Build issue: Fatal Error: "Reading module ‘piodarray’ at line 1600 column 3: Unexpected EOF"

[Anuj]

Dear all,
I checked and run ./check_input_data --download script and downlaoded the datasets, and then confirmed again whether any data remains to download or not, using ./check_input_data script.
And to build the case run ./case.build but getting these errors. please help me regarding this.
Looking for your responce.

Here i have attached the pio.bldlog.200101-123812 file >> (full log file i have attached as a text file please check )

-- The C compiler identification is GNU 7.4.0
-- The Fortran compiler identification is GNU 7.4.0
-- Check for working C compiler: /usr/local/bin/mpicc
-- Check for working C compiler: /usr/local/bin/mpicc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working Fortran compiler: /usr/local/bin/mpif90
-- Check for working Fortran compiler: /usr/local/bin/mpif90 -- works
-- Detecting Fortran compiler ABI info
-- Detecting Fortran compiler ABI info - done
-- Checking whether /usr/local/bin/mpif90 supports Fortran 90
-- Checking whether /usr/local/bin/mpif90 supports Fortran 90 -- yes
-- Found NetCDF_C: /usr/local/lib/libnetcdf.so
-- Checking NetCDF version
-- Checking NetCDF version - 4.6.1./*!<
-- Checking whether NetCDF has parallel support
-- Checking whether NetCDF has parallel support - no
-- Looking for nc_set_log_level
-- Looking for nc_set_log_level - not found
-- Found NetCDF_Fortran: /usr/local/lib/libnetcdff.so
-- MPI Fortran module detected and enabled.
-- Configuring done
-- Generating done
-- Build files have been written to: /home/wcl/CLM_5_run/CLMOutput/test7/bld/gnu/mpich/nodebug/nothreads/pio/pio1
gmake: Leaving directory '/home/wcl/CLM_5_run/CLMOutput/test7/bld/gnu/mpich/nodebug/nothreads/pio/pio1'
cat: Filepath: No such file or directory
cat: Srcfiles: No such file or directory
Building PIO with netcdf support
CMake Warning at pio/CMakeLists.txt:48 (MESSAGE):
Warning: Not building with PNetcdf - cannot run all regression tests.


CMake Warning:
Manually-specified variables were not used by the project:

CMAKE_CXX_FLAGS
GPTL_PATH
PIO_ENABLE_TESTS
gmake -j 4
pio/CMakeFiles/pio.dir/build.make:233: recipe for target 'pio/CMakeFiles/pio.dir/piolib_mod.F90.o' failed
gmake[3]: Leaving directory '/home/wcl/CLM_5_run/CLMOutput/test7/bld/gnu/mpich/nodebug/nothreads/pio/pio1'
pio/CMakeFiles/pio.dir/build.make:249: recipe for target 'pio/CMakeFiles/pio.dir/piolib_mod.F90.o.provides' failed
gmake[2]: Leaving directory '/home/wcl/CLM_5_run/CLMOutput/test7/bld/gnu/mpich/nodebug/nothreads/pio/pio1'
CMakeFiles/Makefile2:88: recipe for target 'pio/CMakeFiles/pio.dir/all' failed
gmake[1]: Leaving directory '/home/wcl/CLM_5_run/CLMOutput/test7/bld/gnu/mpich/nodebug/nothreads/pio/pio1'
Makefile:86: recipe for target 'all' failed

f951: Warning: Nonexistent include directory ‘/home/wcl/CLM_5_run/CLMOutput/test7/bld/gnu/mpich/nodebug/nothreads/mct/noesmf/c1a1l1i1o1r1g1w1e1/include’ [-Wmissing-include-dirs]
f951: Warning: Nonexistent include directory ‘/home/wcl/CLM_5_run/CLMOutput/test7/bld/gnu/mpich/nodebug/nothreads/mct/noesmf/c1a1l1i1o1r1g1w1e1/include’ [-Wmissing-include-dirs]
f951: Fatal Error: Reading module ‘piodarray’ at line 1600 column 3: Unexpected EOF
compilation terminated.
gmake[3]: *** [pio/CMakeFiles/pio.dir/piolib_mod.F90.o] Error 1
gmake[2]: *** [pio/CMakeFiles/pio.dir/piolib_mod.F90.o.provides] Error 2
gmake[1]: *** [pio/CMakeFiles/pio.dir/all] Error 2
gmake: *** [all] Error 2

