成功移植CESM模式（介绍）——Porting CESM via user defined machine files

彭小清

各位大侠，想请教一下 用intel编译的
  我这样做还是报错错误是：

Sun Jul 28 14:21:04 CST 2013 /public1/home/CAS/lzhpc86/software/cesm_intel/run/test1/pio/pio.bldlog.130728-142041
Copying source to CCSM EXEROOT...
ignore pio file alloc_mod.F90
ignore pio file box_rearrange.F90
cp: omitting directory `configure.old'
ignore pio file iompi_mod.F90
ignore pio file mct_rearrange.F90
ignore pio file piodarray.F90
ignore pio file pio_msg_getput_callbacks.F90
ignore pio file pionfatt_mod.F90
ignore pio file pionfget_mod.F90
ignore pio file pionfput_mod.F90
ignore pio file pionfread_mod.F90
ignore pio file pionfwrite_mod.F90
ignore pio file pio_spmd_utils.F90
ignore pio file pio_support.F90
ignore pio file rearrange.F90
New build of PIO
Running configure...
for OS=SUSE Linux MACH=pxq
cat: Filepath: No such file or directory
cat: Srcfiles: No such file or directory
/public1/home/CAS/lzhpc86/software/cesm_intel/scripts/test1/Tools/mkSrcfiles > /public1/home/CAS/lzhpc86/software/cesm_intel/run/test1/pio/Srcfiles
cp -f /public1/home/CAS/lzhpc86/software/cesm_intel/run/test1/pio/Filepath /public1/home/CAS/lzhpc86/software/cesm_intel/run/test1/pio/Deppath
/public1/home/CAS/lzhpc86/software/cesm_intel/scripts/test1/Tools/mkDepends Deppath Srcfiles > /public1/home/CAS/lzhpc86/software/cesm_intel/run/test1/pio/Depends
./configure   --disable-mct --disable-timing  CC="mpicc" F90="mpif90" NETCDF_PATH="/public1/home/CAS/lzhpc86/netcdf-4.0.1-intel" MPI_INC="-I/public1/software/mpi/mvapich2-1.4-intel/include"
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 mpicc accepts -g... yes
checking for mpicc option to accept ISO C89... none needed
checking for mpicc... mpicc
checking for MPI_Init... yes
checking for mpi.h... yes
checking how to run the C preprocessor... mpicc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/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 for char... yes
checking size of char... 1
checking for int... yes
checking size of int... 4
checking for float... yes
checking size of float... 4
checking for double... yes
checking size of double... 8
checking for void *... yes
checking size of void *... 8
checking Fortran 90 filename extension... .F90
checking whether we are using the GNU Fortran 90 compiler... no
checking for mpxlf90_r... no
checking for mpxlf90... no
checking for mpxlf95... no
checking for mpipgf90... no
checking for mpif90... mpif90
checking for mpif.h... yes
checking MPI-IO support in MPI implementation... yes
checking how to get the version output from mpif90... -V
checking whether byte ordering is bigendian... no
configure: WARNING: UNKNOWN FORTRAN 90 COMPILER
checking whether fortran .mod file is uppercase... no
checking for Fortran 90 name-mangling scheme... lower case, underscore
checking for cpp... cpp
checking if Fortran 90 compiler performs preprocessing... yes
checking if C preprocessor can work with Fortran compiler... yes
Full hostname= node74
Hostname=node74
Machine=x86_64
OS=Linux
using NETCDF_PATH from environment
configure: WARNING: PNETCDF_PATH not found in environment,                            defaulting to /usr/local/pnetcdf
configure: WARNING: pnetcdf.inc not found in PNETCDF_PATH/include                              disabling pnetcdf support
configure: WARNING: libpnetcdf.a not found in PNETCDF_PATH/lib                              disabling pnetcdf support
checking Fortran 90 support for sizeof()... yes

