[netCDF #ZXR-914718]: netcdf 4.0.1 with pgi on Linux - 4 errors in tests

Hi Matthias,

Thanks for reporting the problem.  Apparently this has been reported
before and seems to be a vendor problem with the C++ runtime.  Here's
the information we have about this:

 http://www.unidata.ucar.edu/netcdf/docs/known_problems.html#PG_shared

The above information says the problem with the PGI C++ runtime was
"Fixed in version 6.2.1".  If your version of pgCC is later than 6.2.1,
then we should correct this description.

Your configure log included this:

configure:6264: pgCC --version >&5

  pgCC (aka pgcpp) 6.2-5 64-bit target on x86-64 Linux
  Copyright 1989-2000, The Portland Group, Inc. All Rights Reserved.
  Copyright 2000-2006, STMicroelectronics, Inc. All Rights Reserved.

but I don't know the relationship between "6.2-5" and "6.2.1" versions.
If you need the C++ interface for any reason, you may have to upgrade
to 6.2.1.

--Russ

> the compiler option worked well. But I had to disable C++ completely in
> order to pass all checks. If I only disable cxx-4 then I got:
> make[2]: Leaving directory `/home/cuntz/netcdf-4.0.1/nf_test'
> make[1]: Leaving directory `/home/cuntz/netcdf-4.0.1/nf_test'
> Making check in cxx
> make[1]: Entering directory `/home/cuntz/netcdf-4.0.1/cxx'
> make  nctst tst_failure
> make[2]: Entering directory `/home/cuntz/netcdf-4.0.1/cxx'
> source='nctst.cpp' object='nctst.o' libtool=no \
> DEPDIR=.deps depmode=none /bin/sh ../depcomp \
> pgCC -DHAVE_CONFIG_H -I. -I.. -I../fortran  -I../libsrc4
> -I/home/cuntz/lib/hdf5_pgi//include -I/home/cuntz/lib/zlib_pgi//include
> -I/home/cuntz/lib/szip_pgi//include  -DNDEBUG -DpgiFortran  -g -c -o
> nctst.o nctst.cpp
> /bin/sh ../libtool --tag=CXX   --mode=link pgCC  -g
> -L/home/cuntz/lib/hdf5_pgi//lib -L/home/cuntz/lib/zlib_pgi//lib
> -L/home/cuntz/lib/szip_pgi//lib  -o nctst nctst.o
> ../cxx/libnetcdf_c++.la ../libsrc4/libnetcdf.la -lhdf5_hl -lhdf5
> libtool: link: pgCC -g -o .libs/nctst nctst.o
> -L/home/cuntz/lib/hdf5_pgi//lib -L/home/cuntz/lib/zlib_pgi//lib
> -L/home/cuntz/lib/szip_pgi//lib ../cxx/.libs/libnetcdf_c++.so
> /home/cuntz/netcdf-4.0.1/libsrc4/.libs/libnetcdf.so
> ../libsrc4/.libs/libnetcdf.so /home/cuntz/lib/hdf5_pgi//lib/libhdf5_hl.a
> /home/cuntz/lib/hdf5_pgi//lib/libhdf5.a
> /home/cuntz/lib/szip_pgi//lib/libsz.so -lz -lm -Wl,--rpath
> -Wl,/home/cuntz/lib/netcdf4_pgi/lib -Wl,--rpath
> -Wl,/home/cuntz/lib/szip_pgi//lib
> source='tst_failure.cpp' object='tst_failure.o' libtool=no \
> DEPDIR=.deps depmode=none /bin/sh ../depcomp \
> pgCC -DHAVE_CONFIG_H -I. -I.. -I../fortran  -I../libsrc4
> -I/home/cuntz/lib/hdf5_pgi//include -I/home/cuntz/lib/zlib_pgi//include
> -I/home/cuntz/lib/szip_pgi//include  -DNDEBUG -DpgiFortran  -g -c -o
> tst_failure.o tst_failure.cpp
> /bin/sh ../libtool --tag=CXX   --mode=link pgCC  -g
> -L/home/cuntz/lib/hdf5_pgi//lib -L/home/cuntz/lib/zlib_pgi//lib
> -L/home/cuntz/lib/szip_pgi//lib  -o tst_failure tst_failure.o
> ../cxx/libnetcdf_c++.la ../libsrc4/libnetcdf.la -lhdf5_hl -lhdf5
> libtool: link: pgCC -g -o .libs/tst_failure tst_failure.o
> -L/home/cuntz/lib/hdf5_pgi//lib -L/home/cuntz/lib/zlib_pgi//lib
> -L/home/cuntz/lib/szip_pgi//lib ../cxx/.libs/libnetcdf_c++.so
> /home/cuntz/netcdf-4.0.1/libsrc4/.libs/libnetcdf.so
> ../libsrc4/.libs/libnetcdf.so /home/cuntz/lib/hdf5_pgi//lib/libhdf5_hl.a
> /home/cuntz/lib/hdf5_pgi//lib/libhdf5.a
> /home/cuntz/lib/szip_pgi//lib/libsz.so -lz -lm -Wl,--rpath
> -Wl,/home/cuntz/lib/netcdf4_pgi/lib -Wl,--rpath
> -Wl,/home/cuntz/lib/szip_pgi//lib
> make[2]: Leaving directory `/home/cuntz/netcdf-4.0.1/cxx'
> make  check-TESTS
> make[2]: Entering directory `/home/cuntz/netcdf-4.0.1/cxx'
> C++ runtime abort: internal error: static object marked for destruction
> more than once
> /bin/sh: line 1: 28212 Abgebrochen             ${dir}$tst
> FAIL: nctst
> C++ runtime abort: internal error: static object marked for destruction
> more than once
> /bin/sh: line 1: 28235 Abgebrochen             ${dir}$tst
> XFAIL: tst_failure
> 
> *** Testing C++ API test program output.
> *** dumping classic format file to nctst_classic.cdl and comparing...
> /home/cuntz/netcdf-4.0.1/ncdump/.libs/lt-ncdump: nctst_classic.nc: No
> such file or directory
> FAIL: run_nc_tests.sh
> 
