Maria
April 2, 2019, 4:44pm
1
Hi all
I am trying to compile CCTM but an error comes up:
mpiifort -qopenmp se_bndy_copy_info_ext.o se_pe_info_ext.o se_comm_info_ext.o se_data_send_module.o se_domain_info_ext.o se_internal_util_module.o se_data_recv_module.o se_disp_info_ext.o se_subgrid_info_ext.o se_global_sum_module.o se_global_max_module.o se_global_min_module.o se_slice_module.o se_init_module.o se_bndy_copy_module.o se_comm_module.o se_reconfig_grid_info_ext.o se_reconfig_grid_module.o se_gather_module.o se_data_copy_module.o se_term_module.o se_twoway_comm_module.o se_util_module.o se_modules.o swap_sandia.o swap_sandia_routines.o alloc_data_mod.o pinterpb_mod.o parutilio.o piomaps_mod.o boundary.o get_write_map.o growbuf.o gtndxhdv.o interpol.o pinterpb.o pio_init.o pm3err.o pm3exit.o pm3warn.o pshut3.o ptrwrite3.o pwrgrdd.o pwrite3.o readbndy.o subdmap.o wrsubdmap.o UTILIO_DEFN.o HGRD_DEFN.o VGRD_DEFN.o GRID_CONF.o CGRID_SPCS.o PA_DEFN.o PCGRID_DEFN.o AVG_CONC.o DEPVVARS.o BIDI_MOD.o LSM_MOD.o ASX_DATA_MOD.o HGSIM.o MOSAIC_MOD.o RXNS_DATA_MODULE.o BIOG_EMIS.o BEIS_DEFN.o LUS_DEFN.o LTNG_DEFN.o AEROMET_DATA.o AERO_DATA.o UDTYPES.o STK_EMIS.o STK_PRMS.o PTMAP.o PTBILIN.o SSEMIS.o bmatvec.o PTMET.o DEPV_DEFN.o STD_CONC.o CSQY_DATA.o CLOUD_OPTICS.o PHOT_MET_DATA.o DUST_EMIS.o RXNS_FUNC_MODULE.o PRECURSOR_DATA.o MGEMIS.o PT3D_DEFN.o SOA_DEFN.o AERO_EMIS.o AEROSOL_CHEMISTRY.o PAGRD_DEFN.o EMIS_DEFN.o WVEL_DEFN.o distr_env.o mpcomm_init.o advstep.o driver.o hveloc.o sciproc.o wr_aconc.o wr_cgrid.o wr_conc.o wr_init.o diffmsg.o flcheck.o grdcheck.o initscen.o load_cgrid.o opaconc.o opconc.o couplewrf.o advbc_map.o hadvyppm.o hcontvel.o hppm.o rdbcon.o x_ppm.o x_yamo.o y_ppm.o y_yamo.o zfdbc.o vppm.o zadvppmwrf.o deform.o hcdiff3d.o hdiff.o rho_j.o VDIFF_DIAG.o VDIFF_MAP.o SEDIMENTATION.o aero_sedv.o conv_cgrid.o eddyx.o matrix1.o opddep.o opddep_fst.o opddep_mos.o rddepv.o tri.o vdiffacmx.o vdiffproc.o ABFLUX_MOD.o cgrid_depv.o gas_depv_map.o m3dry.o opdepv_diag.o opdepv_fst.o opdepv_mos.o cropcal.o opemis.o tfabove.o tfbelow.o beis3.o checkmem.o chkgrid.o czangle.o getfline.o getparb.o hrno.o parsline.o tmpbeis.o wrdaymsg.o delta_zs.o fire_plmris.o openlayout.o oppt3d_diag.o plmris.o plsprd.o preplm.o ungridb2.o write3_distr.o complex_number_module.o twoway_rrtmg_aero_optics.o AERO_PHOTDATA.o PHOT_MOD.o SEAS_STRAT_O3_MIN.o PHOTOLYSIS_ALBEDO.o o3totcol.o opphot.o phot.o DEGRADE_SETUP_TOX.o hrdata_mod.o degrade_data.o degrade.o final_degrade.o find_degraded.o hrdriver.o hrg1.o hrg2.o hrg3.o hrg4.o hrinit.o hrprodloss.o hrrates.o hrsolver.o init_degrade.o AOD_DEFN.o PMDIAG_DATA.o aero_depv.o aero_driver.o aero_subs.o coags.o getpar.o isocom.o isofwd.o isorev.o opapmdiag.o opavis.o oppmdiag.o opvis.o AQ_DATA.o acmcld.o aqchem.o aq_map.o cldproc_acm.o convcld_acm.o getalpha.o hlconst.o indexn.o opwdep.o rescld.o scavwdep.o PA_GLOBAL.o PA_IPRDEF.o PA_VARS.o