Error in porting CESM

[xuezhen8108@hotmail_com]

Hello, when I porting the CESM 1.0.3 on my local cluster, the log file (pio.bldlog.130609-211143) shows the fatal Error and exit from build.Would someone help me solving this problem. Thanks a lot! the following is the later half of  pio.bldlog.130609-211143 ................................config.status: creating Makefile.conf
Please check the Makefile.conf
Have a nice day!
Making dependencies for pio.F90 --> pio.d
Making dependencies for pio_kinds.F90 --> pio_kinds.d
Making dependencies for nf_mod.F90 --> nf_mod.d
Making dependencies for ionf_mod.F90 --> ionf_mod.d
Making dependencies for pio_types.F90 --> pio_types.d
Making dependencies for piolib_mod.F90 --> piolib_mod.d
Making dependencies for pio_mpi_utils.F90 --> pio_mpi_utils.d
Making dependencies for pio_nf_utils.F90 --> pio_nf_utils.d
Making dependencies for pio_utils.F90 --> pio_utils.d
Making dependencies for pio_quicksort.F90 --> pio_quicksort.d
Making dependencies for pio_msg_mod.F90 --> pio_msg_mod.d
Making dependencies for pio_msg_callbacks.F90 --> pio_msg_callbacks.d
/usr/bin/perl genf90.pl pionfatt_mod.F90.in > pionfatt_mod.F90
Making dependencies for pionfatt_mod.F90 --> pionfatt_mod.d
/usr/bin/perl genf90.pl pionfread_mod.F90.in > pionfread_mod.F90
Making dependencies for pionfread_mod.F90 --> pionfread_mod.d
/usr/bin/perl genf90.pl pionfwrite_mod.F90.in > pionfwrite_mod.F90
Making dependencies for pionfwrite_mod.F90 --> pionfwrite_mod.d
/usr/bin/perl genf90.pl pionfput_mod.F90.in > pionfput_mod.F90
Making dependencies for pionfput_mod.F90 --> pionfput_mod.d
/usr/bin/perl genf90.pl pionfget_mod.F90.in > pionfget_mod.F90
Making dependencies for pionfget_mod.F90 --> pionfget_mod.d
/usr/bin/perl genf90.pl alloc_mod.F90.in > alloc_mod.F90
Making dependencies for alloc_mod.F90 --> alloc_mod.d
/usr/bin/perl genf90.pl box_rearrange.F90.in > box_rearrange.F90
Making dependencies for box_rearrange.F90 --> box_rearrange.d
/usr/bin/perl genf90.pl rearrange.F90.in > rearrange.F90
Making dependencies for rearrange.F90 --> rearrange.d
/usr/bin/perl genf90.pl pio_support.F90.in > pio_support.F90
Making dependencies for pio_support.F90 --> pio_support.d
/usr/bin/perl genf90.pl mct_rearrange.F90.in > mct_rearrange.F90
