pio error (cesm1_2_2)

[huihuojia@163_com]

I have an error when I try to build the case (cesm1_2_2)
command: ./test1.build
error message:
file: test1/intel/openmpi/nodebug/nothreads/pio.bldlog.140708-103452
error:
CC=mpicc CXX=mpicxx FC=mpif90 LDFLAGS="" cmake -D CMAKE_Fortran_FLAGS:STRING="-fp-model source -convert big_endian -assume byterecl -ftz -traceback -assume realloc_lhs -O2 -DLINUX -DNDEBUG -DMCT_INTERFACE -DHAVE_MPI -DFORTRANUNDERSCORE -DNO_R16 -DLINUX -DCPRINTEL -DHAVE_SLASHPROC -I. -I/R2/jia/WorkStation/test1/intel/openmpi/nodebug/nothreads/include -I/R2/jia/WorkStation/test1/intel/openmpi/nodebug/nothreads/MCT/noesmf/a1l1r1i1o1g1w1/csm_share -I/R2/jia/local/intelSET/include -I/R2/jia/WorkStation/test1/intel/openmpi/nodebug/nothreads/include -I/R2/jia/CESM/cesm1_2_2/models/csm_share/shr" -D CMAKE_C_FLAGS:STRING="-O2 -fp-model precise -DLINUX -DNDEBUG -DMCT_INTERFACE -DHAVE_MPI -DFORTRANUNDERSCORE -DNO_R16 -DLINUX -DCPRINTEL -DHAVE_SLASHPROC -I. -I/R2/jia/WorkStation/test1/intel/openmpi/nodebug/nothreads/include -I/R2/jia/WorkStation/test1/intel/openmpi/nodebug/nothreads/MCT/noesmf/a1l1r1i1o1g1w1/csm_share -I/R2/jia/local/intelSET/include -I/R2/jia/WorkStation/test1/intel/openmpi/nodebug/nothreads/include -I/R2/jia/CESM/cesm1_2_2/models/csm_share/shr" -D CMAKE_CXX_FLAGS:STRING="-O2 -fp-model precise -DLINUX -DNDEBUG -DMCT_INTERFACE -DHAVE_MPI -DFORTRANUNDERSCORE -DNO_R16 -DLINUX -DCPRINTEL -DHAVE_SLASHPROC -I. -I/R2/jia/WorkStation/test1/intel/openmpi/nodebug/nothreads/include -I/R2/jia/WorkStation/test1/intel/openmpi/nodebug/nothreads/MCT/noesmf/a1l1r1i1o1g1w1/csm_share -I/R2/jia/local/intelSET/include -I/R2/jia/WorkStation/test1/intel/openmpi/nodebug/nothreads/include -I/R2/jia/CESM/cesm1_2_2/models/csm_share/shr" -D CMAKE_VERBOSE_MAKEFILE:BOOL=ON -D NETCDF_DIR:STRING=USERDEFINED_MUST_EDIT_THIS -D USER_CMAKE_MODULE_DIR:STRING=/R2/jia/CESM/cesm1_2_2/scripts/ccsm_utils/CMake -D WITH_PNETCDF:LOGICAL=FALSE -D USER_CMAKE_MODULE_PATH=/R2/jia/CESM/cesm1_2_2/scripts/ccsm_utils/CMake -D GENF90_PATH=/R2/jia/CESM/cesm1_2_2/tools/cprnc/genf90 /R2/jia/CESM/cesm1_2_2/models/utils/pio
/bin/sh: line 1: cmake: command not found
gmake: *** [test1/intel/openmpi/nodebug/nothreads/pio/Makefile] Error 127
exit 1

And I check the pio directory in cesm1_2_2/models/utils/pio, and compared to older version, there is NO configure executable in the directory, Would it cause the problem?

 

[jedwards]

Here is the error:   /bin/sh: line 1: cmake: command not found You need to install cmake http://www.cmake.org/

 

[huihuojia@163_com]

after install the cmake, the pio build still has errors: (the pio log is attached)-- Configuring doneCMake Error at CMakeLists.txt:190 (ADD_LIBRARY):  Target "pio" links to item " -LNETCDF_LIB_DIR-NOTFOUND -lnetcdf" which has  leading or trailing whitespace.  This is now an error according to policy  CMP0004. and in the log file, it said couldn't find netcdf-fortran lib, but it is actually in directory: /R2/jia/local/intelSET/lib, libnetcdff.so, so is the hdf5 library.

