A problem when building the case.

[makpahr@gmail_com]

Hello,I got the following error when I am building the case.It stopped when building the Atmosphere component, saying "cam.buildexe.csh failed", when I "cat" the bldlog file, It ends like this: mpif90 -c -I. -I/home/mak/exe/1.2/summer/pio -I/export/apps/netcdf-3.6.2-pgi10.6/include -I/export/apps/mpich2-1.4.1p1-pgi10.6/include -I/home/mak/exe/1.2/summer/mct/mct -I/home/mak/exe/1.2/summer/mct/mpeu -I/home/mak/exe/1.2/summer/pio -I/home/mak/exe/1.2/summer/gptl -I/home/mak/cesm1_2_0/models/utils/pio -I/home/mak/exe/1.2/summer/lib/include -I. -I/home/mak/cesm1_2_0/scripts/summer/SourceMods/src.cam -I/home/mak/cesm1_2_0/models/atm/cam/src/chemistry/pp_trop_mozart -I/home/mak/cesm1_2_0/models/atm/cam/src/chemistry/mozart -I/home/mak/cesm1_2_0/models/atm/cam/src/chemistry/bulk_aero -I/home/mak/cesm1_2_0/models/atm/cam/src/chemistry/utils -I/home/mak/cesm1_2_0/models/atm/cam/src/physics/cam -I/home/mak/cesm1_2_0/models/atm/cam/src/dynamics/fv -I/home/mak/cesm1_2_0/models/atm/cam/src/utils/pilgrim -I/home/mak/cesm1_2_0/models/atm/cam/src/cpl_mct -I/home/mak/cesm1_2_0/models/atm/cam/src/cpl_share -I/home/mak/cesm1_2_0/models/atm/cam/src/control -I/home/mak/cesm1_2_0/models/atm/cam/src/utils -I/home/mak/exe/1.2/summer/lib/include -i4 -gopt -Mlist -time -Mextend -byteswapio -Mflushz -Kieee -O2 -Mvect=nosse -DCO2A -DMAXPATCH_PFT=numpft+1 -DLSMLAT=1 -DLSMLON=1 -DPLON=144 -DPLAT=96 -DPLEV=26 -DPCNST=106 -DPCOLS=16 -DPSUBCOLS=1 -DPTRM=1 -DPTRN=1 -DPTRK=1 -DSTAGGERED -DSPMD -DLinux -DMCT_INTERFACE -DHAVE_MPI -DFORTRANUNDERSCORE -DNO_SHR_VMATH -DNO_R16 -DLinux -DCPRPGI -Mfree /home/mak/cesm1_2_0/models/atm/cam/src/physics/cam/rad_constituents.F90
PGF90-S-0084-Illegal use of symbol m_list (/home/mak/cesm1_2_0/models/atm/cam/src/physics/cam/rad_constituents.F90: 514)
PGF90-S-0155-Illegal POINTER assignment - type mismatch (/home/mak/cesm1_2_0/models/atm/cam/src/physics/cam/rad_constituents.F90: 514)
PGF90-S-0084-Illegal use of symbol m_list (/home/mak/cesm1_2_0/models/atm/cam/src/physics/cam/rad_constituents.F90: 523)
PGF90-S-0141-RECORD required on left of % (/home/mak/cesm1_2_0/models/atm/cam/src/physics/cam/rad_constituents.F90: 523)
0 inform, 0 warnings, 4 severes, 0 fatal for rad_cnst_get_info
PGF90-S-0084-Illegal use of symbol m_list (/home/mak/cesm1_2_0/models/atm/cam/src/physics/cam/rad_constituents.F90: 602)
PGF90-S-0155-Illegal POINTER assignment - type mismatch (/home/mak/cesm1_2_0/models/atm/cam/src/physics/cam/rad_constituents.F90: 602)
PGF90-S-0141-RECORD required on left of % (/home/mak/cesm1_2_0/models/atm/cam/src/physics/cam/rad_constituents.F90: 605)
