compilation error of CESM1.1

[ljdiao@gmail_com]

I am installing CESM1.1 on my machine and got the following error as building pio lib. mpif90  -c -Dlinux -DMCT_INTERFACE -DHAVE_MPI -DFORTRANUNDERSCORE -DNO_SHR_VMATH -DNO_R16 -Dlinux -DCPRPGI -DSPMD -DHAVE_MPI -DUSEMPIIO -DSYSLINUX -D_NETCDF -I/opt/netcdf/include -D_NOPNETCDF -DTIMING  -i4 -gopt -Mlist -time -Mextend -byteswapio -Mflushz -Kieee   -Mfree  -I.  -I/opt/netcdf/include -I/opt/pgi/linux86-64/2012/mpi/mpich/include -I/tng4/users/ldiao/CESM/cesm1_1/exe/mct/mct -I/tng4/users/ldiao/CESM/cesm1_1/exe/mct/mpeu -I/tng4/users/ldiao/CESM/cesm1_1/exe/pio -I/tng4/users/ldiao/CESM/cesm1_1/models/utils/pio -I/tng4/users/ldiao/CESM/cesm1_1/exe/lib/include -I/opt/netcdf/include   -I../timing  /tng4/users/ldiao/CESM/cesm1_1/models/utils/pio/ionf_mod.F90
PGF90-F-0004-Unable to open MODULE file perf_utils.mod (/tng4/users/ldiao/CESM/cesm1_1/models/utils/pio/ionf_mod.F90: 18)
PGF90/x86-64 Linux 12.10-0: compilation aborted
gmake[1]: *** [/tng4/users/ldiao/CESM/cesm1_1/models/utils/pio/ionf_mod.o] Error 2
gmake[1]: Leaving directory `/tng4/users/ldiao/CESM/cesm1_1/exe/pio'
gmake: *** [all] Error 2

It looks stange since ionf_mod.F90 doesn't need perf_utils.mod.  Any suggestions will be appreciated.

 

[jedwards]

In fortran 90 you can have dependancy chains of module files, module A uses module B uses module C etc.    In the past most compilers would require module B but not module C be in the include path when compiling module A.   PGI has recently decided that module C also needs to be in the include path.   To fix this an update is required in file scripts/ccsm_utils/Machines/buildlib.pio I've attached an update that should work.    I am concerned that you are using cesm1.1 which has a couple of serious known problems.   I recommend that you start over with cesm1.1.1 (you'll still have the pio build problem though).   Jim

 

[ljdiao@gmail_com]

Hi, Jim:
I already switched to v1.1.1 and updated the buildlib.pio file provided by you. The same error still occurs. Can you guide me working out this error? thank you very much!

 

[jedwards]

Sorry I gave you the wrong fix.  The file perf_utils.mod  should be in /tng4/users/ldiao/CESM/cesm1_1/exe/gptl You can either add -I/tng4/users/ldiao/CESM/cesm1_1/exe/gptl to your include path or copy /tng4/users/ldiao/CESM/cesm1_1/exe/gptl/*.mod /tng4/users/ldiao/CESM/cesm1_1/exe/lib/include  

 

[ljdiao@gmail_com]

Hi, jedwards:Your suggestion works this time. but I got new error message as below still for pio lib:mpif90  -c -Dlinux -DMCT_INTERFACE -DHAVE_MPI -DFORTRANUNDERSCORE -DNO_SHR_VMATH -DNO_R16 -Dlinux -DCPRPGI -DSPMD -DHAVE_MPI -DSYSLINUX -D_NETCDF -I/opt/netcdf/include -D_NOPNETCDF -DTIMING  -i4 -gopt -Mlist -time -Mextend -byteswapio -Mflushz -Kieee   -Mfree  -I.  -I/opt/netcdf/include -I/tng4/users/ldiao/CESM/cesm1_1_1/exe/mct/mct -I/tng4/users/ldiao/CESM/cesm1_1_1/exe/mct/mpeu -I/tng4/users/ldiao/CESM/cesm1_1_1/exe/pio -I/tng4/users/ldiao/CESM/cesm1_1_1/models/utils/pio -I/tng4/users/ldiao/CESM/cesm1_1_1/exe/lib/include -I/opt/netcdf/include   -I../timing  /tng4/users/ldiao/CESM/cesm1_1_1/models/utils/pio/pionfput_mod.F90
PGF90-W-0435-Array declared with zero size (/tng4/users/ldiao/CESM/cesm1_1_1/models/utils/pio/pionfput_mod.F90: 627)I still have no idea about how to fix this problem. I hope you can give me suggestion again. Million thanks.

