[Met_help] Compiling METv2.0
John Halley Gotway
johnhg at rap.ucar.edu
Tue Jul 7 09:12:18 MDT 2009
Ed,
OK, that's what I'd thought. It looks like "pgio_errno" (and all those other undefined symbols) aren't defined in any of those libraries. It looks like there's a problem with the installation of
this version of the PGI compilers. In fact, I found another machine here which does have PGI version 8.0-4 and did find that the library "libpgc.a" does exist with those symbols. And that library is
missing from yours.
You could try the following to see if/where that library does exist:
cd /opt/pgi/linux86
find ./ -name libpgc.a
Or you could try building MET with an older version of the PGI compilers. You may have better luck. Look in /opt/pgi/linux86 to see if there's an earlier version you could use. If not, you could
also try using the GNU "g++/gfortran" compilers if those are present on your machine.
John
Ed Warnken wrote:
> Hey John,
>
> Ok that seemed to work so here is the file.
>
> John Halley Gotway wrote:
>> Ed,
>>
>> Ah, I think when you called the script command it launched a new shell and defaulted to "sh". Try the commands in a little different order:
>>
>> script ~/check_libs.log
>> csh
>> cd /opt/pgi/linux86/8.0-2/lib
>> foreach file (`ls *.a`)
>> echo "*********************** $file ***********************"
>> nm $file | grep "pgio_errno"
>> end
>> CNTRL-D
>>
>>
>> ... OR if that still doesn't work, try this using a different syntax ...
>>
>> script ~/check_libs.log
>> cd /opt/pgi/linux86/8.0-2/lib
>> for file in `ls *.a`
>> do
>> echo "*********************** $file ***********************"
>> nm $file | grep "pgio_errno"
>> done
>> CNTRL-D
>>
>> And then send me that file "~/check_libs.log".
>>
>> Thanks,
>> John
>>
>>
>> Ed Warnken wrote:
>>
>>> John,
>>>
>>> When I copy the line foreach file I get a syntax error message in the
>>> attached file.
>>>
>>> John Halley Gotway wrote:
>>>
>>>> Ed,
>>>>
>>>> So there's still a bunch of undefined references in that compilation log. I pulled out the undefined symbol from each error messages and found that all of them are defined in the library file
>>>> "libpgc.a". That's the library we're trying to link to with when we say "-lpgc". And this is for version 7.1-5, so it's possible that's it's different for version 8.
>>>>
>>>> These errors are rather unusual. I believe that the compiler usually automatically links in these types of standard libraries. Can you tell me, have you used this version of the compiler to compile
>>>> other code? I'm wondering if there may be an issue in how the compiler is installed - which is something you'd need a sys admin's help with.
>>>>
>>>> We could try to locate where one of these undefined symbols is defined for your compiler.
>>>> Try running the following commands:
>>>>
>>>> csh
>>>> script ~/check_libs.log
>>>> cd /opt/pgi/linux86/8.0-2/lib
>>>> foreach file (`ls *.a`)
>>>> echo "*********************** $file ***********************"
>>>> nm $file | grep "pgio_errno"
>>>> end
>>>> CNTRL-D
>>>>
>>>> And then send me the file ~/check_libs.log. That should tell me if and where those undefined symbols are actually defined.
>>>>
>>>> Thanks,
>>>> John
>>>>
>>>>
>>>> Ed Warnken wrote:
>>>>
>>>>
>>>>> Morning John,
>>>>>
>>>>> Well I added the three libraries but it said it couldn't find the pgc
>>>>> one. So for grins I removed just that one and here is the log file.
>>>>>
>>>>> John Halley Gotway wrote:
>>>>>
>>>>>
>>>>>> Ed,
>>>>>>
>>>>>> OK, now we're running into errors I haven't seen before. I'll need to get
>>>>>> a hold of PGI version 8 to do some more testing.
>>>>>>
>>>>>> In your top-level MET Makefile, please try adding three libraries to the
>>>>>> "FC_LIBS" line. So change "FC_LIBS",
>>>>>>
>>>>>> FROM: FC_LIBS = -L/opt/pgi/linux86/8.0-2/lib -lpgftnrtl -lrt -lpthread
>>>>>> TO: FC_LIBS = -L/opt/pgi/linux86/8.0-2/lib -lpgftnrtl -lrt -lpthread
>>>>>> -lpgsse1 -lpgsse2 -lpgc
>>>>>>
>>>>>> And then try recompiling MET. Please let me know how it goes. It looks
>>>>>> like we may need to update the default MET Makefile for PGI version 8.
>>>>>>
>>>>>> Thanks,
>>>>>> John
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>> Hey John,
>>>>>>>
>>>>>>> Well that was weird because I saw that as well the pgf90 was still in
>>>>>>> there. I checked the time on the libbufr.a file and it was the time I
>>>>>>> created it with ar crv, but I didn't delete the .o and .a files so
>>>>>>> that's probably where I messed up. Anyway here is the new make_met.log
>>>>>>> file and I don't see pgf90 in it all.
>>>>>>>
>>>>>>> John Halley Gotway wrote:
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>> Ed,
>>>>>>>>
>>>>>>>> So you (1) rebuilt BUFRLIB using pgf77 and then (2) tried rebuilding
>>>>>>>> MET.
>>>>>>>> But you still saw the same errors.
>>>>>>>>
>>>>>>>> Those errors really look like they're still coming from BUFRLIB being
>>>>>>>> compiled with pgf90. In fact, I tried myself compiling BUFRLIB using
>>>>>>>> pgf90 and then linking a build of MET to that version of BUFRLIB. I was
>>>>>>>> able to reproduce exactly the same error messages you're seeing.
