Hi David: This:
undefined symbol: __pgdbg_stub
seems to indicate that some Portland compiler symbols are still not linked
in.
I did not know you were using Portland compilers. My full recipe for
compiling netCDF with PG compilers is this:
if netcdf is to be installed in /ops/tools
./configure --prefix=/ops/tools FC=pgf90 \
CPPFLAGS="-DNDEBUG -DpgiFortran -fPIC" \
FFLAGS="-I/usr/include -I/ops/tools/include"
make
I think adding -DpgiFortran to the CPPFLAGS for the configure step in the
netCDF compile might help.
Sorry for the hassle. I'm CC'ing the netcdf mailing list in case anyone
on that list has any ideas.
Regards,
Doug Hunt
dhunt@xxxxxxxx
Software Engineer
UCAR - COSMIC, Tel. (303) 497-2611
On Tue, 19 Apr 2011, Bryan, David wrote:
Doug,
Our admin guy recompiled NetCDF with -fPIC. (Though there were some
complications I'll describe below.) The make step worked, but I ran into
problem at the make test step. The log from that is below. After the log,
I've got the description of the compilation.
Thanks,
David
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_harness(0,
'blib/lib', 'blib/arch')" t/*.t
t/01-Netcdf3.t .. 1/46
# Failed test 'use PDL::NetCDF;'
# at t/01-Netcdf3.t line 7.
# Tried to use 'PDL::NetCDF'.
# Error: Can't load '/home/amec/PDL-NetCDF-4.08/blib/arch/auto/PDL/NetCDF/N
etCDF.so' for module PDL::NetCDF: /home/amec/PDL-NetCDF-4.08/blib/arch/auto/PDL/
NetCDF/NetCDF.so: undefined symbol: __pgdbg_stub at /usr/lib64/perl5/5.8.5/x86_6
4-linux-thread-multi/DynaLoader.pm line 230.
# at (eval 39) line 2
# Compilation failed in require at (eval 39) line 2.
# BEGIN failed--compilation aborted at (eval 39) line 2.
Use of inherited AUTOLOAD for non-method PDL::NetCDF::nc_create() is deprecated
at /home/amec/PDL-NetCDF-4.08/blib/lib/PDL/NetCDF.pm line 1063.
Can't locate auto/PDL/NetCDF/nc_create.al in @INC (@INC contains: /home/amec/PDL
-NetCDF-4.08/blib/lib/5.8.5/x86_64-linux-thread-multi /home/amec/PDL-NetCDF-4.08
/blib/lib/5.8.5 /home/amec/PDL-NetCDF-4.08/blib/lib/x86_64-linux-thread-multi /h
ome/amec/PDL-NetCDF-4.08/blib/lib/5.8.4 /home/amec/PDL-NetCDF-4.08/blib/lib/5.8.
3 /home/amec/PDL-NetCDF-4.08/blib/lib/5.8.2 /home/amec/PDL-NetCDF-4.08/blib/lib/
5.8.1 /home/amec/PDL-NetCDF-4.08/blib/lib/5.8.0 /home/amec/PDL-NetCDF-4.08/blib/
lib /home/amec/PDL-NetCDF-4.08/blib/arch/5.8.5/x86_64-linux-thread-multi /home/a
mec/PDL-NetCDF-4.08/blib/arch/5.8.5 /home/amec/PDL-NetCDF-4.08/blib/arch/x86_64-
linux-thread-multi /home/amec/PDL-NetCDF-4.08/blib/arch/5.8.4 /home/amec/PDL-Net
CDF-4.08/blib/arch/5.8.3 /home/amec/PDL-NetCDF-4.08/blib/arch/5.8.2 /home/amec/P
DL-NetCDF-4.08/blib/arch/5.8.1 /home/amec/PDL-NetCDF-4.08/blib/arch/5.8.0 /home/
amec/PDL-NetCDF-4.08/blib/arch /usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi
/usr/lib/perl5/5.8.5 /usr/lib64/perl5/site_perl/5.8.5/x86_64-linux-thread-multi
/usr/lib64/perl5/site_perl/5.8.4/x86_64-linux-thread-multi /usr/lib64/perl5/site
_perl/5.8.3/x86_64-linux-thread-multi /usr/lib64/perl5/site_perl/5.8.2/x86_64-li
nux-thread-multi /usr/lib64/perl5/site_perl/5.8.1/x86_64-linux-thread-multi /usr
/lib64/perl5/site_perl/5.8.0/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/
5.8.5 /usr/lib/perl5/site_perl/5.8.4 /usr/lib/perl5/site_perl/5.8.3 /usr/lib/per
l5/site_perl/5.8.2 /usr/lib/perl5/site_perl/5.8.1 /usr/lib/perl5/site_perl/5.8.0
/usr/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.5/x86_64-linux-thread
-multi /usr/lib64/perl5/vendor_perl/5.8.4/x86_64-linux-thread-multi /usr/lib64/p
erl5/vendor_perl/5.8.3/x86_64-linux-thread-multi /usr/lib64/perl5/vendor_perl/5.
