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error in compiling cesm1_0_4

D

devarajun@gmail_com

Dev
Member
Below is the error when I compile using intel compilers on Linux HPC. I have downloaded cesm1_0_4 and not the alpha release.

ifort -c -I. -I/apps/netcdf-intel/include -I/apps/netcdf-intel/include -I/apps/mpich2-intel/include -I. -I/home/ananya/cesm1_0_4/scripts/CN/SourceMods/src.drv -I/home/ananya/cesm1_0_4/models/drv/driver -I/home/ananya/scratch//CN/lib/include -DMCT_INTERFACE -DHAVE_MPI -DLINUX -DSEQ_ -DFORTRANUNDERSCORE -DNO_R16 -DNO_SHR_VMATH -g -fp-model precise -convert big_endian -assume byterecl -ftz -traceback -O2 -FR /home/ananya/cesm1_0_4/models/drv/driver/mrg_x2g_mct.F90
ifort -c -I. -I/apps/netcdf-intel/include -I/apps/netcdf-intel/include -I/apps/mpich2-intel/include -I. -I/home/ananya/cesm1_0_4/scripts/CN/SourceMods/src.drv -I/home/ananya/cesm1_0_4/models/drv/driver -I/home/ananya/scratch//CN/lib/include -DMCT_INTERFACE -DHAVE_MPI -DLINUX -DSEQ_ -DFORTRANUNDERSCORE -DNO_R16 -DNO_SHR_VMATH -g -fp-model precise -convert big_endian -assume byterecl -ftz -traceback -O2 -FR /home/ananya/cesm1_0_4/models/drv/driver/mrg_x2i_mct.F90
ifort -c -I. -I/apps/netcdf-intel/include -I/apps/netcdf-intel/include -I/apps/mpich2-intel/include -I. -I/home/ananya/cesm1_0_4/scripts/CN/SourceMods/src.drv -I/home/ananya/cesm1_0_4/models/drv/driver -I/home/ananya/scratch//CN/lib/include -DMCT_INTERFACE -DHAVE_MPI -DLINUX -DSEQ_ -DFORTRANUNDERSCORE -DNO_R16 -DNO_SHR_VMATH -g -fp-model precise -convert big_endian -assume byterecl -ftz -traceback -O2 -FR /home/ananya/cesm1_0_4/models/drv/driver/ccsm_comp_mod.F90
/home/ananya/cesm1_0_4/models/drv/driver/ccsm_comp_mod.F90(50): error #7002: Error in opening the compiled module file. Check INCLUDE paths. [ICE_COMP_MCT]
use ice_comp_mct, only: ice_init_mct, ice_run_mct, ice_final_mct
-------^
/home/ananya/cesm1_0_4/models/drv/driver/ccsm_comp_mod.F90(51): error #7002: Error in opening the compiled module file. Check INCLUDE paths. [GLC_COMP_MCT]
use glc_comp_mct, only: glc_init_mct, glc_run_mct, glc_final_mct
-------^
/home/ananya/cesm1_0_4/models/drv/driver/ccsm_comp_mod.F90(50): error #6580: Name in only-list does not exist. [ICE_INIT_MCT]
use ice_comp_mct, only: ice_init_mct, ice_run_mct, ice_final_mct
---------------------------^
/home/ananya/cesm1_0_4/models/drv/driver/ccsm_comp_mod.F90(50): error #6580: Name in only-list does not exist. [ICE_RUN_MCT]
use ice_comp_mct, only: ice_init_mct, ice_run_mct, ice_final_mct
-----------------------------------------^
/home/ananya/cesm1_0_4/models/drv/driver/ccsm_comp_mod.F90(50): error #6580: Name in only-list does not exist. [ICE_FINAL_MCT]
use ice_comp_mct, only: ice_init_mct, ice_run_mct, ice_final_mct
------------------------------------------------------^
/home/ananya/cesm1_0_4/models/drv/driver/ccsm_comp_mod.F90(51): error #6580: Name in only-list does not exist. [GLC_INIT_MCT]
use glc_comp_mct, only: glc_init_mct, glc_run_mct, glc_final_mct
---------------------------^
/home/ananya/cesm1_0_4/models/drv/driver/ccsm_comp_mod.F90(51): error #6580: Name in only-list does not exist. [GLC_RUN_MCT]
use glc_comp_mct, only: glc_init_mct, glc_run_mct, glc_final_mct
-----------------------------------------^
/home/ananya/cesm1_0_4/models/drv/driver/ccsm_comp_mod.F90(51): error #6580: Name in only-list does not exist. [GLC_FINAL_MCT]
use glc_comp_mct, only: glc_init_mct, glc_run_mct, glc_final_mct
------------------------------------------------------^
/home/ananya/cesm1_0_4/models/drv/driver/ccsm_comp_mod.F90(740): error #6406: Conflicting attributes or multiple declaration of name. [ICE_INIT_MCT]
call ice_init_mct( EClock_i, cdata_ii, x2i_ii, i2x_ii, NLFilename=NLFilename )
-----------^
/home/ananya/cesm1_0_4/models/drv/driver/ccsm_comp_mod.F90(758): error #6406: Conflicting attributes or multiple declaration of name. [GLC_INIT_MCT]
call glc_init_mct( EClock_g, cdata_gg, x2g_gg, g2x_gg, NLFilename=NLFilename )
-----------^
/home/ananya/cesm1_0_4/models/drv/driver/ccsm_comp_mod.F90(1759): error #6406: Conflicting attributes or multiple declaration of name. [ICE_RUN_MCT]
call ice_run_mct( EClock_i, cdata_ii, x2i_ii, i2x_ii)
--------------^
/home/ananya/cesm1_0_4/models/drv/driver/ccsm_comp_mod.F90(2185): error #6406: Conflicting attributes or multiple declaration of name. [GLC_RUN_MCT]
call glc_run_mct( EClock_g, cdata_gg, x2g_gg, g2x_gg)
--------------^
/home/ananya/cesm1_0_4/models/drv/driver/ccsm_comp_mod.F90(2485): error #6406: Conflicting attributes or multiple declaration of name. [ICE_FINAL_MCT]
call ice_final_mct( )
-----------^
/home/ananya/cesm1_0_4/models/drv/driver/ccsm_comp_mod.F90(2495): error #6406: Conflicting attributes or multiple declaration of name. [GLC_FINAL_MCT]
call glc_final_mct( )
-----------^
compilation aborted for /home/ananya/cesm1_0_4/models/drv/driver/ccsm_comp_mod.F90 (code 1)
gmake: *** [ccsm_comp_mod.o] Error 1