Making dependencies for mct_rearrange.F90 --> mct_rearrange.d
/usr/bin/perl genf90.pl iompi_mod.F90.in > iompi_mod.F90
Making dependencies for iompi_mod.F90 --> iompi_mod.d
/usr/bin/perl genf90.pl piodarray.F90.in > piodarray.F90
Making dependencies for piodarray.F90 --> piodarray.d
/usr/bin/perl genf90.pl pio_spmd_utils.F90.in > pio_spmd_utils.F90
Making dependencies for pio_spmd_utils.F90 --> pio_spmd_utils.d
/usr/bin/perl genf90.pl pio_msg_getput_callbacks.F90.in > pio_msg_getput_callbacks.F90
Making dependencies for pio_msg_getput_callbacks.F90 --> pio_msg_getput_callbacks.d
Done updating dependencies
gmake[1]: Entering directory `/wps/home/zhangxz/model/cesm/cesm1_0_3/caserun/test4X_f45_g37/pio'
mpicc -c -g -O2 -DFORTRAN_UNDERSCORE_ -DFORTRANUNDERSCORE -DSYSLINUX -DLINUX -DCPRUNKNOWNCPR -DSPMD -DHAVE_MPI -DUSEMPIIO -D_NETCDF -D_NOPNETCDF -D_NOUSEMCT -D_USEBOX -DNO_SIZEOF -I/share/soft/rhel6.2/mpich2-1.3.1/include -I/wps/home/zhangxz/mysoft/include topology.c
mpicc -c -g -O2 -DFORTRAN_UNDERSCORE_ -DFORTRANUNDERSCORE -DSYSLINUX -DLINUX -DCPRUNKNOWNCPR -DSPMD -DHAVE_MPI -DUSEMPIIO -D_NETCDF -D_NOPNETCDF -D_NOUSEMCT -D_USEBOX -DNO_SIZEOF -I/share/soft/rhel6.2/mpich2-1.3.1/include -I/wps/home/zhangxz/mysoft/include pnetcdfversion.c
mpif90 -c -I/share/soft/rhel6.2/mpich2-1.3.1/include -DSYSLINUX -DLINUX -DCPRUNKNOWNCPR -DSPMD -DHAVE_MPI -DUSEMPIIO -D_NETCDF -D_NOPNETCDF -D_NOUSEMCT -D_USEBOX -DNO_SIZEOF -I/share/soft/rhel6.2/mpich2-1.3.1/include -I/wps/home/zhangxz/mysoft/include pio_kinds.F90
mpif.h:503.11:
Included at pio_kinds.F90:23:SAVE /MPIFCMB1/,/MPIFCMB2/
1
Warning: SAVE statement at (1) follows blanket SAVE statement
mpif.h:504.11:
Included at pio_kinds.F90:23:SAVE /MPIFCMB3/,/MPIFCMB4/,/MPIFCMB5/,/MPIFCMB6/
1
Warning: SAVE statement at (1) follows blanket SAVE statement
mpif.h:505.11:
Included at pio_kinds.F90:23:SAVE /MPIFCMB7/,/MPIFCMB8/
1
Warning: SAVE statement at (1) follows blanket SAVE statement
mpif90 -c -I/share/soft/rhel6.2/mpich2-1.3.1/include -DSYSLINUX -DLINUX -DCPRUNKNOWNCPR -DSPMD -DHAVE_MPI -DUSEMPIIO -D_NETCDF -D_NOPNETCDF -D_NOUSEMCT -D_USEBOX -DNO_SIZEOF -I/share/soft/rhel6.2/mpich2-1.3.1/include -I/wps/home/zhangxz/mysoft/include pio_types.F90
