文章目录[隐藏]
without parallel
environment
module load zlib/1.2.6
module load Intel_compiler/13.0
module load autoconf/2.69
install precedure automake libtool & autoconf
Then install omp 4.0.5
compile omp
export HDF5=${HOME}/CESM/hdf5-intel
export PATH=\$HDF5/bin:\$PATH
export LD_LIBRARY_PATH=\$HDF5/lib:\$LD_LIBRARY_PATH
export INCLUDE=\$HDF5/include:$INCLUDE
export CPPFLAGS=-I\$HDF5/include
export LDFLAGS=-L\$HDF5/lib
CC=icc CXX=icpc FC=ifort ./configure --prefix=${HOME}/CESM/netcdf-c-intel --enable-parallel-tests --di^Cble-dap
with parallel
本机的不能用
SUMMARY OF THE HDF5 CONFIGURATION
=================================
General Information:
-------------------
HDF5 Version: 1.12.0
Configured on: Tue Sep 15 00:26:24 CST 2020
Configured by: shlwang@ln8
Host system: x86_64-unknown-linux-gnu
Uname information: Linux ln8 2.6.32-358.11.1.2.ky3.1.x86_64 #1 SMP Mon Jul 8 13:05:58 CST 2013 x86_64 x86_64 x86_64 GNU/Linux
Byte sex: little-endian
Installation point: ${HOME}/CESM/hdf5-intel-parallel
Compiling Options:
------------------
Build Mode: debug
Debugging Symbols: yes
Asserts: yes
Profiling: no
Optimization Level: debug
Linking Options:
----------------
Libraries: static, shared
Statically Linked Executables:
LDFLAGS: -L${HOME}/CESM/hdf5-intel/lib
H5_LDFLAGS:
AM_LDFLAGS:
Extra libraries: -lz -ldl -lm
Archiver: ar
AR_FLAGS: cr
Ranlib: ranlib
Languages:
----------
C: yes
C Compiler: /THL4/software/mpi/mpi-intel2013/bin/mpicc ( MPICH version 3.0.4 built with icc version 13.0.0 (gcc version 4.7.0 compatibility))
CPPFLAGS: -I${HOME}/CESM/hdf5-intel/include
H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200809L -UNDEBUG -DH5AC_DEBUG -DH5B2_DEBUG -DH5CX_DEBUG -DH5D_DEBUG -DH5F_DEBUG -DH5HL_DEBUG -DH5I_DEBUG -DH5O_DEBUG -DH5S_DEBUG -DH5ST_DEBUG -DH5T_DEBUG -DH5Z_DEBUG -DH5_DEBUG_API
AM_CPPFLAGS:
C Flags:
H5 C Flags: -std=c99 -Wall -Wcheck -g -O0
AM C Flags:
Shared C Library: yes
Static C Library: yes
Fortran: no
C++: no
Java: no
Features:
---------
Parallel HDF5: yes
Parallel Filtered Dataset Writes: yes
Large Parallel I/O: yes
High-level library: yes
Build HDF5 Tests: yes
Build HDF5 Tools: yes
Threadsafety: no
Default API mapping: v112
With deprecated public symbols: yes
I/O filters (external): deflate(zlib)
MPE:
Map (H5M) API: no
Direct VFD: no
(Read-Only) S3 VFD: no
(Read-Only) HDFS VFD: no
dmalloc: no
Packages w/ extra debug output: AC,B2,CX,D,F,HL,I,O,S,ST,T,Z
API tracing: yes
Using memory checker: no
Memory allocation sanity checks: yes
Function stack tracing: no
Strict file format checks: yes
Optimization instrumentation: yes
comepiled MPIIO for HDF5
compiled pnet for HDF5
CC=icc CXX=icpc FC=ifort ./configure –prefix=${HOME}/CESM/netcdf-c-intel –enable-parallel-tests –disable-dap
# NetCDF C Configuration Summary
==============================
# General
-------
NetCDF Version: 4.7.4
Dispatch Version: 2
Configured On: Tue Sep 15 00:51:19 CST 2020
Host System: x86_64-pc-linux-gnu
Build Directory: ${HOME}/CESM2/netcdf-c-4.7.4
Install Prefix: ${HOME}/CESM/netcdf-c-intel-parallel
# Compiling Options
-----------------
C Compiler: /THL4/software/mpi/mpi-intel2013/bin/mpicc
CFLAGS:
CPPFLAGS: -I${HOME}/CESM/hdf5-intel-parallel/include
LDFLAGS: -L${HOME}/CESM/hdf5-intel-parallel/lib
AM_CFLAGS:
AM_CPPFLAGS:
AM_LDFLAGS:
Shared Library: yes
Static Library: yes
Extra libraries: -lhdf5_hl -lhdf5 -lm -lz
# Features
--------
NetCDF-2 API: yes
HDF4 Support: no
HDF5 Support: yes
NetCDF-4 API: yes
NC-4 Parallel Support: yes
PnetCDF Support: no
DAP2 Support: no
DAP4 Support: no
Byte-Range Support: no
Diskless Support: yes
MMap Support: no
JNA Support: no
CDF5 Support: yes
ERANGE Fill Support: no
Relaxed Boundary Check: yes
SZIP Support: no
SZIP Write Support: no
Parallel Filters: yes
修改xml credit:MrXun_
$ vim Macros.make
# 修改以下内容
MPIFC := mpiif90
MPICC := mpiicc
MPICXX := mpiicxx
# 在 endif 后面加入
NETCDF_PATH := 你的NetCDF安装路径
HDF5_PATH := 你的HDF5安装路径
SLIBS += -L${NETCDF_PATH}/lib -lnetcdff -lnetcdf -L${HDF5_PATH}/lib -lhdf5_hl -lhdf5 -ldl -lm -lz -lcurl -L${MKLROOT}/lib/intel64 -lmkl_rt -lpthread -ldl
LDFLAGS += -L${NETCDF_PATH}/lib -lnetcdff -lnetcdf -L${HDF5_PATH}/lib -lhdf5_hl -lhdf5 -ld -lm -lz -lcurl -L${MKLROOT}/lib/intel64 -lmkl_rt -lpthread-ldl
# 注释下面的代码
#ifeq ($(MPILIB),mvapich2)
#SLIBS := $(SLIBS) #-mkl=cluster
#endif
#ifeq ($(MPILIB),mpich2)
#SLIBS := $(SLIBS) #-mkl=cluster
#endif
#ifeq ($(MPILIB),mpt)
#SLIBS := $(SLIBS) #-mkl=cluster
#endif
#ifeq ($(MPILIB),openmpi)
#SLIBS := $(SLIBS) #-mkl=cluster
#endif
#ifeq ($(MPILIB),mpich)
#SLIBS := $(SLIBS) #-mkl=cluster
#endif
#ifeq ($(MPILIB),mvapich)
#SLIBS := $(SLIBS) #-mkl=cluster
#endif
#ifeq ($(MPILIB),impi)
#SLIBS := $(SLIBS) #-mkl=cluster
#endif
#ifeq ($(MPILIB),mpi-serial)
#SLIBS := $(SLIBS) #-mkl
#endif
如何创建
/create_newcase --case /data/gpfs01/$USER/cases/g.e20.G1850ECO.f19_g17.test --compset G1850ECO --res f19_g17 --run-unsupported （蓝色标注部分为 创建案例的路径，需修改）
用xmlchange命令修改设定，比如
./xmlchange NTASKS=12
./xmlchange STOP_OPTION=nmonths, STOP_N=5
之后setup、build、submit任务即可：
./case.setup
./case.build
./case.submit