8.2/x86_64-linux-thread-multi /usr/lib64/perl5/vendor_perl/5.8.1/x86_64-linux-th
read-multi /usr/lib64/perl5/vendor_perl/5.8.0/x86_64-linux-thread-multi /usr/lib
/perl5/vendor_perl/5.8.5 /usr/lib/perl5/vendor_perl/5.8.4 /usr/lib/perl5/vendor_
perl/5.8.3 /usr/lib/perl5/vendor_perl/5.8.2 /usr/lib/perl5/vendor_perl/5.8.1 /us
r/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl .) at /home/amec/PDL-Ne
tCDF-4.08/blib/lib/PDL/NetCDF.pm line 1063
# Looks like you planned 46 tests but ran 3.
# Looks like you failed 1 test of 3 run.
# Looks like your test exited with 2 just after 3.
t/01-Netcdf3.t .. Dubious, test returned 2 (wstat 512, 0x200)
Failed 44/46 subtests
t/02-Netcdf4.t .. 1/20
# Failed test 'use PDL::NetCDF;'
# at t/02-Netcdf4.t line 8.
# Tried to use 'PDL::NetCDF'.
# Error: Can't load '/home/amec/PDL-NetCDF-4.08/blib/arch/auto/PDL/NetCDF/N
etCDF.so' for module PDL::NetCDF: /home/amec/PDL-NetCDF-4.08/blib/arch/auto/PDL/
NetCDF/NetCDF.so: undefined symbol: __pgdbg_stub at /usr/lib64/perl5/5.8.5/x86_6
4-linux-thread-multi/DynaLoader.pm line 230.
# at (eval 24) line 2
# Compilation failed in require at (eval 24) line 2.
# BEGIN failed--compilation aborted at (eval 24) line 2.
Bareword "PDL::NetCDF::isNetcdf4" not allowed while "strict subs" in use at t/02
-Netcdf4.t line 14.
Bareword "PDL::NetCDF::isNetcdf4" not allowed while "strict subs" in use at t/02
-Netcdf4.t line 13.
Execution of t/02-Netcdf4.t aborted due to compilation errors.
# Looks like you planned 20 tests but ran 1.
# Looks like you failed 1 test of 1 run.
# Looks like your test exited with 255 just after 1.
t/02-Netcdf4.t .. Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 20/20 subtests
Test Summary Report
-------------------
t/01-Netcdf3.t (Wstat: 512 Tests: 3 Failed: 1)
Failed test: 2
Non-zero exit status: 2
Parse errors: Bad plan. You planned 46 tests but ran 3.
t/02-Netcdf4.t (Wstat: 65280 Tests: 1 Failed: 1)
Failed test: 1
Non-zero exit status: 255
Parse errors: Bad plan. You planned 20 tests but ran 1.
Files=2, Tests=4, 0 wallclock secs ( 0.04 usr 0.01 sys + 0.48 cusr 0.06
csys = 0.59 CPU)
Result: FAIL
Failed 2/2 test programs. 2/4 subtests failed.
make: *** [test_dynamic] Error 255
----> Here's the compilation information:
I've done the following:
Moved previous "libnetcdf" files in /usr/local/lib to /usr/local/lib/BACKUP
Configuration/Compilation settings for NetCDF 4.1.1
(/home/WRF/WRF_Source/netcdf-4.4.1)
CC pgcc
FC pgf90
F77 pgf77
F90 pgf90
CPPFLAGS -DNDEBUG -fPIC
./configure --disable-netcdf-4 -disable-cxx
Where --disable-netcdf-4 -- Do not include HDF5 in compilation
--disable-cxx -- Do not compile C++ library
make check install
... appears to work OK, except that one (1) of the tests in "make check"
fails:
*** Test: varm on URL:
http://test.opendap.org/opendap/data/nc/coads_climatology
.nc
*** Testing: stride case 1
*** nc function failure: -33 NetCDF: Not a valid ID
FAIL: test_varm3
================================================
1 of 4 tests failed
Please report to support-netcdf@xxxxxxxxxxxxxxxx
... not sure what this test is...
Anyway, the following files are available in /home/WRF/WRF_Source/netcdf-4.1.1
./ncdump/ncdump
./ncgen/ncgen
./ncgen3/ncgen3
... and ...
