安装CESM记录
这几天在密云的地球模拟器上安装cesm,遇到很多问题，还是得记一下免得后面又要重新装不知所措
安装移植cesm记录：
首先打开Downloading CESM2 (CESM2.1) — CESM CESM2.1 documentation看看
从CESM2开始，可以通过公共GitHub存储库http://github.com/ESCOMP/CESM获得版本。
要访问这些代码，需要准备好与GitHub和我们的Subversion服务器软件兼容的Git和Subversion客户端软件。您需要访问命令行客户端、git(v1.8或更高版本)和svn(v1.8或更高版本，但低于v1.11)。目前，我们的Subversion服务器软件的版本是1.8.17。有关更多信息或下载开源工具，请访问Subversion和git下载。
在将构建和运行CESM2的计算机上安装有效的GIT和SVN客户端后，用户可以下载最新版本的发布代码：
git clone -b release-cesm2.1.3 https://github.com/ESCOMP/CESM.git my_cesm_sandbox cd my_cesm_sandbox
我来试试！
mkdir cesm_installation
cd cesm_installatioin
git clone -b release-cesm2.1.3 https://github.com/ESCOMP/CESM.git my_cesm_sandbox结果等了半天
Cloning into 'my_cesm_sandbox'...
fatal: unable to access 'https://github.com/ESCOMP/CESM.git/': Encountered end of file我就去百度
好家伙真的可以了，但是报了另个错
[chengxl@server02 cesm_installation]$ git clone -b release-cesm2.1.3 https://github.com/ESCOMP/CESM.git my_cesm_sandbox
Cloning into 'my_cesm_sandbox'...
remote: Enumerating objects: 6393, done.
remote: Counting objects: 100% (547/547), done.
remote: Compressing objects: 100% (334/334), done.
remote: Total 6393 (delta 322), reused 397 (delta 210), pack-reused 5846
Receiving objects: 100% (6393/6393), 10.84 MiB | 868.00 KiB/s, done.
Resolving deltas: 100% (3615/3615), done.
Note: checking out '0596a9760428fb3155310064678f1c7b424d504f'.
You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by performing another checkout.
If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -b with the checkout command again. Example:
git checkout -b new_branch_name最后，要签出所有单独的模型组件，请从/path/to/my_cesm_sandbox运行checkout_outals脚本。
./manage_externals/checkout_externals
我来操作一下！
[chengxl@server02 my_cesm_sandbox]$ ./manage_externals/checkout_externals
Processing externals description file : Externals.cfg
Checking status of externals: clm, mosart, ww3, cime, cice, pop, cism, rtm, cam,
Checking out externals: clm, ERROR:root:Command '[u'git', u'clone', u'--quiet', u'https://github.com/ESCOMP/ctsm/', u'clm']' returned non-zero exit status 128
ERROR:root:Failed with output:
fatal: unable to access 'https://github.com/ESCOMP/ctsm/': Encountered end of file
ERROR: In directory
/public/home/chengxl/cesm_installation/my_cesm_sandbox/components
Process did not run successfully; returned status 128:
git clone --quiet https://github.com/ESCOMP/ctsm/ clm
See above for output from failed command.
ERROR:root:Failed with output:
fatal: unable to access 'https://github.com/ESCOMP/ctsm/': Encountered end of file
ERROR: In directory
/public/home/chengxl/cesm_installation/my_cesm_sandbox/components
Process did not run successfully; returned status 128:
git clone --quiet https://github.com/ESCOMP/ctsm/ clm
See above for output from failed command.
ERROR: Failed with output:
fatal: unable to access 'https://github.com/ESCOMP/ctsm/': Encountered end of file
ERROR: In directory
/public/home/chengxl/cesm_installation/my_cesm_sandbox/components
Process did not run successfully; returned status 128:
git clone --quiet https://github.com/ESCOMP/ctsm/ clm
See above for output from failed command.等了一会，出了问题，分系统没下载下来，根据刚才再来一遍的方法，我再执行一下
[chengxl@server02 my_cesm_sandbox]$ ./manage_externals/checkout_externals
Processing externals description file : Externals.cfg
Processing externals description file : Externals_CLM.cfg
Checking status of externals: clm, fates, ptclm, mosart, ww3, cime, cice, pop, cism, rtm, cam,
Checking out externals: clm, mosart, ww3, cime, Command 'git clone --quiet https://github.com/ESMCI/cime cime'
from directory /public/home/chengxl/cesm_installation/my_cesm_sandbox
has taken 300 seconds. It may be hanging.
The command will continue to run, but you may want to abort
manage_externals with ^C and investigate. A possible cause of hangs is
when svn or git require authentication to access a private
repository. On some systems, svn and git requests for authentication
information will not be displayed to the user. In this case, the program
will appear to hang. Ensure you can run svn and git manually and access
all repositories without entering your authentication information.
cice, ERROR:root:Command '[u'git', u'fetch', u'--quiet', u'--tags', 'origin']' returned non-zero exit status 128
ERROR:root:Failed with output:
fatal: unable to access 'https://github.com/ESCOMP/CESM_CICE5/': Encountered end of file
ERROR: In directory
/public/home/chengxl/cesm_installation/my_cesm_sandbox/components/cice
Process did not run successfully; returned status 128:
git fetch --quiet --tags origin
See above for output from failed command.
ERROR:root:Failed with output:
fatal: unable to access 'https://github.com/ESCOMP/CESM_CICE5/': Encountered end of file
ERROR: In directory
/public/home/chengxl/cesm_installation/my_cesm_sandbox/components/cice
Process did not run successfully; returned status 128:
git fetch --quiet --tags origin
See above for output from failed command.
ERROR: Failed with output:
fatal: unable to access 'https://github.com/ESCOMP/CESM_CICE5/': Encountered end of file
ERROR: In directory
/public/home/chengxl/cesm_installation/my_cesm_sandbox/components/cice
Process did not run successfully; returned status 128:
git fetch --quiet --tags origin
See above for output from failed command.居然可以！相比之前多下载了几个分模式。但还是出了问题，我们再试一下。
不行，百度
git config --global http.sslverify “false”
git config --global url.“https://”.insteadOf git://完蛋出现了这个
[chengxl@server02 my_cesm_sandbox]$ ./manage_externals/checkout_externals
Processing externals description file : Externals.cfg
Processing externals description file : Externals_CLM.cfg
Checking status of externals: clm, fates, ptclm, mosart, ww3, cime, cice, pop, cism, rtm, cam,
Checking out externals: clm, ERROR:root:Command '[u'git', u'fetch', u'--quiet', u'--tags', 'origin']' returned non-zero exit status 128
ERROR:root:Failed with output:
fatal: bad config value for 'http.sslverify' in /public/home/chengxl/.gitconfig
ERROR: In directory
/public/home/chengxl/cesm_installation/my_cesm_sandbox/components/clm
Process did not run successfully; returned status 128:
git fetch --quiet --tags origin
See above for output from failed command.
ERROR:root:Failed with output:
fatal: bad config value for 'http.sslverify' in /public/home/chengxl/.gitconfig
ERROR: In directory
/public/home/chengxl/cesm_installation/my_cesm_sandbox/components/clm
Process did not run successfully; returned status 128:
git fetch --quiet --tags origin
See above for output from failed command.
