[Met_help] fm theo carter dubai re: failure during make
John Halley Gotway
johnhg at rap.ucar.edu
Wed May 27 06:29:09 MDT 2009
Theo,
Great. I'm really glad you got it all to work! I'm sorry that it ended up taking so much effort. I realize that MET could be improved by setting up a nice configure/build script for it. But did
you find anything in particular in the compilation process that should be changed or improved?
We actually have run MET using CentOS (not sure which version number) in the past. When we give the tutorial on MET as part of the WRF-Tutorial twice a year, the classroom machines run CentOS. We
build MET on them using the GNU gfortran/g++ compilers. I wonder what the difference was between those systems and yours that led to the issues you were seeing?
Well I'm glad it's running for you. Please let me know if any questions come up or if you run across any issues or suggestions for improvement in the online tutorial.
Thanks,
John
Theo Carter wrote:
>
> Hi John,
>
>
>
> Thanks for your help!
>
>
>
> Naah - I had download the BUFRLIB from the link on your
> tutorial/website each time - dont even have WRF or WRF var on the PC
> yet. And I used your how-to each time.
>
>
>
> But!! I had done a re-install as a last resort of the OS and everything
> from scratch - only this time I put on the new Intel 11 fortran and C
> compilers, and used that for the installations. Funnily enough, I kept
> getting more warnings throughout, but in the old end the MET Tools
> executables all built!!! Am working my way through the tutorial now.
>
>
>
> If anyone needs a how-to for building using Intel 11 compilers on a
> CentOS 5.3, I kept notes as I went along of the important choices etc.
>
>
>
> Thanks again,
>
> Theo
>
>> Date: Tue, 26 May 2009 07:13:31 -0600
>> From: johnhg at rap.ucar.edu
>> To: thibidottwo at hotmail.com
>> CC: met_help at ucar.edu
>> Subject: Re: [Met_help] fm theo carter dubai re: failure during make
>>
>> Theo,
>>
>> In looking back at our messages back and forth, I still want to make sure you're using the correct version of BUFRLIB - and not one that's distributed with WRF-Var.
>>
>> Here's an excerpt from an earlier message:
>>
>>>>>>>> For compiling MET, be sure to use the version that's distributed by
>>>>>>>> NCEP: http://www.nco.ncep.noaa.gov/sib/decoders/BUFRLIB
>>>>>>>>
>>>>>>>> The following 3 commands should work to compile this version of BUFRLIB
>>>>>>>> with gcc/gfortran:
>>>>>>>> gcc -c -DUNDERSCORE *.c
>>>>>>>> gfortran -c -DUNDERSCORE -fno-second-underscore *.f *.F
>>>>>>>> ar crv libbufr.a *.o
>>>>>>>>
>>>>>>>> These were taken from the METv2.0 Online Tutorial:
>>>>>>>> http://www.dtcenter.org/met/users/support/online_tutorial/METv2.0/compilation/req_libs.php
>>>>>>>>
>>>>>>>> Please try rebuilding BUFRLIB (ignore the warning messages) and recompiling MET to see if that fixes
>>>>>>>> the problem.
>> Once you're sure you're using the right version of BUFRLIB, are you still having any compilation problems with MET?
>>
>> Thanks,
>> John
>>
>>
>> Theo Carter wrote:
>>> Hi John,
>>>
>>> Did get a touch further than yesterday - can now find the BUFRLIB libraries, but am still getting crashes within. On your website you say someone has built this using RHEL, can you ask if I can copy their library and try that maybe?
