Main menu

Navigation

mct not compiling

2 posts / 0 new
Last post
spamiad@...
mct not compiling

Hello, there were some software changes ( general update ) on our HPC and I'm trying to recompile CESM/CLM.

 

However, already when building mct the process fails.

Please find below the config.log from gnu/mpi-serial/nodebug/nothreads/mct

Does it point towards a particular problen?

 

I see the build script is trying to access /include which does not exist, but I'm not sure where this is really coming from.

 

 

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 2.8, which was
generated by GNU Autoconf 2.69.  Invocation command line was

 

 

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 2.8, which was
generated by GNU Autoconf 2.69.  Invocation command line was

  $ /homex/cg41/cg4152/cesm1_2_2/models/utils/mct/configure --enable-mpiserial --enable-mpiserial MCT_PATH=/work/cg41/cg4152/CESM/jc_I_test_24/exe/gnu/mpi-serial/nodebug/nothreads/mct/mpi-serial CC=gcc  FC=gfortran  MPICC=gcc  MPIFC=gfortran  FCFLAGS=-O -fconvert=big-endian -ffree-line-length-none -ffixed-line-length-none  -fno-range-check  -O2  -ffree-form  -I.  -I/work/cg41/cg4152/CESM/jc_I_test_24/exe/gnu/mpi-serial/nodebug/nothreads/include -I/work/cg41/cg4152/CESM/jc_I_test_24/exe/gnu/mpi-serial/nodebug/nothreads/MCT/noesmf/a1l1r1i1o1g1w1/csm_share -I/homey/hbn29/hbn29f/DAS_Depends /include -I/work/cg41/cg4152/CESM/jc_I_test_24/exe/gnu/mpi-serial/nodebug/nothreads/include -I/homex/cg41/cg4152/cesm1_2_2/models/csm_share/shr CPPDEFS= -DLINUX  -DNDEBUG -DMCT_INTERFACE -DNO_MPI2 -DNO_MPIMOD -DFORTRANUNDERSCORE -DNO_R16 -DLINUX -DCPRGNU  -DHAVE_SLASHPROC CFLAGS= -DLINUX  -DNDEBUG -DMCT_INTERFACE -DNO_MPI2 -DNO_MPIMOD -DFORTRANUNDERSCORE -DNO_R16 -DLINUX -DCPRGNU  -DHAVE_SLASHPROC -I.. -I.  -I/work/cg41/cg4152/CESM/jc_I_test_24/exe/gnu/mpi-serial/nodebug/nothreads/include -I/work/cg41/cg4152/CESM/jc_I_test_24/exe/gnu/mpi-serial/nodebug/nothreads/MCT/noesmf/a1l1r1i1o1g1w1/csm_share -I/homey/hbn29/hbn29f/DAS_Depends /include -I/work/cg41/cg4152/CESM/jc_I_test_24/exe/gnu/mpi-serial/nodebug/nothreads/include -I/homex/cg41/cg4152/cesm1_2_2/models/csm_share/shr NETCDF_PATH=/homey/hbn29/hbn29f/DAS_Depends LDFLAGS= LIBS=-lopenblas -lnetcdf -lnetcdff --srcdir /homex/cg41/cg4152/cesm1_2_2/models/utils/mct

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

hostname = jrl06
uname -m = x86_64
uname -r = 3.10.0-514.26.2.el7.x86_64
uname -s = Linux
uname -v = #1 SMP Tue Jul 4 15:04:05 UTC 2017

