
> > > > and so make check cannot find them).
> > > >
> > > > Things look good to me!
> > > >
> > > > Sean
> > > >
> > > > > Hi Sean,
> > > > >
> > > > > Thank you for your help with this. Here are the make.out and
> > > > make_check.out
> > > > > files.
> > > > >
> > > > > Hope you're well,
> > > > >
> > > > > Ben
> > > > >
> > > > > address@hidden> wrote:
> > > > >
> > > > > > Greetings Benjamin,
> > > > > >
> > > > > > Would you kindly send the full output from make and make check?
> > First,
> > > > do
> > > > > >
> > > > > > make clean
> > > > > >
> > > > > > Then, re-run the configure script as you did previously. Next, do
> > > > > >
> > > > > > make &> make.out
> > > > > >
> > > > > > and after that, do
> > > > > >
> > > > > > make check &> make_check.out
> > > > > >
> > > > > > Then, would you mind sending the make.out and make_check.out files?
> > > > They
> > > > > > will be of much help. I looks like the apple gcc-4 is having issues
> > > > finding
> > > > > > the standard c libraries and header files, but the make and make
> > check
> > > > logs
> > > > > > will tell us for sure.
> > > > > >
> > > > > > Thanks so much!
> > > > > >
> > > > > > Sean
> > > > > >
> > > > > > > Full Name: Benjamin Johnson
> > > > > > > Email Address: address@hidden
> > > > > > > Organization: University of Maryland-College Park
> > > > > > > Package Version: netcdf 4.1.3
> > > > > > > Operating System: Mac OS X Lion
> > > > > > > Hardware: Intel processor
> > > > > > > Description of problem: I am trying to configure netcdf to run on
> > Mac
> > > > OS
> > > > > > X Lion's x86_64 architecture (my config.log is attached). Before
> > > > installing
> > > > > > I set my environment variables:
> > > > > > >
> > > > > > > export CFLAG=-m64
> > > > > > > export FFLAG=-m64
> > > > > > >
> > > > > > > Then ran:
> > > > > > >
> > > > > > > sudo ./configure --prefix=/lib --disable-netcdf-4 --enable-shared
> > > > > > > sudo make check install
> > > > > > > sudo make check
> > > > > > >
> > > > > > > Running the last command produced the following:
> > > > > > >
> > > > > > > make check
> > > > > > > Making check in include
> > > > > > > make[1]: Nothing to be done for `check'.
> > > > > > > Making check in libdispatch
> > > > > > > make[1]: Nothing to be done for `check'.
> > > > > > > Making check in oc
> > > > > > > make[1]: Nothing to be done for `check'.
> > > > > > > Making check in libsrc
> > > > > > > make[1]: Nothing to be done for `check'.
> > > > > > > Making check in libdap2
> > > > > > > make[1]: Nothing to be done for `check'.
> > > > > > > Making check in liblib
> > > > > > > make[1]: Nothing to be done for `check'.
> > > > > > > Making check in nctest
> > > > > > > make  nctest tst_rename
> > > > > > > make[2]: `nctest' is up to date.
> > > > > > > make[2]: `tst_rename' is up to date.
> > > > > > > make  check-TESTS
> > > > > > > Testing V2 API with 2 different netCDF formats.
> > > > > > >
> > > > > > >
> > > > > > > Switching to netCDF classic format.
> > > > > > > *** Testing nccreate ...        *** test_nccreate: nccreate
> > failed to
> > > > > > NC_CLOBBER
> > > > > > > *** Testing ncopen ...          *** could not create temp file
> > > > > > > *** Testing ncredef ...         *** test_ncredef: ncopen failed
> > > > > > > *** Testing ncendef ...         *** test_ncendef: ncopen failed
> > > > > > > *** Testing ncclose ...         *** test_ncclose: ncopen failed
> > > > > > > *** Testing ncinquire ...       *** test_ncinquire: ncopen failed
> > > > > > > *** Testing ncsync ...          *** test_ncsync: ncopen in
> > NC_WRITE
> > > > mode
> > > > > > failed
> > > > > > > *** Testing ncabort ...         *** test_ncabort: ncopen failed
> > > > > > > *** Testing ncdimdef ...        *** test_ncdimdef: ncopen failed
> > > > > > > *** Testing ncdimid ...         *** test_ncdimid: ncopen failed
> > > > > > > *** Testing ncdiminq ...        *** test_ncdiminq: ncopen failed
> > > > > > > *** Testing ncdimrename ...     *** test_ncdimrename: ncopen
> > failed
> > > > > > > *** Testing ncvardef ...        *** test_ncvardef: ncopen failed
> > > > > > > *** Testing ncvarid ...         *** test_ncvarid: ncopen failed
> > > > > > > *** Testing ncvarinq ...        *** test_ncvarinq: ncopen failed
> > > > > > > *** Testing ncvarput1 ...       *** test_ncvarput1: ncopen failed
> > > > > > > *** Testing ncvarget1 ...       *** test_ncvarget1: ncopen failed
> > > > > > > *** Testing ncvarput ...        *** test_ncvarput: ncopen failed
> > > > > > > *** Testing ncvarget ...        *** test_ncvarget: ncopen failed
> > > > > > > *** Testing ncvarputg ...       *** test_ncvarputg: ncopen failed
> > > > > > > *** Testing ncvargetg ...       *** test_ncvargetg: ncopen failed
> > > > > > > *** Testing ncrecinq ...        *** test_ncrecinq: ncopen failed
> > > > > > > *** Testing ncrecput ...        *** test_ncrecput: ncopen failed
> > > > > > > *** Testing ncattput ...        *** test_ncattput: ncopen failed
> > > > > > > *** Testing ncattinq ...        *** test_ncattinq: ncopen failed
> > > > > > > *** Testing ncattget ...        *** test_ncattget: ncopen failed
> > > > > > > *** Testing ncattcopy ...       *** test_ncattcopy: ncopen failed
> > > > > > > *** Testing ncattname ...       *** test_ncattname: ncopen failed
> > > > > > > *** Testing ncattrename ...     *** test_ncattrename: ncopen
> > failed
> > > > > > > *** Testing ncattdel ...        *** test_ncattdel: ncopen failed
> > > > > > > *** Testing nctypelen ...       ok ***
> > > > > > >
> > > > > > >
> > > > > > > Switching to 64-bit offset format.