>>>
>>> I have built the BUFR library as you suggested commands-wise, and it still comes with the following:
>>>
>>>
>>>
>>> *** Finished Making grid_stat application ***
>>>
>>> *** Making pb2nc application ***
>>>
>>> /usr/bin/g++ -c pb2nc_Conf.cc -Wall -Wshadow -static \
>>> -I../../lib
>>> /usr/bin/gfortran -c numpbmsg.f -Wall -Wshadow -static -ff2c
>>> /usr/bin/gfortran -c openpb.f -Wall -Wshadow -static -ff2c
>>> /usr/bin/gfortran -c readpb.f -Wall -Wshadow -static -ff2c
>>> /usr/bin/gfortran -c dumppb.f -Wall -Wshadow -static -ff2c
>>>
>>>
>>> /usr/bin/g++ -o pb2nc pb2nc.cc pb2nc_Conf.o numpbmsg.o openpb.o readpb.o dumppb.o \
>>> -Wall -Wshadow -static -DMET_BASE=\"/wrf/METv2.0\" \
>>> -I../../lib -I/usr/local/include -I/usr/local/include/gsl -I/wrf/libraries/BUFRLIB \
>>> -L../../lib -L/usr/local/lib -L/usr/local/lib/gsl -L/wrf/libraries/BUFRLIB -L/usr/lib/gcc/i386-redhat-linux/3.4.6 \
>>> -lbufr -lvx_pb_util \
>>> -lvx_met_util -lvx_analysis_util -lvx_wrfdata -lvx_met_util \
>>> -lvx_contable -lvx_grib_classes \
>>> -lvx_econfig -lvx_gsl_prob -lgsl \
>>> -lvx_plot_util -lvx_render -lvx_pxm -lvx_color -lvx_ps -lvx_afm \
>>> -lvx_data_grids -lvx_gnomon -lvx_nav -lvx_cal -lvx_util -lvx_math -lm \
>>> -lnetcdf_c++ -lnetcdf \
>>> -lg2c -lgfortran
>>> /wrf/libraries/BUFRLIB/libbufr.a(datelen.o): In function `datelen_':
>>> datelen.f:(.text+0x51): undefined reference to `for_write_int_fmt'
>>> /wrf/libraries/BUFRLIB/libbufr.a(openbf.o): In function `openbf_':
>>> openbf.f:(.text+0x4f): undefined reference to `for_cpstr'
>>> openbf.f:(.text+0x91): undefined reference to `for_cpstr'
>>> openbf.f:(.text+0x11b): undefined reference to `for_write_int_fmt'
>>> openbf.f:(.text+0x13e): undefined reference to `for_write_int_fmt_xmit'
>>> openbf.f:(.text+0x19f): undefined reference to `for_write_int_fmt'
>>> etc..............................
>>>
>>>
>>>
>>>
>>> Cheers and thanks for the help,
>>> Theo
>>>
>>>
>>>
>>>
>>>> Date: Fri, 8 May 2009 06:52:24 -0600
>>>> From: johnhg at rap.ucar.edu
>>>> To: thibidottwo at hotmail.com; met_help at ucar.edu
>>>> Subject: Re: [Met_help] fm theo carter dubai re: failure during make
>>>>
>>>> Theo,
>>>>
>>>> If you look closely, those are just warning messages from BUFRLIB. I get them too when compiling with "gfortran", but they won't cause you any problems. Warnings are generally OK - it's the errors
>>>> you should worry about.
>>>>
>>>> You're right that the compiler is complaining that it can't find the file "gsl_cdf.h". Here's what I'd suggest doing:
>>>>
>>>> cd /wrf/libraries/gsl-1.9
>>>> make clean
>>>> ./configure --prefix=`pwd`
>>>> make
>>>> make install
>>>>
>>>> Next, in the top-level MET Makefile, make sure that the following is set:
>>>> GSL_BASE = /wrf/libraries/gsl-1.9
>>>> GSL_INCS = -I$(GSL_BASE)/include
>>>> GSL_LIBS = -L$(GSL_BASE)/lib
>>>>
>>>> And then try rebuilding MET.
>>>>
>>>> Hope that helps.
>>>>
>>>> John
>>>>
>>>> Theo Carter wrote:
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> Hi John,
>>>>>
>>>>> I did put in the file you sent into BUFRLIB, however, I still got the following errors:
>>>>>
>>>>> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
>>>>> [root at localhost BUFRLIB]# gcc -c -DUNDERSCORE *.c
>>>>> [root at localhost BUFRLIB]# gfortran -c -DUNDERSCORE -fno-second-underscore *.f *.F
>>>>> In file nemock.f:77
>>>>>
>>>>> IF(NEMO(I:I).EQ.CHRSET(J:J)) GOTO 10
>>>>> 1
>>>>> In file nemock.f:81
>>>>>
>>>>>
>>>>> 2
>>>>> Warning: Obsolete: GOTO at (1) jumps to END of construct at (2)
>>>>> In file stndrd.f:202
>>>>>
>>>>> GOTO 10
>>>>> 1
>>>>> In file stndrd.f:207
>>>>>
>>>>>
>>>>> 2
>>>>> Warning: Obsolete: GOTO at (1) jumps to END of construct at (2)
>>>>> [root at localhost BUFRLIB]#
>>>>> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
>>>>>
>>>>> I did carry on and install the rest of the libraries etc, and then ran make on mettools version 2 and got to the following point where it is looking for something in the gsl libraries - but the location is strange?
