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Failed to build cesm.exe because of unsuccessfully linking the netcdf and mpi libs

X

xgsun

New Member
I'm trying to build the CESM2.1.2 on my own linux platform by prescribing the machine name "homebrew" for the create_newcase, and I can successfully run the case.setup. However, when I run the case.build, it failed to build the executable file cesm.exe at last and showed the information about unsuccessfully linking the netcdf and mpi libs.

I specified the environment for the NETCDF lib in the config_machines.xml as follows,

<environment_variables>
<env name="NETCDF_PATH">/opt/netcdf/netcdf-c4.6.2-f4.4.4-intel2019</env>
</environment_variables>

In the cesm/cases/*/Tools/Makefile, I can see that netcdf and mpi should be linked while building the cesm.exe.

$(EXEC_SE): $(OBJS) $(ULIBDEP) $(CSMSHARELIB) $(MCTLIBS) $(PIOLIB) $(GPTLLIB)
$(LD) -o $(EXEC_SE) $(OBJS) $(CLIBS) $(ULIBS) $(SLIBS) $(MLIBS) $(LDFLAGS)

I'm not sure whether the settings of netcdf and mpi are needed in other places, any suggestions to solve this problem? Attached please find the config_machines.xml and Macro.make.

Thank you.

Sun
 

Attachments

  • config_machines.xml.txt
    106.4 KB · Views: 14
  • Macros.make.txt
    1.7 KB · Views: 6
J

jedwards

CSEG and Liaisons
Staff member
The machine name homebrew is meant as a generic base for an apple OSx system. The analogous linux platform is centos7-linux.
Without seeing the error I can't determine why you are unable to link netcdf and mpi libraries.
 
X

xgsun

New Member
Though homebrew is used as the machine name, I have made the corresponding settings on my linux platform. I think it should be ok.
Attached is the log file for case.build, and the config_machines.xml was attached before. please help to solve the problem. Thanks.
 

Attachments

  • cesm.bldlog.200608-230607.txt
    222.3 KB · Views: 5
J

jedwards

CSEG and Liaisons
Staff member
Still not sure what is going on here - can you attach the pio.bldlog? You might try defining NETCDF instead of NETCDF_PATH
 
X

xgsun

New Member
I tried to define NETCDF instead of NETCDF_PATH in config_machines.xml, but it comes out errors while running the case.build for mct.bldlog, which indicates the netcdf lib cannot be found,

gmake -f /data1/xgsun/cesm/cases/B1850cmip6.f09_g17/Tools/Makefile -C /home/xgsun/work/cesm/scratch/B1850cmip6.f09_g17/bld/intel/impi/nodebug/nothreads/mct CASEROOT=/data1/xgsun/cesm/cases/B1850cmip6.f09_g17 MODEL=mct /home/xgsun/work/cesm/scratch/B1850cmip6.f09_g17/bld/intel/impi/nodebug/nothreads/mct/Makefile.conf
gmake: Entering directory `/data1/xgsun/cesm/scratch/B1850cmip6.f09_g17/bld/intel/impi/nodebug/nothreads/mct'
gmake: Leaving directory `/data1/xgsun/cesm/scratch/B1850cmip6.f09_g17/bld/intel/impi/nodebug/nothreads/mct'
cat: Filepath: No such file or directory
/data1/xgsun/cesm/cases/B1850cmip6.f09_g17/Tools/Makefile:199: *** NETCDF not found: Define NETCDF_PATH or NETCDF_C_PATH and NETCDF_FORTRAN_PATH in config_machines.xml or config_compilers.xml. Stop.
ERROR: cat: Filepath: No such file or directory
/data1/xgsun/cesm/cases/B1850cmip6.f09_g17/Tools/Makefile:199: *** NETCDF not found: Define NETCDF_PATH or NETCDF_C_PATH and NETCDF_FORTRAN_PATH in config_machines.xml or config_compilers.xml. Stop.

So I think the definition of NETCDF_PATH should be correct, and return back to use the NETCDF_PATH.

