ccsm.exe error despite LD_LIBRARY_PATH

ruk15@psu_edu

New Member
Hi,I am getting the following error, even though I set LD_LIBRARY_PATH in my .bashrc file:export LD_LIBRARY_PATH=/gscratch/vsm/ravi/local/lib:$LD_LIBRARY_PATH

I also have this in my 'env_mach_specific':setenv NETCDF_PATH /gscratch/vsm/ravi/local

I even checked if the LD_LIBRARY_PATH is set on the prompt:echo $LD_LIBRARY_PATH
/gscratch/vsm/ravi/local/lib::/sw/openmpi/lib:/gscratch/vsm/ravi/libcurlBut still I get the following error while execution. The code runs for about 25 seconds and terminates the job../ccsm.exe: error while loading shared libraries: libnetcdff.so.5: cannot open shared object file: No such file or directory ThanksRaviPennsylvania State University
 

jedwards

CSEG and Liaisons
Staff member
Try putting the LD_LIBRARY_PATH into the env_mach_specific file.    You can also you the -Wl,-rpath flag to the linker by adding it to the Macros file.   Make sure that the libnetcdff.so.5 is in the specified directory.
 

ruk15@psu_edu

New Member
Thank you, I did that and the build failed with the following error:******************CCSM PRESTAGE SCRIPT HAS FINISHED SUCCESSFULLY
-------------------------------------------------------------------------
 CCSM BUILDEXE SCRIPT STARTING
 - Build Libraries: mct pio csm_share
Wed Jan 22 07:08:36 PST 2014 /gscratch/vsm/ravi/OUTPUT/Tidallock//Aqua_Tidallock/mct/mct.bldlog.140122-070810
ERROR: mct.buildlib failed, see /gscratch/vsm/ravi/OUTPUT/Tidallock//Aqua_Tidallock/mct/mct.bldlog.140122-070810
ERROR: cat /gscratch/vsm/ravi/OUTPUT/Tidallock//Aqua_Tidallock/mct/mct.bldlog.140122-070810*************************I think this is something related to the mpi path. But when I removed the LD_LIBRARY_PATH from env_mach_specific, the build went well (but of course, we are bakc to the original ./ccsm.exe error that libnetcdff.so.5 is not found). Oh, and my libnetcdff.so.5 is in  /gscratch/vsm/ravi/local/lib  directory which is where I was pointing to in the LD path. Not sure what's happening.RaviPennsylvania State University
 

jedwards

CSEG and Liaisons
Staff member
Look for the error in the config.log file in the directory  /gscratch/vsm/ravi/OUTPUT/Tidallock//Aqua_Tidallock/mct/
 

ruk15@psu_edu

New Member
Thanks, In the beginning of the  config.log file, it says the following. I did load mpi modules. I have given the complete 'config.log' down below. The 'libimf.so' is the only error (after I included LD_LIBRARY_PATH in 'env_mach_specific'. ********************configure:1624: checking for C compiler version
configure:1627: mpicc --version &5
mpicc: error while loading shared libraries: libimf.so: cannot open shared object file: No such file or directory******************* The total config.log file: --------------------------This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.

It was created by MCT configure 2.0, which was
generated by GNU Autoconf 2.59.  Invocation command line was

  $ ./configure CC=mpicc FC=mpif90 F90=mpif90 INCLUDEPATH=-I/include

## --------- ##
## Platform. ##
## --------- ##

hostname = n0365
uname -m = x86_64
uname -r = 2.6.18-371.3.1.el5
uname -s = Linux
uname -v = #1 SMP Mon Nov 11 03:23:58 EST 2013

/usr/bin/uname -p = unknown
/bin/uname -X     = unknown

/bin/arch              = x86_64
/usr/bin/arch -k       = unknown
/usr/convex/getsysinfo = unknown
hostinfo               = unknown
/bin/machine           = unknown
/usr/bin/oslevel       = unknown
/bin/universe          = unknown

PATH: /sw/openmpi-1.6.2_icc-13.0/bin
PATH: /sw/intel/composer_xe_2013.0.079/bin/intel64
PATH: /sw/intel/composer_xe_2013.0.079/mpirt/bin/intel64
PATH: /sw/openmpi-1.6.4_icc-13.1/bin
PATH: /sw/intel/composer_xe_2013.2.146/bin/intel64
PATH: /sw/intel/composer_xe_2013.2.146/mpirt/bin/intel64
PATH: /sw/openmpi/bin
PATH: /sw/local/bin
PATH: /sw/gnu-parallel/bin
PATH: /opt/mx/bin
PATH: /sw/Modules/3.2.9/bin
PATH: /sw/moab/bin
PATH: /sw/moab/sbin
PATH: /sw/torque/bin
PATH: /sw/torque/sbin
PATH: /usr/kerberos/bin
PATH: /usr/lpp/mmfs/bin
PATH: /usr/local/bin
PATH: /bin
PATH: /usr/bin
PATH: /usr/lusers/rkoppara/bin


