CESM Error on Bluegene

[devarajun@gmail_com]

I am getting the following error on Bluegene with front end node OS Linux:

_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/home/caos2/casgbala/dev_blugene/CESM102/30April/cesm1_0_2/casgbala/test1/lib -latm -llnd -lice -locn -lglc -L/home/caos2/casgbala/dev_blugene/CESM102/30April/cesm1_0_2/casgbala/test1/lib -lcsm_share -lmct -lmpeu -lpio-L/opt/ibmmath/essl/4.2/lib -lmass -lmassv -L/home/caos2/casgbala/dev_blugene/netcdf_bgxlf90/lib -lnetcdf -L/bgl/BlueLight/ppcfloor/bglsys/lib -lmpich.rts -lmsglayer.rts -lrts.rts -ldevices.rts -Wl,--allow-multiple-definition
/home/caos2/casgbala/dev_blugene/netcdf_bgxlf90/lib/libnetcdf.a(posixio.o): In function `fgrow':
/home/caos2/casgbala/dev_blugene/netcdf-3.6.2/libsrc/posixio.c:133: undefined reference to `__errno_location'
/home/caos2/casgbala/dev_blugene/netcdf-3.6.2/libsrc/posixio.c:142: undefined reference to `__errno_location'
/home/caos2/casgbala/dev_blugene/netcdf-3.6.2/libsrc/posixio.c:144: undefined reference to `__errno_location'
/home/caos2/casgbala/dev_blugene/netcdf-3.6.2/libsrc/posixio.c:146: undefined reference to `__errno_location'
/home/caos2/casgbala/dev_blugene/netcdf-3.6.2/libsrc/posixio.c:148: undefined reference to `__errno_location'
/home/caos2/casgbala/dev_blugene/netcdf_bgxlf90/lib/libnetcdf.a(posixio.o):/home/caos2/casgbala/dev_blugene/netcdf-3.6.2/libsrc/posixio.c:1474: more undefined references to `__errno_location' follow
gmake: *** [/home/caos2/casgbala/dev_blugene/CESM102/30April/cesm1_0_2/casgbala/test1/run/ccsm.exe] Error 1

Thanks.

 

[eaton]

Since the undefined reference is originating in the netcdf library, this would appear to be a system issue. You need to find out where the '__errno_location' external is defined (perhaps with the help of your systems administrators) and add that library to the link command.

 

[devarajun@gmail_com]

