WRF (Weather Research and Forecast) is a powerful numerical simulation tool in atmospheric science. It is maintained by UCAR, and in continuous development. There has been a lot of official (ARW user guide)/ unofficial installation guide, but not so much information for CentOS 7 system. There are some minor differences in CentOS 7 that we have to configure manually. This, however, is pretty straightforward if you are familiar with Linux. Here I will show how to set up the basic dependencies, and how to compile WRF, as well as the related WPS and RIP4. Here I will give out the steps for Intel compiler installation.
0.My system
It is running CentOS 7, and basically it is after a fresh install.
CentOS 安装及 intel 编译安装参考 “用CentOS 7打造合适的科研环境”.
Intel version
1. Install Intel compiler
There are already a lot of tutorials out there, and I found it good to accept the Intel’s default setting. By default, the software will be in /opt/intel directory. To make icc and ifort available, we need to have our shell read several environment variables setting scripts. I added the following lines to my ~/.bashrc file. Note if you are using csh or tcsh, the files will be a little bit different, and you can find them in these directories.
source /opt/intel/vtune_amplifier_xe_2015/amplxe-vars.sh quiet
source /opt/intel/inspector_xe_2015/inspxe-vars.sh quiet
source /opt/intel/advisor_xe_2015/advixe-vars.sh quiet
source /opt/intel/bin/compilervars.sh intel64
source /opt/intel/bin/ifortvars.sh intel64
source /opt/intel/bin/iccvars.sh intel64(Here, it is better to create a sh file in /etc/profile.d/, and add the lines above in the sh file.) The last two lines are for the installation of NETCDF.
2. Solve dependencies
2.1 NetCDF
NetCDF is available from package manager (which is yum in CentOS). However, if we install it through yum then it is compiled by GNU compiler, which is not what we want. So let’s install from source code. The source codes have been seperated as NetCDF-C and NetCDF-Fortran version now. WRF requires Fortran version, but Fortran version depends on C version, so we will install both. Download the codes at Unidata.
2.1.0 Solve dependencies of netcdf
http://www.unidata.ucar.edu/software/netcdf/docs/getting_and_building_netcdf.html
The usual way of building netCDF requires the HDF5, zlib, and curl libraries. Versions required are at least HDF5 1.8.9, zlib 1.2.5, and curl 7.18.0 or later.
HDF5 and zlib packages are available from the HDF5 downloads site and the zlib home site. If you wish to use the remote data client code, then you will also need libcurl, which can be obtained from the curl website.
The version I installed are hdf5-1.8.16, zlib-1.2.8, and netcdf-4.3.3.1.
If “make check” fails for either zlib or HDF5, the problem must be resolved before the netCDF-4 installation can continue. For HDF5 problems, see the HDF5 help services.
To build zlib from source, specify where you want to install zlib in a shell variable you will also use later (ZDIR, for example), and build it like this from the top-level zlib source directory
$ # Build and install zlib
$ ZDIR=/usr/local
$ ./configure --prefix=${ZDIR}
$ make check
$ make install # or sudo make install, if root permissions requiredNext, specify where you want to install HDF5 in another shell variable, for example H5DIR, and build it from the HDF5 top-level source directory:
$ # Build and install HDF5
$ H5DIR=/usr/local
$ ./configure --with-zlib=${ZDIR} --prefix=${H5DIR}
$ make check
$ make install # or sudo make install, if root permissions requiredadd another line before make check to avoid an error
make In all cases, the installation location specified with the –prefix option must be different from the source directory where the software is being built.
Before building netCDF, you may need to add ${H5DIR}/lib to the LD_LIBRARY_PATH environment variable if that lib directory is not searched by default. See the netCDF FAQ for more details on using shared libraries.
2.1.1 NetCDF-C
First set some environment variables. This is for both icc and ifort. Then install NetCDF-C.
Indicate where you want to install netCDF in another shell variable, for example NCDIR. Then run the netCDF configure script, specifying where HDF5 was installed using the CPPFLAGS and LDFLAGS environment variables. For example, from the top-level netCDF source directory:
$ # Build and install netCDF-4
$ NCDIR=/usr/local
$ CPPFLAGS=-I${H5DIR}/include LDFLAGS=-L${H5DIR}/lib ./configure --prefix=${NCDIR}
$ make check
$ make install # or sudo make installHere there will be problem if just use the lines above.
Just like
icc: warning #10237: -lcilkrts linked in dynamically, static library not available
ld: warning: libimf.so, needed by /usr/local/netcdf4.3-intel/nc430_hdf5_189sz/lib/libnetcdf.so, not found (try using -rpath or -rpath-link)
Use the following lines instead will install the netcdf successfully.
