Building PNetCDF for WRF on ANL LCRC

[Wei-Keng Liao]

Glad to hear that using OpenMPI 4.0.3 resolves the problem.
Thanks for reporting it.

Wei-keng

> On Apr 24, 2020, at 12:48 PM, Robert Fritzen <rfritzen1 at niu.edu> wrote:
> 
> Good Afternoon,
> 
> I installed a version of openmpi-4.0.3 with gcc and the compilation and tests ran successfully.
> 
> Thank you for your help!
> Robert
> 
> -----Original Message-----
> From: Wei-Keng Liao <wkliao at northwestern.edu> 
> Sent: Thursday, April 23, 2020 11:54 PM
> To: Robert Fritzen <rfritzen1 at niu.edu>
> Subject: Re: Building PNetCDF for WRF on ANL LCRC
> 
> Hi, Robert
> 
> File ‘large_coalesce.log' shows an error came from OpenMPI when calling function MPI_File_set_view. The version of OpenMPI you are using is 3.1.3, which is old and may contain bugs. I wonder if you can find a newer version on bebop. If you checked the release log of latest OpenMPI, you should be able to find bug reports related to MPI-IO that have been fixed since 3.1.3.
> 
> Wei-keng
> 
>> On Apr 23, 2020, at 11:32 PM, Robert Fritzen <rfritzen1 at niu.edu> wrote:
>> 
>> Good Evening,
>> 
>> I have attached the two files to the email. Please let me know if anything else is required.
>> 
>> Thanks!
>> Robert
>> 
>> -----Original Message-----
>> From: Wei-Keng Liao <wkliao at northwestern.edu>
>> Sent: Wednesday, April 22, 2020 6:28 PM
>> To: Robert Fritzen <rfritzen1 at niu.edu>
>> Cc: parallel-netcdf at mcs.anl.gov
>> Subject: Re: Building PNetCDF for WRF on ANL LCRC
>> 
>> Hi, Robert
>> 
>> Please send me the following 2 files
>> config.log and
>> test/largefile/large_coalesce.log
>> 
>> They may contain information about the errors.
>> 
>> FYI. When building PnetCDF 1.12.1, you need not set those environment variables. Your configure command can simply be the following.
>> ./configure --prefix=$WRF_LIBRARIES --enable-large-file-test
>> 
>> Wei-keng
>> 
>>> On Apr 22, 2020, at 3:45 PM, Robert Fritzen <rfritzen1 at niu.edu> wrote:
>>> 
>>> Good Afternoon PNetCDF Team,
>>> 
>>> I have been trying to compile PNetCDF for use in the WRF model on 
>>> Bebop (LCRC - ANL) following the following guide for compilation 
>>> (https://urldefense.com/v3/__http://www.hpcadvisorycouncil.com/pdf/WR
>>> F_v3.8*20Installation_Best_Pr__;JQ!!Dq0X2DkFhyF93HkjWTBQKhk!FM81CZq46
>>> pxFHjqlukk-EJzi_-AB7vHKr89ecoB-ViIIfeAhOt4TcKc86sa7TOP8I3cI$
>>> actices.pdf), however I am using the GNU compiler suite instead of 
>>> the intel compiler suite. (The loaded modules on bebop are:
>>> gcc/7.3.0-xyzezhj and openmpi/3.1.3-obi56bx)
>>> 
>>> My issue is with the large file tests which fails:
>>> 
>>> make[4]: Entering directory `/lcrc/project/ACPC/WRF/libs/lib_files/pnetcdf-1.12.1/test/largefile'
>>> PASS: large_files
>>> PASS: large_var
>>> PASS: large_dims_vars_attrs
>>> PASS: high_dim_var
>>> PASS: tst_cdf5_begin
>>> FAIL: large_coalesce
>>> PASS: bigrecords
>>> PASS: tst_flarge
>>> 
>>> The other required libraries prior to PNetCDF compilation (zlib, szip, libpng, jpeg, jasper, and HDF5 (Parallel)) fully compiled and tested without errors. The export statements I am using are:
>>> 
>>> export CC=mpicc
>>> export CXX=mpicxx
>>> export FC=mpif90
>>> export F77=mpif90
>>> export F90=mpif90
>>> export OMPI_MPICC=gcc
>>> export OMPI_MPICXX=g++
>>> export OMPI_MPIFC=gfortran
>>> export OMPI_MPIF77=gfortran
>>> export OMPI_MPIF90=gfortran
>>> export CFLAGS=’-g -O2 -fPIC’
>>> export CXXFLAGS=’-g -O2 -fPIC’
>>> export FFLAGS=’-g -fPIC’
>>> export FCFLAGS=’-g -fPIC’
>>> export FLDFLAGS=’-fPIC’
>>> export F90LDFLAGS=’-fPIC’
>>> export LDFLAGS=’-fPIC’
>>> 
>>> I am running the configure command as such:
>>> 
>>> ./configure --prefix=$WRF_LIBRARIES --enable-fortran 
>>> --enable-large-file-test
>>> 
>>> $WRF_LIBRARIES is the path to where my libraries are being installed on LCRC.
>>> 
>>> Any assistance to help successfully compile PNetCDF would be appreciated. Thanks!
>>> Robert
>>> 
>>> ~
>>> Robert C. Fritzen
>>> Ph.D. Student (NIU)
>>> M.S. Geography & Atmospheric Sciences (NIU, 2017) B.S. Atmospheric 
>>> Sciences (Unv. Illinois Urbana-Champaign, 2013) Office Location: 
>>> Davis Hall 209 ~
>> 
>> <config.log><large_coalesce.log>
>