mpif90 -c -I/share/soft/rhel6.2/mpich2-1.3.1/include -DSYSLINUX -DLINUX -DCPRUNKNOWNCPR -DSPMD -DHAVE_MPI -DUSEMPIIO -D_NETCDF -D_NOPNETCDF -D_NOUSEMCT -D_USEBOX -DNO_SIZEOF -I/share/soft/rhel6.2/mpich2-1.3.1/include -I/wps/home/zhangxz/mysoft/include pio_support.F90
mpif90 -c -I/share/soft/rhel6.2/mpich2-1.3.1/include -DSYSLINUX -DLINUX -DCPRUNKNOWNCPR -DSPMD -DHAVE_MPI -DUSEMPIIO -D_NETCDF -D_NOPNETCDF -D_NOUSEMCT -D_USEBOX -DNO_SIZEOF -I/share/soft/rhel6.2/mpich2-1.3.1/include -I/wps/home/zhangxz/mysoft/include alloc_mod.F90
mpif90 -c -I/share/soft/rhel6.2/mpich2-1.3.1/include -DSYSLINUX -DLINUX -DCPRUNKNOWNCPR -DSPMD -DHAVE_MPI -DUSEMPIIO -D_NETCDF -D_NOPNETCDF -D_NOUSEMCT -D_USEBOX -DNO_SIZEOF -I/share/soft/rhel6.2/mpich2-1.3.1/include -I/wps/home/zhangxz/mysoft/include pio_utils.F90
mpif90 -c -I/share/soft/rhel6.2/mpich2-1.3.1/include -DSYSLINUX -DLINUX -DCPRUNKNOWNCPR -DSPMD -DHAVE_MPI -DUSEMPIIO -D_NETCDF -D_NOPNETCDF -D_NOUSEMCT -D_USEBOX -DNO_SIZEOF -I/share/soft/rhel6.2/mpich2-1.3.1/include -I/wps/home/zhangxz/mysoft/include ionf_mod.F90
mpif90 -c -I/share/soft/rhel6.2/mpich2-1.3.1/include -DSYSLINUX -DLINUX -DCPRUNKNOWNCPR -DSPMD -DHAVE_MPI -DUSEMPIIO -D_NETCDF -D_NOPNETCDF -D_NOUSEMCT -D_USEBOX -DNO_SIZEOF -I/share/soft/rhel6.2/mpich2-1.3.1/include -I/wps/home/zhangxz/mysoft/include pionfread_mod.F90
mpif90 -c -I/share/soft/rhel6.2/mpich2-1.3.1/include -DSYSLINUX -DLINUX -DCPRUNKNOWNCPR -DSPMD -DHAVE_MPI -DUSEMPIIO -D_NETCDF -D_NOPNETCDF -D_NOUSEMCT -D_USEBOX -DNO_SIZEOF -I/share/soft/rhel6.2/mpich2-1.3.1/include -I/wps/home/zhangxz/mysoft/include pio_msg_mod.F90
mpif90 -c -I/share/soft/rhel6.2/mpich2-1.3.1/include -DSYSLINUX -DLINUX -DCPRUNKNOWNCPR -DSPMD -DHAVE_MPI -DUSEMPIIO -D_NETCDF -D_NOPNETCDF -D_NOUSEMCT -D_USEBOX -DNO_SIZEOF -I/share/soft/rhel6.2/mpich2-1.3.1/include -I/wps/home/zhangxz/mysoft/include nf_mod.F90
nf_mod.F90:1203.132:ile%fh, name, dimid, ios%async_interface, ios%iomaster,ios%my_comm,ios%inte
1
Error: 'inte' at (1) is not a member of the 'iosystem_desc_t' structure
nf_mod.F90:1203.132:ile%fh, name, dimid, ios%async_interface, ios%iomaster,ios%my_comm,ios%inte
1
Warning: Line truncated at (1)
gmake[1]: *** [nf_mod.o] Error 1
gmake[1]: Leaving directory `/wps/home/zhangxz/model/cesm/cesm1_0_3/caserun/test4X_f45_g37/pio'
gmake: *** [all] Error 2