ERROR: Failed with output:
fatal: bad config value for 'http.sslverify' in /public/home/chengxl/.gitconfig
ERROR: In directory
/public/home/chengxl/cesm_installation/my_cesm_sandbox/components/clm
Process did not run successfully; returned status 128:
git fetch --quiet --tags origin
See above for output from failed command.vim 看看.gitconfig
把里面乱码去掉了
再试一下./manage_externals/checkout_externals
[chengxl@server02 my_cesm_sandbox]$ ./manage_externals/checkout_externals
Processing externals description file : Externals.cfg
Processing externals description file : Externals_CLM.cfg
Checking status of externals: clm, fates, ptclm, mosart, ww3, cime, cice, pop, cism, rtm, cam,
Checking out externals: clm, mosart, ww3, cime, cice, pop, cism, rtm, cam,
Processing externals description file : Externals_CLM.cfg
Checking out externals: fates, ptclm,
Processing externals description file : Externals_POP.cfg
Checking out externals: cvmix, marbl,
Processing externals description file : Externals_CISM.cfg
Checking out externals: source_cism,
Processing externals description file : Externals_CAM.cfg
Checking out externals: clubb, carma, cosp2, chem_proc, 是不是成功了?
接着做
要确认成功下载所有组件，可以运行带有状态标志的CHECKOUT_EXTERNAL，以显示外部组件的状态：
./manage_externals/checkout_externals -S
我来试试！
[chengxl@server02 my_cesm_sandbox]$ ./manage_externals/checkout_externals -S
Processing externals description file : Externals.cfg
Processing externals description file : Externals_CLM.cfg
Processing externals description file : Externals_POP.cfg
Processing externals description file : Externals_CISM.cfg
Processing externals description file : Externals_CAM.cfg
Checking status of externals: clm, fates, ptclm, mosart, ww3, cime, cice, pop, cvmix, marbl, cism, source_cism, rtm, cam, clubb, carma, cosp2, chem_proc,
./cime
./components/cam
./components/cam/chem_proc
./components/cam/src/physics/carma/base
./components/cam/src/physics/clubb
./components/cam/src/physics/cosp2/src
./components/cice
./components/cism
./components/cism/source_cism
./components/clm
./components/clm/src/fates
./components/clm/tools/PTCLM
./components/mosart
./components/pop
./components/pop/externals/CVMix
./components/pop/externals/MARBL
./components/rtm
./components/ww3看起来不错！
现在，您的/path/to/my_cesm_sandbox中应该有CESM2源代码的完整副本。
至此，cesm的代码都被下载下来了
那么就可以开始进行下一步的操作
机器配置
上一步只是下载好了代码，还有很多需要解决。
首先进行机器配置
cesm需要很多的软件
在超算上就是module
我来列一下：
- CentOS 7（检查：sudo lsb_release -a）
- csh、sh（检查：which csh/sh）
- Perl（ 检查：perl -v）CentOS 7安装Perl环境
- svn 1.4.2+（检查：svn --version）
- PGI（Fortran、C编辑器，检查：pgcc --version）如何部署?
- MPICH（并行程序，可选）
- NetCDF（一系列软件库），如何部署?
- ESMF（Earth System Modeling Framework，可选）
- PnetCDF（Parallel NetCDF，建议使用1.3.1）User Guide Ubuntu根据安装说明执行make的时候，总是会报错，在指针的位置添加->format就可以了。而CentOS不会出现这种情况，所以实际科学计算还是推荐使用CentOS，可以省下不少时间。
- tar（必选）
- MPI C编译器（必选）
- GNU m4（必选，压缩包中已包含）README
- MPI C++编译器（可选）
- MPI Fortran 77编译器（可选）
- MPI Fortran 90编译器（可选）
- Trilinos（某些配置需要）
- LAPACHm（Linear Algebra PACKage，某些配置需要）
- CMake（检查：cmake --version）
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版权声明：本文为CSDN博主「「已注销」」的原创文章，遵循CC 4.0 BY-SA版权协议，转载请附上原文出处链接及本声明。
原文链接：https://blog.csdn.net/weixin_43014927/article/details/99619559
也不知道这篇总结得全部全，先试试！
为了不用每次都module load 我把这个写在~/.bashrc 里
#---------------------------------------------------#
# #
# module #
# #
#---------------------------------------------------#
module purge
module load apps/esmf/intelmpi/7.0.0
#---------- /public/software/modules -----------
#apps/anaconda3/5.3.0
#apps/esmf/intelmpi/7.0.0
#apps/m4/universal/1.4.18
#apps/ncl_ncarg/6.3.0
module load apps/ncl_ncarg/6.6.2
#apps/nco/gnu/4.8.1
#apps/nco/intel/4.8.1
#apps/ncview/gnu/2.1.7
#apps/ncview/intel/2.1.7
#apps/PyTorch/1.7.mmcv/pytorch-1.7-mmcv1.3.8-rocm-4.0.1
#apps/singularity/3.8.0
#apps/TensorFlow/tf1.15.3-rocm4.0.1/hpcx-2.7.4-gcc-7.3.1
#apps/TensorFlow/tf2.5.0-rocm4.0.1/hpcx-2.7.4-gcc-7.3.1
#benchmark/imb/intelmpi/2017
module load compiler/cmake/3.20.1
#compiler/rocm/4.0
#mathlib/antlr/gnu/2.7.7
#mathlib/antlr/intel/2.7.7
#mathlib/cdo/intel/1.10.19
#mathlib/grib_api/intel/1.19.0
#mathlib/hdf4/gnu/4.2.13
#mathlib/hdf4/intel/4.2.13
#mathlib/hdf5/gnu/1.8.20
module load mathlib/hdf5/intel/1.8.20
#mathlib/jasper/gnu/1.900.1
module load mathlib/jasper/intel/1.900.1
#mathlib/jpeg/gnu/9a
module load mathlib/jpeg/intel/9a
#mathlib/libpng/gnu/1.2.12
module load mathlib/libpng/intel/1.2.12
#mathlib/netcdf/gnu/4.4.1
module load mathlib/netcdf/intel/4.4.1
#mathlib/pio/gnu/hpcx-2.7.4-gcc7.3.1-2.5.1
#mathlib/pio/gnu/openmpi-4.0.4-gcc4.8.5-2.5.1
#mathlib/pio/intel/2.5.1
#mathlib/pnetcdf/gnu/hpcx-2.7.4-gcc7.3.1-1.12.1
#mathlib/pnetcdf/gnu/openmpi-4.0.4-gcc4.8.5-1.12.1
module load mathlib/pnetcdf/intel/1.12.1
#mathlib/szip/gnu/2.1.1
#mathlib/szip/intel/2.1.1
#mathlib/udunits/gnu/2.2.28
#mathlib/udunits/intel/2.2.28
#mathlib/wgrib2/2.0.8
#mathlib/zlib/gnu/1.2.11
module load mathlib/zlib/intel/1.2.11
module load mpi/intelmpi/2017.4.239
#mpi/openmpi/gnu/4.0.4
#
##---------- /opt/hpc/software/modules ----------
#compiler/devtoolset/7.3.1
module load compiler/intel/2017.5.239
#compiler/rocm/3.3
#mpi/hpcx/2.7.4/gcc-7.3.1
module load mpi/hpcx/2.7.4/intel-2017.5.239
#mpi/openmpi/4.0.4/gcc-7.3.1打开之前上课的PPT
[chengxl@server02 .cime]$ vim config_machines.xml
[chengxl@server02 .cime]$ vim config_compilers.xml
[chengxl@server02 .cime]$ vim config_batch.xml
[chengxl@server02 .cime]$ ls
config_batch.xml config_compilers.xml config_machines.xml
从cesm里把设置文件考过来;
[chengxl@server02 .cime]$ cp ../cesm_installation/my_cesm_sandbox/cime/config/cesm/machines/config_machines.xml .现在根据超算的情况，编辑一下里面的内容
config_machines.xml - machine specific file
Each
tag requires the following input:
DESC: a text description of the machine
NODENAME_REGEX: a regular expression used to identify the machine. It must work on compute nodes as well as login nodes. | Use themachineoption for create_test or create_newcase if this flag is not available.
