CESM1.2.0移植过程中$case.build出错，请大家帮忙分析

fascism

大家好，最近我正在做CESM1.2.0移植的工作，但是到了$case.build这一步总是出错，我分别用了两组编译器尝试，第一组是pgi和openmpi，另一组是intel和mpich，但是得到的错误信息大同小异，下面主要说一下intel和mpich版本的，具体如下：

-------------------------------------------------------------------------
CESM BUILDNML SCRIPT STARTING
- To prestage restarts, untar a restart.tar file into /labs/climate/jiminglab2/baoqing/cesm1_2_0/mycases/test1/run
infile is /labs/climate/jiminglab2/baoqing/cesm1_2_0/scripts/test1/Buildconf/cplconf/cesm_namelist
CESM BUILDNML SCRIPT HAS FINISHED SUCCESSFULLY
-------------------------------------------------------------------------
-------------------------------------------------------------------------
CESM PRESTAGE SCRIPT STARTING
- Case input data directory, DIN_LOC_ROOT, is /archive/jiminglab07/baoqing/CESM/inputdata
- Checking the existence of input datasets in DIN_LOC_ROOT
CESM PRESTAGE SCRIPT HAS FINISHED SUCCESSFULLY
-------------------------------------------------------------------------
-------------------------------------------------------------------------
CESM BUILDEXE SCRIPT STARTING
COMPILER is intel
- Build Libraries: mct gptl pio csm_share
Sat Oct 12 11:19:19 MDT 2013 /labs/climate/jiminglab2/baoqing/cesm1_2_0/mycases/test1/bld/mct/mct.bldlog.131012-111916
Sat Oct 12 11:20:09 MDT 2013 /labs/climate/jiminglab2/baoqing/cesm1_2_0/mycases/test1/bld/gptl/gptl.bldlog.131012-111916
Sat Oct 12 11:20:12 MDT 2013 /labs/climate/jiminglab2/baoqing/cesm1_2_0/mycases/test1/bld/pio/pio.bldlog.131012-111916
ERROR: buildlib.pio failed, see /labs/climate/jiminglab2/baoqing/cesm1_2_0/mycases/test1/bld/pio/pio.bldlog.131012-111916
ERROR: cat /labs/climate/jiminglab2/baoqing/cesm1_2_0/mycases/test1/bld/pio/pio.bldlog.131012-111916


pio.bldlog.131012-111916文件具体内容是：
Sat Oct 12 11:20:12 MDT 2013 /labs/climate/jiminglab2/baoqing/cesm1_2_0/mycases/test1/bld/pio/pio.bldlog.131012-111916
Copying source to CCSM EXEROOT...
New build of PIO
Running configure...
for OS=LINUX MACH=userdefined
cat: Filepath: No such file or directory
cat: Srcfiles: No such file or directory
/labs/climate/jiminglab2/baoqing/cesm1_2_0/scripts/test1/Tools/mkSrcfiles
cp -f /labs/climate/jiminglab2/baoqing/cesm1_2_0/mycases/test1/bld/pio/Filepath /labs/climate/jiminglab2/baoqing/cesm1_2_0/mycases/test1/bld/pio/Deppath
/labs/climate/jiminglab2/baoqing/cesm1_2_0/scripts/test1/Tools/mkDepends  Deppath Srcfiles > /labs/climate/jiminglab2/baoqing/cesm1_2_0/mycases/test1/bld/pio/Depends
cd /labs/climate/jiminglab2/baoqing/cesm1_2_0/mycases/test1/bld/pio; \
         /labs/climate/jiminglab2/baoqing/cesm1_2_0/models/utils/pio/configure  --enable-timing CC="icc " FC="ifort " MPICC="mpicc  " MPIFC="mpif90 " FCFLAGS="-O2 -fp-model source -convert big_endian -assume byterecl -ftz -traceback  -free  -I.  -I/labs/climate/jiminglab2/baoqing/cesm1_2_0/mycases/test1/bld/pio -I/rc/tools/free/redhat_6_x86_64/datatools-climate-ifort-icc-mvapich2-0//include -I/rc/tools/free/redhat_6_x86_64/datatools-climate-ifort-icc-mvapich2-0//include -I/rc/tools/free/redhat_6_x86_64/datatools-climate-ifort-icc-mvapich2-0//include -I/labs/climate/jiminglab2/baoqing/cesm1_2_0/mycases/test1/bld/mct/mct -I/labs/climate/jiminglab2/baoqing/cesm1_2_0/mycases/test1/bld/mct/mpeu -I/labs/climate/jiminglab2/baoqing/cesm1_2_0/mycases/test1/bld/pio -I/labs/climate/jiminglab2/baoqing/cesm1_2_0/mycases/test1/bld/gptl -I/labs/climate/jiminglab2/baoqing/cesm1_2_0/models/utils/pio -I/labs/climate/jiminglab2/baoqing/cesm1_2_0/mycases/test1/bld/lib/include" CPPDEFS=" -DLINUX  -DMCT_INTERFACE -DHAVE_MPI -DFORTRANUNDERSCORE -DNO_R16 -DLINUX -DCPRINTEL  -DHAVE_SLASHPROC" CFLAGS="-O2 -fp-model precise   -DLINUX  -DMCT_INTERFACE -DHAVE_MPI -DFORTRANUNDERSCORE -DNO_R16 -DLINUX -DCPRINTEL  -DHAVE_SLASHPROC -I.. -I.  -I/labs/climate/jiminglab2/baoqing/cesm1_2_0/mycases/test1/bld/pio -I/rc/tools/free/redhat_6_x86_64/datatools-climate-ifort-icc-mvapich2-0//include -I/rc/tools/free/redhat_6_x86_64/datatools-climate-ifort-icc-mvapich2-0//include -I/rc/tools/free/redhat_6_x86_64/datatools-climate-ifort-icc-mvapich2-0//include -I/labs/climate/jiminglab2/baoqing/cesm1_2_0/mycases/test1/bld/mct/mct -I/labs/climate/jiminglab2/baoqing/cesm1_2_0/mycases/test1/bld/mct/mpeu -I/labs/climate/jiminglab2/baoqing/cesm1_2_0/mycases/test1/bld/pio -I/labs/climate/jiminglab2/baoqing/cesm1_2_0/mycases/test1/bld/gptl -I/labs/climate/jiminglab2/baoqing/cesm1_2_0/models/utils/pio -I/labs/climate/jiminglab2/baoqing/cesm1_2_0/mycases/test1/bld/lib/include" NETCDF_PATH=/rc/tools/free/redhat_6_x86_64/datatools-climate-ifort-icc-mvapich2-0/ LDFLAGS="" LIBS="" PNETCDF_PATH=/rc/tools/free/redhat_6_x86_64/datatools-climate-ifort-icc-mvapich2-0/   --srcdir /labs/climate/jiminglab2/baoqing/cesm1_2_0/models/utils/pio
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether icc  accepts -g... yes
checking for icc  option to accept ISO C89... none needed
checking how to run the C preprocessor... icc  -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes

checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking whether byte ordering is bigendian... no
checking whether we are using the GNU Fortran compiler... no
checking whether ifort  accepts -g... yes
checking for Fortran flag to compile .F90 files... none
checking for Fortran flag needed to accept free-form source... none
checking for Fortran flag needed to accept 132 column source lines... none
checking for Fortran flag to compile preprocessed .F files... none
checking how to define symbols for preprocessed Fortran... -D
checking for ftn... mpif90
checking for mpif.h... yes
checking for Fortran flag to compile .F90 files... (cached) none
checking for mpi.mod... yes
checking Fortran support for c_sizeof()... yes
checking MPI-IO support in MPI implementation... yes
Full hostname= login-02
Hostname=login-02.rc.usu.edu
Machine=x86_64
OS=Linux
checking Fortran 90 module extension... mod

checking Fortran 90 module inclusion flag... -I
using NETCDF_PATH from environment
checking for Fortran flag to compile .F90 files... (cached) none
checking for hdf5... yes
checking for H5open in -lhdf5... no
checking for H5Dclose in -lhdf5_hl... no
configure: Fortran not checked for yet
checking for netcdf... /rc/tools/free/redhat_6_x86_64/datatools-climate-ifort-icc-mvapich2-0/
checking for library containing nc_inq_libvers... -lnetcdf
checking for library containing NF_INQ_LIBVERS... no
configure: error: cannot find netCDF fortran library
gmake: *** [/labs/climate/jiminglab2/baoqing/cesm1_2_0/mycases/test1/bld/pio/Makefile.conf] Error 1
cp: cannot stat `Makefile.conf': No such file or directory
Makefile:25: Makefile.conf: No such file or directory
gmake: *** No rule to make target `Makefile.conf'.  Stop.



我感觉是netcdf有问题，但是我的netcdf已经安装测试过了，应该好着呢。
我看了天道酬勤发表的帖子：http://bbs.06climate.com/forum.php?mod=viewthread&tid=14380
感觉很有道理，应该是没有
cp: cannot stat `Makefile.conf.old': No such file or directory
cp: cannot stat `Makefile.conf': No such file or directory
Makefile:4: Makefile.conf: No such file or directory
make: *** No rule to make target `Makefile.conf'.  Stop.
感觉是缺少Makefile.conf.old以及Makefile.conf。然后按照他的方法，
cd  ...../cesm/models/utils/mct
./configure这一步正常完成了，但是当我
cd  ...../cesm/models/utils/pio
./configure的时候，又出错了，具体作物信息如下：
checking for xlc... no
checking for cc... cc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether cc accepts -g... yes
checking for cc option to accept ISO C89... none needed
checking how to run the C preprocessor... cc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking whether byte ordering is bigendian... no
checking for gfortran... gfortran
checking whether we are using the GNU Fortran compiler... yes
checking whether gfortran accepts -g... yes
checking for Fortran flag to compile .F90 files... none
checking for Fortran flag needed to accept free-form source... none
checking for Fortran flag needed to accept 132 column source lines... none
checking for Fortran flag to compile preprocessed .F files... none
checking how to define symbols for preprocessed Fortran... -D
checking for ftn... no
checking for mpif90... mpif90
checking for MPI_Init... yes
checking for mpif.h... yes
checking for Fortran flag to compile .F90 files... (cached) none
checking for mpi.mod... yes
checking Fortran support for c_sizeof()... no
checking Fortran support for sizeof()... yes
checking MPI-IO support in MPI implementation... no
Full hostname= login-02
Hostname=login-02.rc.usu.edu
Machine=x86_64
OS=Linux
checking Fortran 90 module extension... mod
checking Fortran 90 module inclusion flag... -I
configure: WARNING: NETCDF_PATH not found in environment,                            defaulting to /usr/local/netcdf
checking for Fortran flag to compile .F90 files... (cached) none
checking for hdf5... yes
checking for H5open in -lhdf5... no
checking for H5Dclose in -lhdf5_hl... no
configure: Fortran not checked for yet
checking for netcdf... yes
checking for library containing nc_inq_libvers... no
configure: error: cannot find netCDF C library