 

[jedwards]

cesm1.0.3 is extremely old.  I recommend that you update to 1.1.1 or at least 1.0.5    The error above indicates that your compiler is truncating fortran source after 80 columns.   Look for a compiler flag that allows for 132 or ulimited column length in your source files.

 

[xuezhen8108@hotmail_com]

Thanks for you reply.  By refering your reply, I install a new netcdf (3.6.2) and openmpi (1.6.4) compiled by intel compiler (12.1). The above error has not occurred yet. However, I get the following error in the file "ccsm.bldlog.130613-221802", the end lines as the following:mpif90 -c -I.  -I/wps/home/zhangxz/mysoft/netcdf-3.6.2/include -I/wps/home/zhangxz/mysoft/netcdf-3.6.2/include -I/wps/home/zhangxz/mysoft/openmpi-1.6.4/include -I. -I/wps/home/zhangxz/model/cesm/cesm1_0_3/scripts/test5X_f45_g37/SourceMods/src.drv -I/wps/home/zhangxz/model/cesm/cesm1_0_3/models/drv/driver -I/wps/home/zhangxz/model/cesm/cesm1_0_3/caserun/test5X_f45_g37/lib/include   -DMCT_INTERFACE -DHAVE_MPI -DGLC_NEC_10 -DLINUX -DSEQ_ -DFORTRANUNDERSCORE -DNO_R16 -DNO_SHR_VMATH  -g -fp-model precise -convert big_endian -assume byterecl -ftz -traceback -O2 -FR  /wps/home/zhangxz/model/cesm/cesm1_0_3/models/drv/driver/ccsm_driver.F90mpif90 -o /wps/home/zhangxz/model/cesm/cesm1_0_3/caserun/test5X_f45_g37/run/ccsm.exe ccsm_comp_mod.o ccsm_driver.o map_atmatm_mct.o map_atmice_mct.o map_atmlnd_mct.o map_atmocn_mct.o map_glcglc_mct.o map_iceice_mct.o map_iceocn_mct.o map_lndlnd_mct.o map_ocnocn_mct.o map_rofocn_mct.o map_rofrof_mct.o map_snoglc_mct.o map_snosno_mct.o mrg_x2a_mct.o mrg_x2g_mct.o mrg_x2i_mct.o mrg_x2l_mct.o mrg_x2o_mct.o mrg_x2s_mct.o seq_avdata_mod.o seq_diag_mct.o seq_domain_mct.o seq_flux_mct.o seq_frac_mct.o seq_hist_mod.o seq_rearr_mod.o seq_rest_mod.o -L/wps/home/zhangxz/model/cesm/cesm1_0_3/caserun/test5X_f45_g37/lib -latm -llnd -lice -locn -lglc -L/wps/home/zhangxz/model/cesm/cesm1_0_3/caserun/test5X_f45_g37/lib -lcsm_share -lmct -lmpeu -lpio  -L/wps/home/zhangxz/mysoft/netcdf-3.6.2/lib -lnetcdf  -L/wps/home/zhangxz/mysoft/openmpi-1.6.4/lib -limpild: cannot find -limpigmake: *** [/wps/home/zhangxz/model/cesm/cesm1_0_3/caserun/test5X_f45_g37/run/ccsm.exe] Error 1 Could you help me again? Thanks. By the we, becase I have carried out a 1000-year control simulation using CESM 1.0.3, I have to use this version to do ohter sensitivity experiment. 

 

[jedwards]

It looks like now you are using openmpi but still trying to link against impi.    Search for impi in your Macros and or Makefile and replace with mpi.   

 

[xuezhen8108@hotmail_com]

Thanks a lot again. Following your suggestion, I changed the impi to mpi. The last error does not exist. However, I meet a new error when build ocean (POP2). The error occur in the file "ocn.bldlog.130614-215107"  as the following,mpif90 -c -I.  -I/wps/home/zhangxz/mysoft/netcdf-3.6.2/include -I/wps/home/zhangxz/mysoft/netcdf-3.6.2/include -I/wps/home/zhangxz/mysoft/openmpi-1.6.4/include -I. -I/wps/home/zhangxz/model/cesm/cesm1_0_3/caserun/test1850/ocn/source -I/wps/home/zhangxz/model/cesm/cesm1_0_3/caserun/test1850/lib/include  -DCCSMCOUPLED -DBLCKX=40 -DBLCKY=48 -DMXBLCKS=1 -DMCT_INTERFACE -DHAVE_MPI -DCO2A -DLINUX -DSEQ_ -DFORTRANUNDERSCORE -DNO_R16 -DNO_SHR_VMATH  -g -fp-model precise -convert big_endian -assume byterecl -ftz -traceback -O2 -FR  /wps/home/zhangxz/model/cesm/cesm1_0_3/caserun/test1850/ocn/source/passive_tracers.F90/wps/home/zhangxz/model/cesm/cesm1_0_3/caserun/test1850/ocn/source/passive_tracers.F90(309): error #7938: Character length argument mismatch.   [TADVECT_CTYPE_PASSIVE_TRACERS]                       tadvect_ctype_passive_tracers(ecosys_ind_begin:ecosys_ind_end), &-----------------------^compilation aborted for /wps/home/zhangxz/model/cesm/cesm1_0_3/caserun/test1850/ocn/source/passive_tracers.F90 (code 1)gmake: *** [passive_tracers.o] Error 1 Could you help me again ?  

 

[jedwards]

As I stated earlier you should be using the cesm1_0_5 release which is functionally equivalent to the 1.0.3 release but includes bug fixes for problems like this one.