 

[jedwards]

> PGF90-W-0435-Array declared with zero size (/tng4/users/ldiao/CESM/cesm1_1_1/models/utils/pio/pionfput_mod.F90: 627) That is a warning that you can safely ignore.  

 

[ljdiao@gmail_com]

Hi, Jedward:Ok, then the true problem is the following which caused the installation failed. mpif90  -c -Dlinux -DMCT_INTERFACE -DHAVE_MPI -DFORTRANUNDERSCORE -DNO_SHR_VMATH -DNO_R16 -Dlinux -DCPRPGI -DSPMD -DHAVE_MPI -DSYSLINUX -D_NETCDF -I/opt/netcdf/include -D_NOPNETCDF -DTIMING  -i4 -gopt -Mlist -time -Mextend -byteswapio -Mflushz -Kieee   -Mfree  -I.  -I/opt/netcdf/include -I/tng4/users/ldiao/CESM/cesm1_1_1/exe/mct/mct -I/tng4/users/ldiao/CESM/cesm1_1_1/exe/mct/mpeu -I/tng4/users/ldiao/CESM/cesm1_1_1/exe/pio -I/tng4/users/ldiao/CESM/cesm1_1_1/models/utils/pio -I/tng4/users/ldiao/CESM/cesm1_1_1/exe/lib/include -I/opt/netcdf/include   -I../timing  /tng4/users/ldiao/CESM/cesm1_1_1/models/utils/pio/pionfput_mod.F90PGF90-S-0155-Could not resolve generic procedure mpi_bcast (/tng4/users/ldiao/CESM/cesm1_1_1/models/utils/pio/pionfput_mod.F90: 1040)
  0 inform,   0 warnings,   1 severes, 0 fatal for put_var_3d_text

PGF90-S-0155-Could not resolve generic procedure mpi_bcast (/tng4/users/ldiao/CESM/cesm1_1_1/models/utils/pio/pionfput_mod.F90: 4368)
  0 inform,   0 warnings,   1 severes, 0 fatal for put_vara_4d_text

PGF90-S-0155-Could not resolve generic procedure mpi_bcast (/tng4/users/ldiao/CESM/cesm1_1_1/models/utils/pio/pionfput_mod.F90: 5061)
  0 inform,   0 warnings,   1 severes, 0 fatal for put_vara_5d_int

gmake[1]: *** [/tng4/users/ldiao/CESM/cesm1_1_1/models/utils/pio/pionfput_mod.o] Error 2
gmake[1]: Leaving directory `/tng4/users/ldiao/CESM/cesm1_1_1/exe/pio'
gmake: *** [all] Error 2

there are dozens of similar error messages. Thanks for your help!

 

[jedwards]

Hi Lijun,I've not seen this problem before - what MPI library and version are you using?   It looks like a problem in the F90 module mpi.mod.    A workaround would be to add the flag-DNO_MPIMOD to your cppdefs. 