Any suggestions, How do I solve this issue. Thanks in advance.

Dev
 
erik

erik

Erik Kluzek
CSEG and Liaisons
Staff member
You don't give the specifics of the case you are trying to run. But, from the error messages it's not able to find the GLC and ICE models that you are trying to link in. so you'll want to make sure they are available and they were already compiled and in the lib directory of your case. You would need to give us more specifics in order to help any further...
 
D

devarajun@gmail_com

Dev
Member
Hi Erik,

Thanks for asking this. I am running a case I_1850_CN with resolution f19_g16 on generic linux intel machine with
FC = ifort, CC = icc

Below is the error message
Fri Sep 14 12:43:52 IST 2012 /home/ananya/scratch//CN/mct/mct.bldlog.120914-124218
Fri Sep 14 12:45:07 IST 2012 /home/ananya/scratch//CN/pio/pio.bldlog.120914-124218
Fri Sep 14 12:45:57 IST 2012 /home/ananya/scratch//CN/csm_share/csm_share.bldlog.120914-124218
Fri Sep 14 12:46:48 IST 2012 /home/ananya/scratch//CN/run/cpl.bldlog.120914-124218
Fri Sep 14 12:46:48 IST 2012 /home/ananya/scratch//CN/run/atm.bldlog.120914-124218
Fri Sep 14 12:46:54 IST 2012 /home/ananya/scratch//CN/run/lnd.bldlog.120914-124218
Fri Sep 14 12:52:52 IST 2012 /home/ananya/scratch//CN/run/ice.bldlog.120914-124218
Fri Sep 14 12:52:54 IST 2012 /home/ananya/scratch//CN/run/ocn.bldlog.120914-124218
Fri Sep 14 12:52:55 IST 2012 /home/ananya/scratch//CN/run/glc.bldlog.120914-124218
Fri Sep 14 12:52:57 IST 2012 /home/ananya/scratch//CN/run/ccsm.bldlog.120914-124218
ERROR: ccsm.buildexe.csh failed, see /home/ananya/scratch//CN/run/ccsm.bldlog.120914-124218
ERROR: cat /home/ananya/scratch//CN/run/ccsm.bldlog.120914-124218