f951: Warning: Nonexistent include directory /home/wcl/CLM_5_run/CLMOutput/test7/bld/gnu/mpich/nodebug/nothreads/mct/noesmf/c1a1l1i1o1r1g1w1e1/include [-Wmissing-include-dirs]
f951: Fatal Error: Reading module piodarray at line 1600 column 3: Unexpected EOF
compilation terminated.
gmake[3]: *** [pio/CMakeFiles/pio.dir/piolib_mod.F90.o] Error 1
gmake[2]: *** [pio/CMakeFiles/pio.dir/piolib_mod.F90.o.provides] Error 2
gmake[1]: *** [pio/CMakeFiles/pio.dir/all] Error 2
gmake: *** [all] Error 2

 

[sacks]

Can you please provide information on the version of the code you are using (running git describe and ./manage_externals/checkout_externals --status --verbose from the top level of your code checkout), as well as the other information under the "Always" heading in this post. Also, have you confirmed that you get the same error if you do a fresh checkout of the code and create a new case from scratch?

 

[Anuj]

Can you please provide information on the version of the code you are using (running git describe and ./manage_externals/checkout_externals --status --verbose from the top level of your code checkout), as well as the other information under the "Always" heading in this post. Also, have you confirmed that you get the same error if you do a fresh checkout of the code and create a new case from scratch?

Dear sir,
As per your suggestion here i have provided the information of version etc. Please suggest where i am getting error. Looking for your response.

wcl@wcl:~/clm5.0/cime/scripts$ git describe
cime5.6.25

wcl@wcl:~/clm5.0$ ./manage_externals/checkout_externals --status
Processing externals description file : Externals.cfg
Processing externals description file : Externals_CISM.cfg
Processing externals description file : Externals_CLM.cfg
Checking status of externals: cism, source_cism, clm, fates, ptclm, mosart, cime, rtm,
M ./cime
./components/cism
./components/cism/source_cism
./components/mosart
./components/rtm
./src/fates
./tools/PTCLM

wcl@wcl:~/clm5.0$ ./manage_externals/checkout_externals --verbose
Processing externals description file : Externals.cfg
Processing externals description file : Externals_CISM.cfg
Processing externals description file : Externals_CLM.cfg
Checking status of externals: cism, source_cism, clm, fates, ptclm, mosart, cime, rtm,
M ./cime
modified sandbox, on cime5.6.25
./components/cism
clean sandbox, on release-cesm2.0.04
./components/cism/source_cism
clean sandbox, on release-cism2.1.03
./components/mosart
clean sandbox, on release-cesm2.0.03
./components/rtm
clean sandbox, on release-cesm2.0.03
./src/fates
clean sandbox, on fates_s1.21.0_a7.0.0_br_rev2
./tools/PTCLM
clean sandbox, on PTCLM2_180611
----------------------------------------------------------------------
The external repositories labeled with 'M' above are not in a clean state.

The following are two options for how to proceed:

(1) Go into each external that is not in a clean state and issue either
an 'svn status' or a 'git status' command. Either revert or commit
your changes so that all externals are in a clean state. (Note,
though, that it is okay to have untracked files in your working
directory.) Then rerun checkout_externals.

(2) Alternatively, you do not have to rely on checkout_externals. Instead, you
can manually update out-of-sync externals (labeled with 's' above)
as described in the configuration file Externals.cfg.


The external repositories labeled with '?' above are not under version
control using the expected protocol. If you are sure you want to switch
protocols, and you don't have any work you need to save from this
directory, then run "rm -rf [directory]" before re-running the
checkout_externals tool.

----------------------------------------------------------------------

 

[Anuj]

Can you please provide information on the version of the code you are using (running git describe and ./manage_externals/checkout_externals --status --verbose from the top level of your code checkout), as well as the other information under the "Always" heading in this post. Also, have you confirmed that you get the same error if you do a fresh checkout of the code and create a new case from scratch?