I attached the pio.bldlog and cesm.bldlog. From the output errors in cesm.bldlog, I understand that to finally build the cesm.exe, it should link the netcdf and mpi libs, but I cannot see the flags in the command line

mpiifort -o /home/xgsun/work/cesm/scratch/B1850cmip6.f09_g17/bld/cesm.exe cime_comp_mod.o cime_driver.o component_mod.o component_type_mod.o cplcomp_exchange_mod.o map_glc2lnd_mod.o map_lnd2glc_mod.o map_lnd2rof_irrig_mod.o mrg_mod.o prep_aoflux_mod.o prep_atm_mod.o prep_glc_mod.o prep_ice_mod.o prep_lnd_mod.o prep_ocn_mod.o prep_rof_mod.o prep_wav_mod.o seq_diag_mct.o seq_domain_mct.o seq_flux_mct.o seq_frac_mct.o seq_hist_mod.o seq_io_mod.o seq_map_mod.o seq_map_type_mod.o seq_rest_mod.o t_driver_timers_mod.o -L/home/xgsun/work/cesm/scratch/B1850cmip6.f09_g17/bld/lib/ -latm -L/home/xgsun/work/cesm/scratch/B1850cmip6.f09_g17/bld/lib/ -lice -L../../intel/impi/nodebug/nothreads/mct/noesmf/lib/ -lclm -L/home/xgsun/work/cesm/scratch/B1850cmip6.f09_g17/bld/lib/ -locn -L/home/xgsun/work/cesm/scratch/B1850cmip6.f09_g17/bld/lib/ -lrof -L/home/xgsun/work/cesm/scratch/B1850cmip6.f09_g17/bld/lib/ -lglc -L/home/xgsun/work/cesm/scratch/B1850cmip6.f09_g17/bld/lib/ -lwav -L/home/xgsun/work/cesm/scratch/B1850cmip6.f09_g17/bld/lib/ -lesp -L../../glc/lib/ -lglimmercismfortran -L../../intel/impi/nodebug/nothreads/mct/noesmf/c1a1l1i1o1r1g1w1e1/lib -lcsm_share -L../../intel/impi/nodebug/nothreads/lib -lpio -lgptl -lmct -lmpeu -mkl=cluster

I'm wondering where I can add the link flags for netcdf and mpi in the "mpiifort -o ....", in other words, in which file I can specify the link flags manually.
Any suggestions? Thanks.
 

Attachments

  • cesm.bldlog.200609-084601.txt
    248.5 KB · Views: 6
  • pio.bldlog.200609-084601.txt
    65.6 KB · Views: 4
J

jedwards

CSEG and Liaisons
Staff member
Try setting NETCDF_PATH in the config_compilers.xml file instead of in config_machines.xml, you will find several examples in that file of how to do that.
 
X

xgsun

New Member
The model can finally be successfully be built when I set the NETCDF_PATH in the config_compliers.xml file. Thanks.
But another problem comes out when I run the case.submit, I just show the error information in the cesm.log.xxx

[proxy:0:0@intel1] HYD_spawn (../../../../../src/pm/i_hydra/libhydra/spawn/intel/hydra_spawn.c:57): pipe error (Too many open files)
[proxy:0:0@intel1] launch_processes (../../../../../src/pm/i_hydra/proxy/proxy.c:550): error creating process
[proxy:0:0@intel1] main (../../../../../src/pm/i_hydra/proxy/proxy.c:892): error launching_processes
[mpiexec@intel1] wait_proxies_to_terminate (../../../../../src/pm/i_hydra/mpiexec/intel/i_mpiexec.c:528): downstream from host intel1 exited with status 3
[mpiexec@intel1] main (../../../../../src/pm/i_hydra/mpiexec/mpiexec.c:2077): assert (exitcodes != NULL) failed

I think it may be due to that too many nodes are required when I run the cesm.exe. I checked the run information by ./preview_run, and it shows

CASE INFO:
nodes: 9
total tasks: 864
tasks per node: 96
thread count: 1

BATCH INFO:
FOR JOB: case.run

ENV:
Setting Environment NETCDF_PATH=/opt/netcdf/netcdf-c4.6.2-f4.4.4-intel2019
Setting Environment OMP_NUM_THREADS=1

SUBMIT CMD:
None

MPIRUN (job=case.run):
mpirun -np 864 -prepend-rank /home/xgsun/work/cesm/scratch/B1850cmip6.f09_g17/bld/cesm.exe >> cesm.log.$LID 2>&1

FOR JOB: case.st_archive
ENV:
Setting Environment NETCDF_PATH=/opt/netcdf/netcdf-c4.6.2-f4.4.4-intel2019
Setting Environment OMP_NUM_THREADS=1

SUBMIT CMD:
None


I did set the tasks per node 96 in the config_machines.xml, but I didn't prescribe 9 nodes since my platform only has one node. I'm wondering where it comes from. Any suggestions about the number of nodes and the running error? Thanks.
 
J

jedwards

CSEG and Liaisons
Staff member
You are getting a default setup. You can change it in the case with
./xmlchange NTASKS=96
./xmlchange ROOTPE=0

You can probably tune that for better performance, but these settings should at least run.
 
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