Temp variables: {F90=mpif90} {MPIF90=mpif90}

Output Variables: {CC=mpicc} {MPICC=mpicc} {ALLCFLAGS=-g -O2 -DFORTRAN_UNDERSCORE_ -DFORTRANUNDERSCORE -DSYSLINUX -DLINUX -DCPRUNKNOWNCPR} {EXPLICIT_FPP=no} {FPP=cpp} {FPPFLAGS=-P -C -N -traditional} {FC=mpif90} {MPIF90=mpif90}{OPT=} {BIT64=} {REAL8=} {ENDIAN=} {FFLAGS= -I/public1/software/mpi/mvapich2-1.4-intel/include} {CFLAGS=-g -O2} {F90FLAGS=} {MACHDEFS=-DSYSLINUX -DLINUX -DCPRUNKNOWNCPR} {MPI_INC=-I/public1/software/mpi/mvapich2-1.4-intel/include} {MPI_LIB=} {MODINC=-I} {INCLUDEPATH=} {AR=ar} {ARFLAGS=cq} {USE_PNETCDF=no} {PNETCDF_PATH=/usr/local/pnetcdf} {USE_NETCDF=yes} {NETCDF_PATH=/public1/home/CAS/lzhpc86/netcdf-4.0.1-intel} {USE_MCT=no} {USEBOX=yes} {PDEFS= -DSPMD -DHAVE_MPI -DUSEMPIIO -D_NETCDF -D_NOPNETCDF -D_NOUSEMCT -D_USEBOX} {PDEFSF= -DSPMD -DHAVE_MPI -DUSEMPIIO -D_NETCDF -D_NOPNETCDF -D_NOUSEMCT -D_USEBOX} {PINCS=-I/public1/software/mpi/mvapich2-1.4-intel/include -I/public1/home/CAS/lzhpc86/netcdf-4.0.1-intel/include} {LDLIBS= -L/public1/home/CAS/lzhpc86/netcdf-4.0.1-intel/lib -lnetcdf } {DEBUG=no}

