CESM1_0_6 - Porting to a new cluster - PGI and Openmpi

[divy@mit_edu]

Hi,
I'm trying to port CESM1.0.6. I'm using PGI13.8 and OPENMPI 1.7.2.

Initially I get this error during the build stage for ccsm.
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/net/fs02/d3/divy/cesm/test_blah4/lib/libpio.a(pionfget_mod.o): In function `pionfget_mod_get_var_5d_int_':
/net/fs02/d3/divy/cesm/test_blah4/pio/./pionfget_mod.F90:5406: undefined reference to `netcdf_nf90_get_var_5d_fourbyteint_'
/net/fs02/d3/divy/cesm/test_blah4/pio/./pionfget_mod.F90:5410: undefined reference to `netcdf_nf90_get_var_5d_fourbyteint_'
/net/fs02/d3/divy/cesm/test_blah4/lib/libpio.a(pionfget_mod.o): In function `.C73_305':
pionfget_mod.F90:(.data+0x103c): undefined reference to `netcdf_'
pionfget_mod.F90:(.data+0x1044): undefined reference to `typesizes_'
/net/fs02/d3/divy/cesm/test_blah4/lib/libpio.a(pio_msg_getput_callbacks.o): In function `.C24_284':
pio_msg_getput_callbacks.F90:(.data+0x388): undefined reference to `typesizes_'
pio_msg_getput_callbacks.F90:(.data+0x390): undefined reference to `netcdf_'
gmake: *** [/net/fs02/d3/divy/cesm/test_blah4/run/ccsm.exe] Error 2
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I included a linking flag to my Macros file:
SLIBS += -L$(LIB_NETCDF) -lnetcdff

However, the build seems to stop even earlier with this error message.

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mpif90 -o /net/fs02/d3/divy/cesm/test_blah_link2/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/net/fs02/d3/divy/cesm/test_blah_link2/lib -latm -llnd -lice -locn -lglc -L/net/fs02/d3/divy/cesm/test_blah_link2/lib -lcsm_share -lmct -lmpeu -lpio -L/home/software/pgi/pgi-13.8/pkg/netcdf/netcdf-20130909/lib -lnetcdff -L/home/software/pgi/pgi-13.8/pkg/netcdf/netcdf-20130909/lib -lnetcdf -L/home/software/pgi/pgi-13.8/pkg/openmpi/openmpi-1.7.2/lib -lmpi
/net/fs02/d3/divy/cesm/test_blah_link2/lib/liblnd.a(abortutils.o): In function `abortutils_endrun_':
/home/divy/cesm1_0_6/models/lnd/clm/src/main/abortutils.F90:55: multiple definition of `..Dm_abortutils'
/net/fs02/d3/divy/cesm/test_blah_link2/lib/libatm.a(abortutils.o):/home/divy/cesm1_0_6/models/atm/cam/src/utils/abortutils.F90:35: first defined here
/net/fs02/d3/divy/cesm/test_blah_link2/lib/liblnd.a(abortutils.o): In function `abortutils_':
abortutils.F90:(.text+0x0): multiple definition of `abortutils_'
/net/fs02/d3/divy/cesm/test_blah_link2/lib/libatm.a(abortutils.o):abortutils.F90:(.text+0x0): first defined here
/net/fs02/d3/divy/cesm/test_blah_link2/lib/liblnd.a(abortutils.o): In function `abortutils_endrun_':
(.text+0x10): multiple definition of `abortutils_endrun_'
/net/fs02/d3/divy/cesm/test_blah_link2/lib/libatm.a(abortutils.o):(.text+0x10): first defined here
gmake: *** [/net/fs02/d3/divy/cesm/test_blah_link2/run/ccsm.exe] Error 2
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Any help would be greatly appreciated!
Thanks,
Diane

 

[jedwards]

Try adding the flag -Wl,-z,muldefs to your LDFLAGS.

 

[jedwards]

Try adding the flag -Wl,-z,muldefs to your LDFLAGS.

 

[divy@mit_edu]

That worked! Thanks so much!Diane

 

[divy@mit_edu]

That worked! Thanks so much!Diane

 

[zhuchenxia]

I also met the similar problem. With the error information below:
pionfget_mod.F90:(.data+0x10c8): undefined reference to `netcdf_'
pionfget_mod.F90:(.data+0x10d8): undefined reference to `typesizes_'
/nuist/u/home/wangguojie/wgj_zhucx/cases/XcomUser/bld/pgi/mpich/nodebug/nothreads/lib/libpio.a(pio_msg_getput_callbacks.F90.o): In function `.C24_284':
pio_msg_getput_callbacks.F90:(.data+0x3a0): undefined reference to `typesizes_'
pio_msg_getput_callbacks.F90:(.data+0x3a8): undefined reference to `netcdf_'
gmake: *** [/nuist/u/home/wangguojie/wgj_zhucx/cases/XcomUser/bld/cesm.exe] Error 2

I have tried the solution above. Go to the config_compilers, and add the -Wl,-z into LDFLAGS. However, it didn't work.

Could you please give some suggestions?