1501-510 Compilation successful for file ccsm_driver.F90.
bgxlf90 -o /home/caos2/casgbala/dev_blugene/CESM102/30April/cesm1_0_2/casgbala/test1/run/ccsm.exe 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/home/caos2/casgbala/dev_blugene/CESM102/30April/cesm1_0_2/casgbala/test1/lib -latm -llnd -lice -locn -lglc -L/home/caos2/casgbala/dev_blugene/CESM102/30April/cesm1_0_2/casgbala/test1/lib -lcsm_share -lmct -lmpeu -lpio .rts -L/opt/ibmmath/essl/4.2/lib -lmass -lmassv -L/home/caos2/casgbala/dev_blugene/netcdf_bgxlf90/lib -lnetcdf -L/bgl/BlueLight/ppcfloor/bglsys/lib -lmpich.rts -lmsglayer.rts -lrts.rts -ldevices.rts -Wl,--allow-multiple-definition -L/usr/lib -lc
/opt/ibmcmp/xlf/bg/11.1/blrts_lib/libxlf90.a(open.o): In function `SetDefaults':
/build/xlf/111_com/xlf.111.bg-prod-opt-bgl/xlf/rte2/src/io/shr/open.c:(.text+0x1a3c): warning: the use of `mktemp' is dangerous, better use `mkstemp'
/bgl/BlueLight/ppcfloor/bglsys/lib/libmpich.rts.a(mpidtime.o): In function `MPID_Wtime_init':
/bglhome/usr6/bgbuild/V1R3M4_300_2008-080728/ppc/src/bglsw/comm/lib/mpi/mpich2/src/mpi/timer/mpidtime.c:124: undefined reference to `rts_get_personality'
/bgl/BlueLight/ppcfloor/bglsys/lib/libmpich.rts.a(mpid_init.o): In function `MPID_Init':
/bglhome/usr6/bgbuild/V1R3M4_300_2008-080728/ppc/src/bglsw/comm/lib/mpi/mpich2/src/mpid/bgltorus5/src/mpid_init.c:167: undefined reference to `rts_get_personality'
/bglhome/usr6/bgbuild/V1R3M4_300_2008-080728/ppc/src/bglsw/comm/lib/mpi/mpich2/src/mpid/bgltorus5/src/mpid_init.c:81: undefined reference to `rts_alloc_lockbox'
/bgl/BlueLight/ppcfloor/bglsys/lib/libmpich.rts.a(mpid_collectives.o): In function `MPIDI_Coll_Comm_create':
/bglhome/usr6/bgbuild/V1R3M4_300_2008-080728/ppc/src/bglsw/comm/lib/mpi/mpich2/src/mpid/bgltorus5/src/coll/mpid_collectives.c:30: undefined reference to `rts_get_personality'
/bgl/BlueLight/ppcfloor/bglsys/lib/libmpich.rts.a(mpid_coll_utils.o): In function `MPIDI_BGLTS_findRect':
/bglhome/usr6/bgbuild/V1R3M4_300_2008-080728/ppc/src/bglsw/comm/lib/mpi/mpich2/src/mpid/bgltorus5/src/coll/mpid_coll_utils.c:307: undefined reference to `rts_get_personality'
/bgl/BlueLight/ppcfloor/bglsys/lib/libmpich.rts.a(mpidi_physical_cart.o): In function `MPIDI_PhysicalCart_init':
/bglhome/usr6/bgbuild/V1R3M4_300_2008-080728/ppc/src/bglsw/comm/lib/mpi/mpich2/src/mpid/bgltorus5/src/topo/mpidi_physical_cart.c:68: undefined reference to `rts_get_personality'
/bgl/BlueLight/ppcfloor/bglsys/lib/libmpich.rts.a(bgltorus_simple_pmi.o): In function `PMI_Cart_comm_create':
/bglhome/usr6/bgbuild/V1R3M4_300_2008-080728/ppc/src/bglsw/comm/lib/mpi/mpich2/src/pmi/bgltorus_simple/bgltorus_simple_pmi.c:176: undefined reference to `rts_get_personality'
/bgl/BlueLight/ppcfloor/bglsys/lib/libmpich.rts.a(bgltorus_simple_pmi.o): In function `PMI_Pset_same_comm_create':
/bglhome/usr6/bgbuild/V1R3M4_300_2008-080728/ppc/src/bglsw/comm/lib/mpi/mpich2/src/pmi/bgltorus_simple/bgltorus_simple_pmi.c:225: undefined reference to `rts_get_personality'
/bgl/BlueLight/ppcfloor/bglsys/lib/libmpich.rts.a(bgltorus_simple_pmi.o):/bglhome/usr6/bgbuild/V1R3M4_300_2008-080728/ppc/src/bglsw/comm/lib/mpi/mpich2/src/pmi/bgltorus_simple/bgltorus_simple_pmi.c:239: more undefined references to `rts_get_personality' follow
/bgl/BlueLight/ppcfloor/bglsys/lib/libmsglayer.rts.a(BGLML_Init.rts.o): In function `BGLML_Messager_VM_Init':
/bglhome/usr6/bgbuild/V1R3M4_300_2008-080728/ppc/src/bglsw/comm/sys/msglayer/base/messager/BGLML_Init.c:277: undefined reference to `rts_get_scratchpad_window'

 

[jedwards]

On my bluegene system rts_get_personality is located in /bgl/BlueLight/ppcfloor/bglsys/lib/libmpich.rts.a
and ppcfloor points to version
V1R3M4_300_2008-080728/ppc

It should be in the same location on your system - I suggest that you find someone experienced with building on
your bluegene system to help you with this issue.

- Jim