 

[jedwards]

NETCDF_DIR:STRING=USERDEFINED_MUST_EDIT_THIS<br /><br /><br />You need to edit the path to NETCDF in the case Macros file  this is copied from ccsm_utils/Machines/config_compilers.xml <br /><br />Check your case directory for other occurances of the string USERDEFINED

 

[huihuojia@163_com]

after I change the USERDEFINED variables in Macro, the pio build is OK. But csm_share build has error (the csm_share log is attached):: catastrophic error: **Internal compiler error: internal abort** Please report this error along with the circumstances in which it occurred in a Software Problem Report.  Note: File and line given may not be explicit cause of this error. compilation aborted for /R2/jia/CESM/cesm1_2_2/models/csm_share/shr/shr_dmodel_mod.F90 (code 3)

 

[jedwards]

What version of the intel compiler are you using?   We are currently using 13.1.2.   If you have an older one try updating, if you are using a newer version thanyou should report the problem to intel.

 

[huihuojia@163_com]

my intel version is 11.1

 

[huihuojia@163_com]

When I try the CESM 1.1.1, the build process is OK with intel version 11.1But I have a strange error after I porting the CESM 1.1.1 and try to run the same case again. The error occurs when I use the command:./test1.runerror message is :./Tools/ccsm_getenv: line 11: syntax error near unexpected token `('./Tools/ccsm_getenv: line 11: `foreach i (env_case.xml env_run.xml env_mach_pes.xml env_build.xml)'But ./Tools/ccsm_getenv is fine when I use the userdefined machine.

 

[huihuojia@163_com]

And the problem didn't occur in the build process.I test the Tools/ccsm_getenv, and find that "Tools/ccsm_getenv" command is OK, but "source Tools/ccsm_getenv " command has the error mentioned above.

 

[huihuojia@163_com]

solve the problem by the posting:alberto.sadde@...Thought of posting my workaround to this strange error.You will need to run the script using csh your_model.run. My guess is that the the system tries to run the csh as a normal sh script in this case.when I use csh ./test1.run, it is OK (my env is sh)

 

[jbuzan@purdue_edu]