OS: the machine’s operating system
PROXY: optional http proxy for access to the internet
COMPILERS: compilers supported on the machine, in comma-separated list, default first
MPILIBS: mpilibs supported on the machine, in comma-separated list, default first
PROJECT: a project or account number used for batch jobs; can be overridden in environment or in $HOME/.cime/config
SAVE_TIMING_DIR: (E3SM only) target directory for archiving timing output
SAVE_TIMING_DIR_PROJECTS: (E3SM only) projects whose jobs archive timing output
CIME_OUTPUT_ROOT: Base directory for case output; the bld and run directories are written below here
DIN_LOC_ROOT: location of the input data directory
DIN_LOC_ROOT_CLMFORC: optional input location for clm forcing data
DOUT_S_ROOT: root directory of short-term archive files
DOUT_L_MSROOT: root directory on mass store system for long-term archive files
BASELINE_ROOT: root directory for system test baseline files
CCSM_CPRNC: location of the cprnc tool, which compares model output in testing
GMAKE: gnu-compatible make tool; default is “gmake”
GMAKE_J: optional number of threads to pass to the gmake flag
TESTS: (E3SM only) list of tests to run on the machine
BATCH_SYSTEM: batch system used on this machine (none is okay)
SUPPORTED_BY: contact information for support for this system
MAX_TASKS_PER_NODE: maximum number of threads/tasks per shared memory node on the machine
MAX_MPITASKS_PER_NODE: number of physical PES per shared node on the machine. In practice the MPI tasks per node will not exceed this value.
PROJECT_REQUIRED: Does this machine require a project to be specified to the batch system?
mpirun: The mpi exec to start a job on this machine. This is itself an element that has sub-elements that must be filled:
Must have a required
elementMay have optional attributes of
compiler,mpiliband/orthreadedMay have an optional
element which in turn contains one or moreelements. These specify the arguments to the mpi executable and are dependent on your mpi library implementation.May have an option
element which overrides thedefault_run_exeMay have an option
element which overrides thedefault_run_misc_suffix
module_system: How and what modules to load on this system. Module systems allow you to easily load multiple compiler environments on a machine. CIME provides support for two types of module tools: module and soft. If neither of these is available on your machine, simply set.
environment_variables: environment_variables to set on the systemThis contains sub-elements
with thenameattribute specifying the environment variable name, and the element value specifying the corresponding environment variable value. If the element value is not set, the corresponding environment variable will be unset in your shell.For example, the following sets the environment variable
OMP_STACKSIZEto 256M:256M The following unsets this environment variable in the shell:
Note
These changes are ONLY activated for the CIME build and run environment, BUT NOT for your login shell. To activate them for your login shell, source either $CASEROOT/.env_mach_specific.sh or $CASEROOT/.env_mach_specific.csh, depending on your shell.
[chengxl@server02 .cime]$ cat config_machines.xml
Example port to centos7 linux system with gcc, netcdf, pnetcdf and mpich
using modules from http://www.admin-magazine.com/HPC/Articles/Environment-Modules
regex.expression.matching.your.machine
LINUX
https://howto.get.out
gnu
mpich
none
$ENV{HOME}/cesm/scratch
$ENV{HOME}/cesm/inputdata
$ENV{HOME}/cesm/inputdata/lmwg
$ENV{HOME}/cesm/archive/$CASE
$ENV{HOME}/cesm/cesm_baselines
$ENV{HOME}/cesm/tools/cime/tools/cprnc/cprnc
make
8
none
[email protected]
8
8
FALSE
mpiexec
-np {{ total_tasks }}
/usr/share/Modules/init/perl.pm
/usr/share/Modules/init/python.py
/usr/share/Modules/init/csh
/usr/share/Modules/init/sh
/usr/bin/modulecmd perl
/usr/bin/modulecmd python
module
module
compiler/gnu/8.2.0
mpi/3.3/gcc-8.2.0
tool/netcdf/4.6.1/gcc-8.1.0
256M
-1
${EXEROOT}/cesm.exe
>> cesm.log.$LID 2>&1
改啊改。。。
[chengxl@server02 .cime]$ cat config_machines.xml
Example port to centos7 linux system with gcc, netcdf, pnetcdf and mpich
using modules from http://www.admin-magazine.com/HPC/Articles/Environment-Modules
regex.expression.matching.your.machine
LINUX
https://howto.get.out
intel
mpich
none
$ENV{HOME}/cesm/scratch
$ENV{HOME}/cesm/inputdata
$ENV{HOME}/cesm/inputdata/lmwg
$ENV{HOME}/cesm/archive/$CASE
$ENV{HOME}/cesm/cesm_baselines
$ENV{HOME}/cesm/tools/cime/tools/cprnc/cprnc
make
8
none
[email protected]
8
8
FALSE
mpiexec
-np {{ total_tasks }}
/usr/share/Modules/init/perl.pm
/usr/share/Modules/init/python.py
/usr/share/Modules/init/csh
/usr/share/Modules/init/sh
/usr/bin/modulecmd perl
/usr/bin/modulecmd python
module
module
compiler/intel/2017.5.239
mpi/hpcx/2.7.4/intel-2017.5.239
mathlib/netcdf/4.4.1/
256M
-1
${EXEROOT}/cesm.exe
>> cesm.log.$LID 2>&1
接下来改这个config_compiler:
@server02 .cime]$ cat config_compilers.xml
-D_USE_FLOW_CONTROL
FALSE
-qopenmp
-O2 -debug minimal
-O0 -g
-DFORTRANUNDERSCORE -DCPRINTEL
FORTRAN
-qopenmp
-O0 -g -check uninit -check bounds -check pointers -fpe0 -check noarg_temp_created
-O2 -debug minimal
-qopenmp
-qopenmp
mpicc
mpicxx
mpif90
icc
icpc
ifort
-mkl=cluster
-mkl=cluster
-mkl=cluster
-mkl=cluster
-mkl=cluster
-mkl=cluster
-mkl=cluster
-mkl
TRUE
通过执行以下操作，检查以确保您的config_machines.xml文件符合CIME架构定义：
xmllint --noout --schema $CIME/config/xml_schemas/config_machines.xsd $HOME/.cime/config_machines.xml
就是检查一下刚才设置的机器配置对不对
@server02 ~]$ xmllint --noout --schema $CIME/config/xml_schemas/config_machines.xsd $HOME/.cime/config_machines.xml
warning: failed to load external entity "/config/xml_schemas/config_machines.xsd"
Schemas parser error : Failed to locate the main schema resource at '/config/xml_schemas/config_machines.xsd'.