>>>>>
>>>>> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
>>>>>
>>>>> *** Making vx_contable Library ***
>>>>>
>>>>> /usr/bin/g++ vx_contable.cc -Wall -Wshadow -static -c -I..
>>>>> /usr/bin/g++ vx_contable_stats.cc -Wall -Wshadow -static -c -I.. -I/wrf/libraries/gsl-1.9/include -I/usr/local/include
>>>>> In file included from ../vx_gsl_prob/vx_gsl_prob.h:17,
>>>>> from ../vx_met_util/compute_ci.h:16,
>>>>> from ../vx_met_util/vx_met_util.h:17,
>>>>> from vx_contable_stats.cc:21:
>>>>> ../vx_gsl_prob/gsl_cdf.h:17:25: error: gsl/gsl_cdf.h: No such file or directory
>>>>> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
>>>>>
>>>>> I did a 'locate' and found the library here??
>>>>>
>>>>> [wrf at localhost gsl-1.9]$ locate gsl_cdf.h
>>>>> /wrf/METv2.0/lib/vx_gsl_prob/gsl_cdf.h
>>>>> /wrf/libraries/gsl-1.9/cdf/gsl_cdf.h
>>>>> [wrf at localhost gsl-1.9]$
>>>>>
>>>>> How do I get past this problem?
>>>>>
>>>>> Cheers and thanks for the help so far,
>>>>> Theo
>>>>>
>>>>>
>>>>>> Date: Wed, 6 May 2009 15:24:18 -0600
>>>>>> Subject: RE: [Met_help] fm theo carter dubai re: failure during make
>>>>>> From: johnhg at rap.ucar.edu
>>>>>> To: thibidottwo at hotmail.com
>>>>>> CC: met_help at ucar.edu
>>>>>>
>>>>>> Theo,
>>>>>>
>>>>>> Good news. When I compile the current version of BUFRLIB using
>>>>>> gcc/gfortran, I see the exact same warning and error messages. In fact,
>>>>>> when I use gfortran on the latest version of Debian Linux (Lenny), I see
>>>>>> even more warning messages.
>>>>>>
>>>>>> I've also been in touch with BUFRLIB support about this, and they're aware
>>>>>> of the issue with compiling BUFRLIB with the GNU compilers. There is a
>>>>>> very simple fix to get that file "nvnwin.f" to compile without error.
>>>>>> However, I don't believe that you need it to get MET working.
>>>>>>
>>>>>> Try compiling BUFRLIB using the following 3 commands:
>>>>>> gcc -c -DUNDERSCORE *.c
>>>>>> gfortran -c -DUNDERSCORE -fno-second-underscore *.f *.F
>>>>>> ar crv libbufr.a *.o
>>>>>>
>>>>>> Ignore the warnings and error, and then try building MET. I believe it
>>>>>> should work fine.
>>>>>>
>>>>>> If you'd like to get rid of that BUFRLIB error message, you're welcome to
>>>>>> replace your version of the file "BUFRLIB/nvnwin.f" with the version I've
>>>>>> attached. It includes the simple fix which should get rid of that error
>>>>>> message from gfortran.
>>>>>>
>>>>>> Thanks and good luck,
>>>>>> John
>>>>>>
>>>>>>> Hi John,
>>>>>>>
>>>>>>> I have tried to install BUFRLIB on fedora 10 and centos 5.3 now, and in
>>>>>>> both cases I get the same following problem, have you come across this
>>>>>>> before. It is disheartening to fail at the first hurdle like this. My
>>>>>>> system is standard desktop (two different ones, here at home and at work).
>>>>>>>
>>>>>>> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
>>>>>>> [root at localhost BUFRLIB]# whereis gcc
>>>>>>> gcc: /usr/bin/gcc /usr/lib/gcc /usr/libexec/gcc
>>>>>>> /usr/share/man/man1/gcc.1.gz
>>>>>>> [root at localhost BUFRLIB]# whereis gfortran
>>>>>>> gfortran: /usr/bin/gfortran /usr/share/man/man1/gfortran.1.gz
>>>>>>> [root at localhost BUFRLIB]# gcc -c -DUNDERSCORE *.c
>>>>>>> [root at localhost BUFRLIB]# gfortran -c -DUNDERSCORE -fno-second-underscore
>>>>>>> *.f *.