## ----------- ##
## Core tests. ##
## ----------- ##

configure:1624: checking for C compiler version
configure:1627: mpicc --version &5
mpicc: error while loading shared libraries: libimf.so: cannot open shared object file: No such file or directory
configure:1630: $? = 127
configure:1632: mpicc -v &5
mpicc: error while loading shared libraries: libimf.so: cannot open shared object file: No such file or directory
configure:1635: $? = 127
configure:1637: mpicc -V &5
mpicc: error while loading shared libraries: libimf.so: cannot open shared object file: No such file or directory
configure:1640: $? = 127
configure:1663: checking for C compiler default output file name
configure:1666: mpicc    conftest.c  >&5
mpicc: error while loading shared libraries: libimf.so: cannot open shared object file: No such file or directory
configure:1669: $? = 127
configure: failed program was:
| /* confdefs.h.  */
|
| #define PACKAGE_NAME "MCT"
| #define PACKAGE_TARNAME "mct"
| #define PACKAGE_VERSION "2.0"
| #define PACKAGE_STRING "MCT 2.0"
| #define PACKAGE_BUGREPORT ""
| /* end confdefs.h.  */
|
| int
| main ()
| {
|
|   ;
|   return 0;
| }
configure:1708: error: C compiler cannot create executables
See `config.log' for more details.

## ---------------- ##
## Cache variables. ##
## ---------------- ##

ac_cv_env_ALLCFLAGS_set=
ac_cv_env_ALLCFLAGS_value=
ac_cv_env_AR_set=
ac_cv_env_AR_value=
ac_cv_env_BABELROOT_set=
ac_cv_env_BABELROOT_value=
ac_cv_env_BIT64_set=
ac_cv_env_BIT64_value=
ac_cv_env_CC_set=set
ac_cv_env_CC_value=mpicc
ac_cv_env_CFLAGS_set=
ac_cv_env_CFLAGS_value=
ac_cv_env_COMPILER_ROOT_set=
ac_cv_env_COMPILER_ROOT_value=
ac_cv_env_CPPFLAGS_set=
ac_cv_env_CPPFLAGS_value=
ac_cv_env_ENDIAN_set=
ac_cv_env_ENDIAN_value=
ac_cv_env_F90FLAGS_set=
ac_cv_env_F90FLAGS_value=
ac_cv_env_F90SUFFIX_set=
ac_cv_env_F90SUFFIX_value=
ac_cv_env_F90_set=set
ac_cv_env_F90_value=mpif90
ac_cv_env_FCFLAGS_set=
ac_cv_env_FCFLAGS_value=
ac_cv_env_FC_set=set
ac_cv_env_FC_value=mpif90
ac_cv_env_FORT_SIZE_set=
ac_cv_env_FORT_SIZE_value=
ac_cv_env_FPPFLAGS_set=
ac_cv_env_FPPFLAGS_value=
ac_cv_env_FPP_set=
ac_cv_env_FPP_value=
ac_cv_env_INCLUDEFLAG_set=
ac_cv_env_INCLUDEFLAG_value=
ac_cv_env_INCLUDEPATH_set=set
ac_cv_env_INCLUDEPATH_value=-I/include
ac_cv_env_LDFLAGS_set=
ac_cv_env_LDFLAGS_value=
ac_cv_env_MACHDEFS_set=
ac_cv_env_MACHDEFS_value=
ac_cv_env_MPIF90_set=
ac_cv_env_MPIF90_value=
ac_cv_env_MPIHEADER_set=
ac_cv_env_MPIHEADER_value=
ac_cv_env_MPILIBS_set=
ac_cv_env_MPILIBS_value=
ac_cv_env_OPT_set=
ac_cv_env_OPT_value=
ac_cv_env_REAL8_set=
ac_cv_env_REAL8_value=
ac_cv_env_build_alias_set=
ac_cv_env_build_alias_value=
ac_cv_env_host_alias_set=
ac_cv_env_host_alias_value=
ac_cv_env_target_alias_set=
ac_cv_env_target_alias_value=