PA_PARSE.o PA_IPRVARS.o pa_compmech.o pa_datagen.o pa_errcheck.o pa_getcoef.o pa_getcycle.o pa_getdesc.o pa_getfamily.o pa_getiprout.o pa_getirrout.o pa_getrxns.o pa_getrxnsum.o pa_init.o pa_irr_ctl.o pa_irr.o pa_mkhdr.o pa_molcloss.o pa_molcprod.o pa_output.o pa_read.o pa_report.o pa_setup_ipr.o pa_setup_irr.o pa_update.o pa_wrtpadefn.o cksummer.o findex.o get_envlist.o lstepf.o setup_logdev.o subhdomain.o subhfile.o -L/media/maria/Backup/CMAQ_Project/PREP/mcip/src/lib/x86_64/intel/ioapi/lib -lioapi -L/media/maria/Backup/CMAQ_Project/PREP/mcip/src/lib/x86_64/intel/netcdf/lib -lnetcdff -lnetcdf -L/media/maria/Backup/CMAQ_Project/PREP/mcip/src/lib/x86_64/intel/mpi/lib -lcurl -o CCTM_v52.exe
I am not a specialist about compilers or programming. I was searching on Internet a possible solution, however I didn’t find anything about it.
Do you have any idea?
Maria
Hi Maria,
It may be something as simple of adding -lmpi to your config_cmaq.csh
config_cmaq.csh: setenv mpi_lib “-lmpi”
If this doesn’t work, please send the following information:
module list
If not, use the command which mpiifort to reveal what compiler you are using:
which mpiifort
Maria
April 2, 2019, 8:57pm
3
Thank you for your reply.
When I typed “which mpiifort” the result is:
/media/maria/Backup/intel/compilers_and_libraries_2019.3.199/linux/mpi/intel64/bin/mpiifort
Then, I decided to change the path in:
But a new error comes up:
So, I suppose that the change is not in the correct environment variable. Do I have to change the path in other place?
Maria
Hi Maria,
Please try adding the following environment variable to your config_cmaq.csh
setenv myLINK_FLAG "-qopenmp"
Liz
Maria
April 4, 2019, 9:10pm
5
Hi Liz
In my current config_cmaq.csh file, I have that environment variable but the error persists:
setenv IOAPI_MOD_DIR /media/maria/Backup/IOAPI3.1/Linux2_x86_64ifort/ #> I/O API precompiled modules
#> Compiler Aliases and Flags
setenv myFC mpiifort
setenv myCC icc
setenv myFSTD "-O3 -fno-alias -mp1 -fp-model source"
setenv myDBG "-O0 -g -check bounds -check uninit -fpe0 -fno-alias -ftrapuv -traceback"
setenv myLINK_FLAG "-qopenmp"
setenv myFFLAGS "-fixed -132"
setenv myFRFLAGS "-free"
setenv myCFLAGS "-O2"
setenv extra_lib "-lcurl"
#setenv extra_lib ""
setenv mpi_lib ""
I really appreciate your help
Maria
@lizadams Hello
Please, below is the response I got while trying to configure CMAQ:
ERROR: /home/catalyst/Desktop/Build_WRF/CMAQ-5.2.1/lib/x86_64/gcc/netcdf/lib/libnetcdf.a does not exist in your CMAQ_LIB directorysource config_cmaq.csh gcc! Check your installation before proceeding with CMAQ build.
Also, while compiling ICON and BCON:
ERROR
Kindly help, please.
Please use the following instructions to install the required software.
## CMAQ Tutorial ##
### Getting Started ###
Purpose: This tutorial describes the steps required to prepare your Linux system for installing and running CMAQ.