WXS schema /config/xml_schemas/config_machines.xsd failed to compile好像出了问题。。。
原因是没设置$CIME,直接用￥CIMEROOT好了
@server02 xml_schemas]$ xmllint --noout --schema $CIMEROOT/config/xml_schemas/config_machines.xsd $HOME/.cime/config_machines.xml
/public/home/chengxl/.cime/config_machines.xml validates这下成功了！
再验证一下config_compiler.xml
@server02 xml_schemas]$ xmllint --noout --schema $CIMEROOT/config/xml_schemas/config_compilers_v2.xsd $HOME/.cime/config_compilers.xml
/public/home/chengxl/.cime/config_compilers.xml validates又成功了！
这样机器可能就配置好了吧！
创建CASE
这一部分应该算在跑模式里了，但是这一步可以检验上一步是否配置成功了。
首先进目录
cd $CIMEROOT/scripts有个验证的命令：
./create_test --xml-category prealpha --xml-machine cheyenne --xml-compiler intel --machine --compiler 就会出现问题：
Finished CREATE_NEWCASE for test SMS_D_Ln9.f09_g17.BWSSP585.server02_intel.allactive-defaultio_min in 2.140936 seconds (FAIL). [COMPLETED 1 of 70]
Case dir: /public/home/chengxl/cesm/scratch/SMS_D_Ln9.f09_g17.BWSSP585.server02_intel.allactive-defaultio_min.20211229_140226_j2iq1q
Errors were:
Could not find machine match for 'server02' or 'server02'
ERROR: Expected one child
Finished CREATE_NEWCASE for test ERS_Ld5.f09_g17.B1850_BPRP.server02_intel.allactive-defaultio_min in 2.073376 seconds (FAIL). [COMPLETED 2 of 70]
Case dir: /public/home/chengxl/cesm/scratch/ERS_Ld5.f09_g17.B1850_BPRP.server02_intel.allactive-defaultio_min.20211229_140226_j2iq1q
Errors were:
Could not find machine match for 'server02' or 'server02'
ERROR: Expected one child
Finished CREATE_NEWCASE for test NCK.f19_g17.B1850.server02_intel.allactive-defaultiomi in 2.242019 seconds (FAIL). [COMPLETED 3 of 70]
Case dir: /public/home/chengxl/cesm/scratch/NCK.f19_g17.B1850.server02_intel.allactive-defaultiomi.20211229_140226_j2iq1q
Errors were:
Could not find machine match for 'server02' or 'server02'
ERROR: Expected one child新建一个case 也出现问题：
@server02 scripts]$ ./create_newcase --case FHIST_f19 --res f19_f19 --compset FHIST --run-unsupported --compiler intel --mach CAS-ESM
Compset longname is HIST_CAM60_CLM50%SP_CICE%PRES_DOCN%DOM_MOSART_CISM2%NOEVOLVE_SWAV
Compset specification file is /public/home/chengxl/CESM/cime/../components/cam//cime_config/config_compsets.xml
Compset forcing is Historic transient
ATM component is CAM cam6 physics:
LND component is clm5.0:Satellite phenology:
ICE component is Sea ICE (cice) model version 5 :prescribed cice
OCN component is DOCN prescribed ocean mode
ROF component is MOSART: MOdel for Scale Adaptive River Transport
GLC component is cism2 (default, higher-order, can run in parallel):cism ice evolution turned off (this is the standard configuration unless you're explicitly interested in ice evolution):
WAV component is Stub wave component
ESP component is
Pes specification file is /public/home/chengxl/CESM/cime/../components/cam//cime_config/config_pes.xml
Compset specific settings: name is RUN_STARTDATE and value is 1950-01-01
Compset specific settings: name is SSTICE_DATA_FILENAME and value is $DIN_LOC_ROOT/atm/cam/sst/sst_HadOIBl_bc_1.9x2.5_1850_2017_c180507.nc
Compset specific settings: name is SSTICE_GRID_FILENAME and value is $DIN_LOC_ROOT/atm/cam/ocnfrac/domain.camocn.1.9x2.5_gx1v6_090403.nc
Compset specific settings: name is SSTICE_YEAR_END and value is 2016
Could not find machine match for 'server02' or 'server02'
Machine is CAS-ESM
ERROR: Expected one child这百度不到怎么解决。。。
很奇怪为什么会把我的节点名字给读进去了。。
是不是只在.cime里改配置不行？
我再把这个粘贴到$CIMEROOT/config/...里面看看
结果
@server02 scripts]$ ./create_test --xml-category prealpha --xml-machine cheyenne --xml-compiler intel --machine server02 --compiler intel
ERROR: No machine server02 found这下ERROR更干脆了。。。
是不是没验证
@server02 scripts]$ cd $CIMEROOT/config/cesm/machines/
xmllint -noout -schema ../../../config/xml_schemas/config_machines.xsd ./config_machines.xml
xmllint -noout -schema ../../../config/xml_schemas/config_compilers_v2.xsd ./config_compilers.xml
@server02 scripts]$ cd /public/home/chengxl/cesm/cime/scripts/
@server02 scripts]$ ./create_test --xml-category prealpha --xml-machine cheyenne --xml-compiler intel --machine server02 --compiler intel
ERROR: No machine server02 found着很奇怪啊。。。
我在想是不是名字有问题，改成miyun？
[chengxl@server02 scripts]$ vim /public/home/chengxl/cesm/cime/config/cesm/machines/config_machines.xml
[chengxl@server02 scripts]$ vim /public/home/chengxl/cesm/cime/config/cesm/machines/config_compilers.xml
[chengxl@server02 scripts]$ vim ~/.cime/config_machines.xml
[chengxl@server02 scripts]$ vim ~/.cime/config_compilers.xml是不是machines里的这个干扰到了，去掉看看
[chengxl@server02 scripts]$ cd /public/home/chengxl/cesm/cime/config/cesm/machines/
[chengxl@server02 machines]$ mv config_machines.xml config_machines.xml.log
[chengxl@server02 machines]$ mv config_compilers.xml config_compilers.xml.log
cd /public/home/chengxl/cesm/cime/scripts/
./create_test --xml-category prealpha --xml-machine cheyenne --xml-compiler intel --machine miyun --compiler intel
ERROR: Makes no sense to have empty read-only file好家伙，出现了新的错误
只读文件为空是没有意义的。。。
看来还是把它给还原吧
[chengxl@server02 scripts]$ cd /public/home/chengxl/cesm/cime/config/cesm/machines/