/usr/local/lib/libnetcdf.a
/usr/local/lib/libnetcdf.la
... plus several other files under /home/WRF/WRF_Source/netcdf-4.1.1
________________________________________
From: Doug Hunt [dhunt@xxxxxxxx]
Sent: Monday, April 18, 2011 12:28 PM
To: Bryan, David
Subject: RE: module PDL::NetCDF not on CPAN
Hi David: It looks like you are on a 64 bit Linux machine, but your
netcdf installation was not compiled with -fPIC. This is a hassle.
For my local installation, I compile netcdf like this:
./configure --prefix=/where/to/install/netcdf \
CPPFLAGS="-DNDEBUG -fPIC"
make
make install
You may have to adapt your ./configure line according to your local
needs--the important thing is the -fPIC.
Regards,
Doug
dhunt@xxxxxxxx
Software Engineer
UCAR - COSMIC, Tel. (303) 497-2611
On Mon, 18 Apr 2011, Bryan, David wrote:
Doug,
Thanks for the information. Below you'll see the log from the make step. Do
you have any suggestions about this?
Thanks,
David
/usr/bin/perl -I/usr/lib64/perl5/site_perl/5.8.5/x86_64-linux-thread-multi
"-MPDL::PP qw/PDL::NetCDF PDL::NetCDF NetCDF/" netcdf.pd
cp NetCDF.pm blib/lib/PDL/NetCDF.pm
/usr/bin/perl /usr/lib/perl5/5.8.5/ExtUtils/xsubpp -typemap
/usr/lib/perl5/5.8.5/ExtUtils/typemap -typemap
/usr/lib64/perl5/site_perl/5.8.5/x86_64-linux-thread-multi/PDL/Core/typemap.pdl -typemap
typemap NetCDF.xs > NetCDF.xsc && mv NetCDF.xsc NetCDF.c
gcc -c -I/usr/lib64/perl5/site_perl/5.8.5/x86_64-linux-thread-multi/PDL/Core -I/usr/local/include/
-Dbool=int -g -O2 -g -pipe -m64 -DVERSION=\"4.08\" -DXS_VERSION=\"4.08\" -fPIC
"-I/usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi/CORE" NetCDF.c
In file included from
/usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi/CORE/perl.h:1813,
from NetCDF.xs:6:
/usr/lib64/perl5/5.8.5/x86_64-linux-thread-multi/CORE/handy.h:85:1: warning:
"bool" redefined
<command line>:1:1: warning: this is the location of the previous definition
Running Mkbootstrap for PDL::NetCDF ()
chmod 644 NetCDF.bs
rm -f blib/arch/auto/PDL/NetCDF/NetCDF.so
gcc -shared NetCDF.o -o blib/arch/auto/PDL/NetCDF/NetCDF.so \
-L/usr/local/lib/ -lnetcdf \
/usr/bin/ld: /usr/local/lib//libnetcdf.a(attr.o): relocation R_X86_64_32S
against `a local symbol' can not be used when making a shared object; recompile
with -fPIC
/usr/local/lib//libnetcdf.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
make: *** [blib/arch/auto/PDL/NetCDF/NetCDF.so] Error 1
________________________________________
From: Doug Hunt [dhunt@xxxxxxxx]
Sent: Friday, April 15, 2011 7:04 PM
To: Bryan, David
Cc: rt-cpan-admin@xxxxxxxxxxxxxxxxx
Subject: Re: module PDL::NetCDF not on CPAN
Hi David: I've been having problems getting PDL::NetCDF indexed on CPAN
for a while now, and don't know how to fix them.
For the moment, you can just download the
http://search.cpan.org/CPAN/authors/id/D/DH/DHUNT/PDL-NetCDF-4.08.tar.gz
tarball and then:
tar -xvzf PDL-NetCDF-4.08.tar.gz
cd PDL-NetCDF-4.08
export NETCDF_LIBDIR=/where/netcdf/libs/are
export NETCDF_INCDIR=/where/netcdf/include/files/are
perl Makefile.PL
make
make test
make install
Regards,
Doug
dhunt@xxxxxxxx
Software Engineer
UCAR - COSMIC, Tel. (303) 497-2611
On Fri, 15 Apr 2011, Bryan, David wrote:
Iʼve tried installing PDL::NetCDF module with CPAN but I get the message that
itʼs not available from CPAN. Can you address
this?
Thanks,
David Bryan
Wind Modeler
AMEC Earth and Environmental
133 Crosbie Rd
St. John's, NL A1B 4A5
Canada
709-724-1929 ext. 321
fax: 709-722-7353
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