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undefined reference to `ddot_' when building CESM1.2.2

W

wadewei

Wade Wei
New Member
Hi everyone,

I used to run F1850 compset with my CESM1.2.2. Today when I was trying out -compset F_1850_CN_GLC_CISM1, build failed with the following message. A bit of googling tells me this has something to do with lapack but didn't yield much else. I am using intel compiler and mkl 2016u2 FYI. Does anyone have a clue? Thank you very much!

Wade


I have mpiifort -o /home/wade/cesmcasedata/archive/test_CISM__1014/bld/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/wade/cesmcasedata/archive/test_CISM__1014/bld/lib/ -latm -L/home/wade/cesmcasedata/archive/test_CISM__1014/bld/lib/ -lice -L/home/wade/cesmcasedata/archive/test_CISM__1014/bld/lib/ -llnd -L/home/wade/cesmcasedata/archive/test_CISM__1014/bld/lib/ -locn -L/home/wade/cesmcasedata/archive/test_CISM__1014/bld/lib/ -lrof -L/home/wade/cesmcasedata/archive/test_CISM__1014/bld/lib/ -lglc -L/home/wade/cesmcasedata/archive/test_CISM__1014/bld/lib/ -lwav -L/home/wade/cesmcasedata/archive/test_CISM__1014/bld/glc/lib/ -lglimmercismfortran -L/home/wade/cesmcasedata/archive/test_CISM__1014/bld/intel/impi/nodebug/nothreads/MCT/noesmf/a1l1r1i1o1g1w1/csm_share -lcsm_share -L/home/wade/cesmcasedata/archive/test_CISM__1014/bld/intel/impi/nodebug/nothreads/lib -lpio -lgptl -lmct -lmpeu -L/opt/netcdf/4.3.2-intel16/lib -lnetcdf -L/opt/intel/2016u2/compilers_and_libraries/linux/mpi/bin64/lib -lmpi -L/opt/hdf5/1.8.18-intel16/lib -lhdf5 -L/opt/netcdf/4.3.2-intel16/lib -lnetcdf -lnetcdff
/home/wade/cesmcasedata/archive/test_CISM__1014/bld/glc/lib//libglimmercismfortran.a(dcgs.f.o): In function `dcgs_':
dcgs.f:(.text+0x54b): undefined reference to `ddot_'
dcgs.f:(.text+0x9ab): undefined reference to `ddot_'
dcgs.f:(.text+0xcb5): undefined reference to `daxpy_'
dcgs.f:(.text+0xd3f): undefined reference to `daxpy_'
/home/wade/cesmcasedata/archive/test_CISM__1014/bld/glc/lib//libglimmercismfortran.a(dcgs.f.o): In function `isdcgs_':
dcgs.f:(.text+0x1178): undefined reference to `dnrm2_'
dcgs.f:(.text+0x1196): undefined reference to `dnrm2_'
dcgs.f:(.text+0x11c5): undefined reference to `dnrm2_'
dcgs.f:(.text+0x1260): undefined reference to `dnrm2_'
dcgs.f:(.text+0x12c4): undefined reference to `dnrm2_'
/home/wade/cesmcasedata/archive/test_CISM__1014/bld/glc/lib//libglimmercismfortran.a(dcgs.f.o):dcgs.f:(.text+0x1442): more undefined references to `dnrm2_' follow
/home/wade/cesmcasedata/archive/test_CISM__1014/bld/glc/lib//libglimmercismfortran.a(dcgs.f.o): In function `dsdcgs_':
dcgs.f:(.text+0x1ca5): undefined reference to `ddot_'
dcgs.f:(.text+0x215a): undefined reference to `ddot_'
dcgs.f:(.text+0x2465): undefined reference to `daxpy_'
dcgs.f:(.text+0x24f4): undefined reference to `daxpy_'
 
W

wadewei

Wade Wei
New Member
Added -mkl=cluster to config_compilers.xml directly will result in mct compilation to fail from the beginning.

