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error in building CESM on Blegene

D

devarajun@gmail_com

Dev
Member
Hi

I am trying to build CESM on Bluegene/L with Linux OS system. I have choose the machine as prototype_frost. I have compiled all the components successfully and and getting error at the last as below:
1501-510 Compilation successful for file ccsm_driver.F90.
blrts_xlf90 -o /home/caos2/casgbala/dev_blugene/CESM102/cesm_intel/cesm1_0_2/scripts/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/cesm_intel/cesm1_0_2/scripts/casgbala/test1/lib -latm -llnd -lice -locn -lglc -L/home/caos2/casgbala/dev_blugene/CESM102/cesm_intel/cesm1_0_2/scripts/casgbala/test1/lib -lcsm_share -lmct -lmpeu -lpio -L/opt/ibmmath/essl/4.2/lib -lmass -lmassv -L/contrib/memmon2 -lmemmon2 -L/home/caos2/casgbala/dev_blugene/netcdf_blugen/netcdf-3.6.3_installed/lib -lnetcdf -L/bgl/BlueLight/ppcfloor/bglsys/lib -lmpich.rts -lmsglayer.rts -lrts.rts -ldevices.rts -Wl,--allow-multiple-definition
/bgl/BlueLight/ppcfloor/blrts-gnu/powerpc-bgl-blrts-gnu/bin/ld: cannot find -lmemmon2
gmake: *** [/home/caos2/casgbala/dev_blugene/CESM102/cesm_intel/cesm1_0_2/scripts/casgbala/test1/run/ccsm.exe] Error 1

It says cannot find -lmemmon2,and there is no such /contrib/ directory in our system, also my system admin says its not a Blugene/L system library..

I am not able to figure out ..
Please clarify if any one knows about the problem...

Thanks.
Dev
 
J

jedwards

CSEG and Liaisons
Staff member
Try removing -lmemmon2 and adding the flag -bloadmap:map to LDFLAGS in the Macros.prototype_frost file in your case directory.

When you rebuild you will get a file called map that will indicate the place in the code where that library is being used at which point you can probably just comment it out.
 
D

devarajun@gmail_com

Dev
Member
Hi

Thanks for the suggestion. I removed -lmemmon2 and added the flag -bloadmap:map to LDFLAGS.

After rebuld, I am getting the following error: I am not able to find map file:

1501-510 Compilation successful for file ccsm_driver.F90.
blrts_xlf90 -o /home/caos2/casgbala/dev_blugene/CESM102/cesm_intel/cesm1_0_2/scripts/casgbala/test1/run/ccsm.exe ccsm_driver.o map_atmatm_mct.o map_atmice_mct.o map_atmlnd_mct.o map_atmocn_mc
t.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_x2
i_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/ca
sgbala/dev_blugene/CESM102/cesm_intel/cesm1_0_2/scripts/casgbala/test1/lib -latm -llnd -lice -locn -lglc -L/home/caos2/casgbala/dev_blugene/CESM102/cesm_intel/cesm1_0_2/scripts/casgbala/test1
/lib -lcsm_share -lmct -lmpeu -lpio -L/opt/ibmmath/essl/4.2/lib -lmass -lmassv -L/contrib/memmon2 -L/home/caos2/casgbala/dev_blugene/netcdf_blugen/netcdf-3.6.3_installed/lib -lnetcdf -L/bg
l/BlueLight/ppcfloor/bglsys/lib -lmpich.rts -lmsglayer.rts -lrts.rts -ldevices.rts -Wl,--allow-multiple-definition -bloadmap:map
/bgl/BlueLight/ppcfloor/blrts-gnu/powerpc-bgl-blrts-gnu/bin/ld: invalid BFD target `loadmap:map'
gmake: *** [/home/caos2/casgbala/dev_blugene/CESM102/cesm_intel/cesm1_0_2/scripts/casgbala/test1/run/ccsm.exe] Error 1

Thanks.
 
J

jedwards

CSEG and Liaisons
Staff member
Sorry - The machine frost is down and so I haven't been able to test what I am telling you. Try once more without the -bloadmap:map flag (and still without -lmemon2) - hopefully I'll be able to get on frost later today and have a look.
 
D

devarajun@gmail_com

Dev
Member
Hi,

I removed both -bloadmap:map flag and -lmemon2, But much error as below: Our system admin says "bloadmap option works on AIX(regatta), it will not work linux (BGL) system": Please guide me how to go.......

Thu Apr 28 21:38:06 IST 2011 /home/caos2/casgbala/dev_blugene/CESM102/cesm_intel/cesm1_0_2/scripts/casgbala/test1/run/ccsm.bldlog.110428-213429
-------------------------------------------------------------------------
Building a single executable version of CCSM
-------------------------------------------------------------------------
cat: Srcfiles: No such file or directory