PGF90-S-0084-Illegal use of symbol m_list (/home/mak/cesm1_2_0/models/atm/cam/src/physics/cam/rad_constituents.F90: 612)
PGF90-S-0141-RECORD required on left of % (/home/mak/cesm1_2_0/models/atm/cam/src/physics/cam/rad_constituents.F90: 612)
PGF90-S-0075-Subscript, substring, or argument illegal in this context for (/home/mak/cesm1_2_0/models/atm/cam/src/physics/cam/rad_constituents.F90: 612)
PGF90-S-0038-Symbol, n_list, has not been explicitly declared (/home/mak/cesm1_2_0/models/atm/cam/src/physics/cam/rad_constituents.F90)
0 inform, 0 warnings, 7 severes, 0 fatal for rad_cnst_get_info_by_mode
PGF90-S-0084-Illegal use of symbol m_list (/home/mak/cesm1_2_0/models/atm/cam/src/physics/cam/rad_constituents.F90: 661)
PGF90-S-0155-Illegal POINTER assignment - type mismatch (/home/mak/cesm1_2_0/models/atm/cam/src/physics/cam/rad_constituents.F90: 661)
PGF90-S-0084-Illegal use of symbol m_list (/home/mak/cesm1_2_0/models/atm/cam/src/physics/cam/rad_constituents.F90: 664)
PGF90-S-0141-RECORD required on left of % (/home/mak/cesm1_2_0/models/atm/cam/src/physics/cam/rad_constituents.F90: 664)
PGF90-S-0084-Illegal use of symbol m_list (/home/mak/cesm1_2_0/models/atm/cam/src/physics/cam/rad_constituents.F90: 671)
PGF90-S-0141-RECORD required on left of % (/home/mak/cesm1_2_0/models/atm/cam/src/physics/cam/rad_constituents.F90: 671)
PGF90-S-0075-Subscript, substring, or argument illegal in this context for (/home/mak/cesm1_2_0/models/atm/cam/src/physics/cam/rad_constituents.F90: 671)
0 inform, 0 warnings, 7 severes, 0 fatal for rad_cnst_get_info_by_mode_spec
PGF90-S-0084-Illegal use of symbol m_list (/home/mak/cesm1_2_0/models/atm/cam/src/physics/cam/rad_constituents.F90: 718)
PGF90-S-0155-Illegal POINTER assignment - type mismatch (/home/mak/cesm1_2_0/models/atm/cam/src/physics/cam/rad_constituents.F90: 718)
PGF90-S-0084-Illegal use of symbol m_list (/home/mak/cesm1_2_0/models/atm/cam/src/physics/cam/rad_constituents.F90: 721)
PGF90-S-0141-RECORD required on left of % (/home/mak/cesm1_2_0/models/atm/cam/src/physics/cam/rad_constituents.F90: 721)
PGF90-S-0084-Illegal use of symbol m_list (/home/mak/cesm1_2_0/models/atm/cam/src/physics/cam/rad_constituents.F90: 728)
PGF90-S-0141-RECORD required on left of % (/home/mak/cesm1_2_0/models/atm/cam/src/physics/cam/rad_constituents.F90: 728)
PGF90-S-0075-Subscript, substring, or argument illegal in this context for (/home/mak/cesm1_2_0/models/atm/cam/src/physics/cam/rad_constituents.F90: 728)0 inform, 0 warnings, 7 severes, 0 fatal for rad_cnst_get_info_by_spectype
gmake: *** [rad_constituents.o] Error 2 The model seems to have some syntax error( illegal use of m_list ) that I dont know what to do with. Can anybody help me with this? I would really appreciate your help, Thanks.