configure: creating ./config.status
config.status: creating Makefile.conf
Please check the Makefile.conf
Have a nice day!
Making dependencies for pio.F90 --> pio.d
Making dependencies for pio_kinds.F90 --> pio_kinds.d
Making dependencies for nf_mod.F90 --> nf_mod.d
Making dependencies for ionf_mod.F90 --> ionf_mod.d
Making dependencies for pio_types.F90 --> pio_types.d
Making dependencies for piolib_mod.F90 --> piolib_mod.d
Making dependencies for pio_mpi_utils.F90 --> pio_mpi_utils.d
Making dependencies for pio_nf_utils.F90 --> pio_nf_utils.d
Making dependencies for pio_utils.F90 --> pio_utils.d
Making dependencies for pio_quicksort.F90 --> pio_quicksort.d
Making dependencies for pio_msg_mod.F90 --> pio_msg_mod.d
Making dependencies for pio_msg_callbacks.F90 --> pio_msg_callbacks.d
Making dependencies for calcdecomp.F90 --> calcdecomp.d
Making dependencies for calcdisplace_mod.F90 --> calcdisplace_mod.d
/usr/bin/perl genf90.pl pionfatt_mod.F90.in > pionfatt_mod.F90
Making dependencies for pionfatt_mod.F90 --> pionfatt_mod.d
/usr/bin/perl genf90.pl pionfread_mod.F90.in > pionfread_mod.F90
Making dependencies for pionfread_mod.F90 --> pionfread_mod.d
/usr/bin/perl genf90.pl pionfwrite_mod.F90.in > pionfwrite_mod.F90
Making dependencies for pionfwrite_mod.F90 --> pionfwrite_mod.d
/usr/bin/perl genf90.pl pionfput_mod.F90.in > pionfput_mod.F90
Making dependencies for pionfput_mod.F90 --> pionfput_mod.d
/usr/bin/perl genf90.pl pionfget_mod.F90.in > pionfget_mod.F90
Making dependencies for pionfget_mod.F90 --> pionfget_mod.d
/usr/bin/perl genf90.pl alloc_mod.F90.in > alloc_mod.F90
Making dependencies for alloc_mod.F90 --> alloc_mod.d
/usr/bin/perl genf90.pl box_rearrange.F90.in > box_rearrange.F90
Making dependencies for box_rearrange.F90 --> box_rearrange.d
/usr/bin/perl genf90.pl rearrange.F90.in > rearrange.F90
Making dependencies for rearrange.F90 --> rearrange.d
/usr/bin/perl genf90.pl pio_support.F90.in > pio_support.F90
Making dependencies for pio_support.F90 --> pio_support.d
/usr/bin/perl genf90.pl mct_rearrange.F90.in > mct_rearrange.F90
Making dependencies for mct_rearrange.F90 --> mct_rearrange.d
/usr/bin/perl genf90.pl iompi_mod.F90.in > iompi_mod.F90
Making dependencies for iompi_mod.F90 --> iompi_mod.d
/usr/bin/perl genf90.pl piodarray.F90.in > piodarray.F90
Making dependencies for piodarray.F90 --> piodarray.d
/usr/bin/perl genf90.pl pio_spmd_utils.F90.in > pio_spmd_utils.F90
Making dependencies for pio_spmd_utils.F90 --> pio_spmd_utils.d
/usr/bin/perl genf90.pl pio_msg_getput_callbacks.F90.in > pio_msg_getput_callbacks.F90
Making dependencies for pio_msg_getput_callbacks.F90 --> pio_msg_getput_callbacks.d
Done updating dependencies
gmake[1]: Entering directory `/public1/home/CAS/lzhpc86/software/cesm_intel/run/test1/pio'
mpicc -c -g -O2 -DFORTRAN_UNDERSCORE_ -DFORTRANUNDERSCORE -DSYSLINUX -DLINUX -DCPRUNKNOWNCPR -DSPMD -DHAVE_MPI -DUSEMPIIO -D_NETCDF -D_NOPNETCDF -D_NOUSEMCT -D_USEBOX  -I/public1/software/mpi/mvapich2-1.4-intel/include -I/public1/home/CAS/lzhpc86/netcdf-4.0.1-intel/include topology.c
mpif90 -c -I/public1/software/mpi/mvapich2-1.4-intel/include  -DSYSLINUX -DLINUX -DCPRUNKNOWNCPR -DSPMD -DHAVE_MPI -DUSEMPIIO -D_NETCDF -D_NOPNETCDF -D_NOUSEMCT -D_USEBOX -I/public1/software/mpi/mvapich2-1.4-intel/include -I/public1/home/CAS/lzhpc86/netcdf-4.0.1-intel/include pio_kinds.F90
mpif90 -c -I/public1/software/mpi/mvapich2-1.4-intel/include  -DSYSLINUX -DLINUX -DCPRUNKNOWNCPR -DSPMD -DHAVE_MPI -DUSEMPIIO -D_NETCDF -D_NOPNETCDF -D_NOUSEMCT -D_USEBOX -I/public1/software/mpi/mvapich2-1.4-intel/include -I/public1/home/CAS/lzhpc86/netcdf-4.0.1-intel/include pio_types.F90
PGF90-F-0004-Corrupt or Old Module file /public1/home/CAS/lzhpc86/netcdf-4.0.1-intel/include/netcdf.mod (pio_types.F90: 8)
PGF90/x86-64 Linux 7.1-4: compilation aborted
gmake[1]: *** [pio_types.o] Error 2
gmake[1]: Leaving directory `/public1/home/CAS/lzhpc86/software/cesm_intel/run/test1/pio'
gmake: *** [all] Error 2

andrewsoong

彭小清 发表于 2013-7-28 14:25

                               
登录/注册后可看大图

各位大侠，想请教一下 用intel编译的
  我这样做还是报错错误是：

你这个netcdf是用intel编译的？我看不是3.6.3版本呢，我用其他版本的报错。另外你的这个并行mpi建议使用intel的那个impi。既然你是用的是intel的ifort，为什么倒数第第四行出现了PGF90 ？？？