[chengxl@server02 machines]$ mv config_machines.xml.log config_machines.xml
[chengxl@server02 machines]$ mv config_compilers.xml.log config_compilers.xml还是去看看帮助文档吧。。。
我打开原先上课时候用的曙光集群的config_machines.xml
-- IAP Shuguang, 24 pes/node, batch system is PBS something.matching.your.machine.hostname Linux intel intelmpi $ENV{HOME}/Myb/cesm2.1.3/output /5600/CESMinput /5600/CESMinput/atm/datm7 $CIME_OUTPUT_ROOT/archive/$CASE $ENV{HOME}/Myb/cesm2.1.3/baselines $ENV{HOME}/Myb/cesm2.1.3/cime/tools/cprnc 4 none Myb 24 24 -mpirun --np $TOTALPES - 64M $ENV{HOME}/bin:$ENV{PATH} /public/software/intel/netcdf4
再看看4. Defining the machine — CIME master documentation
我把之前的config文件考进去，然后再链接到.cime文件夹省的老改两个
[chengxl@login04 ~]$ cd .cime
[chengxl@login04 .cime]$ ln -s /public/home/chengxl/cesm/cime/config/cesm/machines/config_machines.xml ./config_machines.xml
[chengxl@login04 .cime]$ ln -s /public/home/chengxl/cesm/cime/config/cesm/machines/config_compilers.xml ./config_compilers.xml这时的config_machines.xml
IAP miyun diqiuxitongmoniqi , 24 pes/node, batch system is PBS
something.matching.your.machine.hostname
Linux
intel
intelmpi
${HOME}/cesm/cime_output
${HOME}/cesm/din_loc_root
/${HOME}/cesm/din_loc_root_clmforc
${HOME}/cesm/dout_s_root
${HOME}/cesm/baseline_root
${HOME}/cesm/ccsm_cprnc
4
none
Myb
24
24
mpirun
-np $TOTALPES
64M
$ENV{HOME}/bin:$ENV{PATH}
/mathlib/netcdf/intel/4.4.1
config_compilers.xml
[chengxl@login04 machines]$ cat config_compilers.xml
-qopenmp
-O2 -debug minimal
-O0 -g
-DFORTRANUNDERSCORE -DCPRINTEL
FORTRAN
-qopenmp
-O0 -g -check uninit -check bounds -check pointers -fpe0 -check noarg_temp_created
-O2 -debug minimal
-qopenmp
-qopenmp
mpiicc
mpiicpc
mpiifort
icc
icpc
ifort
/mpi/intelmpi/2017.4.239
-mkl=cluster
-mkl=cluster
-mkl=cluster
-mkl=cluster
-mkl=cluster
-mkl=cluster
-mkl=cluster
-mkl
TRUE
/5600/soft/lapack/lib
再试试建立新case
./create_newcase --case FHIST_f19 --res f19_f19 --compset FHIST --run-unsupported --compiler intel --mach IAP-MYB
还是不行啊
[chengxl@login04 scripts]$ ./create_newcase --case FHIST_f19 --res f19_f19 --compset FHIST --run-unsupported --compiler intel --mach IAP-MYB
Compset longname is HIST_CAM60_CLM50%SP_CICE%PRES_DOCN%DOM_MOSART_CISM2%NOEVOLVE_SWAV
Compset specification file is /public/home/chengxl/cesm/cime/../components/cam//cime_config/config_compsets.xml
Compset forcing is Historic transient
ATM component is CAM cam6 physics:
LND component is clm5.0:Satellite phenology:
ICE component is Sea ICE (cice) model version 5 :prescribed cice
OCN component is DOCN prescribed ocean mode
ROF component is MOSART: MOdel for Scale Adaptive River Transport
GLC component is cism2 (default, higher-order, can run in parallel):cism ice evolution turned off (this is the standard configuration unless you're explicitly interested in ice evolution):
WAV component is Stub wave component
ESP component is
Pes specification file is /public/home/chengxl/cesm/cime/../components/cam//cime_config/config_pes.xml
Compset specific settings: name is RUN_STARTDATE and value is 1950-01-01
Compset specific settings: name is SSTICE_DATA_FILENAME and value is $DIN_LOC_ROOT/atm/cam/sst/sst_HadOIBl_bc_1.9x2.5_1850_2017_c180507.nc
Compset specific settings: name is SSTICE_GRID_FILENAME and value is $DIN_LOC_ROOT/atm/cam/ocnfrac/domain.camocn.1.9x2.5_gx1v6_090403.nc
Compset specific settings: name is SSTICE_YEAR_END and value is 2016
ERROR: No machine IAP-MYB found不行，去看看别人文章怎么做的
配置文件详解
这里重点有下面几个方面：COMPILERS：一般大型服务器上都会部署 mpi 编译器，根据你的需求选择有 pgi，intel，gnu 等等
MPILIBS：Intel 编译器一般选择 impi，gnu 可以搭配 openmpi，mpich，如果你不需要 mpi 这里就填 mpi-serial 即可
DIN_LOC_ROOT：这个文件夹的位置可以选择一个固定的目录，这样所有的 inputdata 都会放在同一个文件夹中，方便后续使用
DIN_LOC_ROOT_CLMFORC：同上
BATCH_SYSTEM：如果你是普通的服务器没有部署作业调度系统这一项填写 none 即可。一般大型服务器或超算上都会部署类似 slurm，pbs 或者 lsf 等等作业调度系统，还有部分作业调度系统是定制版本，这就需要联系系统管理员或者自己熟读用户手册之后再修改这两项
GMAKE_J：编译时候可以并行的最大核数，这个数字填你使用的机器的 CPU 核数即可
PES_PER_NODE 和 MAX_TASKS_PER_NODE：这两个数字需要视情况而定，如果你使用的机器是一般的服务器，没有计算节点这些东西的话直接填写机器的 CPU 核数即可；如果你使用的是大型服务器或超算则需要填写计算节点的 CPU 核数。如果这里填的数字超过你的 CPU 核数一般都是会再运行时报错
RUNDIR、EXEROOT、DOUT_S_ROOT、BASELINE_ROOT：这些都是可以使用环境变量的形式填写，这样的好处是多人使用的时候每个人只需要设置 WORKDIR 变量就可以了，方便每个人管理自己的 case
上面的几点如果熟悉 CESM 1.x 的朋友们应该已经很熟悉了，下面几点是 2.x 版本新添加的功能，这里需要大家根据自己的配置来设置mpirun 标签：如果你只使用一种 mpi 模式，后面 mpilib 的值填 default 即可，如果你有多种模式的 mpi ，例如 openmpi、mpich 等。这里就需要对每种 mpi 模式选择对应的提交方式，我这里就只有 intelmpi ，所以选择 default
executable 标签：指 mpi 提交作业的方式，没有作业调度系统的情况下填写 mpirun 或 mpiexec 即可。如果有作业调度系统，这里一般不能直接填写 mpirun，应选择对应的作业提交方式，类似 srun、qsub等
arguments 标签：指 mpi 提交作业的其他参数，每个参数都可以单独写一个 arg 标签，例如指定 -n 核数
-n {{ total_tasks }}
1
module_system 标签：指定在软件运行前需要使用 module 命令加载的软件或者库，如果没有 module 或不需要软件提醒，自己手动加载的，这里的 type 选择 none 就可以了
init_path 标签：指加载 module 命令的初始命令，一般情况下系统中都会自动加载，后面的 lang 参数是指初始化 module 时使用的语言
cmd_path 标签：指使用 module 时的命令，一般情况下都是 module
modules 标签：指在运行 CESM 之前需要使用的命令，如果是指定 compiler 则是指在使用某个编译器时需要加载的命令
modules 下 command 标签：执行 module 命令的参数，name = load 就相当于执行了 module load 命令
environment_variables 标签：指定在运行前需要手动设置的环境变量，例如：
/public/lib/netcdf/intel/4.7.4
1
