compilation errors: No executables

All things involving the setup (compiling, NetCDF, etc.) of the WRF Model itself.

compilation errors: No executables

Postby alberto » Thu Apr 04, 2013 5:35 am

Hello guys,

I am having problem when building or compiling my wrf.
This is what I have done so far:
My zlib i got through my synaptics manager and it is installed as shared library I think cuz it is under /usr/local.. and then its respective files in /lib, /include /bin.

For netcdf 4.2
I did :
>> ./configure FC=gfortran
and then in my .bashrc file I snet the environment varaible:
export NETCDF=/usr/local

I did the same for NETCDF fortran libraries to get netcdf.inc

all were instaled in /usr/local and their respective locations /bin , /lib, /include

I have gfortran adn gcc

I also have the JASPERLIB AND JASPERINC variables defined ans instaled in
/usr/local/lib_compiled_with_gfortran/jasper-install/lib
/usr/local/lib_compiled_with_gfortran/jasper-install/include

I got the jasper from the compilation script from the FAQ in the WRF users page.

I also set my LD_LIBRARY_PATH
export LD_LIBRARY_PATH=/usr/local/lib:${LD_LIBRARY_PATH}

Ok..

So now I try with wrf..... I go and inside the wrfv3 folder I type
>> ./configure
I then get the set of option, I hade not problem with NETCDF and JASPER cuz I changed the configure.wrf file to get the grib2 data types as well

So the options, 23 is sfor gfortran with gcc and serial

then 1 for simple nesting option
then ./compile em_real >&compile.log
so I can obtain my log as well..... it takes a while but finally it makes the log and I see errors , but moft o them say (igored). Then I CHEKC MY MAIN FOLDER TO FIND THE EXECUTABLES and the procees only reached until making the .f90 files. So they are basicaly frotran files but not compiled yet.



I I have tried this many many times like 10 time aloready. I tried installing netcdf ina separate folder as /usr/local/netcdf-gfortran

but nothing changed, the same thing happened.


Can somebody help me out and tell me what or earth is going on with my procedure.


Thanks in advance guys, and I hope to see responses.
alberto
 
Posts: 54
Joined: Mon Mar 25, 2013 7:48 am

Re: compilation errors: No executables

Postby scaine2 » Sun Apr 07, 2013 10:42 pm

Is there a specific reason you want grib2 support in WRF?
the standard way of using grib2 support is with WPS. Which will mean you can ingest grib2 files.

If you include your zlib and jasper libraries with WRF, it still does not use them unless you modify some of the config files.
If you really need grib2 support for WRF (i.e. you want to output the data in grib2) I suggest first compiling
WRF without grib2 support, to make sure you can build it, then move on to having grib2 support.

In my experience, you will want to compile netcdf with the following arguements
./configure --prefix="path_you_choose" --disable-netcdf4 --disable-dap
if you do not use the --prefix option it should go to /usr/local i believe

when you are done you need to set
export NETCDF="path_you_choose"
export NETCDF_LIB="path_you_choose/lib"
export NETCDF_INC="path_you_choose/include"

This should be all you need to get WRF to compile,
if you have an error in the compilation you might want to replace
DM_FC = mpif90 -f90=$(SFC)
with
DM_FC =mpif90

and
DM_CC = mpicc -cc$(SCC) -DMPI2_SUPPORT
with
DM_CC = mpicc -DMPI2_SUPPORT

make sure you always start fresh when you are recompiling netcdf and WRF
i.e. do one of
make clean, make dist clean, ./clean -a , which ever is required for your program

Good luck,
Simon
scaine2
 
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Joined: Wed Jan 16, 2013 6:25 pm

Re: compilation errors: No executables

Postby alberto » Thu Apr 11, 2013 9:59 am

I will try that when I get home, one question though.. the changes you have just said are in my configure file, am I right??

thanks for the response =)
regards,
Alberto Striedinger
alberto
 
Posts: 54
Joined: Mon Mar 25, 2013 7:48 am

Re: compilation errors: No executables

Postby alberto » Thu Apr 11, 2013 8:00 pm

I just realized that my configuration of netcdf does not recognize the disable options of netcdf 4: Here is hte partial result from the ./configure::