>>>>>>> F
>>>>>>> In file nemock.f:77
>>>>>>>
>>>>>>> IF(NEMO(I:I).EQ.CHRSET(J:J)) GOTO 10
>>>>>>> 1
>>>>>>> In file nemock.f:81
>>>>>>>
>>>>>>>
>>>>>>> 2
>>>>>>> Warning: Obsolete: GOTO at (1) jumps to END of construct at (2)
>>>>>>> In file nvnwin.f:84
>>>>>>>
>>>>>>> INVN(I) = BMISS
>>>>>>> 1
>>>>>>> Error: Arithmetic overflow converting REAL(8) to INTEGER(4) at (1)
>>>>>>> In file stndrd.f:202
>>>>>>>
>>>>>>> GOTO 10
>>>>>>> 1
>>>>>>> In file stndrd.f:207
>>>>>>>
>>>>>>>
>>>>>>> 2
>>>>>>> Warning: Obsolete: GOTO at (1) jumps to END of construct at (2)
>>>>>>> [root at localhost BUFRLIB]#
>>>>>>>
>>>>>>> xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
>>>>>>>
>>>>>>> Any help you can give will be great - I sent off a query to the bufrlib
>>>>>>> helpdesk on their website, but have had no reply.
>>>>>>> Thanks,
>>>>>>> Theo Carter, Forecaster, Dubai Met Office.
>>>>>>>
>>>>>>>> Date: Wed, 29 Apr 2009 06:38:24 -0600
>>>>>>>> From: johnhg at rap.ucar.edu
>>>>>>>> To: thibidottwo at hotmail.com
>>>>>>>> CC: met_help at ucar.edu
>>>>>>>> Subject: Re: [Met_help] fm theo carter dubai re: failure during make
>>>>>>>>
>>>>>>>> Theo,
>>>>>>>>
>>>>>>>> Based on that error message, I'd guess that there's an issue with your
>>>>>>>> version of BUFRLIB.
>>>>>>>>
>>>>>>>> Where did you obtain the version of BUFRLIB you're using? Is by any
>>>>>>>> chance part of WRF-Var? If so, that version may or may not work.
>>>>>>>>
>>>>>>>> For compiling MET, be sure to use the version that's distributed by
>>>>>>>> NCEP: http://www.nco.ncep.noaa.gov/sib/decoders/BUFRLIB
>>>>>>>>
>>>>>>>> The following 3 commands should work to compile this version of BUFRLIB
>>>>>>>> with gcc/gfortran:
>>>>>>>> gcc -c -DUNDERSCORE *.c
>>>>>>>> gfortran -c -DUNDERSCORE -fno-second-underscore *.f *.F
>>>>>>>> ar crv libbufr.a *.o
>>>>>>>>
>>>>>>>> These were taken from the METv2.0 Online Tutorial:
>>>>>>>> http://www.dtcenter.org/met/users/support/online_tutorial/METv2.0/compilation/req_libs.php
>>>>>>>>
>>>>>>>> Please try rebuilding BUFRLIB and recompiling MET to see if that fixes
>>>>>>>> the problem.
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>> John Halley Gotway
>>>>>>>> johnhg at ucar.edu
>>>>>>>>
>>>>>>>>
>>>>>>>> Theo Carter wrote:
>>>>>>>>> Hi,
>>>>>>>>>
>>>>>>>>> I wonder if you can help or if you have come across this problem
>>>>>>>> before? While running make on a very generic basic Pentium 4 32-bit
>>>>>>>> using gfortran, gcc and g++ compilers within a CentOS 5.3 OS (RHEL 5
>>>>>>>> clone) the build fails with the following output.
>>>>>>>>> /wrf/extralibraries/libbufr.a(ufbevn.o): In function `ufbevn_':
>>>>>>>>> ufbevn.f:(.text+0xa6e): undefined reference to `nvnwin_'
>>>>>>>>> collect2: ld returned 1 exit status
>>>>>>>>> make[3]: *** [pb2nc] Error 1
>>>>>>>>> make[2]: *** [all] Error 2
>>>>>>>>> make[1]: *** [targets] Error 2
>>>>>>>>> make: *** [all] Error 2
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> BUFRLIB was built on the same machine.
>>>>>>>>>
>>>>>>>>> I then end up with only gen_poly_mask, grid_stat, mode and pcp_combine
>>>>>>>> executables in my /bin.
>>>>>>>>> Any help would be appreciated,
>>>>>>>>> Thanks,
>>>>>>>>> Theo Carter
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> ------------------------------------------------------------------------
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> Met_help mailing list
>>>>>>>>> Met_help at mailman.ucar.edu
>>>>>>>>> http://mailman.ucar.edu/mailman/listinfo/met_help
>
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