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pio error (cesm1_2_2)

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huihuojia@...
pio error (cesm1_2_2)

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/

CESM Software Engineer

huihuojia@...

after install the cmake, the pio build still has errors: (the pio log is attached)

-- Configuring done

CMake 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


You need to edit the path to NETCDF in the case Macros file this is copied from ccsm_utils/Machines/config_compilers.xml

Check your case directory for other occurances of the string USERDEFINED

CESM Software Engineer

huihuojia@...

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 than

you should report the problem to intel.

CESM Software Engineer

huihuojia@...

my intel version is 11.1

huihuojia@...

When I try the CESM 1.1.1, the build process is OK with intel version 11.1

But 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.run

error 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@...

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@...

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@...

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.160406-221952

WARNING: did not find netcdf fortran library

NETCDF 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 done

CMake 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.

CESM Software Engineer

conte@...

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 1

I 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.   

CESM Software Engineer

conte@...

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?

CESM Software Engineer

conte@...

I got the cesm code from this site:

https://svn-ccsm-models.cgd.ucar.edu/cesm1/release_tags/cesm1_2_2

I attach the pio build log...

Thanks!

conte@...

 

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.

CESM Software Engineer

conte@...

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!

jedwards
This is not the version of pio downloaded from https://svn-ccsm-models.cgd.ucar.edu/cesm1/release_tags/cesm1_2_2 it's a newer version which is not compatible with cesm1_2_2.

CESM Software Engineer

conte@...

OK. Thank you.

Could you please tell me which version should I download? I mean, which one is compatible with cesm1_2_2?

Thanks!

jedwards
PIO comes with the cesm1_2_2 distribution, cesm originates in several different source repositories and sometimes one or more of them fail, I think that in your case the pio download failed when you first got cesm and you missed the error message that was output.

CESM Software Engineer

conte@...

Thank you very much for your last comment. It was really helpful.

I managed to download the correct pio version, and tried everything again.

However I have encountered another problem... Pio is succesfully compiled, but not installed in the right place. And I don't know why.

I could try to hack it, but I think it is better that pio files are installed by the scripts.

I am attaching the pio and csm_share build logs. In the first one you will see (at the end) the cp files have no match.

I would appreciate any advice.

And thanks again!

jedwards

It looks like you tried to build again over an old build directory.   Completly remove the build directory and try again.

CESM Software Engineer

conte@...

Hi,

I finally made it run. I was able to "execute" the file "case.run".

When it finished, I got the following message:

 

CESM PRESTAGE SCRIPT HAS FINISHED SUCCESSFULLY

-------------------------------------------------------------------------

Fri May  6 15:22:27 CEST 2016 -- CSM EXECUTION BEGINS HERE

Fri May  6 15:35:26 CEST 2016 -- CSM EXECUTION HAS FINISHED

(seq_mct_drv): ===============       SUCCESSFUL TERMINATION OF CPL7-CCSM ===============

Archiving cesm output to /home/*****/export/scratch/archive/waccm_2

Calling the short-term archiving script st_archive.sh

st_archive.sh: start of short-term archiving

st_archive.sh: restart files from end of run will be saved, 

                   interim restart files will be deleted

st_archive.sh: short-term archiving completed successfully

/homenas/home/*****/export/waccm/builtrun/waccm_2/Tools/ccsm_getenv: No such file or directory.

gzip: timing/ccsm_timing_stats.160506-152159: No such file or directory

 

Could you please give me any advice on the two errors at the end of the message? I mean the lack of the files...

(Apologies for this question but, as I said before, I am new at this)

Thank you!!

 

 

jedwards

What is the value of the environment variable $USER?    It looks like that variable either isn't set or is set to something incorrect. 

CESM Software Engineer

conte@...

Hi!

There is no problem. I just changed changed the user variable to "*****" for the post.