Dear sir,
As per your suggestion here i have provided the information of version etc. Please suggest where i am getting error. Looking for your response.

>>Here I have attached the log files and steps using for case creation to case.build (file = clm_used_steps1.txt)<<

wcl@wcl:~/clm5.0/cime/scripts$ git describe
cime5.6.25

wcl@wcl:~/clm5.0$ ./manage_externals/checkout_externals --status
Processing externals description file : Externals.cfg
Processing externals description file : Externals_CISM.cfg
Processing externals description file : Externals_CLM.cfg
Checking status of externals: cism, source_cism, clm, fates, ptclm, mosart, cime, rtm,
M ./cime
./components/cism
./components/cism/source_cism
./components/mosart
./components/rtm
./src/fates
./tools/PTCLM

wcl@wcl:~/clm5.0$ ./manage_externals/checkout_externals --verbose
Processing externals description file : Externals.cfg
Processing externals description file : Externals_CISM.cfg
Processing externals description file : Externals_CLM.cfg
Checking status of externals: cism, source_cism, clm, fates, ptclm, mosart, cime, rtm,
M ./cime
modified sandbox, on cime5.6.25
./components/cism
clean sandbox, on release-cesm2.0.04
./components/cism/source_cism
clean sandbox, on release-cism2.1.03
./components/mosart
clean sandbox, on release-cesm2.0.03
./components/rtm
clean sandbox, on release-cesm2.0.03
./src/fates
clean sandbox, on fates_s1.21.0_a7.0.0_br_rev2
./tools/PTCLM
clean sandbox, on PTCLM2_180611
----------------------------------------------------------------------
The external repositories labeled with 'M' above are not in a clean state.

The following are two options for how to proceed:

(1) Go into each external that is not in a clean state and issue either
an 'svn status' or a 'git status' command. Either revert or commit
your changes so that all externals are in a clean state. (Note,
though, that it is okay to have untracked files in your working
directory.) Then rerun checkout_externals.

(2) Alternatively, you do not have to rely on checkout_externals. Instead, you
can manually update out-of-sync externals (labeled with 's' above)
as described in the configuration file Externals.cfg.


The external repositories labeled with '?' above are not under version
control using the expected protocol. If you are sure you want to switch
protocols, and you don't have any work you need to save from this
directory, then run "rm -rf [directory]" before re-running the
checkout_externals tool.

----------------------------------------------------------------------

##Setps and machine info

#Other Configuration
> machine -ubuntu 18.04 (64 bit)
a)The C compiler identification is GNU 7.4.0
b)The Fortran compiler identification is GNU 7.4.0
c)Netcdf 4.6.1

compiler using= gnu

#Created Case
>sudo ./create_newcase --case /home/wcl/CLM_5_run/case/test6 --compset IHistClm50BgcCrop --res f09_g17 --mach wcl

#Setting up case
>cd /home/wcl/CLM_5_run/case/test7/
>sudo./case.setup

#Building case
>./check_input_data
>./check_input_data --download
>sudo ./case.build
>>>>when i am trying to build getting error

 

[sacks]

Thank you for providing this additional information. I'm still not sure what the error is. The following information would help us to help you further:

1. Have you tried starting over, doing a new clone of the code (followed by ./manage_externals/checkout_externals, then copying your config_compilers and config_machines files into the new location) and creating a new case? I'd like to get confirmation that you run into the same problem a second time, and if you do, I'd like to see the pio bldlog file from the first time you try to build with a fresh case. (If it's too much of a pain to do a fresh clone, you can skip that step, but please at least try a new case from the beginning.)

2. Can you do this without using sudo? Normally you shouldn't need sudo when building and running CESM, and I'm wondering if there are permission errors here, for example, if some of the build process is being run with sudo, but for some reason some part of it isn't.

3. Can you rerun git describe from the top level – that is from the directory containing cime, components, etc. (the same directory where you ran manage_externals/checkout_externals)

4. Can you give the output from running git status from your cime directory? I want to see if there are any changes there besides config_machines.xml and config_compilers.xml.