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Build Error

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Y

Yue_Ma

New member
Hi，
I am first trying to compiling the MPAS following tutorial practice guide. While I build init_atmosphere core, I put
Code: 
make gfortran CORE=init_atmosphere PRECISION=single
I get
Code: 
( make all \
"FC_PARALLEL = mpif90" \
"CC_PARALLEL = mpicc" \
"CXX_PARALLEL = mpicxx" \
"FC_SERIAL = gfortran" \
"CC_SERIAL = gcc" \
"CXX_SERIAL = g++" \
"FFLAGS_PROMOTION = -fdefault-real-8 -fdefault-double-8" \
"FFLAGS_OPT = -O3 -m64 -ffree-line-length-none -fconvert=big-endian -ffree-form" \
"CFLAGS_OPT = -O3 -m64" \
"CXXFLAGS_OPT = -O3 -m64" \
"LDFLAGS_OPT = -O3 -m64" \
"FFLAGS_DEBUG = -g -m64 -ffree-line-length-none -fconvert=big-endian -ffree-form -fbounds-check -fbacktrace -ffpe-trap=invalid,zero,overflow" \
"CFLAGS_DEBUG = -g -m64" \
"CXXFLAGS_DEBUG = -O3 -m64" \
"LDFLAGS_DEBUG = -g -m64" \
"FFLAGS_OMP = -fopenmp" \
"CFLAGS_OMP = -fopenmp" \
"CORE = init_atmosphere" \
"DEBUG = " \
"USE_PAPI = " \
"OPENMP = " \
"CPPFLAGS =  -D_MPI -DUNDERSCORE" )
make[1]: Entering directory '/home/lennovo/MPAS/MPAS-Model-6.1'
cd src; make FC="mpif90" \
                 CC="mpicc" \
                 CXX="mpicxx" \
                 SFC="gfortran" \
                 SCC="gcc" \
                 LINKER="mpif90" \
                 CFLAGS="-O3 -m64 "-DSINGLE_PRECISION"" \
                 CXXFLAGS="-O3 -m64 "-DSINGLE_PRECISION"" \
                 FFLAGS="-O3 -m64 -ffree-line-length-none -fconvert=big-endian -ffree-form" \
                 LDFLAGS="-O3 -m64" \
                 RM="rm -f" \
                 CPP="cpp -P -traditional" \
                 CPPFLAGS="-D_MPI -DUNDERSCORE -DCORE_INIT_ATMOSPHERE -DMPAS_NAMELIST_SUFFIX=init_atmosphere -DMPAS_EXE_NAME=init_atmosphere_model "-DSINGLE_PRECISION" -DMPAS_NATIVE_TIMERS -DMPAS_GIT_VERSION="unknown"" \
                 LIBS="-L/usr/local/ParallelIO/lib -lpio -L/usr/local/PnetCDF/lib -lpnetcdf -L/usr/local/NETCDF/lib -lnetcdff -lnetcdf" \
                 CPPINCLUDES="-I/usr/local/ParallelIO/include -I/usr/local/PnetCDF/include -I/usr/local/NETCDF/include" \
                 FCINCLUDES="-I/usr/local/ParallelIO/include -I/usr/local/PnetCDF/include -I/usr/local/NETCDF/include" \
                 CORE="init_atmosphere"\
                 AUTOCLEAN="false" \
                 GEN_F90="false" \
                 NAMELIST_SUFFIX="init_atmosphere" \
                 EXE_NAME="init_atmosphere_model"
make[2]: Entering directory '/home/lennovo/MPAS/MPAS-Model-6.1/src'