cat /home/ananya/scratch//CN/run/ccsm.bldlog.120914-124218

ifort -c -I. -I/apps/netcdf-intel/include -I/apps/netcdf-intel/include -I/apps/mpich2-intel/include -I. -I/home/ananya/cesm1_0_4/scripts/CN/SourceMods/src.drv -I/home/ananya/cesm1_0_4/models/drv/driver -I/home/ananya/scratch//CN/lib/include -DMCT_INTERFACE -DHAVE_MPI -DLINUX -DSEQ_ -DFORTRANUNDERSCORE -DNO_R16 -DNO_SHR_VMATH -g -fp-model precise -convert big_endian -assume byterecl -ftz -traceback -O2 -FR /home/ananya/cesm1_0_4/models/drv/driver/mrg_x2g_mct.F90
ifort -c -I. -I/apps/netcdf-intel/include -I/apps/netcdf-intel/include -I/apps/mpich2-intel/include -I. -I/home/ananya/cesm1_0_4/scripts/CN/SourceMods/src.drv -I/home/ananya/cesm1_0_4/models/drv/driver -I/home/ananya/scratch//CN/lib/include -DMCT_INTERFACE -DHAVE_MPI -DLINUX -DSEQ_ -DFORTRANUNDERSCORE -DNO_R16 -DNO_SHR_VMATH -g -fp-model precise -convert big_endian -assume byterecl -ftz -traceback -O2 -FR /home/ananya/cesm1_0_4/models/drv/driver/mrg_x2i_mct.F90
ifort -c -I. -I/apps/netcdf-intel/include -I/apps/netcdf-intel/include -I/apps/mpich2-intel/include -I. -I/home/ananya/cesm1_0_4/scripts/CN/SourceMods/src.drv -I/home/ananya/cesm1_0_4/models/drv/driver -I/home/ananya/scratch//CN/lib/include -DMCT_INTERFACE -DHAVE_MPI -DLINUX -DSEQ_ -DFORTRANUNDERSCORE -DNO_R16 -DNO_SHR_VMATH -g -fp-model precise -convert big_endian -assume byterecl -ftz -traceback -O2 -FR /home/ananya/cesm1_0_4/models/drv/driver/ccsm_comp_mod.F90
/home/ananya/cesm1_0_4/models/drv/driver/ccsm_comp_mod.F90(50): error #7002: Error in opening the compiled module file. Check INCLUDE paths. [ICE_COMP_MCT]
use ice_comp_mct, only: ice_init_mct, ice_run_mct, ice_final_mct
-------^
/home/ananya/cesm1_0_4/models/drv/driver/ccsm_comp_mod.F90(51): error #7002: Error in opening the compiled module file. Check INCLUDE paths. [GLC_COMP_MCT]
use glc_comp_mct, only: glc_init_mct, glc_run_mct, glc_final_mct
-------^
/home/ananya/cesm1_0_4/models/drv/driver/ccsm_comp_mod.F90(50): error #6580: Name in only-list does not exist. [ICE_INIT_MCT]
use ice_comp_mct, only: ice_init_mct, ice_run_mct, ice_final_mct
---------------------------^
/home/ananya/cesm1_0_4/models/drv/driver/ccsm_comp_mod.F90(50): error #6580: Name in only-list does not exist. [ICE_RUN_MCT]
use ice_comp_mct, only: ice_init_mct, ice_run_mct, ice_final_mct
-----------------------------------------^
/home/ananya/cesm1_0_4/models/drv/driver/ccsm_comp_mod.F90(50): error #6580: Name in only-list does not exist. [ICE_FINAL_MCT]
use ice_comp_mct, only: ice_init_mct, ice_run_mct, ice_final_mct
------------------------------------------------------^
/home/ananya/cesm1_0_4/models/drv/driver/ccsm_comp_mod.F90(51): error #6580: Name in only-list does not exist. [GLC_INIT_MCT]
use glc_comp_mct, only: glc_init_mct, glc_run_mct, glc_final_mct
---------------------------^
/home/ananya/cesm1_0_4/models/drv/driver/ccsm_comp_mod.F90(51): error #6580: Name in only-list does not exist. [GLC_RUN_MCT]
use glc_comp_mct, only: glc_init_mct, glc_run_mct, glc_final_mct
-----------------------------------------^
/home/ananya/cesm1_0_4/models/drv/driver/ccsm_comp_mod.F90(51): error #6580: Name in only-list does not exist. [GLC_FINAL_MCT]
use glc_comp_mct, only: glc_init_mct, glc_run_mct, glc_final_mct
------------------------------------------------------^
/home/ananya/cesm1_0_4/models/drv/driver/ccsm_comp_mod.F90(740): error #6406: Conflicting attributes or multiple declaration of name. [ICE_INIT_MCT]
call ice_init_mct( EClock_i, cdata_ii, x2i_ii, i2x_ii, NLFilename=NLFilename )
-----------^
/home/ananya/cesm1_0_4/models/drv/driver/ccsm_comp_mod.F90(75: error #6406: Conflicting attributes or multiple declaration of name. [GLC_INIT_MCT]
call glc_init_mct( EClock_g, cdata_gg, x2g_gg, g2x_gg, NLFilename=NLFilename )
-----------^
/home/ananya/cesm1_0_4/models/drv/driver/ccsm_comp_mod.F90(1759): error #6406: Conflicting attributes or multiple declaration of name. [ICE_RUN_MCT]
call ice_run_mct( EClock_i, cdata_ii, x2i_ii, i2x_ii)
--------------^
/home/ananya/cesm1_0_4/models/drv/driver/ccsm_comp_mod.F90(2185): error #6406: Conflicting attributes or multiple declaration of name. [GLC_RUN_MCT]
call glc_run_mct( EClock_g, cdata_gg, x2g_gg, g2x_gg)
--------------^
/home/ananya/cesm1_0_4/models/drv/driver/ccsm_comp_mod.F90(2485): error #6406: Conflicting attributes or multiple declaration of name. [ICE_FINAL_MCT]
call ice_final_mct( )
-----------^
/home/ananya/cesm1_0_4/models/drv/driver/ccsm_comp_mod.F90(2495): error #6406: Conflicting attributes or multiple declaration of name. [GLC_FINAL_MCT]
call glc_final_mct( )
-----------^
compilation aborted for /home/ananya/cesm1_0_4/models/drv/driver/ccsm_comp_mod.F90 (code 1)
gmake: *** [ccsm_comp_mod.o] Error 1