 

[jedwards]

I think that this may be a problem with the version of the PGI compiler that you are using.   We have tested this code with versions 12.5, 12.10 and 13.3  of the compiler without any errors.   If you are using an older version I would suggest updateing your compiler.    

 

[makpahr@gmail_com]

Hi jedwards,Thanks for your swift reply to my problem.Yes, our PGI compiler version is lower, but we can not update that in a short time but it is already in plan. Though, we found a method to solve the error. What we did was to change the name of this varible from "m_list" to "m_list_new", and it worked.But the building process was stopped in the last component when building the cesm.exe. End of the log file is like this, hope you can help.mpif90  -o /home/mak/exe/1.1.1/hope/cesm.exe ccsm_comp_mod.o ccsm_driver.o mrg_mod.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_map_esmf.o seq_map_mod.o seq_mctext_mod.o seq_rest_mod.o -L/home/mak/exe/1.1.1/hope/lib -latm -llnd -lice -locn -lglc -lrof -L/home/mak/exe/1.1.1/hope/lib -lcsm_share  -L/home/mak/exe/1.1.1/hope/mct/mct -lmct -L/home/mak/exe/1.1.1/hope/mct/mpeu -lmpeu -L/home/mak/exe/1.1.1/hope/pio -lpio -lgptl -L/export/apps/netcdf-3.6.2-pgi10.6/lib -lnetcdf  -L/export/apps/mpich2-1.5-pgi10.6/lib  -time -Wl,--allow-multiple-definition /share/apps/pgi10.6/linux86-64/10.6/lib/libpgf90.a(initpar.o): In function `__hpf_myprocnum':initpar.c:(.text+0x2): relocation truncated to fit: R_X86_64_PC32 against symbol `__hpf_lcpu' defined in COMMON section in /share/apps/pgi10.6/linux86-64/10.6/lib/libpgf90.a(initpar.o)/share/apps/pgi10.6/linux86-64/10.6/lib/libpgf90.a(initpar.o): In function `__hpf_ncpus':initpar.c:(.text+0x12): relocation truncated to fit: R_X86_64_PC32 against symbol `__hpf_tcpus' defined in COMMON section in /share/apps/pgi10.6/linux86-64/10.6/lib/libpgf90.a(initpar.o)/share/apps/pgi10.6/linux86-64/10.6/lib/libpgf90.a(initpar.o): In function `__hpf_getioproc':initpar.c:(.text+0x22): relocation truncated to fit: R_X86_64_PC32 against symbol `__hpf_ioproc' defined in COMMON section in /share/apps/pgi10.6/linux86-64/10.6/lib/libpgf90.a(initpar.o)/share/apps/pgi10.6/linux86-64/10.6/lib/libpgf90.a(initpar.o): In function `__hpf_is_ioproc':initpar.c:(.text+0x32): relocation truncated to fit: R_X86_64_PC32 against symbol `__hpf_ioproc' defined in COMMON section in /share/apps/pgi10.6/linux86-64/10.6/lib/libpgf90.a(initpar.o)initpar.c:(.text+0x38): relocation truncated to fit: R_X86_64_PC32 against symbol `__hpf_lcpu' defined in COMMON section in /share/apps/pgi10.6/linux86-64/10.6/lib/libpgf90.a(initpar.o)/share/apps/pgi10.6/linux86-64/10.6/lib/libpgf90.a(initpar.o): In function `__hpf_abort':initpar.c:(.text+0x5f): relocation truncated to fit: R_X86_64_PC32 against symbol `__hpf_lcpu' defined in COMMON section in /share/apps/pgi10.6/linux86-64/10.6/lib/libpgf90.a(initpar.o)/share/apps/pgi10.6/linux86-64/10.6/lib/libpgf90.a(initpar.o): In function `__hpf_abortp':initpar.c:(.text+0xeb): relocation truncated to fit: R_X86_64_PC32 against symbol `__hpf_lcpu' defined in COMMON section in /share/apps/pgi10.6/linux86-64/10.6/lib/libpgf90.a(initpar.o)/share/apps/pgi10.6/linux86-64/10.6/lib/libpgf90.a(initpar.o): In function `__hpf_istat':initpar.c:(.text+0x60c): relocation truncated to fit: R_X86_64_PC32 against symbol `__hpf_quiet' defined in COMMON section in /share/apps/pgi10.6/linux86-64/10.6/lib/libpgf90.a(initpar.o)initpar.c:(.text+0x63d): relocation truncated to fit: R_X86_64_PC32 against symbol `__hpf_quiet' defined in COMMON section in /share/apps/pgi10.6/linux86-64/10.6/lib/libpgf90.a(initpar.o)initpar.c:(.text+0x658): relocation truncated to fit: R_X86_64_PC32 against symbol `__hpf_quiet' defined in COMMON section in /share/apps/pgi10.6/linux86-64/10.6/lib/libpgf90.a(initpar.o)initpar.c:(.text+0x673): additional relocation overflows omitted from the outputgmake: *** [/home/mak/exe/1.1.1/hope/cesm.exe] Error 2 We didn't know which part of configuration went wrong and what we should do to fix it.I have done some search on google for a while, and they say something about flag addition.Hope you can help. 