/usr/bin/uname -p = x86_64
/bin/uname -X     = unknown

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

PATH: /usr/local/software/jc/Stages/2016a/software/libxml2/2.9.3-GCCcore-5.3.0/bin
PATH: /usr/local/software/jc/Stages/2016a/software/Perl/5.22.1-GCCcore-5.3.0/bin
PATH: /usr/local/software/jc/Stages/2016a/software/ncview/2.1.6-gpsmpi-2016a/bin
PATH: /usr/local/software/jc/Stages/2016a/software/libXpm/3.5.11-GCCcore-5.3.0/bin
PATH: /usr/local/software/jc/Stages/2016a/software/UDUNITS/2.2.20-GCC-5.3.0-2.26/bin
PATH: /usr/local/software/jc/Stages/2016a/software/netCDF/4.4.0-gpsmpi-2016a/bin
PATH: /usr/local/software/jc/Stages/2016a/software/HDF5/1.8.16-gpsmpi-2016a/bin
PATH: /usr/local/software/jc/Stages/2016a/software/FFTW/3.3.4-gpsmpi-2016a/bin
PATH: /usr/local/software/jc/Stages/2016a/software/git/2.7.2-GCCcore-5.3.0/bin
PATH: /usr/local/software/jc/Stages/2016a/software/gettext/0.19.7-GCCcore-5.3.0/bin
PATH: /usr/local/software/jc/Stages/2016a/software/expat/2.1.0-GCCcore-5.3.0/bin
PATH: /usr/local/software/jc/Stages/2016a/software/cURL/7.47.1-GCCcore-5.3.0/bin
PATH: /usr/local/software/jc/Stages/2016a/software/psmpi/5.1.5-1-GCC-5.3.0-2.26/bin
PATH: /usr/local/software/jc/Stages/2016a/software/CMake/3.4.3-GCCcore-5.3.0/bin
PATH: /usr/local/software/jc/Stages/2016a/software/ncurses/6.0-GCCcore-5.3.0/bin
PATH: /usr/local/software/jc/Stages/2016a/software/binutils/2.26-GCCcore-5.3.0/bin
PATH: /usr/local/software/jc/Stages/2016a/software/GCCcore/5.3.0/bin
PATH: /usr/local/software/jc/Stages/2016a/software/pscom/Default/bin
PATH: /homey/hbn29/hbn29f/DAS_Depends/lib
PATH: /homey/hbn29/hbn29f/DAS_Depends/bin
PATH: /usr/local/jsc/bin
PATH: /usr/bin
PATH: /usr/sbin
PATH: /opt/ibutils/bin
PATH: /usr/lpp/mmfs/bin


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

configure:2358: checking for C compiler version
configure:2367: gcc  --version >&5
gcc (GCC) 5.3.0
Copyright (C) 2015 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

configure:2378: $? = 0
configure:2367: gcc  -v >&5
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/local/software/jc/Stages/2016a/software/GCCcore/5.3.0/libexec/gcc/x86_64-unknown-linux-gnu/5.3.0/lto-wrapper
Target: x86_64-unknown-linux-gnu
Configured with: ../configure --enable-languages=c,c++,fortran --enable-lto --enable-checking=release --disable-multilib --enable-shared=yes --enable-static=yes --enable-threads=posix --enable-gold=default --enable-plugins --enable-ld --with-plugin-ld=ld.gold --prefix=/usr/local/software/jc/Stages/2016a/software/GCCcore/5.3.0 --with-local-prefix=/usr/local/software/jc/Stages/2016a/software/GCCcore/5.3.0 --enable-bootstrap --with-isl=/dev/shm/swmanage/GCCcore/5.3.0/dummy-/gcc-5.3.0/stage2_stuff
Thread model: posix
gcc version 5.3.0 (GCC)
configure:2378: $? = 0
configure:2367: gcc  -V >&5
gcc: error: unrecognized command line option '-V'
gcc: fatal error: no input files
compilation terminated.
configure:2378: $? = 1
configure:2367: gcc  -qversion >&5
gcc: error: unrecognized command line option '-qversion'
gcc: fatal error: no input files
compilation terminated.
configure:2378: $? = 1
configure:2398: checking whether the C compiler works
configure:2420: gcc   -DLINUX  -DNDEBUG -DMCT_INTERFACE -DNO_MPI2 -DNO_MPIMOD -DFORTRANUNDERSCORE -DNO_R16 -DLINUX -DCPRGNU  -DHAVE_SLASHPROC -I.. -I.  -I/work/cg41/cg4152/CESM/jc_I_test_24/exe/gnu/mpi-serial/nodebug/nothreads/include -I/work/cg41/cg4152/CESM/jc_I_test_24/exe/gnu/mpi-serial/nodebug/nothreads/MCT/noesmf/a1l1r1i1o1g1w1/csm_share -I/homey/hbn29/hbn29f/DAS_Depends /include -I/work/cg41/cg4152/CESM/jc_I_test_24/exe/gnu/mpi-serial/nodebug/nothreads/include -I/homex/cg41/cg4152/cesm1_2_2/models/csm_share/shr   conftest.c -lopenblas -lnetcdf -lnetcdff >&5
gcc: error: /include: No such file or directory
configure:2424: $? = 1
configure:2462: result: no
configure: failed program was:
| /* confdefs.h */
| #define PACKAGE_NAME "MCT"
| #define PACKAGE_TARNAME "mct"
| #define PACKAGE_VERSION "2.8"
| #define PACKAGE_STRING "MCT 2.8"
| #define PACKAGE_BUGREPORT ""
| #define PACKAGE_URL ""
| /* end confdefs.h.  */
|
| int
| main ()
| {
|
|   ;
|   return 0;
| }
configure:2467: error: in `/work/cg41/cg4152/CESM/jc_I_test_24/exe/gnu/mpi-serial/nodebug/nothreads/mct':
configure:2469: error: C compiler cannot create executables
See `config.log' for more details

