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Error in porting CESM

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xuezhen8108@...
Error in porting CESM

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.

CESM Software Engineer

xuezhen8108@...

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.F90

mpif90 -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 -limpi

ld: cannot find -limpi

gmake: *** [/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.   

CESM Software Engineer

xuezhen8108@...

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.  

CESM Software Engineer

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