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[netCDF #EPQ-640599]: make check failed

Subject: [netCDF #EPQ-640599]: make check failed
Date: Wed, 24 Aug 2011 12:49:08 -0600
> New Staff Reply: 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

He'll also need -lnetcdf:

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

and depending on which version he's compiling (if shared libraries were
not the default) he'll need more, such as

  gfortran -g -O2 -L/lib/lib -o simple_xy_wr simple_xy_wr.o -lnetcdff \
           -lnetcdf -lhdf5 -lz ...

whatever the "nc-config --flibs" shows.

--Russ

> 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 che
> ck
> > > > > specifically looks in some temporary folders for the compiled librari
> es
> > > -
> > > > > 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 file
> s?
> > > > > They
> > > > > > > will be of much help. I looks like the apple gcc-4 is having issu
> es
> > > > > 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-shar
> ed
> > > > > > > > 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 fail
> ed
> > > > > > > > *** Testing ncsync ...          *** test_ncsync: ncopen in
> > > NC_WRITE
> > > > > mode
> > > > > > > failed
> > > > > > > > *** Testing ncabort ...         *** test_ncabort: ncopen failed
> > > > > > > > *** Testing ncdimdef ...        *** test_ncdimdef: ncopen faile
> d
> > > > > > > > *** Testing ncdimid ...         *** test_ncdimid: ncopen failed
> > > > > > > > *** Testing ncdiminq ...        *** test_ncdiminq: ncopen faile
> d
> > > > > > > > *** Testing ncdimrename ...     *** test_ncdimrename: ncopen
> > > failed
> > > > > > > > *** Testing ncvardef ...        *** test_ncvardef: ncopen faile
> d
> > > > > > > > *** Testing ncvarid ...         *** test_ncvarid: ncopen failed
> > > > > > > > *** Testing ncvarinq ...        *** test_ncvarinq: ncopen faile
> d
> > > > > > > > *** Testing ncvarput1 ...       *** test_ncvarput1: ncopen fail
> ed
> > > > > > > > *** Testing ncvarget1 ...       *** test_ncvarget1: ncopen fail
> ed
> > > > > > > > *** Testing ncvarput ...        *** test_ncvarput: ncopen faile
> d
> > > > > > > > *** Testing ncvarget ...        *** test_ncvarget: ncopen faile
> d
> > > > > > > > *** Testing ncvarputg ...       *** test_ncvarputg: ncopen fail
> ed
> > > > > > > > *** Testing ncvargetg ...       *** test_ncvargetg: ncopen fail
> ed
> > > > > > > > *** Testing ncrecinq ...        *** test_ncrecinq: ncopen faile
> d
> > > > > > > > *** Testing ncrecput ...        *** test_ncrecput: ncopen faile
> d
> > > > > > > > *** Testing ncattput ...        *** test_ncattput: ncopen faile
> d
> > > > > > > > *** Testing ncattinq ...        *** test_ncattinq: ncopen faile
> d
> > > > > > > > *** Testing ncattget ...        *** test_ncattget: ncopen faile
> d
> > > > > > > > *** Testing ncattcopy ...       *** test_ncattcopy: ncopen fail
> ed
> > > > > > > > *** Testing ncattname ...       *** test_ncattname: ncopen fail
> ed
> > > > > > > > *** Testing ncattrename ...     *** test_ncattrename: ncopen
> > > failed
> > > > > > > > *** Testing ncattdel ...        *** test_ncattdel: ncopen faile
> d
> > > > > > > > *** 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 fail
> ed
> > > > > > > > *** Testing ncsync ...          *** test_ncsync: ncopen in
> > > NC_WRITE
> > > > > mode
> > > > > > > failed
> > > > > > > > *** Testing ncabort ...         *** test_ncabort: ncopen failed
> > > > > > > > *** Testing ncdimdef ...        *** test_ncdimdef: ncopen faile
> d
> > > > > > > > *** Testing ncdimid ...         *** test_ncdimid: ncopen failed
> > > > > > > > *** Testing ncdiminq ...        *** test_ncdiminq: ncopen faile
> d
> > > > > > > > *** Testing ncdimrename ...     *** test_ncdimrename: ncopen
> > > failed
> > > > > > > > *** Testing ncvardef ...        *** test_ncvardef: ncopen faile
> d
> > > > > > > > *** Testing ncvarid ...         *** test_ncvarid: ncopen failed
> > > > > > > > *** Testing ncvarinq ...        *** test_ncvarinq: ncopen faile
> d
> > > > > > > > *** Testing ncvarput1 ...       *** test_ncvarput1: ncopen fail
> ed
> > > > > > > > *** Testing ncvarget1 ...       *** test_ncvarget1: ncopen fail
> ed
> > > > > > > > *** Testing ncvarput ...        *** test_ncvarput: ncopen faile
> d
> > > > > > > > *** Testing ncvarget ...        *** test_ncvarget: ncopen faile
> d
> > > > > > > > *** Testing ncvarputg ...       *** test_ncvarputg: ncopen fail
> ed
> > > > > > > > *** Testing ncvargetg ...       *** test_ncvargetg: ncopen fail
> ed
> > > > > > > > *** Testing ncrecinq ...        *** test_ncrecinq: ncopen faile
> d
> > > > > > > > *** Testing ncrecput ...        *** test_ncrecput: ncopen faile
> d
> > > > > > > > *** Testing ncrecget ...        *** test_ncrecget: ncopen faile
> d
> > > > > > > > *** Testing ncvarrename ...     *** test_ncvarrename: ncopen
> > > failed
> > > > > > > > *** Testing ncattput ...        *** test_ncattput: ncopen faile
> d
> > > > > > > > *** Testing ncattinq ...        *** test_ncattinq: ncopen faile
> d
> > > > > > > > *** Testing ncattget ...        *** test_ncattget: ncopen faile
> d
> > > > > > > > *** Testing ncattcopy ...       *** test_ncattcopy: ncopen fail
> ed
> > > > > > > > *** Testing ncattname ...       *** test_ncattname: ncopen fail
> ed
> > > > > > > > *** Testing ncattrename ...     *** test_ncattrename: ncopen
> > > failed
> > > > > > > > *** Testing ncattdel ...        *** test_ncattdel: ncopen faile
> d
> > > > > > > > *** 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
> Link:  https://www.unidata.ucar.edu/esupport/staff/index.php?_m=tickets&_a=vi
> ewticket&ticketid=18641



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