 

[santos]

This is a problem with linking in the PGI runtime, not anything in CESM itself. I did a quick Google search and it looks like you might need "-mcmodel=medium" for this version of PGI (hopefully the right mcmodel was already used to compile netCDF and your MPI implementation on this machine). I can't help much beyond that, since this is really a PGI 10.6 issue, and I don't have that version.

 

[fischer]

There is also a bug in the PGI-10.X compilers that is exposed by CAM, not related to your problem.  I would recommend that youupgrade to at least 11.

 

[makpahr@gmail_com]

Thanks for your reply. We are trying to update our pgi but it will take some time.So I'd like to try our best with what we got, But I dont know where exactly should I add some flags stuff. Can you help me out? And what should I do to check if our NetCDF and MPI is already compiled with the right mcmodel? And what should I do to fix it?Im an undergred and major in Environmental science, sorry to intertupt you with some basic questions.

 

[jedwards]

To check your netcdf and mpi libraries write a simple test program which makes calls to the mpi and netcdf libraries (an example that calls mpi is available in the cesm users guide.)Compile your program with the -mcmodel=medium and link the libraries.   If you get an error you need to rebuild the libraries.   Having said this, I think that you really need to wait to get a new compiler version.  

 

[makpahr@gmail_com]

Hi JedwardsWe updated our compiler to pgi13.7, but we are having the same error as before:here is the log file:------------------------------------------------------------------------- Building a single executable version of CESM -------------------------------------------------------------------------/home/mak/cesm1_1_1/scripts/newpgi/Tools/mkSrcfiles cp -f /home/mak/exe/1.1.1/newpgi/cesm/obj/Filepath /home/mak/exe/1.1.1/newpgi/cesm/obj/Deppath/home/mak/cesm1_1_1/scripts/newpgi/Tools/mkDepends Deppath Srcfiles > /home/mak/exe/1.1.1/newpgi/cesm/obj/Depends/home/mak/cesm1_1_1/scripts/newpgi/Tools/mkSrcfiles mpif90  -o /home/mak/exe/1.1.1/newpgi/cesm.exe ccsm_comp_mod.o ccsm_driver.o mrg_mod.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_map_esmf.o seq_map_mod.o seq_mctext_mod.o seq_rest_mod.o -L/home/mak/exe/1.1.1/newpgi/lib -latm -llnd -lice -locn -lglc -lrof -L/home/mak/exe/1.1.1/newpgi/lib -lcsm_share  -L/home/mak/exe/1.1.1/newpgi/mct/mct -lmct -L/home/mak/exe/1.1.1/newpgi/mct/mpeu -lmpeu -L/home/mak/exe/1.1.1/newpgi/pio -lpio -lgptl -L/share/apps/netcdf-4.3.0-fortran-4.2-pgi13.7/lib -lnetcdf -lnetcdff  -L/share/apps/mpich2-1.5-pgi13.7/lib -lmpich  -time -Wl,--allow-multiple-definition /usr/bin/ld: warning: libnetcdf.so.6, needed by /share/apps/netcdf-4.3.0-fortran-4.2-pgi13.7/lib/libnetcdff.so, may conflict with libnetcdf.so.7/share/apps/pgi13.7/linux86-64/13.7/lib/libpgf90.a(initpar.o): In function `__hpf_myprocnum':initpar.c:(.text+0x6): relocation truncated to fit: R_X86_64_PC32 against symbol `__hpf_lcpu' defined in COMMON section in /share/apps/pgi13.7/linux86-64/13.7/lib/libpgf90.a(initpar.o)/share/apps/pgi13.7/linux86-64/13.7/lib/libpgf90.a(initpar.o): In function `__hpf_ncpus':initpar.c:(.text+0x16): relocation truncated to