这就是指你在编译运行前需要设置 NETCDF_PATH 参数：export NETCDF_PATH=/public/lib/netcdf/intel/4.7.4，如果你使用 openmpi ，可以在这里写
这里重点有下面几个方面（依旧以 Intel 编译器为例）：首先需要修改的还是 MPICC 等几个 mpi 编译器的名称
SLIBS 标签下原先缺少了 netcdf 库的各种链接，需要手动添加，base 的意思是无论你的 MPILIB 是什么都会自动加载
————————————————
版权声明：本文为CSDN博主「MrXun_」的原创文章，遵循CC 4.0 BY-SA版权协议，转载请附上原文出处链接及本声明。
原文链接：https://blog.csdn.net/qq_32115939/article/details/115377142
Expected one child 这个报错，让我摸不着头脑，今天先到这里。
我又来了，继续配置，看之前说节点名字有关系，我改
./create_newcase --case FHIST_f19 --res f19_f19 --compset FHIST --run-unsupported --compiler intel --mach afw
Compset longname is HIST_CAM60_CLM50%SP_CICE%PRES_DOCN%DOM_MOSART_CISM2%NOEVOLVE_SWAV
Compset specification file is /public/home/chengxl/cesm/cime/../components/cam//cime_config/config_compsets.xml
Compset forcing is Historic transient
ATM component is CAM cam6 physics:
LND component is clm5.0:Satellite phenology:
ICE component is Sea ICE (cice) model version 5 :prescribed cice
OCN component is DOCN prescribed ocean mode
ROF component is MOSART: MOdel for Scale Adaptive River Transport
GLC component is cism2 (default, higher-order, can run in parallel):cism ice evolution turned off (this is the standard configuration unless you're explicitly interested in ice evolution):
WAV component is Stub wave component
ESP component is
Pes specification file is /public/home/chengxl/cesm/cime/../components/cam//cime_config/config_pes.xml
Compset specific settings: name is RUN_STARTDATE and value is 1950-01-01
Compset specific settings: name is SSTICE_DATA_FILENAME and value is $DIN_LOC_ROOT/atm/cam/sst/sst_HadOIBl_bc_1.9x2.5_1850_2017_c180507.nc
Compset specific settings: name is SSTICE_GRID_FILENAME and value is $DIN_LOC_ROOT/atm/cam/ocnfrac/domain.camocn.1.9x2.5_gx1v6_090403.nc
Compset specific settings: name is SSTICE_YEAR_END and value is 2016
Traceback (most recent call last):
File "./create_newcase", line 218, in
_main_func(__doc__)
File "./create_newcase", line 213, in _main_func
input_dir=input_dir, driver=driver, workflowid=workflow)
File "/public/home/chengxl/cesm/cime/scripts/Tools/../../scripts/lib/CIME/case/case.py", line 1448, in create
input_dir=input_dir, driver=driver, workflowid=workflowid)
File "/public/home/chengxl/cesm/cime/scripts/Tools/../../scripts/lib/CIME/case/case.py", line 813, in configure
machobj = Machines(machine=machine_name)
File "/public/home/chengxl/cesm/cime/scripts/Tools/../../scripts/lib/CIME/XML/machines.py", line 43, in __init__
GenericXML.read(self, local_infile, schema)
File "/public/home/chengxl/cesm/cime/scripts/Tools/../../scripts/lib/CIME/XML/generic_xml.py", line 87, in read
self.read_fd(fd)
File "/public/home/chengxl/cesm/cime/scripts/Tools/../../scripts/lib/CIME/XML/generic_xml.py", line 99, in read_fd
addroot = _Element(ET.parse(fd).getroot())
File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1182, in parse
tree.parse(source, parser)
File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 656, in parse
parser.feed(data)
File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1642, in feed
self._raiseerror(v)
File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1506, in _raiseerror
raise err
xml.etree.ElementTree.ParseError: mismatched tag: line 57, column 3
这个原因是xml的某一行可能没<> 没对应
我就是少写了一个/
@login04 scripts]$ vim ~/.cime/config_machines.xml
[chengxl@login04 scripts]$ ./create_newcase --case FHIST_f19 --res f19_f19 --compset FHIST --run-unsupported --compiler intel --mach afw
Compset longname is HIST_CAM60_CLM50%SP_CICE%PRES_DOCN%DOM_MOSART_CISM2%NOEVOLVE_SWAV
Compset specification file is /public/home/chengxl/cesm/cime/../components/cam//cime_config/config_compsets.xml
Compset forcing is Historic transient
ATM component is CAM cam6 physics:
LND component is clm5.0:Satellite phenology:
ICE component is Sea ICE (cice) model version 5 :prescribed cice
OCN component is DOCN prescribed ocean mode
ROF component is MOSART: MOdel for Scale Adaptive River Transport
GLC component is cism2 (default, higher-order, can run in parallel):cism ice evolution turned off (this is the standard configuration unless you're explicitly interested in ice evolution):
WAV component is Stub wave component
ESP component is
Pes specification file is /public/home/chengxl/cesm/cime/../components/cam//cime_config/config_pes.xml
Compset specific settings: name is RUN_STARTDATE and value is 1950-01-01
Compset specific settings: name is SSTICE_DATA_FILENAME and value is $DIN_LOC_ROOT/atm/cam/sst/sst_HadOIBl_bc_1.9x2.5_1850_2017_c180507.nc
Compset specific settings: name is SSTICE_GRID_FILENAME and value is $DIN_LOC_ROOT/atm/cam/ocnfrac/domain.camocn.1.9x2.5_gx1v6_090403.nc
Compset specific settings: name is SSTICE_YEAR_END and value is 2016
ERROR: Command: '/usr/bin/xmllint --noout --schema /public/home/chengxl/cesm/cime/config/xml_schemas/config_machines.xsd /public/home/chengxl/.cime/config_machines.xml' failed with error '/public/home/chengxl/.cime/config_machines.xml:8: element NODENAME_REGEX: Schemas validity error : Element 'NODENAME_REGEX': This element is not expected. Expected is ( COMPILERS ).