--------astriedinger@s117555 ~/Downloads/Libraries/NETCDF_files/netcdf-4.2.1.1 $ ./configure FC=gfortran --disable-netcfd4 --disable-dap
configure: WARNING: unrecognized options: --disable-netcfd4
configure: netCDF 4.2.1.1
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking target system type... x86_64-unknown-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
configure: checking user options
checking whether a win32 DLL is desired... no
checking whether a NCIO_MINBLOCKSIZE was specified... 256
checking if fsync support is enabled... yes
checking whether extra valgrind tests should be run... no
checking whether we should try to build netCDF-4... yes
checking whether reading of HDF4 SD files is to be enabled... no
checking whether to fetch some sample HDF4 files from Unidata ftp site to test HDF4 reading (requires wget)... no
checking whether parallel I/O for classic and 64-bit offset files using parallel-netcdf is to be enabled... no
checking whether extra example tests should be run... no
checking whether parallel IO tests should be run... no
checking whether a default chunk size in bytes was specified... 4194304
checking whether a maximum per-variable cache size for HDF5 was specified... 67108864
checking whether a number of chunks for the default per-variable cache was specified... 10
checking whether a default file cache size for HDF5 was specified... 4194304
checking whether a default file cache maximum number of elements for HDF5 was specified... 1009
checking whether a default cache preemption for HDF5 was specified... 0.75
checking whether netCDF-4 logging is enabled... no
checking whether cdmremote client is to be built... no
checking whether DAP client is to be built... no
checking for style of include used by make... GNU
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking dependency style of gcc... gcc3
checking for curl_easy_setopt in -lcurl... no
checking whether dap remote testing should be enabled (default on)... no
checking whether netcdf4 group names should be enabled (default on)... configure: dap groups disabled because dap disabled or netcdf-4 disabled
no
checking whether the time-consuming dap tests should be enabled (default off)... no
checking whether netCDF extra tests should be run (developers only)... no
checking whether FFIO will be used... no
checking whether examples should be built... yes
checking whether v2 netCDF API should be built... yes
checking whether the ncgen/ncdump/nccopy should be built... yes
checking whether test should be built and run... yes
checking whether large file (> 2GB) tests should be run... no
checking whether benchmaks should be run (experimental)... no
checking whether extreme numbers should be used in tests... yes
checking where to put large temp files if large file tests are run... .
configure: finding C compiler
checking for gcc... (cached) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking dependency style of gcc... (cached) gcc3
checking whether gcc and cc understand -c and -o together... yes
checking for an ANSI C-conforming const... yes
checking whether a CURLOPT_KEYPASSWD is defined... no
configure: setting up libtool
checking how to print strings... printf
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for ar... ar
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for mt... mt
checking if mt is a manifest tool... no
checking how to run the C preprocessor... gcc -E
checking for ANSI C header files... ^Castriedinger@s117555 ~/Downloads/Libraries/NETCDF_files/netcdf-4.2.1.1 $
alberto
 
Posts: 54
Joined: Mon Mar 25, 2013 7:48 am

Re: compilation errors: No executables

Postby bassline » Fri Apr 12, 2013 6:15 am

Try to not disable netcdf 4. Maybe you should disable f90... see ./configure --help for other options.

What's your WRF version?
bassline
 
Posts: 55
Joined: Tue Jan 29, 2013 3:25 pm

Re: compilation errors: No executables

Postby alberto » Fri Apr 12, 2013 11:23 am

the lastest version 3.4.1
that is teh one I am trying to install in my personal notebook. why disabeling the f-90, what does it impley??? fortran 90 capabilities or something?? I am using gfrotran, wouldnt that compromise something...(sorry for typos).

regards,
Alberto
alberto
 
Posts: 54
Joined: Mon Mar 25, 2013 7:48 am

Re: compilation errors: No executables

Postby alberto » Fri Apr 12, 2013 3:39 pm

HUm,,, so If I want to instal it again but it is already in the shaerd library, /usr/local, is it safe if I just manualy remove all the files from lib, bin, include, ...? and the configure and compile? I just read my configure script, the delault mode with with no netcdf4 ability, so what is why the option is not recognized.... I will try to just configure and compile fro the source I have and it willl I supose replace the existing files in the /usr/local.... and then apply the flags you just said. the configure wrf and compile to see the results... I will get back and post ... :? :)
alberto
 
Posts: 54
Joined: Mon Mar 25, 2013 7:48 am

Re: compilation errors: No executables

Postby bassline » Mon Apr 15, 2013 5:37 am

You can export your NETCDF path as described in WRF's manual.

The '--disable-f90' flag won't try to build the netCDF Fortran 90 API.

Regards
bassline
 
Posts: 55
Joined: Tue Jan 29, 2013 3:25 pm

Re: compilation errors: No executables

Postby alberto » Tue Apr 16, 2013 9:36 am

Ok thanks, I will have it in consideration for another occasion. WRF help responded and they told me to change some flags in my configure script, then save it, clean and re compile. This is the asnwer they provided:

Alberto,


In your configure script, you have this line:


FCOPTIM = -O3 -ftree-vectorize -ftree-loop-linear -funroll-loops


Try removing the -ftree-loop-linear so that it will read like this:


FCOPTIM = -O3 -ftree-vectorize -funroll-loops


Once you do that, save that file as something else (like configure.wrf.save). Then do a clean -a. After that, copy that file back to the original


cp configure.wrf.save configure.wrf


Then recompile. Do not reconfigure. See if that helps at all.


~wrfhelp~

------it did.... I just asked them why did it help...
alberto
 
Posts: 54
Joined: Mon Mar 25, 2013 7:48 am

Re: compilation errors: No executables

Postby bassline » Fri Apr 19, 2013 5:27 am

alberto wrote:Ok thanks, I will have it in consideration for another occasion. WRF help responded and they told me to change some flags in my configure script, then save it, clean and re compile. This is the asnwer they provided:

Alberto,


In your configure script, you have this line:


FCOPTIM = -O3 -ftree-vectorize -ftree-loop-linear -funroll-loops


Try removing the -ftree-loop-linear so that it will read like this:


FCOPTIM = -O3 -ftree-vectorize -funroll-loops


Once you do that, save that file as something else (like configure.wrf.save). Then do a clean -a. After that, copy that file back to the original


cp configure.wrf.save configure.wrf


Then recompile. Do not reconfigure. See if that helps at all.


~wrfhelp~

------it did.... I just asked them why did it help...


mmmm... interesting!!!

maybe your GCC wasn't configured with --with-ppl and --with-cloog. So, you had to remove this option!!!

Did you compiled or installed via repository?

[]'s
bassline
 
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