## ----------------- ##
## Output variables. ##
## ----------------- ##

ALLCFLAGS=''
AR=''
BABELROOT=''
BIT64=''
CC='mpicc'
CFLAGS=''
COMPILER_ROOT=''
CPPFLAGS=''
CRULE=''
DEFS=''
ECHO_C=''
ECHO_N='-n'
ECHO_T=''
ENDIAN=''
EXEEXT=''
F90='mpif90'
F90FLAGS=''
F90RULE=''
F90RULECPP=''
F90SUFFIX=''
FC='mpif90'
FCFLAGS=''
FORT_SIZE=''
FPP=''
FPPFLAGS=''
INCLUDEFLAG=''
INCLUDEPATH='-I/include'
LDFLAGS=''
LIBOBJS=''
LIBS=''
LTLIBOBJS=''
MACHDEFS=''
MPIF90=''
MPIHEADER=''
MPILIBS=''
MPISERPATH=''
OBJEXT=''
OPT=''
PACKAGE_BUGREPORT=''
PACKAGE_NAME='MCT'
PACKAGE_STRING='MCT 2.0'
PACKAGE_TARNAME='mct'
PACKAGE_VERSION='2.0'
PATH_SEPARATOR=':'
PYTHON=''
PYTHONOPTS=''
REAL8=''
SHELL='/bin/sh'
ac_ct_CC=''
ac_ct_F90=''
bindir='${exec_prefix}/bin'
build_alias=''
datadir='${prefix}/share'
exec_prefix='NONE'
host_alias=''
includedir='${prefix}/include'
infodir='${prefix}/info'
libdir='${exec_prefix}/lib'
libexecdir='${exec_prefix}/libexec'
localstatedir='${prefix}/var'
mandir='${prefix}/man'
oldincludedir='/usr/include'
prefix='NONE'
program_transform_name='s,x,x,'
sbindir='${exec_prefix}/sbin'
sharedstatedir='${prefix}/com'
sysconfdir='${prefix}/etc'
target_alias=''

## ----------- ##
## confdefs.h. ##
## ----------- ##

#define PACKAGE_BUGREPORT ""
#define PACKAGE_NAME "MCT"
#define PACKAGE_STRING "MCT 2.0"
#define PACKAGE_TARNAME "mct"
#define PACKAGE_VERSION "2.0"

configure: exit 77
--------------------------
 

ruk15@psu_edu

New Member
At least I solved the build problem now. The issue is that in the 'env_mach_specific', I did the following:setenv LD_LIBRARY_PATH /gscratch/vsm/ravi/local/libThe correct syntax is:setenv LD_LIBRARY_PATH /gscratch/vsm/ravi/local/lib:${LD_LIBRARY_PATH}Now it builds fine, but gives the following error when the code is executed:LD_LIBRARY_PATH: Undefined variable.

It does not recognize this variable in the 'env_mach_specific' for some reason.ThanksRavi 
 

jedwards

CSEG and Liaisons
Staff member
This has more to do with the configuration of your machine than with CESM - I would guess that the environment from your login node is not being exported to your compute nodes andLD_LIBRARY_PATH is not defined on the compute nodes.   
 

rajkmsaini

Dr. Raj Saini
Member
Dear Jedwards,

I am new for this CESM.

$ ./cesm_setup
Macros script already created ...skipping
Machine/Decomp/Pes configuration has already been done ...skipping
Running preview_namelist script
LD_LIBRARY_PATH: Undefined variable.
ERROR: /scratch/am/irdstaff/ird12765/cas/raj/IITD_COE_EXP1/preview_namelists failed: 65280

I am getting same type of error.

Can you help me where I need to change? In the folloing below:


======================================
setenv intelhome /home/soft/intel2015
setenv intehome /home/soft/intel2015
setenv CC $intehome/bin/icc
setenv FC $intelhome/bin/ifort
setenv F90 $intelhome/bin/ifort
setenv CXX $intelhome/bin/icpc
setenv PATH $intelhome/bin:$PATH
setenv LD_LIBRARY_PATH $intelhome/lib/intel64:$LD_LIBRARY_PATH
setenv MANPATH $intelhome/man:$MANPATH

#PGI mpi environment
setenv PATH $intelhome/impi/5.0.3.048/intel64/bin:$PATH
setenv LD_LIBRARY_PATH $intelhome/impi/5.0.3.048/intel64/lib:$LD_LIBRARY_PATH
setenv INCLUDE_PATH $intelhome/impi/5.0.3.048/intel64/include:$INCLUDE_PATH

#Deps
setenv PATH /home/soft/centOS/apps/wrf/impi20152/bin:$PATH
setenv LD_LIBRARY_PATH /home/soft/centOS/apps/wrf/impi20152/lib:$LD_LIBRARY_PATH
setenv MANPATH $PREFIX/share/man:$MANPATH
setenv PKG_CONFIG_PATH $PREFIX/lib/pkgconfig:$PKG_CONFIG_PATH
setenv LD_RUN_PATH /home/soft/centOS/apps/wrf/impi20152/lib:$LD_RUN_PATH

#Extra
setenv HDF5_INCLUDE_DIRS /home/soft/centOS/apps/wrf/impi20152/include
setenv HDF5_ROOT /home/soft/centOS/apps/wrf/impi20152/dep2
setenv HDF5_PATH /home/soft/centOS/apps/wrf/impi20152/dep2
setenv HDF5_LIBRARY_PATH /home/soft/centOS/apps/wrf/impi20152/lib
setenv INC_HDF5 /home/soft/centOS/apps/wrf/impi20152/include
setenv NETCDF_PATH /home/soft/centOS/apps/wrf/impi20152
setenv NetCDF /home/soft/centOS/apps/wrf/impi20152
setenv NETCDF /home/soft/centOS/apps/wrf/impi20152
setenv PNETCDF_PATH /home/soft/centOS/apps/wrf/impi20152

================================================================


Thank you in advanced.


Thanks,
Best,
Raj
 
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