----
Several steps are required to prepare your Linux system for compiling and running CMAQ. Complete all of these steps before installing CMAQ.
Several of these steps are facilitated by having either root or sudo privileges on your system. If you do not have these privileges, work with the system administrator to complete these steps.
1. Install Fortran and C compilers
-----
There are several options for Fortran and C compilers. The [Fortran wiki](http://fortranwiki.org/fortran/show/Compilers) includes a full list of free and commercial Fortran compilers.
Most Linux systems include the Gnu gfortran compiler by default. Other options that have been tested with CMAQ include the **Intel, Portland Group, and Absoft** compilers.
The following instructions are for Gnu compilers. For other Fortran compilers, follow the instructions from the vendor.
Check for the Gnu gfortran compiler:
show original
Thanks for your response. But the problems still persist after installing netcdf-c-4.6.3 and netcdf-fortran-4.4.4 following your instructions.
source config_cmaq.csh gcc 7.3.0
I’ll appreciate your further help. Thanks.
Below is what I got:
Makefile:95: home/catalyst/Desktop/Build_WRF/LIBRARIES/ioapi-3.2/ioapi/Makeinclude.Linux2_x86_64gfort: No such file or directory
Where did you get this ioapi-3.2/ioapi/ ? Going to the CMAS web-server, I see:longleaf:download % tar tfz ioapi-3.2.tar.gz | grep gfort ioapi/Makeinclude.Linux2_x86_64gfort_360 ioapi/Makeinclude.Linux2_x86_64gfort ioapi/Makeinclude.WIN_x86_64gfort_medium ioapi/Makeinclude.Linux2_ia64gfort ioapi/Makeinclude.Linux2_x86_64gfort_365 ioapi/Makeinclude.Linux2_x86_64gfortmpi ioapi/Makeinclude.OSX_x86_gfortran ioapi/Makeinclude.Linux2_x86_64gfort_medium ioapi/Makeinclude.Linux2_x86_64gfortdbg ioapi/Makeinclude.WIN_x86gfort ioapi/Makeinclude.WIN_x86_64gfort
and similarly on the GitHub server… You did follow the I/O API installation instructions https://cjcoats.github.io/ioapi/AVAIL.html#build
Hello,
Below is what I got while building CCTM:
gfortran -c -ffixed-form -ffixed-line-length-132 -funroll-loops -finit-character=32 -O3 -funroll-loops -finit-character=32 -Wtabs -Wsurprising -I /home/catalyst/Desktop/Build_WRF/CMAQ-5.2/lib/x86_64/gcc7.3.0/ioapi/modules -I /home/catalyst/Desktop/Build_WRF/CMAQ-5.2/lib/x86_64/gcc7.3.0/ioapi/include_files -I /home/catalyst/Desktop/Build_WRF/CMAQ-5.2/lib/x86_64/gcc7.3.0/mpi -I. pinterpb.f
Error: Syntax error in COMMON statement at (1)
Error: Syntax error in COMMON statement at (1)ERROR while running make command
else if ( 0 ) then
Please, help me out as usual. Thanks a lot.
Still on CCTM, kindly assist me. Thanks.