 

[ljdiao@gmail_com]

Hi, Jedward: Although adding -DNO_MPIMOD option works, but what does it actally mean and will it affect the parallel execution of the cesm.exe?I got the last error message in the command line as:-L/opt/pgi/linux86-64/2012/mpi/mpich/lib –lmpi  /usr/bin/ld: cannot find -lmpigmake: *** [/tng4/users/ldiao/CESM/cesm1_1_1/exe/cesm.exe] Error 2in my path there is indeed no mpi lib, but I do have mpich lib. Can I change it from -lmpi to -lmpich?I feel if it is not my fault, CESM1.1.1 has deficiencies on installing. But anyway I am very indebted to your efforts.

 

[jedwards]

Yes change it to mpich. 

 

[ljdiao@gmail_com]

Hi, can someone tell me how to add the netcdf libs netcdff and netcdf on compiling by modifying SLIBS. thanks very much

 

[jedwards]

It should be something iikeSLIBS+= $(shell $(NETCDF_PATH)/bin/nf-config --flibs) In your case Macros file.   Look in file scripts/ccsm_utils/Machines/config_compilers.xml  for the place to change it permanently.

 

[rajshekharsingh@berkeley_edu]

I am having the same error. I could compile the code earlier but had to change the pgi compiler to 12.10 instead of 12.5 I was using earlier and now I am getting this error. I saw the solution above but that path does not exist in my script. I hope someoen can help.

mpif90  -c -DLINUX -DMCT_INTERFACE -DHAVE_MPI -DFORTRANUNDERSCORE -DNO_SHR_VMATH -DNO_R16 -DLINUX -DCPRPGI -DHAVE_SLASHPROC -DSPMD -DHAVE_MPI -DUSEMPIIO -DSYSLINUX -D_NETCDF -I/global/software/sl-6.x86_64/modules/pgi/12.10/netcdf/4.2.1.1-pgi-s/include -D_NOPNETCDF -DTIMING  -i4 -gopt -Mlist -time -Mextend -byteswapio -Mflushz -Kieee   -Mfree  -I.  -I/global/software/sl-6.x86_64/modules/pgi/12.10/netcdf/4.2.1.1-pgi-s/include -I/global/software/sl-6.x86_64/modules/pgi/12.10/netcdf/4.2.1.1-pgi-s/include -I/global/scratch/rsingh/cesm1_1_1/cesmrun/sfrec_assim_test/bld/mct/mct -I/global/scratch/rsingh/cesm1_1_1/cesmrun/sfrec_assim_test/bld/mct/mpeu -I/global/scratch/rsingh/cesm1_1_1/cesmrun/sfrec_assim_test/bld/pio -I/global/scratch/rsingh/cesm1_1_1/models/utils/pio -I/global/scratch/rsingh/cesm1_1_1/cesmrun/sfrec_assim_test/bld/lib/include -I/global/software/sl-6.x86_64/modules/pgi/12.10/netcdf/4.2.1.1-pgi-s/include   -I../timing  /global/scratch/rsingh/cesm1_1_1/models/utils/pio/ionf_mod.F90PGF90-F-0004-Unable to open MODULE file perf_utils.mod (/global/scratch/rsingh/cesm1_1_1/models/utils/pio/ionf_mod.F90: 18)PGF90/x86-64 Linux 12.10-0: compilation abortedgmake[1]: *** [/global/scratch/rsingh/cesm1_1_1/models/utils/pio/ionf_mod.o] Error 2gmake[1]: Leaving directory `/global/scratch/rsingh/cesm1_1_1/cesmrun/sfrec_assim_test/bld/pio' gmake: *** [all] Error 2 

 

[jedwards]

The file perf_utils.mod  should be in /tng4/users/ldiao/CESM/cesm1_1/exe/gptl You can either add -I/tng4/users/ldiao/CESM/cesm1_1/exe/gptl to your include path orcopy /tng4/users/ldiao/CESM/cesm1_1/exe/gptl/*.mod /tng4/users/ldiao/CESM/cesm1_1/exe/lib/include Just replace /tng4/users/ldiao/CESM/cesm1_1  with/global/scratch/rsingh/cesm1_1_1/cesmrun/sfrec_assim_test/