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

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='gcc '
ac_cv_env_CFLAGS_set=set
ac_cv_env_CFLAGS_value=' -DLINUX  -DNDEBUG -DMCT_INTERFACE -DNO_MPI2 -DNO_MPIMOD -DFORTRANUNDERSCORE -DNO_R16 -DLINUX -DCPRGNU  -DHAVE_SLASHPROC -I.. -I.  -I/work/cg41/cg4152/CESM/jc_I_test_24/exe/gnu/mpi-serial/nodebug/nothreads/include -I/work/cg41/cg4152/CESM/jc_I_test_24/exe/gnu/mpi-serial/nodebug/nothreads/MCT/noesmf/a1l1r1i1o1g1w1/csm_share -I/homey/hbn29/hbn29f/DAS_Depends /include -I/work/cg41/cg4152/CESM/jc_I_test_24/exe/gnu/mpi-serial/nodebug/nothreads/include -I/homex/cg41/cg4152/cesm1_2_2/models/csm_share/shr'
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_CPP_set=
ac_cv_env_CPP_value=
ac_cv_env_DEBUG_set=set
ac_cv_env_DEBUG_value=FALSE
ac_cv_env_ENDIAN_set=
ac_cv_env_ENDIAN_value=
ac_cv_env_FCFLAGS_set=set
ac_cv_env_FCFLAGS_value='-O -fconvert=big-endian -ffree-line-length-none -ffixed-line-length-none  -fno-range-check  -O2  -ffree-form  -I.  -I/work/cg41/cg4152/CESM/jc_I_test_24/exe/gnu/mpi-serial/nodebug/nothreads/include -I/work/cg41/cg4152/CESM/jc_I_test_24/exe/gnu/mpi-serial/nodebug/nothreads/MCT/noesmf/a1l1r1i1o1g1w1/csm_share -I/homey/hbn29/hbn29f/DAS_Depends /include -I/work/cg41/cg4152/CESM/jc_I_test_24/exe/gnu/mpi-serial/nodebug/nothreads/include -I/homex/cg41/cg4152/cesm1_2_2/models/csm_share/shr'
ac_cv_env_FC_set=set
ac_cv_env_FC_value='gfortran '
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=
ac_cv_env_INCLUDEPATH_value=
ac_cv_env_LDFLAGS_set=set
ac_cv_env_LDFLAGS_value=
ac_cv_env_LIBS_set=set
ac_cv_env_LIBS_value='-lopenblas -lnetcdf -lnetcdff'
ac_cv_env_MPIFC_set=set
ac_cv_env_MPIFC_value='gfortran '
ac_cv_env_MPIHEADER_set=
ac_cv_env_MPIHEADER_value=
ac_cv_env_MPILIBS_set=set
ac_cv_env_MPILIBS_value=mpich,mpi-serial
ac_cv_env_OPT_set=
ac_cv_env_OPT_value=
ac_cv_env_PROGFCFLAGS_set=
ac_cv_env_PROGFCFLAGS_value=
ac_cv_env_RANLIB_set=
ac_cv_env_RANLIB_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. ##
## ----------------- ##