driver.o: In function MAIN__': driver.F:(.text+0x11e3): undefined reference tompi_wtime_’mpi_finalize_' se_data_send_module.o: In functionse_data_send_module_MOD_se_5d_data_send’:mpi_send_' se_data_send_module.f:(.text+0x55b): undefined reference tompi_send ’mpi_send_' se_data_send_module.o: In functionse_data_send_module_MOD_se_4de_data_send’:mpi_send_' se_data_send_module.o: In functionse_data_send_module_MOD_se_4d_data_send’:mpi_send_' se_data_send_module.o:se_data_send_module.f:(.text+0xf03): more undefined references tompi_send ’ follow__se_internal_util_module_MOD_se_generate_map': se_internal_util_module.f:(.text+0xe45): undefined reference tompi_gathermpi_bcast_' se_data_recv_module.o: In functionse_data_recv_module_MOD_se_5d_data_recv’:mpi_recv_' se_data_recv_module.o: In functionse_data_recv_module_MOD_se_4de_data_recv’:mpi_recv_' se_data_recv_module.f:(.text+0xa6b): undefined reference tompi_recv ’__se_data_recv_module_MOD_se_4d_data_recv': se_data_recv_module.f:(.text+0xc26): undefined reference tompi_recv__se_data_recv_module_MOD_se_3de_data_recv': se_data_recv_module.f:(.text+0x1077): undefined reference tompi_recv ’mpi_recv_' follow se_global_sum_module.o: In functionse_global_sum_module_MOD_se_global_rasum’:mpi_reduce_' se_global_sum_module.f:(.text+0x2a1): undefined reference tompi_bcast ’__se_global_sum_module_MOD_se_global_iasum': se_global_sum_module.f:(.text+0x3dc): undefined reference tompi_reducempi_bcast_' se_global_sum_module.o: In functionse_global_sum_module_MOD_se_global_rsum’:mpi_reduce_' se_global_sum_module.f:(.text+0x5fa): undefined reference tompi_bcast ’__se_global_sum_module_MOD_se_global_isum': se_global_sum_module.f:(.text+0x647): undefined reference tompi_reducempi_bcast_' se_global_max_module.o: In functionse_global_max_module_MOD_se_global_rmax’:mpi_reduce_' se_global_max_module.f:(.text+0x5f): undefined reference tompi_bcast ’__se_global_max_module_MOD_se_global_imax': se_global_max_module.f:(.text+0xba): undefined reference tompi_reducempi_bcast_' se_global_min_module.o: In functionse_global_min_module_MOD_se_global_rmin’:mpi_reduce_' se_global_min_module.f:(.text+0x63): undefined reference tompi_bcast ’__se_global_min_module_MOD_se_global_imin': se_global_min_module.f:(.text+0xbe): undefined reference tompi_reducempi_bcast_' se_slice_module.o: In functionse_slice_module_MOD_se_slice4r’:mpi_recv_' se_slice_module.f:(.text+0xa2a): undefined reference tompi_send ’__se_slice_module_MOD_se_slice4i': se_slice_module.f:(.text+0xfac): undefined reference tompi_recvmpi_send_' se_slice_module.o: In functionse_slice_module_MOD_se_slice3r’:mpi_recv_' se_slice_module.f:(.text+0x1e28): undefined reference tompi_send ’mpi_recv_' se_slice_module.o: In functionse_slice_module_MOD_se_slice3i’:mpi_recv_' se_slice_module.f:(.text+0x26a6): undefined reference tompi_send ’mpi_recv_' se_slice_module.o: In functionse_slice_module_MOD_se_slice2r’:mpi_recv_' se_slice_module.f:(.text+0x2e2b): undefined reference tompi_send ’mpi_recv_' se_slice_module.o: In functionse_slice_module_MOD_se_slice2i’:mpi_recv_' se_slice_module.f:(.text+0x34ca): undefined reference tompi_send ’mpi_recv_' se_slice_module.o: In functionse_slice_module_MOD_se_slice1r’:mpi_recv_' se_slice_module.f:(.text+0x364f): undefined reference tompi_send ’__se_slice_module_MOD_se_slice1i': se_slice_module.f:(.text+0x36ea): undefined reference tompi_recvmpi_send_' se_init_module.o: In functionse_init_module_MOD_se_init’:mpi_comm_dup_' se_init_module.F:(.text+0xce): undefined reference tompi_comm_dup ’mpi_comm_group_' se_init_module.F:(.text+0xeb3): undefined reference tompi_group_inclmpi_group_excl_' se_init_module.F:(.text+0xeed): undefined reference tompi_comm_creatempi_comm_create_' se_gather_module.o: In functionse_gather_module_MOD_se_gather4i’:mpi_gather_' se_gather_module.f:(.text+0x2d9): undefined reference tompi_gather ’__se_gather_module_MOD_se_gather3i': se_gather_module.f:(.text+0xef1): undefined reference tompi_gathermpi_gather_' se_gather_module.o: In functionse_gather_module_MOD_se_gather2i’:mpi_gather_' se_gather_module.o:se_gather_module.f:(.text+0x1b32): more undefined references tompi_gather ’ follow__se_twoway_comm_module_MOD_se_twoway_recv4': se_twoway_comm_module.f:(.text+0x689): undefined reference tompi_recv__se_twoway_comm_module_MOD_se_twoway_send4': se_twoway_comm_module.f:(.text+0xf5e): undefined reference tompi_send__se_twoway_comm_module_MOD_se_cmaq_wrf_comm4': se_twoway_comm_module.f:(.text+0x1f94): undefined reference tompi_sendmpi_recv_' se_twoway_comm_module.f:(.text+0x285b): undefined reference tompi_sendmpi_recv_' se_twoway_comm_module.f:(.text+0x29a9): undefined reference tompi_send__se_twoway_comm_module_MOD_se_cmaq_wrf_comm3': se_twoway_comm_module.f:(.text+0x34b7): undefined reference tompi_send ’mpi_recv_' se_twoway_comm_module.f:(.text+0x3c4f): undefined reference tompi_sendmpi_send_' se_twoway_comm_module.f:(.text+0x3e25): undefined reference tompi_recv__se_twoway_comm_module_MOD_se_cmaq_wrf_comm2': se_twoway_comm_module.f:(.text+0x4761): undefined reference tompi_send_’mpi_recv_' se_twoway_comm_module.o: In functionse_twoway_comm_module_MOD_se_wrf_cmaq_comm4’:mpi_send_' se_twoway_comm_module.f:(.text+0x5ba9): undefined reference tompi_recv ’mpi_send_' se_twoway_comm_module.f:(.text+0x63f9): undefined reference tompi_recvmpi_send_' se_twoway_comm_module.o: In functionse_twoway_comm_module_MOD_se_wrf_cmaq_comm3’:mpi_send_' se_twoway_comm_module.f:(.text+0x70b4): undefined reference tompi_recv ’mpi_send_' se_twoway_comm_module.f:(.text+0x7893): undefined reference tompi_sendmpi_recv_' se_twoway_comm_module.o: In functionse_twoway_comm_module_MOD_se_wrf_cmaq_comm2’:mpi_send_' se_twoway_comm_module.f:(.text+0x8359): undefined reference tompi_recv ’__se_util_module_MOD_se_collect': se_util_module.f:(.text+0x2d9): undefined reference tompi_recvmpi_send_' se_util_module.o: In functionse_util_module_MOD_se_in_syn’:mpi_bcast_' se_util_module.o: In functionse_util_module_MOD_se_global_logical’:mpi_reduce_' se_util_module.f:(.text+0x44d4): undefined reference tompi_bcast ’__se_util_module_MOD_se_my_region': se_util_module.f:(.text+0x460e): undefined reference tompi_reducempi_bcast_' se_util_module.o: In functionse_util_module_MOD_se_rsum_chk’:mpi_reduce_' se_util_module.f:(.text+0x46f3): undefined reference tompi_bcast ’__se_util_module_MOD_se_isum_chk': se_util_module.f:(.text+0x47a0): undefined reference tompi_reducempi_bcast_' se_util_module.o: In functionse_util_module_MOD_se_global_min_data’:mpi_reduce_' se_util_module.f:(.text+0x4a5b): undefined