How do I go about it please help.

Dev
 
J

jedwards

CSEG and Liaisons
Staff member
It looks like the ice_comp_mct failed to build, have a look in the ice.bldlog:

/home/ananya/scratch//CN/run/ice.bldlog.120914-124218

and see if you have any errors. Are you trying to build with mpi or a serial version?
 
D

devarajun@gmail_com

Dev
Member
Hi Jim,
Thanks for the reply. It seems no error showing up in ice.bldlog.120914-124218 and below is the content of the file. I am building with mpi compiled with Intel compilers.

Fri Sep 14 12:52:52 IST 2012 /home/ananya/scratch//CN/run/ice.bldlog.120914-124218
cat: Srcfiles: No such file or directory
/home/ananya/cesm1_0_4/scripts/CN/Tools/mkSrcfiles > /home/ananya/scratch/CN/ice/obj/Srcfiles
cp -f /home/ananya/scratch/CN/ice/obj/Filepath /home/ananya/scratch/CN/ice/obj/Deppath
/home/ananya/cesm1_0_4/scripts/CN/Tools/mkDepends Deppath Srcfiles > /home/ananya/scratch/CN/ice/obj/Depends
mpif90 -c -I. -I/apps/netcdf-intel/include -I/apps/mpich2-intel/include -I. -I/home/ananya/cesm1_0_4/scripts/CN/SourceMods/src.sice -I/home/ananya/cesm1_0_4/models/ice/sice -I/home/ananya/cesm1_0_4/models/ice/sice/cpl_mct -I/home/ananya/scratch//CN/lib/include -DMCT_INTERFACE -DHAVE_MPI -DLINUX -DSEQ_ -DFORTRANUNDERSCORE -DNO_R16 -DNO_SHR_VMATH -g -fp-model precise -convert big_endian -assume byterecl -ftz -traceback -O2 -FR /home/ananya/cesm1_0_4/models/ice/sice/cpl_mct/ice_comp_mct.F90
ar -r /home/ananya/scratch//CN/lib/libice.a ice_comp_mct.o
ar: creating /home/ananya/scratch//CN/lib/libice.a
touch /home/ananya/scratch/CN/ice/obj/Filepath
 