vi test_CISM_1014/bld/intel/impi/nodebug/nothreads/mct/config.log
configure:2398: checking whether the C compiler works
configure:2420: icc -O2 -fp-model precise -xHost -DLINUX -DNDEBUG -DMCT_INTERFACE -DHAVE_MPI -DFORTRANUNDERSCORE -DNO_R16 -DLINUX -DCPRINTEL -DHAVE_SLASHPROC -I.. -I. -I/home/wade/cesmcasedata/archive/test_CISM_1014/bld/intel/impi/nodebug/nothreads/include -I/home/wade/cesmcasedata/archive/test_CISM_1014/bld/intel/impi/nodebug/nothreads/MCT/noesmf/a1l1r1i1o1g1w1/csm_share -I/opt/netcdf/4.3.2-intel16/include -I/opt/intel/2016u2/compilers_and_libraries/linux/mpi/bin64/include -I/home/wade/cesmcasedata/archive/test_CISM_1014/bld/intel/impi/nodebug/nothreads/include -I/home/wade/cesm1_2_2/models/csm_share/shr -L/opt/hdf5/1.8.18-intel16/lib -lhdf5 -L/opt/netcdf/4.3.2-intel16/lib -lnetcdf -lnetcdff conftest.c /opt/intel/2016/compilers_and_libraries_2016/linux/mkl/lib/intel64/libmkl_blas95_lp64.a /opt/intel/2016/compilers_and_libraries_2016/linux/mkl/lib/intel64/libmkl_lapack95_lp64.a -L/opt/intel/2016/compilers_and_libraries_2016/linux/mkl/lib/intel64 -liomp5 -lpthread -lm -ldl -mkl=cluster >&5
/opt/intel/2016/compilers_and_libraries_2016/linux/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.so: undefined reference to `MPI_Waitall'
/opt/intel/2016/compilers_and_libraries_2016/linux/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.so: undefined reference to `MPI_Abort'
/opt/intel/2016/compilers_and_libraries_2016/linux/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.so: undefined reference to `MPI_Waitany'
/opt/intel/2016/compilers_and_libraries_2016/linux/mkl/lib/intel64/libmkl_blacs_intelmpi_lp64.so: undefined reference to `MPI_Wtime'
 
W

wadewei

Wade Wei
New Member
jedwards said:
The compiler should not be icc it should be mpicc or mpiicc
Click to expand...
Emmm I took a look at previous F-compset cases that were working, they seem to have the same icc -o test here at the beginning of config.log.
MPICC were indeed set to mpiicc in config_compilers.xml. I wonder though, what the SCC option in that file is meant for.

Below is the machine-specific contents in config_compilers.xml

<compiler MACH="paleo">
<MPICC>mpiicc</MPICC>
<MPIFC>mpiifort</MPIFC>
<MPICXX>mpiicpc</MPICXX>
<SFC>ifort</SFC>
<SCC>icc</SCC>
<SCXX>icpc</SCXX>
<ADD_FFLAGS> -xHost </ADD_FFLAGS>
<ADD_CFLAGS> -xHost </ADD_CFLAGS>
<ADD_LDFLAGS>-L/opt/hdf5/1.8.18-intel16/lib -lhdf5 -L/opt/netcdf/4.3.2-intel16/lib -lnetcdf -lnetcdff</ADD_LDFLAGS>
<NETCDF_PATH>/opt/netcdf/4.3.2-intel16</NETCDF_PATH>
<ADD_SLIBS>/opt/intel/2016/compilers_and_libraries_2016/linux/mkl/lib/intel64/libmkl_blas95_lp64.a /opt/intel/2016/compilers_and_libraries_2016/linux/mkl/lib/intel64/libmkl_lapack95_lp64.a -L/opt/intel/2016/compilers_and_libraries_2016/linux/mkl/lib/intel64 -liomp5 -lpthread -lm -ldl</ADD_SLIBS>
<MPI_PATH>/opt/intel/2016u2/compilers_and_libraries/linux/mpi/bin64</MPI_PATH>
</compiler>
 
J

jedwards

CSEG and Liaisons
Staff member
Ah I see. I think that you added the mkl=cluster to LDFLAGS, it should be SLIBS instead.
 
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