还是netcdf的问题，我现在严重怀疑我的netcdf版本有问题，我用的是netcdf 4.3.0. 不知道netcdf用什么版本的比较好呢？

或者有什么其他原因，请大家帮我分析一下！我已经卡了快10天了，不胜感激！希望能尽快解决

andrewsoong

CESM1.2.0要求netcdf4.2及其以上版本~~~但是我师姐用netcdf3.6.3也转通了~~~
另外值得提醒你的是：从netcdf4.1.3以后的版本开始，netcdf-c 和netcdf-fortran分开发行了，也就是说你在安装netcdf的时候需要将这两个安装在一起~~~
我记得我以前写过这个帖子，关于如何将他们安装在一起~~~

另外值得提醒你的是，CESM1.2.0要求最新版本的intel fortran，也就是2013版的~~~以前的版本有bug~~~

祝你成功~~~

fascism

andrewsoong 发表于 2013-10-13 08:25

                               
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CESM1.2.0要求netcdf4.2及其以上版本~~~但是我师姐用netcdf3.6.3也转通了~~~
另外值得提醒你的是：从netcd ...

好的，非常感谢，我试试先，我看错误信息里面说是找不到netcdf-c，我感觉是因为我只有netcdf-fortran

fascism

andrewsoong 发表于 2013-10-13 08:25

                               
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CESM1.2.0要求netcdf4.2及其以上版本~~~但是我师姐用netcdf3.6.3也转通了~~~
另外值得提醒你的是：从netcd ...

我试了好多次，用netcdf 4.3总是出现找不到netcdf c Lib或者fortran lib，很苦恼啊。当时您师姐用的netcdf3.6.3也是转的cesm1.2吗？不行了我就考虑用netcdf3.6.3，这东西太熬人。非常感谢

andrewsoong

fascism 发表于 2013-10-17 00:54

                               
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我试了好多次，用netcdf 4.3总是出现找不到netcdf c Lib或者fortran lib，很苦恼啊。当时您师姐用的netcd ...

转1.2使用的是netcdf3.6.3~~~你这样出错，肯定是netcdf没有安装好~~~
另外intel fortran 版本不能低于2012版~~~

fascism

andrewsoong 发表于 2013-10-17 08:32

                               
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转1.2使用的是netcdf3.6.3~~~你这样出错，肯定是netcdf没有安装好~~~
另外intel fortran 版本不能低于20 ...

好的，我也换成3.6.3吧，只要能转通就行。本来总是纠结，看看能否用4.3转起来，现在不想再试了，呵呵。

andrewsoong

fascism 发表于 2013-10-17 12:28

                               
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好的，我也换成3.6.3吧，只要能转通就行。本来总是纠结，看看能否用4.3转起来，现在不想再试了，呵呵。

移植新模式就是这么消磨人~~~尤其是这种比较矫情的模式~~~

fascism

andrewsoong 发表于 2013-10-17 14:50

                               
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移植新模式就是这么消磨人~~~尤其是这种比较矫情的模式~~~

好的，谢谢鼓励。对了，我用svn下载的cesm1.2.0，大概是1.7GB。只是想确认一下模式是否下载完整了，您那个模式刚下载下来大概多大啊？

andrewsoong

fascism 发表于 2013-10-18 00:05

                               
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好的，谢谢鼓励。对了，我用svn下载的cesm1.2.0，大概是1.7GB。只是想确认一下模式是否下载完整了，您那个 ...

没这么大啊~~~不到100M~~~inputdata比较大一些~~~
使用如下命令：svn co https://svn-ccsm-release.cgd.ucar.edu/model_versions/cesm1_2_0/

fascism

andrewsoong 发表于 2013-10-18 08:24

                               
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没这么大啊~~~不到100M~~~inputdata比较大一些~~~
使用如下命令：svn co https://svn-ccsm-release.cgd. ...

那奇怪了啊，我就用的这个命令下载的，我一会再看看。好像这次netcdf lib弄对了