Here I transcribe the complete message:

 

-------------------------------------------------------------------------

 CESM BUILDNML SCRIPT STARTING

 - To prestage restarts, untar a restart.tar file into /home/ma017/export/waccm/builtrun/waccm_2

 infile is /home/ma017/export/waccm/case/waccm_2/Buildconf/cplconf/cesm_namelist 

 CESM BUILDNML SCRIPT HAS FINISHED SUCCESSFULLY

-------------------------------------------------------------------------

-------------------------------------------------------------------------

 CESM PRESTAGE SCRIPT STARTING

 - Case input data directory, DIN_LOC_ROOT, is /home/ma017/export/scratch/inputdata

 - Checking the existence of input datasets in DIN_LOC_ROOT

 CESM PRESTAGE SCRIPT HAS FINISHED SUCCESSFULLY

-------------------------------------------------------------------------

Mon May  9 10:02:27 CEST 2016 -- CSM EXECUTION BEGINS HERE

Mon May  9 10:15:38 CEST 2016 -- CSM EXECUTION HAS FINISHED

(seq_mct_drv): ===============       SUCCESSFUL TERMINATION OF CPL7-CCSM ===============

Archiving cesm output to /home/ma017/export/scratch/archive/waccm_2

Calling the short-term archiving script st_archive.sh

 

st_archive.sh: start of short-term archiving

st_archive.sh: restart files from end of run will be saved, 

               interim restart files will be deleted

st_archive.sh: short-term archiving completed successfully

/homenas/home/ma017/export/waccm/builtrun/waccm_2/Tools/ccsm_getenv: No such file or directory.

gzip: timing/ccsm_timing_stats.160509-100200: No such file or directory



Thanks!

 
jedwards
No such file or directory: /homenas/home/ma017/export/waccm/builtrun/waccm_2/Tools/ccsm_getenv

CESM Software Engineer

conte@...

Yes, that's clear.

But why is not there and for what is it needed?

jadhavom91@...

I am getting error while building CESM1_2_2_CAMChem. On one forum it has mentioned that 'to set proper path to netcdf.inc' (which I have already set !). It works properly with shared libraries but throughs following error while building statistically. Please suggest solution as I am really stuck to this point.

 

PGF90-W-0435-Array declared with zero size (/home/cc/vfaculty/omjadhav.vfaculty/cesm1_2_2_CAMChem2/models/utils/pio/nf_mod.F90: 1617)
PGF90-S-0079-Keyword form of argument illegal in this context for comm (/home/cc/vfaculty/omjadhav.vfaculty/cesm1_2_2_CAMChem2/models/utils/pio/ionf_mod.F90: 82)
PGF90-S-0079-Keyword form of argument illegal in this context for info (/home/cc/vfaculty/omjadhav.vfaculty/cesm1_2_2_CAMChem2/models/utils/pio/ionf_mod.F90: 101)
  0 inform,   0 warnings,   2 severes, 0 fatal for create_nf
PGF90-S-0187-Too many arguments specified for nf90_open (/home/cc/vfaculty/omjadhav.vfaculty/cesm1_2_2_CAMChem2/models/utils/pio/ionf_mod.F90: 204)
PGF90-S-0079-Keyword form of argument illegal in this context for info (/home/cc/vfaculty/omjadhav.vfaculty/cesm1_2_2_CAMChem2/models/utils/pio/ionf_mod.F90: 208)
  0 inform,   0 warnings,   2 severes, 0 fatal for open_nf
PGF90-S-0038-Symbol, nf90_def_var_fill, has not been explicitly declared (/home/cc/vfaculty/omjadhav.vfaculty/cesm1_2_2_CAMChem2/models/utils/pio/nf_mod.F90)
PGF90-S-0038-Symbol, nf90_def_var_deflate, has not been explicitly declared (/home/cc/vfaculty/omjadhav.vfaculty/cesm1_2_2_CAMChem2/models/utils/pio/nf_mod.F90)
  0 inform,   0 warnings,   2 severes, 0 fatal for def_var_md
gmake[2]: *** [CMakeFiles/pio.dir/nf_mod.F90.o] Error 2
gmake[2]: *** Waiting for unfinished jobs....
gmake[2]: *** [CMakeFiles/pio.dir/ionf_mod.F90.o] Error 2

Om Jadhav

jedwards

I think that you may be building with a netcdf library that is not compatible with the pio library you are using.   From the line above

NETCDF_DIR:STRING=USERDEFINED_MUST_EDIT_THIS  suggests that you haven't defined the path to netcdf properly, this is probably the root of the problem.

 

CESM Software Engineer

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