>>>>>>>>
>>>>>>>> Here's what you can do. Execute the command:
>>>>>>>> nm /usr/local/lib/libbufr.a
>>>>>>>>
>>>>>>>> That will list the contents of the BUFRLIB library to which MET is
>>>>>>>> linking. If you see a bunch of "pgf90" strings in there, you'll know
>>>>>>>> that
>>>>>>>> BUFRLIB still isn't compiled properly.
>>>>>>>>
>>>>>>>> If that's the case try recompiling BUFRLIB again:
>>>>>>>> cd /usr/local/src/BUFRLIB
>>>>>>>> rm *.o *.a
>>>>>>>> pgcc -c -DUNDERSCORE *.c
>>>>>>>> pgf77 -c -DUNDERSCORE -Mnosecond_underscore *.f *.F
>>>>>>>> ar crv libbufr.a *.o
>>>>>>>> cp libbufr.a /usr/local/lib/.
>>>>>>>>
>>>>>>>> And then try recompiling MET again. I'm wondering if you did rebuild it
>>>>>>>> using pgf77, but forget to copy it over to /usr/local/lib. That's where
>>>>>>>> you've set in the Makefile for the linker to look.
>>>>>>>>
>>>>>>>> Let me know how it goes. It looks like there may be some other errors
>>>>>>>> after the BUFRLIB ones that we'll need to address. But let's fix this
>>>>>>>> BUFRLIB issue first.
>>>>>>>>
>>>>>>>> John
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>> Hey John,
>>>>>>>>>
>>>>>>>>> Well I got the same errors so I'm also attaching the MET Makefile so
>>>>>>>>> you
>>>>>>>>> can see if I'm messing up in that too.
>>>>>>>>>
>>>>>>>>> Ed
>>>>>>>>>
>>>>>>>>> John Halley Gotway wrote:
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>> Ed,
>>>>>>>>>>
>>>>>>>>>> No, you shouldn't have to. MET doesn't use the Fortran interface to
>>>>>>>>>> NetCDF and there's no Fortran in GSL... so those compilations should
>>>>>>>>>> be
>>>>>>>>>> fine.
>>>>>>>>>>
>>>>>>>>>> You should just need to recompile BUFRLIB and then MET.
>>>>>>>>>>
>>>>>>>>>> Just let me know if you run across any more errors.
>>>>>>>>>>
>>>>>>>>>> Thanks,
>>>>>>>>>> John
>>>>>>>>>>
>>>>>>>>>> Ed Warnken wrote:
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> Hi John,
>>>>>>>>>>>
>>>>>>>>>>> Just wondering if I also have to re-compile netcdf and gsl?
>>>>>>>>>>>
>>>>>>>>>>> John Halley Gotway wrote:
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>> Ed,
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks for sending the MET compilation log. It makes it a lot
>>>>>>>>>>>> easier
>>>>>>>>>>>> to diagnose the problem.
>>>>>>>>>>>>
>>>>>>>>>>>> You should be using a Fortan-77 compiler instead of a Fortran-90
>>>>>>>>>>>> compiler. So in the top-level MET Makefile, try setting "FC" to the
>>>>>>>>>>>> "pgf77" compiler. Also, you'll need to recompile BUFRLIB using
>>>>>>>>>>>> the same "pgf77" compiler. You could use the following 3 commands
>>>>>>>>>>>> to
>>>>>>>>>>>> compile BUFRLIB:
>>>>>>>>>>>>
>>>>>>>>>>>> pgcc -c -DUNDERSCORE *.c
>>>>>>>>>>>> pgf77 -c -DUNDERSCORE -Mnosecond_underscore *.f *.F
>>>>>>>>>>>> ar crv libbufr.a *.o
>>>>>>>>>>>>
>>>>>>>>>>>> These are taken from the METv2.0 online tutorial:
>>>>>>>>>>>> http://www.dtcenter.org/met/users/support/online_tutorial/METv2.0/compilation/req_libs.php
>>>>>>>>>>>>
>>>>>>>>>>>> I've compiled MET using PGI versions 6 and 7, but not version 8 - to
>>>>>>>>>>>> which we don't have access yet. I'll be interested to hear how it
>>>>>>>>>>>> goes.
>>>>>>>>>>>>
>>>>>>>>>>>> Thanks and good luck,
>>>>>>>>>>>> John Halley Gotway
>>>>>>>>>>>> johnhg at ucar.edu
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>> Ed Warnken wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>>> Hello,
>>>>>>>>>>>>>
>>>>>>>>>>>>> I'm running into issues when compiling METv2.0. I've attached the
>>>>>>>>>>>>> make_met.log file to this email for you. The system I'm trying
>>>>>>>>>>>>> install
>>>>>>>>>>>>> this on is RHEL5 32bit. I've compiled the BUFRLIB, GSL-1.12 and
>>>>>>>>>>>>> netcdf-3.6.3 using the portland (ver 8.0-2) fortran compilers.
>>>>>>>>>>>>> Thank
>>>>>>>>>>>>> you for your time.
>>>>>>>>>>>>>
>>>>>>>>>>>>> Ed Warnken
>>>>>>>>>>>>> NOAA/PSD
>>>>>>>>>>>>> Phone 303-497-7264
>>>>>>>>>>>>>
>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>> Met_help mailing list
>>>>>>>>>>>>> Met_help at mailman.ucar.edu
>>>>>>>>>>>>> http://mailman.ucar.edu/mailman/listinfo/met_help
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>
>>>>>>
>>>>>>
More information about the Met_help
mailing list