reference tompi_bcast ’mpi_bcast_' se_util_module.o: In functionse_util_module_MOD_se_barrier’:mpi_comm_dup_' se_util_module.f:(.text+0x4d12): undefined reference tompi_barrier ’mpi_comm_free_' se_util_module.f:(.text+0x4d3f): undefined reference tompi_barrier__swap_sandia_MOD_swap_init_snl': swap_sandia.f:(.text+0x20): undefined reference tompi_comm_rankmpi_comm_size_' swap_sandia_routines.o: In functionswap1d ’:mpi_irecv_' swap_sandia_routines.f:(.text+0x10f): undefined reference tompi_sendmpi_wait_' swap_sandia_routines.f:(.text+0x1d0): undefined reference tompi_wait_’swap2d_': swap_sandia_routines.f:(.text+0x2e2): undefined reference tompi_irecv_’mpi_send_' swap_sandia_routines.f:(.text+0x590): undefined reference tompi_wait_’mpi_wait_' swap_sandia_routines.o: In functionswap3d_’:mpi_irecv_' swap_sandia_routines.f:(.text+0xa34): undefined reference tompi_send_’mpi_wait_' swap_sandia_routines.f:(.text+0xb18): undefined reference tompi_wait_’swap4d_': swap_sandia_routines.f:(.text+0xd9f): undefined reference tompi_wait_’mpi_irecv_' swap_sandia_routines.f:(.text+0x106c): undefined reference tompi_send_’pm3err_': pm3err.f:(.text+0xce2): undefined reference tompi_abort_’pm3exit_': pm3exit.f:(.text+0x8f2): undefined reference tompi_abort_’pshut3_': pshut3.F:(.text+0x665): undefined reference tompi_bcast_’ptrwrite3_': ptrwrite3.f:(.text+0x1ff): undefined reference tompi_bcast_’mpi_bcast_' ptrwrite3.f:(.text+0x279): undefined reference tompi_bcast_’mpi_bcast_' ptrwrite3.o:ptrwrite3.f:(.text+0x9fc): more undefined references tompi_bcast_’ followpwrgrdd_': pwrgrdd.f:(.text+0x651): undefined reference tompi_recv_’mpi_recv_' pwrgrdd.f:(.text+0xc9a): undefined reference tompi_send_’mpi_send_' pwrgrdd.f:(.text+0xd2e): undefined reference tompi_allreduce_’pwrite3_': pwrite3.f:(.text+0x206): undefined reference tompi_bcast_’mpi_bcast_' pwrite3.f:(.text+0x280): undefined reference tompi_bcast_’mpi_bcast_' pwrite3.f:(.text+0x98c): undefined reference tompi_bcast_’distr_env_': distr_env.c:(.text+0xd6): undefined reference toompi_mpi_comm_world’ompi_mpi_int' distr_env.c:(.text+0xe9): undefined reference toMPI_Bcast’ompi_mpi_comm_world' distr_env.c:(.text+0xfb): undefined reference toompi_mpi_char’MPI_Bcast' distr_env.c:(.text+0x10c): undefined reference toompi_mpi_comm_world’MPI_Barrier' distr_env.c:(.text+0x148): undefined reference toompi_mpi_comm_world’ompi_mpi_int' distr_env.c:(.text+0x163): undefined reference toMPI_Bcast’ompi_mpi_comm_world' distr_env.c:(.text+0x175): undefined reference toompi_mpi_char’MPI_Bcast' mpcomm_init.o: In functionmpcomm_init_’:mpi_init_' mpcomm_init.F:(.text+0x60): undefined reference tompi_wtime_’mpi_comm_size_' mpcomm_init.F:(.text+0xa2): undefined reference tompi_comm_rank_’setup_logdev_': setup_logdev.F:(.text+0x6d): undefined reference tompi_comm_rank_’ERROR while running make command
You have an error with specifying the MPI libraries in the link-line. Note that what is required is dependent upon which MPI implementation you are using – the MPICH implementation of MPI uses different libraries than OPENMPI (and further note that it is also dependent upon the vendor of the underlying C and Fortran libraries…
Ok. I am using OPENMPI and netcdf-4.1.3. What’s the way forward now, please? Kindly assist me. Thanks.