1501-510 Compilation successful for file ccsm_driver.F90.
blrts_xlf90 -o /home/caos2/casgbala/dev_blugene/CESM102/cesm_intel/cesm1_0_2/scripts/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/cesm_intel/cesm1_0_2/scripts/casgbala/test1/lib -latm -llnd -lice -locn -lglc -L/home/caos2/casgbala/dev_blugene/CESM102/cesm_intel/cesm1_0_2/scripts/casgbala/test1/lib -lcsm_share -lmct -lmpeu -lpio -L/opt/ibmmath/essl/4.2/lib -lmass -lmassv -L/contrib/memmon2 -L/home/caos2/casgbala/dev_blugene/netcdf_blugen/netcdf-3.6.3_installed/lib -lnetcdf -L/bgl/BlueLight/ppcfloor/bglsys/lib -lmpich.rts -lmsglayer.rts -lrts.rts -ldevices.rts -Wl,--allow-multiple-definition
ccsm_driver.o: In function `ccsm_driver':
/home/caos2/casgbala/dev_blugene/CESM102/cesm_intel/cesm1_0_2/models/drv/driver/ccsm_driver.F90:2: undefined reference to `__func_trace_enter'
ccsm_driver.o: In function `seq_ccsm_printlogheader':

/home/caos2/casgbala/dev_blugene/CESM102/cesm_intel/cesm1_0_2/models/csm_share/shr/shr_ncread_mod.F90:426: undefined reference to `__func_trace_exit'
/home/caos2/casgbala/dev_blugene/CESM102/cesm_intel/cesm1_0_2/scripts/casgbala/test1/lib/libcsm_share.a(shr_ncread_mod.o): In function `shr_ncread_vardimsizename':
/home/caos2/casgbala/dev_blugene/CESM102/cesm_intel/cesm1_0_2/models/csm_share/shr/shr_ncread_mod.F90:229: undefined reference to `__func_trace_enter'
/home/caos2/casgbala/dev_blugene/CESM102/cesm_intel/cesm1_0_2/models/csm_share/shr/shr_ncread_mod.F90:259: undefined reference to `__func_trace_exit'
/home/caos2/casgbala/dev_blugene/CESM102/cesm_intel/cesm1_0_2/scripts/casgbala/test1/lib/libpio.a(pionfput_mod.o): In function `__pionfput_mod_NMOD_put_var_0d_text':
pionfput_mod.F90:(.text+0x216c): undefined reference to `nf_put_vars_text'
pionfput_mod.F90:(.text+0x21c4): undefined reference to `nf_put_vars_text'
pionfput_mod.F90:(.text+0x2230): undefined reference to `nf_put_vars_text'
/home/caos2/casgbala/dev_blugene/netcdf_blugen/netcdf-3.6.3_installed/lib/libnetcdf.a(posixio.o): In function `fgrow':
/home/caos2/casgbala/dev_blugene/netcdf_blugen/netcdf-3.6.3/libsrc/posixio.c:133: undefined reference to `__errno_location'
/home/caos2/casgbala/dev_blugene/netcdf_blugen/netcdf-3.6.3/libsrc/posixio.c:142: undefined reference to `__errno_location'
/home/caos2/casgbala/dev_blugene/netcdf_blugen/netcdf-3.6.3/libsrc/posixio.c:144: undefined reference to `__errno_location'
/home/caos2/casgbala/dev_blugene/netcdf_blugen/netcdf-3.6.3/libsrc/posixio.c:146: undefined reference to `__errno_location'
/home/caos2/casgbala/dev_blugene/netcdf_blugen/netcdf-3.6.3/libsrc/posixio.c:148: undefined reference to `__errno_location'
/home/caos2/casgbala/dev_blugene/netcdf_blugen/netcdf-3.6.3_installed/lib/libnetcdf.a(posixio.o):/home/caos2/casgbala/dev_blugene/netcdf_blugen/netcdf-3.6.3/libsrc/posixio.c:1474: more undefined references to `__errno_location' follow
gmake: *** [/home/caos2/casgbala/dev_blugene/CESM102/cesm_intel/cesm1_0_2/scripts/casgbala/test1/run/ccsm.exe] Error 1
 
J

jedwards

CSEG and Liaisons
Staff member
The functions __func_trace_exit __func_trace_enter seem to indicate that the -qdebug=function_trace flag was used and so you should include -lmpitrace_f or remove that flag. The other __errno_location should be in libc but seems to indicate a problem with your netcdf build.
 
D

devarajun@gmail_com

Dev
Member
I too guess its netCDF problem. I compiled netCDF as below:

The compilers used are:

setenv PATH /opt/ibmcmp/xlf/bg/11.1/bin/blrts_xlf90
setenv PATH /opt/ibmcmp/vac/bg/9.0/bin/blrts_xlc
setenv PATH /opt/ibmcmp/vacpp/bg/9.0/bin/blrts_xlC

set FC=blrts_xlf90
set CC=blrts_xlc
set CXX=blrts_xlC
set F90=blrts_xlf90
set F77=blrts_xlf
cd netcdf-3.6.3
./configure --enable-f90 --prefix=/home/caos2/casgbala/dev_blugene/netcdf_blugen/netcdf-3.6.3_installed/ FCFLAGS=-qsuffix=f=f90 -qextname FFLAGS=-qextname CPPFLAGS=-DIBMR2Fortran -Dextname F90FLAGS=-qsuffix=f=f90

and then I got warning message
make[1]: warning: Clock skew detected. Your build may be incomplete.
make[1]: Leaving directory `/home/caos2/casgbala/dev_blugene/netcdf_blugen/netcdf_crosscompile/netcdf-3.6.3'
make: warning: Clock skew detected. Your build may be incomplete.

Am I done right netCDF compilation?
 
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