彭小清

没有报错了  输出的结果没有数据出来    不知道为啥

andrewsoong

彭小清 发表于 2013-7-31 22:07

                               
登录/注册后可看大图

没有报错了  输出的结果没有数据出来    不知道为啥

竟然没有数据？？？？@奥兰多@奥兰多

奥兰多

andrewsoong 发表于 2013-8-1 08:21

                               
登录/注册后可看大图

竟然没有数据？？？？@奥兰多@奥兰多

一般服务器有自己的提交方式，你必须按服务的提交要求提交作业。否则，只显示你提交成功，不会有结果输出。如不想提交作业，你也可以直接在服务器前台上运行。输./******.run文件即可。

彭小清

串行的结果还是报错   
lzhpc86@node74:~/software/cesm_intel/scripts/test7> ./test7.pxq.run
XLSF_UIDDIR=/apps/lsf/7.0/linux2.6-glibc2.3-x86_64/lib/uid
CCSM_COMPSET=I_TEST_2003 (ITEST)
COMP_ATM=datm
COMP_LND=clm
COMP_ICE=sice
COMP_GLC=sglc
COMP_OCN=socn
COMP_CPL=cpl
CCSM_LCOMPSET=I_TEST_2003
CCSM_SCOMPSET=ITEST
COMP_RUN_BARRIERS=FALSE
COMP_INTERFACE=MCT
BUILD_COMPLETE=TRUE
SMP_BUILD=a0l0i0o0g0c0
SMP_VALUE=a0l0i0o0g0c0
-------------------------------------------------------------------------
CCSM BUILDNML SCRIPT STARTING
- To prestage restarts, untar a restart.tar file into /public1/home/CAS/lzhpc86/software/cesm_intel/run/test7/run
- Create modelio namelist input files
CCSM BUILDNML SCRIPT HAS FINISHED SUCCESSFULLY
-------------------------------------------------------------------------
CCSM PRESTAGE SCRIPT STARTING
- CCSM input data directory, DIN_LOC_ROOT_CSMDATA, is /public1/home/CAS/lzhpc86/software/cesm_intel/inputdata
- Case input data directory, DIN_LOC_ROOT, is /public1/home/CAS/lzhpc86/software/cesm_intel/inputdata
- Checking the existence of input datasets in DIN_LOC_ROOT
CCSM PRESTAGE SCRIPT HAS FINISHED SUCCESSFULLY
Mon Aug  5 16:01:09 CST 2013 -- CSM EXECUTION BEGINS HERE
Mon Aug  5 16:05:26 CST 2013 -- CSM EXECUTION HAS FINISHED
(seq_mct_drv): ===============       SUCCESSFUL TERMINATION OF CPL7-CCSM ===============
cp: No match.
Archiving ccsm output to /public1/home/CAS/lzhpc86/software/cesm_intel/run/archive/test7
Calling the short-term archiving script st_archive.sh

st_archive.sh: start of short-term archiving
mv: cannot stat `/public1/home/CAS/lzhpc86/software/cesm_intel/run/archive/test7/*': No such file or directory
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
mv: cannot stat `/public1/home/CAS/lzhpc86/software/cesm_intel/scripts/test7/timing/ccsm_timing.test7.130805-160043': No such file or directory

彭小清

求指导   不知道错在哪里了

andrewsoong

彭小清 发表于 2013-8-5 22:12

                               
登录/注册后可看大图

串行的结果还是报错   
lzhpc86@node74:~/software/cesm_intel/scripts/test7> ./test7.pxq.run
XLSF_UI ...

@奥兰多 这个问题你是不是遇见过？

奥兰多

andrewsoong 发表于 2013-8-6 08:29

                               
登录/注册后可看大图

@奥兰多 这个问题你是不是遇见过？

恩，和我的相似，我也没解决，这些是后续处理的东西，已经运行成功了，不影响模拟结果的。

andrewsoong

彭小清 发表于 2013-8-5 22:12

                               
登录/注册后可看大图

求指导   不知道错在哪里了

奥兰多说他也遇到了类似的情况，不过不影响结果~~~