> *** Testing C++ API test program output for netCDF-4.
> *** dumping netcdf-4 format file to nctst_netcdf4.cdl and comparing...
> /home/cuntz/netcdf-4.0.1/ncdump/.libs/lt-ncdump: nctst_netcdf4.nc: No
> such file or directory
> FAIL: run_nc4_tests.sh
> =========================================
> 3 of 4 tests failed
> Please report to address@hidden
> =========================================
> make[2]: *** [check-TESTS] Fehler 1
> make[2]: Leaving directory `/home/cuntz/netcdf-4.0.1/cxx'
> make[1]: *** [check-am] Fehler 2
> make[1]: Leaving directory `/home/cuntz/netcdf-4.0.1/cxx'
> make: *** [check-recursive] Fehler 1
> 
> 
> 
> Looks like that it is still checking cxx-4 even that I said:
> % ./configure --prefix=/home/cuntz/lib/netcdf4_pgi/ --enable-shared
> --enable-netcdf-4 \
> --enble-extra-example-tests --enable-extra-tests
> --enable-large-file-tests \
> --with-hdf5=/home/cuntz/lib/hdf5_pgi/
> --with-zlib=/home/cuntz/lib/zlib_pgi/ \
> --with-szlib=/home/cuntz/lib/szip_pgi/ --disable-cxx-4
> --enable-ncgen4 && make check
> 
> putting also --disable-cxx into configure works.
> 
> Cheers
> Matthias
> 
> 
> 
> 
> Unidata netCDF Support schrieb:
> > Hi Matthias,
> >
> >
> >> I am compiling netcdf 4.0.1 on Linux with the Portland Group (pg)
> >> compilers. I have compiled zlib, szip and hdf5 with the pg-compilers
> >> builiding shared and static libraries without problems.
> >>
> >> Now I am compiling netcdf 4:
> >>
> >> % uname -a
> >> Linux compile.liclus.leipzig.ufz.de 2.6.9-55.ELsmp #1 SMP Fri Apr 20
> >> 16:36:54 EDT 2007 x86_64 x86_64 x86_64 GNU/Linux
> >> % export CC=pgcc
> >> % export CXX=pgCC
> >> % export FC=pgf90
> >> % ./configure --prefix=/home/cuntz/lib/netcdf4_pgi/ --enable-shared
> >> --enable-netcdf-4 --enable-cxx-4 \
> >>     --enable-extra-example-tests --enable-extra-tests
> >> --enable-large-file-tests \
> >>     --with-hdf5=/home/cuntz/lib/hdf5_pgi/ --with-zlib=/home/cuntz/lib/
> >> --with-szlib=/home/cuntz/lib/
> >> % make | tee make.log
> >> % make check | tee make_check.log
> >>
> >> I get:
> >>
> >> =========================================
> >> 4 of 46 tests failed
> >> Please report to address@hidden
> >> =========================================
> >>
> >
> > Portland Group has published recommendations for compiling netCDF with
> > their compilers:
> >
> >   http://www.pgroup.com/resources/netcdf/netcdf362_pgi71.htm
> >
> > and in that recommendation, they have set
> >
> >   CFLAGS="-O2 -Msignextend -V"
> >
> > before running the configure script.  I'm not sure how necessary the -O2
> > and -V are (I think that just prints the version), but we have tested the
> > 4.0.1 version using the CFLAGS above on a 64-bit Linux platform with all
> > PG compilers, and it worked.  The exact settings we used were:
> >
> >   CPPFLAGS="-DNDEBUG -DpgiFortran"
> >   CC=pgcc
> >   CFLAGS="-O2 -Msignextend -V"
> >   CXX=pgCC
> >   CXXFLAGS=-g
> >   FC=pgf90
> >   FCFLAGS=-g
> >   F77=pgf90
> >   FFLAGS="-O2 -w -V"
> >
> > and the configure script was called as:
> >
> >   ./configure --enable-netcdf-4 --with-hdf5=/upc/share/ed/local/shecky
> >
> > before running
> >
> >   make check install
> >
> > The output from this working build is here:
> >
> >   
> > http://www.unidata.ucar.edu/netcdf/builds/4_0_1/out_shecky_2009042811_20_1.txt
> >
> > As a side note, the cxx4 API is very incomplete and untested. It is
> > experimental. If you want to use it, count on having to debug and
> > improve it yourself. We hope to get the cxx4 API ready for the 4.2
> > release.  I recommend you omit --enable-cxx-4 unless you really need
> > it and are prepared to do some work on it.  That's why it's currently
> > disabled by default.
> >
> > I hope this helps.
> >
> > --Russ
> >
> > Russ Rew                                         UCAR Unidata Program
> > address@hidden                     http://www.unidata.ucar.edu
> >
> >
> >
> > Ticket Details
> > ===================
> > Ticket ID: ZXR-914718
> > Department: Support netCDF
> > Priority: Normal
> > Status: Closed
> >
> >
> 
> 

Russ Rew                                         UCAR Unidata Program
address@hidden                     http://www.unidata.ucar.edu



Ticket Details
===================
Ticket ID: ZXR-914718
Department: Support netCDF
Priority: Normal
Status: Closed