AR=''
BABELROOT=''
BIT64=''
CC='gcc '
CFLAGS=' -DLINUX  -DNDEBUG -DMCT_INTERFACE -DNO_MPI2 -DNO_MPIMOD -DFORTRANUNDERSCORE -DNO_R16 -DLINUX -DCPRGNU  -DHAVE_SLASHPROC -I.. -I.  -I/work/cg41/cg4152/CESM/jc_I_test_24/exe/gnu/mpi-serial/nodebug/nothreads/include -I/work/cg41/cg4152/CESM/jc_I_test_24/exe/gnu/mpi-serial/nodebug/nothreads/MCT/noesmf/a1l1r1i1o1g1w1/csm_share -I/homey/hbn29/hbn29f/DAS_Depends /include -I/work/cg41/cg4152/CESM/jc_I_test_24/exe/gnu/mpi-serial/nodebug/nothreads/include -I/homex/cg41/cg4152/cesm1_2_2/models/csm_share/shr'
COMPILER_ROOT=''
CPP=''
CPPDEFS=' -DLINUX  -DNDEBUG -DMCT_INTERFACE -DNO_MPI2 -DNO_MPIMOD -DFORTRANUNDERSCORE -DNO_R16 -DLINUX -DCPRGNU  -DHAVE_SLASHPROC'
CPPFLAGS=''
CRULE=''
DEBUG='FALSE'
DEFS=''
ECHO_C=''
ECHO_N='-n'
ECHO_T=''
EGREP=''
ENDIAN=''
EXEEXT=''
FC='gfortran '
FCFLAGS='-O -fconvert=big-endian -ffree-line-length-none -ffixed-line-length-none  -fno-range-check  -O2  -ffree-form  -I.  -I/work/cg41/cg4152/CESM/jc_I_test_24/exe/gnu/mpi-serial/nodebug/nothreads/include -I/work/cg41/cg4152/CESM/jc_I_test_24/exe/gnu/mpi-serial/nodebug/nothreads/MCT/noesmf/a1l1r1i1o1g1w1/csm_share -I/homey/hbn29/hbn29f/DAS_Depends /include -I/work/cg41/cg4152/CESM/jc_I_test_24/exe/gnu/mpi-serial/nodebug/nothreads/include -I/homex/cg41/cg4152/cesm1_2_2/models/csm_share/shr'
FCFLAGS_F90=''
FCFLAGS_F=''
FCLIBS=''
FC_DEFINE=''
FORT_SIZE=''
FPP=''
FPPFLAGS=''
GREP=''
INCLUDEFLAG=''
INCLUDEPATH=''
LDFLAGS=''
LIBOBJS=''
LIBS='-lopenblas -lnetcdf -lnetcdff'
LTLIBOBJS=''
MPIFC='gfortran '
MPIHEADER=''
MPILIBS='mpich,mpi-serial'
MPISERPATH=''
OBJEXT=''
OPT=''
PACKAGE_BUGREPORT=''
PACKAGE_NAME='MCT'
PACKAGE_STRING='MCT 2.8'
PACKAGE_TARNAME='mct'
PACKAGE_URL=''
PACKAGE_VERSION='2.8'
PATH_SEPARATOR=':'
PROGFCFLAGS=''
PYTHON=''
PYTHONOPTS=''
RANLIB=''
REAL8=''
SHELL='/bin/sh'
ac_ct_CC=''
ac_ct_FC=''
bindir='${exec_prefix}/bin'
build_alias=''
datadir='${datarootdir}'
datarootdir='${prefix}/share'
docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
dvidir='${docdir}'
exec_prefix='NONE'
host_alias=''
htmldir='${docdir}'
includedir='${prefix}/include'
infodir='${datarootdir}/info'
libdir='${exec_prefix}/lib'
libexecdir='${exec_prefix}/libexec'
localedir='${datarootdir}/locale'
localstatedir='${prefix}/var'
mandir='${datarootdir}/man'
oldincludedir='/usr/include'
pdfdir='${docdir}'
prefix='NONE'
program_transform_name='s,x,x,'
psdir='${docdir}'
sbindir='${exec_prefix}/sbin'
sharedstatedir='${prefix}/com'
sysconfdir='${prefix}/etc'
target_alias=''

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

/* confdefs.h */
#define PACKAGE_NAME "MCT"
#define PACKAGE_TARNAME "mct"
#define PACKAGE_VERSION "2.8"
#define PACKAGE_STRING "MCT 2.8"
#define PACKAGE_BUGREPORT ""
#define PACKAGE_URL ""

configure: exit 77

jedwards

The problem is that there is an extra space after DAS_Depends in this line:

  -I/homey/hbn29/hbn29f/DAS_Depends /include 

This could either be a problem in your Makefile or perhaps a problem in the way the system module is defined - I think that it's a system module problem and you need to talk to your administrator.


CESM Software Engineer

Log in or register to post comments

Who's new

  • Nicholas.Davis@...
  • numarsanifa@...
  • bingdian_46@...
  • mxy2832029@...
  • nthg2000@...