( cd external; make FC="mpif90" SFC="gfortran" CC="mpicc" SCC="gcc" FFLAGS="-O3 -m64 -ffree-line-length-none -fconvert=big-endian -ffree-form" CFLAGS="-O3 -m64 -DSINGLE_PRECISION" CPP="cpp -P -traditional" NETCDF="/usr/local/NETCDF" CORE="init_atmosphere" all )
make[3]: Entering directory '/home/lennovo/MPAS/MPAS-Model-6.1/src/external'
( cd esmf_time_f90; make FC="mpif90 -O3 -m64 -ffree-line-length-none -fconvert=big-endian -ffree-form" CPP="cpp -P -traditional" CPPFLAGS="-D_MPI -DUNDERSCORE -DCORE_INIT_ATMOSPHERE -DMPAS_NAMELIST_SUFFIX=init_atmosphere -DMPAS_EXE_NAME=init_atmosphere_model -DSINGLE_PRECISION -DMPAS_NATIVE_TIMERS -DMPAS_GIT_VERSION=unknown -DHIDE_MPI" GEN_F90=false )
make[4]: Entering directory '/home/lennovo/MPAS/MPAS-Model-6.1/src/external/esmf_time_f90'
ar -ru libesmf_time.a *.o
ar: `u' modifier ignored since `D' is the default (see `U')
make[4]: Leaving directory '/home/lennovo/MPAS/MPAS-Model-6.1/src/external/esmf_time_f90'
( cd ezxml; make )
make[4]: Entering directory '/home/lennovo/MPAS/MPAS-Model-6.1/src/external/ezxml'
rm -f *.o *.i
make -j 1 library
make[5]: Entering directory '/home/lennovo/MPAS/MPAS-Model-6.1/src/external/ezxml'
mpicc -O3 -m64 -DSINGLE_PRECISION -D_MPI -DUNDERSCORE -DCORE_INIT_ATMOSPHERE -DMPAS_NAMELIST_SUFFIX=init_atmosphere -DMPAS_EXE_NAME=init_atmosphere_model -DSINGLE_PRECISION -DMPAS_NATIVE_TIMERS -DMPAS_GIT_VERSION=unknown -c ezxml.c
make[5]: Leaving directory '/home/lennovo/MPAS/MPAS-Model-6.1/src/external/ezxml'
make[4]: Leaving directory '/home/lennovo/MPAS/MPAS-Model-6.1/src/external/ezxml'
make[3]: Leaving directory '/home/lennovo/MPAS/MPAS-Model-6.1/src/external'
( cd framework; make CPPFLAGS="-D_MPI -DUNDERSCORE -DCORE_INIT_ATMOSPHERE -DMPAS_NAMELIST_SUFFIX=init_atmosphere -DMPAS_EXE_NAME=init_atmosphere_model -DSINGLE_PRECISION -DMPAS_NATIVE_TIMERS -DMPAS_GIT_VERSION=unknown" CPPINCLUDES="-I/usr/local/ParallelIO/include -I/usr/local/PnetCDF/include -I/usr/local/NETCDF/include" all ) 
make[3]: Entering directory '/home/lennovo/MPAS/MPAS-Model-6.1/src/framework'
rm -f mpas_io.o mpas_io.mod
mpif90 -D_MPI -DUNDERSCORE -DCORE_INIT_ATMOSPHERE -DMPAS_NAMELIST_SUFFIX=init_atmosphere -DMPAS_EXE_NAME=init_atmosphere_model -DSINGLE_PRECISION -DMPAS_NATIVE_TIMERS -DMPAS_GIT_VERSION=unknown -O3 -m64 -ffree-line-length-none -fconvert=big-endian -ffree-form -c mpas_io.F -I/usr/local/ParallelIO/include -I/usr/local/PnetCDF/include -I/usr/local/NETCDF/include -I/usr/local/ParallelIO/include -I/usr/local/PnetCDF/include -I/usr/local/NETCDF/include -I../external/esmf_time_f90
mpas_io.F:30:43:

    integer, parameter :: MPAS_INT_FILLVAL = NF_FILL_INT
                                           1
Error: Parameter ‘nf_fill_int’ at (1) has not been declared or is a variable, which does not reduce to a constant expression
mpas_io.F:31:53:

    character, parameter :: MPAS_CHAR_FILLVAL = achar(NF_FILL_CHAR)
                                                     1
Error: Parameter ‘nf_fill_char’ at (1) has not been declared or is a variable, which does not reduce to a constant expression
mpas_io.F:42:54:

    real (kind=RKIND), parameter :: MPAS_REAL_FILLVAL = NF_FILL_FLOAT
                                                      1
Error: Parameter ‘nf_fill_float’ at (1) has not been declared or is a variable, which does not reduce to a constant expression
mpas_io.F:566:79:

 io_ierr = PIO_def_dim(handle % pio_file, trim(dimname), PIO_unlimited, new_dimlist_node % dimhandle % dimid)
                                                                     1
Error: Symbol ‘pio_unlimited’ at (1) has no IMPLICIT type
mpas_io.F:278:37:

             pio_mode = PIO_64BIT_DATA
                                     1
Error: Symbol ‘pio_64bit_data’ at (1) has no IMPLICIT type
Makefile:119: recipe for target 'mpas_io.o' failed
make[3]: *** [mpas_io.o] Error 1
make[3]: Leaving directory '/home/lennovo/MPAS/MPAS-Model-6.1/src/framework'
Makefile:31: recipe for target 'frame' failed
make[2]: *** [frame] Error 2
make[2]: Leaving directory '/home/lennovo/MPAS/MPAS-Model-6.1/src'
Makefile:694: recipe for target 'mpas_main' failed
make[1]: *** [mpas_main] Error 2
make[1]: Leaving directory '/home/lennovo/MPAS/MPAS-Model-6.1'
Makefile:214: recipe for target 'gfortran' failed
make: *** [gfortran] Error 2
how can I build init_atmosphere core?
 
Sorry for the late reply! Which version of the PIO library are you using? If you're using the newer PIO 2.x library, you'll need to add "USE_PIO2=true" to your build command.

In case you're using the older PIO 1.x library, this could be an issue with the netCDF library. Which versions of the parallel-netCDF and netCDF libraries are you using?
 
What does the output look like from Test #4 on the web pgae you linked for compiling WRF? It is a little surprising that, if the gcc and gfortran compilers are both from the GNU 7.3.0 release, that they wouldn't be able to create compatible object files.
 
I have installed multiple versions of gcc and i set wrong permissions. Now it is fine.
But i meet a new problem. While I build init_atmosphere core,
Code: 
/usr/bin/ld: /home/ubuntu/MPAS/mpas-libs/lib/libmpi.a(ad_iwrite.o): undefined reference to symbol 'aio_read64@@GLIBC_2.2.5'
//lib/x86_64-linux-gnu/librt.so.1: error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status
Makefile:18: recipe for target 'mpas' failed
make[2]: *** [mpas] Error 1
make[2]: Leaving directory '/home/ubuntu/MPAS/MPAS-Model-master/src'
Makefile:694: recipe for target 'mpas_main' failed
make[1]: *** [mpas_main] Error 2
make[1]: Leaving directory '/home/ubuntu/MPAS/MPAS-Model-master'
Makefile:214: recipe for target 'gfortran' failed
make: *** [gfortran] Error 2

It looks like MPI can't find some lib? If that is the case, where should i add '-lm' ?
 
How was your MPI library installed? Was it compiled from source using the GNU 7.3.0 compilers? It might be worth seeing whether the attached MPI test program compiles and runs correctly with
Code: 
mpif90 -O3 -m64 -ffree-line-length-none -fconvert=big-endian -ffree-form -o mpi_test mpitest.f90
The above command-line uses the same Fortran compiler flags as are used when compiling MPAS.
 

Attachments

  • mpitest.f90
    1.7 KB · Views: 77
Thanks for your test program. This test program runs correctly and gets an executable file ‘mpi_test’. Now MPAS compiles correctly!
I get packages from http://www2.mmm.ucar.edu/people/duda/files/mpas/sources/ compiled by GNU 5.4.0 compilers or GNU 7.3.0. Of course, i simple modify the 'iolib_installation.sh' , adding
Code: 
# Download packages
wget -P ${LIBSRC} http://www2.mmm.ucar.edu/people/duda/files/mpas/sources/mpich-3.2.tar.gz    #mpich
wget -P ${LIBSRC} http://www2.mmm.ucar.edu/people/duda/files/mpas/sources/zlib-1.2.8.tar.gz   #zlib
wget -P ${LIBSRC} http://www2.mmm.ucar.edu/people/duda/files/mpas/sources/hdf5-1.8.19.tar.bz2 #hdf5
wget -P ${LIBSRC} http://www2.mmm.ucar.edu/people/duda/files/mpas/sources/parallel-netcdf-1.8.1.tar.gz  #pnetcdf
wget -P ${LIBSRC} http://www2.mmm.ucar.edu/people/duda/files/mpas/sources/netcdf-4.4.1.1.tar.gz #netcdf-c
wget -P ${LIBSRC} http://www2.mmm.ucar.edu/people/duda/files/mpas/sources/netcdf-fortran-4.4.4.tar.gz #netcdf-fortran
Both version 5.4.0 and version 7.3.0 could work!
Thank you again for your patience.
 
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