/home/catalyst/Desktop/Build_WRF/CMAQ-5.2/lib/x86_64/gcc7.3.0/ioapi/lib/libioapi.a(wrdict3.o): In function wrdict3_': wrdict3.f90:(.text+0x3a7): undefined reference toGOMP_critical_name_start’GOMP_critical_name_start' wrdict3.f90:(.text+0x55e): undefined reference toGOMP_critical_name_end’GOMP_critical_name_end' wrdict3.f90:(.text+0x8f3): undefined reference toGOMP_critical_name_end’GOMP_critical_name_end' wrdict3.f90:(.text+0x15b0): undefined reference toGOMP_critical_name_end’GOMP_critical_name_end' follow /home/catalyst/Desktop/Build_WRF/CMAQ-5.2/lib/x86_64/gcc7.3.0/ioapi/lib/libioapi.a(wriddata.o): In functionwriddata_’:GOMP_critical_name_start' wriddata.f90:(.text+0x50): undefined reference toGOMP_critical_name_start’GOMP_critical_name_end' wriddata.f90:(.text+0x190): undefined reference toGOMP_critical_name_end’GOMP_critical_name_end' wriddata.f90:(.text+0x231): undefined reference toGOMP_critical_name_end’wrsmatrx_': wrsmatrx.f90:(.text+0xd3): undefined reference toGOMP_critical_name_start’GOMP_critical_name_start' wrsmatrx.f90:(.text+0x214): undefined reference toGOMP_critical_name_end’GOMP_critical_name_end' wrsmatrx.f90:(.text+0x2aa): undefined reference toGOMP_critical_name_end’GOMP_critical_name_end' /home/catalyst/Desktop/Build_WRF/CMAQ-5.2/lib/x86_64/gcc7.3.0/ioapi/lib/libioapi.a(crtfil3.o): In functioncrtfil3_’:GOMP_critical_name_start' crtfil3.F90:(.text+0x46): undefined reference toGOMP_critical_name_end’GOMP_critical_name_start' crtfil3.F90:(.text+0x4a5): undefined reference toGOMP_critical_name_end’GOMP_critical_name_end' crtfil3.F90:(.text+0x57c): undefined reference toGOMP_critical_name_start’GOMP_critical_name_end' crtfil3.F90:(.text+0xa49): undefined reference toGOMP_critical_name_end’wrtflag_': wrtflag.F90:(.text+0xaa): undefined reference toGOMP_critical_name_start’GOMP_critical_name_end' wrtflag.F90:(.text+0x731): undefined reference toGOMP_critical_name_start’GOMP_critical_name_end' /home/catalyst/Desktop/Build_WRF/CMAQ-5.2/lib/x86_64/gcc7.3.0/ioapi/lib/libioapi.a(rdatt3.o): In functionmaster.0.rdatt3_’:GOMP_critical_name_start' rdatt3.F90:(.text+0x681): undefined reference toGOMP_critical_name_end’GOMP_critical_name_end' rdatt3.F90:(.text+0x1cd5): undefined reference toGOMP_critical_name_end’GOMP_critical_name_end' rdatt3.F90:(.text+0x1da3): undefined reference toGOMP_critical_name_end’master.0.wratt3_': wratt3.F90:(.text+0x659): undefined reference toGOMP_critical_name_start’GOMP_critical_name_end' wratt3.F90:(.text+0xb3b): undefined reference toGOMP_critical_name_end’ERROR while running make command
What’s your underlying compiler for OpenMPI? Since the I/O API is openmp-enabled (with various other programs using omp shared-memory parallelism), you need to include the appropriate OpenMP flag in your link step (-qopenmp for Intel, -fopenmp for GNU, -mp for PGI, …)
Thanks for your response. Below is my Compiler Aliases and Flags:
#> Compiler Aliases and Flags#setenv myFC mpifort#setenv myDBG “$myDBG -fimplicit-none”#setenv mpi_lib “-lmpi_mpifh” #> -lmpich for mvapich or -lmpi for openmpi
sp you need to add -fopenmp to your link-flags
For my CCTM Script"
setenv FC ${myFC} #> path of Fortan compiler; set in config.cmaqFC #> path of Fortan preprocessor; set in config.cmaq
set CC = {myCC} #> path of C compiler; set in config.cmaq{CMAQ_HOME}/UTIL/bldmake/bldmake_ {compilerString}.exe #> name of model builder executable
#> Libraries/include files{IOAPI_DIR}/lib {ioapi_lib}” #> I/O API library directory{IOAPI_DIR}/include" #> I/O API module directory
set NETCDF = " {NETCDF_DIR}/lib {netcdf_lib}" #> netCDF library directory
#set PNETCDF = " {PNETCDF_DIR}/lib {pnetcdf_lib}" #> Parallel netCDF library directory
#set PIO_INC = " {IOAPI_DIR}/src”
#> Compiler flags set in config.cmaq{myFSTD}"
set DBG = " {myDBG}”{myFFLAGS}" #> F77 flags
set F90_FLAGS = " {myFRFLAGS}” #> F90 flags{myCFLAGS} -DFLDMN -I" #> C flags
set LINK_FLAGS = " {myLINK_FLAG}” # Link flags
I have been able to successfully compile CCTM after so many manipulations of my scripts. Thanks so much for your guide. I’m available to help those facing the challenges I have faced in the course of compiling CMAQ and its related models.
Cheers.
Catalyst