J

jedwards

CSEG and Liaisons
Staff member
I think I see what is going on, in your ice build you used the mpi wrapper to the compiler mpif90
but in your link step you are using ifort directly. My bet is that the mpif90 is referring to a compiler other than
ifort (or perhaps a different ifort version) and so the created .mod files are incompatible. Try checking the
versions with
mpif90 --version
ifort --version

If they are not the same you need to fix things in your path, remove that build and try again.
 
D

devarajun@gmail_com

Dev
Member
Hi Jim,

I have now mpif90 and ifort version is same:
mpif90 --version
ifort (IFORT) 12.1.0 20110811
Copyright (C) 1985-2011 Intel Corporation. All rights reserved.

ifort --version
ifort (IFORT) 12.1.0 20110811
Copyright (C) 1985-2011 Intel Corporation. All rights reserved.

I have cleaned the build and tried building again. Below is error again: please help
Fri Sep 28 15:42:54 IST 2012 /home/ananya/scratch//cn/mct/mct.bldlog.120928-154250
Fri Sep 28 15:43:30 IST 2012 /home/ananya/scratch//cn/pio/pio.bldlog.120928-154250
Fri Sep 28 15:44:15 IST 2012 /home/ananya/scratch//cn/csm_share/csm_share.bldlog.120928-154250
Fri Sep 28 15:44:50 IST 2012 /home/ananya/scratch//cn/run/cpl.bldlog.120928-154250
Fri Sep 28 15:44:50 IST 2012 /home/ananya/scratch//cn/run/atm.bldlog.120928-154250
Fri Sep 28 15:44:53 IST 2012 /home/ananya/scratch//cn/run/lnd.bldlog.120928-154250
Fri Sep 28 15:50:17 IST 2012 /home/ananya/scratch//cn/run/ice.bldlog.120928-154250
Fri Sep 28 15:50:18 IST 2012 /home/ananya/scratch//cn/run/ocn.bldlog.120928-154250
Fri Sep 28 15:50:19 IST 2012 /home/ananya/scratch//cn/run/glc.bldlog.120928-154250
Fri Sep 28 15:50:20 IST 2012 /home/ananya/scratch//cn/run/ccsm.bldlog.120928-154250
ERROR: ccsm.buildexe.csh failed, see /home/ananya/scratch//cn/run/ccsm.bldlog.120928-154250
ERROR: cat /home/ananya/scratch//cn/run/ccsm.bldlog.120928-154250
[ananya@mandhan cn]$ cat /home/ananya/scratch//cn/run/ccsm.bldlog.120928-154250
Fri Sep 28 15:50:20 IST 2012 /home/ananya/scratch//cn/run/ccsm.bldlog.120928-154250
-------------------------------------------------------------------------
Building a single executable version of CCSM
-------------------------------------------------------------------------
cat: Srcfiles: No such file or directory
/home/ananya/cesm1_0_4/scripts/cn/Tools/mkSrcfiles > /home/ananya/scratch/cn/ccsm/obj/Srcfiles
cp -f /home/ananya/scratch/cn/ccsm/obj/Filepath /home/ananya/scratch/cn/ccsm/obj/Deppath
/home/ananya/cesm1_0_4/scripts/cn/Tools/mkDepends Deppath Srcfiles > /home/ananya/scratch/cn/ccsm/obj/Depends
ifort -c -I. -I/apps/netcdf-with-hdf5-1.8.4-patch1/include -I/apps/netcdf-with-hdf5-1.8.4-patch1/include -I/apps/mpich2-intel/include -I. -I/home/ananya/cesm1_0_4/scripts/cn/SourceMods/src.drv -I/home/ananya/cesm1_0_4/models/drv/driver -I/home/ananya/scratch//cn/lib/include -DMCT_INTERFACE -DHAVE_MPI -DLINUX -DSEQ_ -DFORTRANUNDERSCORE -DNO_R16 -DNO_SHR_VMATH -g -fp-model precise -convert big_endian -assume byterecl -ftz -traceback -O2 -FR /home/ananya/cesm1_0_4/models/drv/driver/seq_diag_mct.F90