Hello,  I am having a PIO error with the same netcdf issue. error: cat /scratch/rice/j/jbuzan/output/I.MO.12_repeat_0_CN_cru_x1_122_wb/intel/openmpi/nodebug/nothreads/pio.bldlog.160406-221952WARNING: did not find netcdf fortran libraryNETCDF built without MPIIO-- Found HDF5: /usr/lib64/libz.so;/usr/lib64/libm.so;/usr/lib64/libhdf5_hl.so;/usr/lib64/libhdf5.so  -- Adding hdf5 libraries -- Could NOT find NETCDF (missing:  NETCDF_Fortran_LIBRARY) -- Found pnetcdf: /depot/huberm/apps/jon_messing_around/PNetcdf_Build/lib/libpnetcdf.a  -- MPIIO detected and enabled.-- MPI Fortran module detected and enabled.-- Configuring doneCMake Error at CMakeLists.txt:190 (ADD_LIBRARY):  Target "pio" links to item "  -L/apps/rhel6/netcdf/4.1.1_intel-13.0.1.117/lib -lnetcdf" which has leading  or trailing whitespace.  This is now an error according to policy CMP0004.  I have set NETCDF_DIR: and NETCDF_PATH.  I am not sure what else to do. -Jonathan Macros File:# Makefile Macros generated from /scratch/rice/j/jbuzan/cesm/cesm1_2_2-Change/scripts/ccsm_utils/Machines/config_compilers.xml using# COMPILER=intel# OS=LINUX# MACH=rice#CPPDEFS+= -DFORTRANUNDERSCORE -DNO_R16 -DLINUX -DCPRINTEL  SLIBS+=-L/apps/rhel6/netcdf/4.1.1_intel-13.0.1.117/lib -lnetcdff -lnetcdf -Bstatic -Wl,--start-group /apps/rhel6/intel/composer_xe_2013.1.117/mkl/lib/intel64/libmkl_intel_lp64.a /apps/rhel6/intel/composer_xe_2013.1.117/mkl/lib/intel64/libmkl_intel_thread.a /apps/rhel6/intel/composer_xe_2013.1.117/mkl/lib/intel64/libmkl_core.a -Wl,--end-group -Bdynamic -liomp5 -lpthread -Xlinker -rpath -Xlinker /apps/rhel6/intel/composer_xe_2013.1.117/compiler/lib/intel64 -I/depot/huberm/apps/jon_messing_around/PNetcdf_Build/include -L/depot/huberm/apps/jon_messing_around/PNetcdf_Build/lib -lpnetcdf CFLAGS:= -O2 -fp-model precise  CXX_LDFLAGS:= -cxxlib  CXX_LINKER:=FORTRAN FC_AUTO_R8:= -r8  FFLAGS:= -O2 -fp-model source -convert big_endian -assume byterecl -ftz -traceback  FFLAGS_NOOPT:= -O0  FIXEDFLAGS:= -fixed -132  FREEFLAGS:= -free  MPICC:= mpicc   MPICXX:= mpicxx  MPIFC:= mpif90  MPI_PATH:=/apps/rhel6/openmpi/1.8.1/intel-13.0.1.117 NETCDF_DIR:=/apps/rhel6/netcdf/4.1.1_intel-13.0.1.117 NETCDF_PATH:=/apps/rhel6/netcdf/4.1.1_intel-13.0.1.117 PIO_PATH:=/depot/huberm/apps/jon_messing_around/PIO_Install PNETCDF_PATH:=/depot/huberm/apps/jon_messing_around/PNetcdf_Build SCC:= icc  SCXX:= icpc  SFC:= ifort  SUPPORTS_CXX:=TRUE ifeq ($(DEBUG), TRUE)    FFLAGS += -g -CU -check pointers -fpe0  endif ifeq ($(compile_threaded), true)                                           

 

[jedwards]

This is the problem: Target "pio" links to item "  -L/apps/rhel6/netcdf/4.1.1_intel-13.0.1.117/lib -lnetcdf" which has leading  or trailing whitespace.  This is now an error according to policy CMP0004.Somehow there is a lot of extra whtespace at the beginnig of that line, but I can't tell the root cause from what you've sent me.   THe netcdf version that you are using is very old and the solution may be to build and link to a newer version.

 

[conte@iap-kborn_de]

I am also having problems when building the pio library.I got these 2 error messages:CMake Error: The source directory "/home/ma017/cesm1_2_2/models/utils/pio" does not exist.gmake: *** [/home/ma017/export/waccm/builtrun/waccm_1/intel/mpich/nodebug/nothreads/pio/Makefile] Error 1I am attaching the complete error message. I would appreciate any comment on this matter. Thanks! Fede.

 

[jedwards]

> The source directory "/home/ma017/cesm1_2_2/models/utils/pio" does not exist.I suspect that there was an error when you checked the code out - Try checking out the code again.   

 

[conte@iap-kborn_de]

I was able to somehow solve the problem with pio library... However, I have problems when building the csm_share library.I am attaching the error message. It looks like cesm is not compatible with pio version.Thanks!Fede.

 

[jedwards]

Looks like there is still a problem with the pio build - can you attach that build log.   Also where / how did you get the cesm source code?

 

[conte@iap-kborn_de]

I got the cesm code from this site:https://svn-ccsm-models.cgd.ucar.edu/cesm1/release_tags/cesm1_2_2I attach the pio build log...Thanks!

 

[conte@iap-kborn_de]

 Hi again. Sorry to insist with this, but have you found a solution to the problem I reported?I would appreciate any advice, because I am really stucked at this point and can't go forward.Thanks! 

 

[jedwards]

From the latest pio log it looks like your build directory is corrupted by an earlier attempt to build run  rm -fr test1/intel/   and try again.

 

[conte@iap-kborn_de]

I did what you recommended. However, I still can't build the csm_share library.I am attaching both the pio and csm_share build logs.Thanks!