/public/home/chengxl/.cime/config_machines.xml fails to validate' from dir '/public/home/chengxl/cesm/cime/scripts'难道位置也有关系吗？
改到上面去确实没这个问题了
但是又出现 expected one child 了
[chengxl@login04 scripts]$ cat ~/.cime/config_machines.xml
module
login04
LINUX
https://howto.get.out
intel
intelmpi
none
${HOME}/cesm/scratch
${HOME}/cesm/inputdata
${HOME}/cesm/inputdata
${HOME}/cesm/archive/dout_s_root
${HOME}/cesm/cesm_baselines
${HOME}/cesm/tools/cime/tools/cprnc
make
8
none
myb
8
8
FALSE
mpirun
-np {{ total_tasks }}
/usr/share/Modules/init/perl.pm
/usr/share/Modules/init/python.py
/usr/share/Modules/init/csh
/usr/share/Modules/init/sh
/usr/bin/modulecmd perl
/usr/bin/modulecmd python
module
module
compiler/intel/2017.5.239
mpi/hpcx/2.7.4/intel-2017.5.239
mathlib/netcdf/4.4.1/
256M
-1
${EXEROOT}/cesm.exe
>> cesm.log.$LID 2>&1
我把default_run_suffix 那个元素删了，确实是那个原因
./create_newcase --case FHIST_f19 --res f19_f19 --compset FHIST --run-unsupported --compiler intel --mach afw
Compset longname is HIST_CAM60_CLM50%SP_CICE%PRES_DOCN%DOM_MOSART_CISM2%NOEVOLVE_SWAV
Compset specification file is /public/home/chengxl/cesm/cime/../components/cam//cime_config/config_compsets.xml
Compset forcing is Historic transient
ATM component is CAM cam6 physics:
LND component is clm5.0:Satellite phenology:
ICE component is Sea ICE (cice) model version 5 :prescribed cice
OCN component is DOCN prescribed ocean mode
ROF component is MOSART: MOdel for Scale Adaptive River Transport
GLC component is cism2 (default, higher-order, can run in parallel):cism ice evolution turned off (this is the standard configuration unless you're explicitly interested in ice evolution):
WAV component is Stub wave component
ESP component is
Pes specification file is /public/home/chengxl/cesm/cime/../components/cam//cime_config/config_pes.xml
Compset specific settings: name is RUN_STARTDATE and value is 1950-01-01
Compset specific settings: name is SSTICE_DATA_FILENAME and value is $DIN_LOC_ROOT/atm/cam/sst/sst_HadOIBl_bc_1.9x2.5_1850_2017_c180507.nc
Compset specific settings: name is SSTICE_GRID_FILENAME and value is $DIN_LOC_ROOT/atm/cam/ocnfrac/domain.camocn.1.9x2.5_gx1v6_090403.nc
Compset specific settings: name is SSTICE_YEAR_END and value is 2016
Machine is afw
Pes setting: grid match is a%1.9x2.5
Pes setting: grid is a%1.9x2.5_l%1.9x2.5_oi%1.9x2.5_r%r05_g%gland4_w%null_m%gx1v6
Pes setting: compset is HIST_CAM60_CLM50%SP_CICE%PRES_DOCN%DOM_MOSART_CISM2%NOEVOLVE_SWAV
Pes setting: tasks is {'NTASKS_ATM': -2, 'NTASKS_ICE': -2, 'NTASKS_CPL': -2, 'NTASKS_LND': -2, 'NTASKS_WAV': -2, 'NTASKS_ROF': -2, 'NTASKS_OCN': -2, 'NTASKS_GLC': -2}
Pes setting: threads is {'NTHRDS_ICE': 1, 'NTHRDS_ATM': 1, 'NTHRDS_ROF': 1, 'NTHRDS_LND': 1, 'NTHRDS_WAV': 1, 'NTHRDS_OCN': 1, 'NTHRDS_CPL': 1, 'NTHRDS_GLC': 1}
Pes setting: rootpe is {'ROOTPE_OCN': 0, 'ROOTPE_LND': 0, 'ROOTPE_ATM': 0, 'ROOTPE_ICE': 0, 'ROOTPE_WAV': 0, 'ROOTPE_CPL': 0, 'ROOTPE_ROF': 0, 'ROOTPE_GLC': 0}
Pes setting: pstrid is {}
Pes other settings: {}
Pes comments: none
Compset is: HIST_CAM60_CLM50%SP_CICE%PRES_DOCN%DOM_MOSART_CISM2%NOEVOLVE_SWAV
Grid is: a%1.9x2.5_l%1.9x2.5_oi%1.9x2.5_r%r05_g%gland4_w%null_m%gx1v6
Components in compset are: ['cam', 'clm', 'cice', 'docn', 'mosart', 'cism', 'swav', 'sesp', 'drv', 'dart']
Using project from config_machines.xml: none
No charge_account info available, using value from PROJECT
Using project from config_machines.xml: none
cesm model version found: cesm2.1.3-rc.01
Batch_system_type is none
Traceback (most recent call last):
File "./create_newcase", line 218, in
_main_func(__doc__)
File "./create_newcase", line 213, in _main_func
input_dir=input_dir, driver=driver, workflowid=workflow)
File "/public/home/chengxl/cesm/cime/scripts/Tools/../../scripts/lib/CIME/case/case.py", line 1448, in create
input_dir=input_dir, driver=driver, workflowid=workflowid)
File "/public/home/chengxl/cesm/cime/scripts/Tools/../../scripts/lib/CIME/case/case.py", line 945, in configure
batch = Batch(batch_system=batch_system_type, machine=machine_name, files=files)
File "/public/home/chengxl/cesm/cime/scripts/Tools/../../scripts/lib/CIME/XML/batch.py", line 38, in __init__
GenericXML.read(self, infile)
File "/public/home/chengxl/cesm/cime/scripts/Tools/../../scripts/lib/CIME/XML/generic_xml.py", line 87, in read
self.read_fd(fd)
File "/public/home/chengxl/cesm/cime/scripts/Tools/../../scripts/lib/CIME/XML/generic_xml.py", line 99, in read_fd
addroot = _Element(ET.parse(fd).getroot())
File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1182, in parse
tree.parse(source, parser)
File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 657, in parse
self._root = parser.close()
File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1654, in close
self._raiseerror(v)
File "/usr/lib64/python2.7/xml/etree/ElementTree.py", line 1506, in _raiseerror
raise err
xml.etree.ElementTree.ParseError: no element found: line 1, column 0 我突然想到是不是我建立的空config_batch.xml 干扰了
于是删了它
@login04 scripts]$ rm ~/.cime/config_batch.xml
[chengxl@login04 scripts]$ ./create_newcase --case FHIST_f19 --res f19_f19 --compset FHIST --run-unsupported --compiler intel --mach afw
Compset longname is HIST_CAM60_CLM50%SP_CICE%PRES_DOCN%DOM_MOSART_CISM2%NOEVOLVE_SWAV
Compset specification file is /public/home/chengxl/cesm/cime/../components/cam//cime_config/config_compsets.xml
Compset forcing is Historic transient
ATM component is CAM cam6 physics:
LND component is clm5.0:Satellite phenology:
ICE component is Sea ICE (cice) model version 5 :prescribed cice
OCN component is DOCN prescribed ocean mode
ROF component is MOSART: MOdel for Scale Adaptive River Transport
GLC component is cism2 (default, higher-order, can run in parallel):cism ice evolution turned off (this is the standard configuration unless you're explicitly interested in ice evolution):
WAV component is Stub wave component
ESP component is
Pes specification file is /public/home/chengxl/cesm/cime/../components/cam//cime_config/config_pes.xml
Compset specific settings: name is RUN_STARTDATE and value is 1950-01-01
Compset specific settings: name is SSTICE_DATA_FILENAME and value is $DIN_LOC_ROOT/atm/cam/sst/sst_HadOIBl_bc_1.9x2.5_1850_2017_c180507.nc
Compset specific settings: name is SSTICE_GRID_FILENAME and value is $DIN_LOC_ROOT/atm/cam/ocnfrac/domain.camocn.1.9x2.5_gx1v6_090403.nc
Compset specific settings: name is SSTICE_YEAR_END and value is 2016
Machine is afw
Pes setting: grid match is a%1.9x2.5
Pes setting: grid is a%1.9x2.5_l%1.9x2.5_oi%1.9x2.5_r%r05_g%gland4_w%null_m%gx1v6
Pes setting: compset is HIST_CAM60_CLM50%SP_CICE%PRES_DOCN%DOM_MOSART_CISM2%NOEVOLVE_SWAV
Pes setting: tasks is {'NTASKS_ATM': -2, 'NTASKS_ICE': -2, 'NTASKS_CPL': -2, 'NTASKS_LND': -2, 'NTASKS_WAV': -2, 'NTASKS_ROF': -2, 'NTASKS_OCN': -2, 'NTASKS_GLC': -2}
Pes setting: threads is {'NTHRDS_ICE': 1, 'NTHRDS_ATM': 1, 'NTHRDS_ROF': 1, 'NTHRDS_LND': 1, 'NTHRDS_WAV': 1, 'NTHRDS_OCN': 1, 'NTHRDS_CPL': 1, 'NTHRDS_GLC': 1}
Pes setting: rootpe is {'ROOTPE_OCN': 0, 'ROOTPE_LND': 0, 'ROOTPE_ATM': 0, 'ROOTPE_ICE': 0, 'ROOTPE_WAV': 0, 'ROOTPE_CPL': 0, 'ROOTPE_ROF': 0, 'ROOTPE_GLC': 0}
Pes setting: pstrid is {}
Pes other settings: {}
Pes comments: none
Compset is: HIST_CAM60_CLM50%SP_CICE%PRES_DOCN%DOM_MOSART_CISM2%NOEVOLVE_SWAV
Grid is: a%1.9x2.5_l%1.9x2.5_oi%1.9x2.5_r%r05_g%gland4_w%null_m%gx1v6
Components in compset are: ['cam', 'clm', 'cice', 'docn', 'mosart', 'cism', 'swav', 'sesp', 'drv', 'dart']
Using project from config_machines.xml: none
No charge_account info available, using value from PROJECT
Using project from config_machines.xml: none
cesm model version found: cesm2.1.3-rc.01
Batch_system_type is none
Creating Case directory /public/home/chengxl/cesm/cime/scripts/FHIST_f19
[chengxl@login04 scripts]$ ls
create_clone create_test FHIST_f19 lib query_testlists Tools
create_newcase data_assimilation fortran_unit_testing query_config tests
[chengxl@login04 scripts]$ 这下果然成功了！！！
搞了三天，心态崩了，终于成功了！
放上我的config_machines.xml
module
login04
LINUX
https://howto.get.out
intel
intelmpi
none
${HOME}/cesm/scratch
${HOME}/cesm/inputdata
${HOME}/cesm/inputdata
${HOME}/cesm/archive/dout_s_root
${HOME}/cesm/cesm_baselines
${HOME}/cesm/tools/cime/tools/cprnc
make
8
none
myb
8
8
FALSE
mpirun
-np {{ total_tasks }}
/usr/share/Modules/init/perl.pm
/usr/share/Modules/init/python.py
/usr/share/Modules/init/csh
/usr/share/Modules/init/sh
/usr/bin/modulecmd perl
/usr/bin/modulecmd python
module
module
compiler/intel/2017.5.239
mpi/hpcx/2.7.4/intel-2017.5.239
mathlib/netcdf/4.4.1/
256M
-1
附录
两个目录
scripts
cd /public/home/chengxl/cesm/cime/scriptsmachines
cd /public/home/chengxl/cesm/cime/config/cesm/machines创建case
./create_newcase --case FHIST_f19 --res f19_f19 --compset FHIST --run-unsupported --compiler intel --mach afw
查看一下可以加载的模块
[chengxl@server02 .cime]$ module avail
----------------------------------- /opt/hpc/software/modules -----------------------------------
compiler/devtoolset/7.3.1 mpi/hpcx/2.4.1/gcc-7.3.1 mpi/openmpi/4.0.4/gcc-7.3.1
compiler/intel/2017.5.239 mpi/hpcx/2.7.4/gcc-7.3.1
compiler/rocm/3.3 mpi/hpcx/2.7.4/intel-2017.5.239
----------------------------------- /public/software/modules ------------------------------------
apps/anaconda3/5.3.0
apps/esmf/intelmpi/7.0.0
apps/m4/universal/1.4.18
apps/ncl_ncarg/6.3.0
apps/ncl_ncarg/6.6.2
apps/nco/gnu/4.8.1
apps/nco/intel/4.8.1
apps/ncview/gnu/2.1.7
apps/ncview/intel/2.1.7
apps/PyTorch/1.7.mmcv/pytorch-1.7-mmcv1.3.8-rocm-4.0.1
apps/singularity/3.8.0
apps/TensorFlow/tf1.15.3-rocm4.0.1/hpcx-2.7.4-gcc-7.3.1
apps/TensorFlow/tf2.5.0-rocm4.0.1/hpcx-2.7.4-gcc-7.3.1
benchmark/imb/intelmpi/2017
compiler/cmake/3.20.1
compiler/rocm/4.0
mathlib/antlr/gnu/2.7.7
mathlib/antlr/intel/2.7.7
mathlib/cdo/intel/1.10.19
mathlib/grib_api/intel/1.19.0
mathlib/hdf4/gnu/4.2.13
mathlib/hdf4/intel/4.2.13
mathlib/hdf5/gnu/1.8.20
mathlib/hdf5/intel/1.8.20
mathlib/jasper/gnu/1.900.1
mathlib/jasper/intel/1.900.1
mathlib/jpeg/gnu/9a
mathlib/jpeg/intel/9a
mathlib/libpng/gnu/1.2.12
mathlib/libpng/intel/1.2.12
mathlib/netcdf/gnu/4.4.1
mathlib/netcdf/intel/4.4.1
mathlib/pio/gnu/hpcx-2.7.4-gcc7.3.1-2.5.1
mathlib/pio/gnu/openmpi-4.0.4-gcc4.8.5-2.5.1
mathlib/pio/intel/2.5.1
mathlib/pnetcdf/gnu/hpcx-2.7.4-gcc7.3.1-1.12.1
mathlib/pnetcdf/gnu/openmpi-4.0.4-gcc4.8.5-1.12.1
mathlib/pnetcdf/intel/1.12.1
mathlib/szip/gnu/2.1.1
mathlib/szip/intel/2.1.1
mathlib/udunits/gnu/2.2.28
mathlib/udunits/intel/2.2.28
mathlib/wgrib2/2.0.8
mathlib/zlib/gnu/1.2.11
mathlib/zlib/intel/1.2.11
mpi/intelmpi/2017.4.239
mpi/openmpi/gnu/4.0.4查看当前可用的modulefile
命令：moduleavormoduleavail
#查看可用的module：
module av
module avail
#加载module：
module add xxx
module load xxx
#查看已经加载的module:
module li
module list
#删除当前已经加载的module:
module rm xxx
module unload xxx
#删除所有已经加载的module:
module purge
#添加自定义的MODULEPATH:
exportMODULEPATH=[YOUR_NEW_MODULEPATH]:$MODULEPATH
或者
moduleuseYOUR_NEW_MODULEPATH调度系统命令介绍：
这一部分有点多之后再写。
vim 操作：
3、在 10 - 20 行添加 # 注释
:10,20s/^/#/g4、在 10 - 20 行删除 # 注释
:10,20s/#//g