ifort -c -I. -I/apps/netcdf-with-hdf5-1.8.4-patch1/include -I/apps/netcdf-with-hdf5-1.8.4-patch1/include -I/apps/mpich2-intel/include -I. -I/home/ananya/cesm1_0_4/scripts/cn/SourceMods/src.drv -I/home/ananya/cesm1_0_4/models/drv/driver -I/home/ananya/scratch//cn/lib/include -DMCT_INTERFACE -DHAVE_MPI -DLINUX -DSEQ_ -DFORTRANUNDERSCORE -DNO_R16 -DNO_SHR_VMATH -g -fp-model precise -convert big_endian -assume byterecl -ftz -traceback -O2 -FR /home/ananya/cesm1_0_4/models/drv/driver/ccsm_comp_mod.F90
/home/ananya/cesm1_0_4/models/drv/driver/ccsm_comp_mod.F90(50): error #7002: Error in opening the compiled module file. Check INCLUDE paths. [ICE_COMP_MCT]
use ice_comp_mct, only: ice_init_mct, ice_run_mct, ice_final_mct
-------^
/home/ananya/cesm1_0_4/models/drv/driver/ccsm_comp_mod.F90(51): error #7002: Error in opening the compiled module file. Check INCLUDE paths. [GLC_COMP_MCT]
use glc_comp_mct, only: glc_init_mct, glc_run_mct, glc_final_mct
-------^

-----------------------------------------^
/home/ananya/cesm1_0_4/models/drv/driver/ccsm_comp_mod.F90(51): error #6580: Name in only-list does not exist. [GLC_FINAL_MCT]
use glc_comp_mct, only: glc_init_mct, glc_run_mct, glc_final_mct
------------------------------------------------------^
/home/ananya/cesm1_0_4/models/drv/driver/ccsm_comp_mod.F90(740): error #6406: Conflicting attributes or multiple declaration of name. [ICE_INIT_MCT]
call ice_init_mct( EClock_i, cdata_ii, x2i_ii, i2x_ii, NLFilename=NLFilename )
-----------^
/home/ananya/cesm1_0_4/models/drv/driver/ccsm_comp_mod.F90(758): error #6406: Conflicting attributes or multiple declaration of name. [GLC_INIT_MCT]
call glc_init_mct( EClock_g, cdata_gg, x2g_gg, g2x_gg, NLFilename=NLFilename )
-----------^
/home/ananya/cesm1_0_4/models/drv/driver/ccsm_comp_mod.F90(1759): error #6406: Conflicting attributes or multiple declaration of name. [ICE_RUN_MCT]
call ice_run_mct( EClock_i, cdata_ii, x2i_ii, i2x_ii)
--------------^
/home/ananya/cesm1_0_4/models/drv/driver/ccsm_comp_mod.F90(2185): error #6406: Conflicting attributes or multiple declaration of name. [GLC_RUN_MCT]
call glc_run_mct( EClock_g, cdata_gg, x2g_gg, g2x_gg)
--------------^
/home/ananya/cesm1_0_4/models/drv/driver/ccsm_comp_mod.F90(2485): error #6406: Conflicting attributes or multiple declaration of name. [ICE_FINAL_MCT]
call ice_final_mct( )
-----------^
/home/ananya/cesm1_0_4/models/drv/driver/ccsm_comp_mod.F90(2495): error #6406: Conflicting attributes or multiple declaration of name. [GLC_FINAL_MCT]
call glc_final_mct( )
-----------^
compilation aborted for /home/ananya/cesm1_0_4/models/drv/driver/ccsm_comp_mod.F90 (code 1)
gmake: *** [ccsm_comp_mod.o] Error 1
 
D

devarajun@gmail_com

Dev
Member
I am trying to debug the error posted above and not able to fix it. If any suggestions on this error will be helpful for us to compile CESM104.

Thanks in advance.
 
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