fit: R_X86_64_PC32 against symbol `__hpf_tcpus' defined in COMMON section in /share/apps/pgi13.7/linux86-64/13.7/lib/libpgf90.a(initpar.o)/share/apps/pgi13.7/linux86-64/13.7/lib/libpgf90.a(initpar.o): In function `__hpf_getioproc':initpar.c:(.text+0x26): relocation truncated to fit: R_X86_64_PC32 against symbol `__hpf_ioproc' defined in COMMON section in /share/apps/pgi13.7/linux86-64/13.7/lib/libpgf90.a(initpar.o)/share/apps/pgi13.7/linux86-64/13.7/lib/libpgf90.a(initpar.o): In function `__hpf_is_ioproc':initpar.c:(.text+0x36): relocation truncated to fit: R_X86_64_PC32 against symbol `__hpf_lcpu' defined in COMMON section in /share/apps/pgi13.7/linux86-64/13.7/lib/libpgf90.a(initpar.o)initpar.c:(.text+0x3e): relocation truncated to fit: R_X86_64_PC32 against symbol `__hpf_ioproc' defined in COMMON section in /share/apps/pgi13.7/linux86-64/13.7/lib/libpgf90.a(initpar.o)/share/apps/pgi13.7/linux86-64/13.7/lib/libpgf90.a(initpar.o): In function `__hpf_abort':initpar.c:(.text+0x7a): relocation truncated to fit: R_X86_64_PC32 against symbol `__hpf_lcpu' defined in COMMON section in /share/apps/pgi13.7/linux86-64/13.7/lib/libpgf90.a(initpar.o)/share/apps/pgi13.7/linux86-64/13.7/lib/libpgf90.a(initpar.o): In function `__hpf_abortp':initpar.c:(.text+0xe0): relocation truncated to fit: R_X86_64_PC32 against symbol `__hpf_lcpu' defined in COMMON section in /share/apps/pgi13.7/linux86-64/13.7/lib/libpgf90.a(initpar.o)/share/apps/pgi13.7/linux86-64/13.7/lib/libpgf90.a(initpar.o): In function `__hpf_getenv':initpar.c:(.text+0x13d): relocation truncated to fit: R_X86_64_PC32 against `.bss'/share/apps/pgi13.7/linux86-64/13.7/lib/libpgf90.a(initpar.o): In function `__hpf_getopt':initpar.c:(.text+0x1de): relocation truncated to fit: R_X86_64_PC32 against `.bss'initpar.c:(.text+0x202): relocation truncated to fit: R_X86_64_PC32 against `.bss'initpar.c:(.text+0x213): additional relocation overflows omitted from the outputgmake: *** [/home/mak/exe/1.1.1/newpgi/cesm.exe] Error 2 Hope you can help us with this error. 

 

[jedwards]

Now that you have the new compiler version you need to recompile netcdf and mpi including the flag:-mcmodel=medium then you should be able to compile and link CESM

 

[makpahr@gmail_com]

We successfully recompiled our mpich2 with this flag, but having trouble with netcdf compiling.We tried to switch to higher version of netcdf 4.3.0, but we found out that netcdf 4.3 has C stable releases, fortran releases and c++ releases. Do we have to download them all and compile in one directoty? Why I am asking this is that, CESM has been built successfully, but when we try to run the case, it shows:/home/mak/exe/1.1.1/newpgi/cesm.exe: error while loading shared libraries: libnetcdf.so.6: cannot open shared object file: No such file or directoryIt seems like our netcdf compiling has some problems(And we dont know what this libnetcdf.so.6 is). Can you help some a little more concretly on how we should compile netcdf? Or do you have a preference on a netcdf version that you could recommend us?Thanks for your great help. 

 

[jedwards]

With 4.3.0 you need the c and fortran libraries.   Help with building netcdf is available through their website at http://www.unidata.ucar.edu/software/netcdf/