> > > > > > > *** Testing nccreate ...        *** test_nccreate: nccreate
> > failed to
> > > > > > NC_CLOBBER
> > > > > > > *** Testing ncopen ...          *** could not create temp file
> > > > > > > *** Testing ncredef ...         *** test_ncredef: ncopen failed
> > > > > > > *** Testing ncendef ...         *** test_ncendef: ncopen failed
> > > > > > > *** Testing ncclose ...         *** test_ncclose: ncopen failed
> > > > > > > *** Testing ncinquire ...       *** test_ncinquire: ncopen failed
> > > > > > > *** Testing ncsync ...          *** test_ncsync: ncopen in
> > NC_WRITE
> > > > mode
> > > > > > failed
> > > > > > > *** Testing ncabort ...         *** test_ncabort: ncopen failed
> > > > > > > *** Testing ncdimdef ...        *** test_ncdimdef: ncopen failed
> > > > > > > *** Testing ncdimid ...         *** test_ncdimid: ncopen failed
> > > > > > > *** Testing ncdiminq ...        *** test_ncdiminq: ncopen failed
> > > > > > > *** Testing ncdimrename ...     *** test_ncdimrename: ncopen
> > failed
> > > > > > > *** Testing ncvardef ...        *** test_ncvardef: ncopen failed
> > > > > > > *** Testing ncvarid ...         *** test_ncvarid: ncopen failed
> > > > > > > *** Testing ncvarinq ...        *** test_ncvarinq: ncopen failed
> > > > > > > *** Testing ncvarput1 ...       *** test_ncvarput1: ncopen failed
> > > > > > > *** Testing ncvarget1 ...       *** test_ncvarget1: ncopen failed
> > > > > > > *** Testing ncvarput ...        *** test_ncvarput: ncopen failed
> > > > > > > *** Testing ncvarget ...        *** test_ncvarget: ncopen failed
> > > > > > > *** Testing ncvarputg ...       *** test_ncvarputg: ncopen failed
> > > > > > > *** Testing ncvargetg ...       *** test_ncvargetg: ncopen failed
> > > > > > > *** Testing ncrecinq ...        *** test_ncrecinq: ncopen failed
> > > > > > > *** Testing ncrecput ...        *** test_ncrecput: ncopen failed
> > > > > > > *** Testing ncrecget ...        *** test_ncrecget: ncopen failed
> > > > > > > *** Testing ncvarrename ...     *** test_ncvarrename: ncopen
> > failed
> > > > > > > *** Testing ncattput ...        *** test_ncattput: ncopen failed
> > > > > > > *** Testing ncattinq ...        *** test_ncattinq: ncopen failed
> > > > > > > *** Testing ncattget ...        *** test_ncattget: ncopen failed
> > > > > > > *** Testing ncattcopy ...       *** test_ncattcopy: ncopen failed
> > > > > > > *** Testing ncattname ...       *** test_ncattname: ncopen failed
> > > > > > > *** Testing ncattrename ...     *** test_ncattrename: ncopen
> > failed
> > > > > > > *** Testing ncattdel ...        *** test_ncattdel: ncopen failed
> > > > > > > *** Testing nctypelen ...       ok ***
> > > > > > >
> > > > > > > Total number of failures: 64
> > > > > > > nctest FAILURE!!!
> > > > > > > FAIL: nctest
> > > > > > >
> > > > > > > *** Testing v3/v4 API versions of some v2 tests.
> > > > > > > *** testing simple dim rename...Sorry! Unexpected result,
> > > > tst_rename.c,
> > > > > > line: 219
> > > > > > > FAIL: tst_rename
> > > > > > > PASS: compare_test_files.sh
> > > > > > > ================================================
> > > > > > > 2 of 3 tests failed
> > > > > > > Please report to address@hidden
> > > > > > > ================================================
> > > > > > > make[2]: *** [check-TESTS] Error 1
> > > > > > > make[1]: *** [check-am] Error 2
> > > > > > > make: *** [check-recursive] Error 1
> > > > > > >
> > > > > > >
> > > > > >
> > > > > >
> > > > > > Ticket Details
> > > > > > ===================
> > > > > > Ticket ID: EPQ-640599
> > > > > > Department: Support netCDF
> > > > > > Priority: Normal
> > > > > > Status: Open
> > > > > >
> > > > > >
> > > > >
> > > > >
> > > >
> > > >
> > > > Ticket Details
> > > > ===================
> > > > Ticket ID: EPQ-640599
> > > > Department: Support netCDF
> > > > Priority: Normal
> > > > Status: Open
> > > >
> > > >
> > >
> > >
> >
> >
> > Ticket Details
> > ===================
> > Ticket ID: EPQ-640599
> > Department: Support netCDF
> > Priority: Normal
> > Status: Open
> >
> >
> 
> 


Ticket Details
===================
Ticket ID: EPQ-640599
Department: Support netCDF
Priority: Normal
Status: Open