ZDIR=/usr/local
H5DIR=/usr/local
export CC=icc
export CXX=icpc
export CFLAGS='-O3 -xHost -ip -no-prec-div -static-intel'
export CXXFLAGS='-O3 -xHost -ip -no-prec-div -static-intel'
export F77=ifort
export FC=ifort
export F90=ifort
export FFLAGS='-O3 -xHost -ip -no-prec-div -static-intel'
export CPP='icc -E'
export CXXCPP='icpc -E'
CPPFLAGS=-I${H5DIR}/include LDFLAGS=-L${H5DIR}/lib
LD_LIBRARY_PATH=/usr/local/lib:${LD_LIBRARY_PATH}
./configure --prefix=/usr/intel/netcdf
make
make check # This is just to check the compilation. You can skip this if you want.
make install2.1.2 NetCDF-Fortran
Most of the environment variables needed should have been set by the above lines. But there is still one more:
export CPPFLAGS="-I/usr/intel/netcdf/include"Now go ahead and install it:
tar -zxf netcdf-fortran-4.4.2.tar.gz
cd netcdf-fortran-4.4.2
configure --prefix=/usr/intel/netcdf
make
make check # Similarly, you can skip this is you want.
make installThe lines above are not enough.
Follow the instructions on ucar:
http://www.unidata.ucar.edu/software/netcdf/docs/netcdf-fortran-install.html
First make sure the netCDF C library has been built, tested, and installed under directory ${DIR1}, as specified by –prefix=${DIR1} to the C library configure script, or under directory /usr/local by default.
For the Fortran netCDF library, use the same C compiler as used to create the netCDF C library, specified with the CC environment variable, if necessary.
If the netCDF C library was installed as a shared library in a location that is not searched by default, you will need to set the LD_LIBRARY_PATH environment variable (or DYLD_LIBRARY_PATH on OSX) to specify that directory before running the configure script, for example:
export LD_LIBRARY_PATH=${DIR1}/lib:${LD_LIBRARY_PATH}
If you set the LD_LIBRARY_PATH (or DYLD_LIBRARY_PATH) environment variable in the previous step, don’t use the “sudo” command before the following “configure” or “make check” commands. Using “sudo” causes the LD_* environment variables to be ignored, as a security precaution. You can use “sudo make install” as the last step, but you shouldn’t need to use “sudo” before that.
For the configure script, set CPPFLAGS and LDFLAGS variables to specify the include and lib directories for the netCDF C library. For example, to install the Fortran libraries in the same directory ${DIR1} where the C netCDF library is installed:
CPPFLAGS=-I\${DIR1}/include LDFLAGS=-L\${DIR1}/lib ./configure –prefix=\${DIR1}
If you are cross-compiling, you should also include the configure option “–disable-fortran-type-check”, as in:
CPPFLAGS=-I\${DIR1}/include LDFLAGS=-L\${DIR1}/lib \
./configure –disable-fortran-type-check –prefix=\${DIR1}
If that succeeds, run “make check”.
If that succeeds, run “make install” or “sudo make install”.
The codes are:
DIR1=/usr/intel/netcdf
export LD_LIBRARY_PATH=${DIR1}/lib:${LD_LIBRARY_PATH}
CPPFLAGS=-I${DIR1}/include LDFLAGS=-L${DIR1}/lib ./configure --prefix=${DIR1}
make
make check
sudo make installAdd the following line to .bashrc file in the user home directory, then can use the commands like ”ncdump”.
export PATH=$PATH:/usr/intel/netcdf/bin/2.2 MPICH
I am not sure if OpenMP works. Theoritically it should work, but I did not have enough time to try it. Set the following environmental variables first. These blank values are to erase the values we just wrote above, for NetCDF.
export F90=
export F90FLAGS=
export FC=ifort
export FCLAGS='-O3 -xHost -ip -no-prec-div -static-intel'Download mpich from http://www.mpich.org/downloads/, and then install it as below:
tar xvzf mpich-3.2.tar.gz
cd mpich-3.2/
./configure --prefix=/usr/intel/mpich
make
make check
make install
(error occur... but seems that WRF does not need mpich if only runs on one pc, so check later)2.3 zlib
Have these two variables set, then install the zlib.
(have installed, check the context above)
2.4 libpng
Download the package from http://www.libpng.org/pub/png/libpng.html.
tar xvzf libpng-1.6.21.tar.gz
cd libpng-1.6.21/
export CC=icc
export CXX=icpc
./configure --prefix=/usr/intel/libpng
make
make check
sudo make install2.5 jasper
Nothing special here. Just follow the general procedure of installing from source codes.
Download the code from http://www.ece.uvic.ca/~frodo/jasper/#download
tar -zxf jasper-1.900.1.tar.gz
cd jasper-1.900.1
export CC=icc
export CXX=icpc
./configure --prefix=/usr/intel/jasper
make
make check
sudo make installNow we need to modify the PATH variable, adding these new paths.
export PATH=$PATH:/usr/intel/netcdf/bin/
export PATH=$PATH:/usr/intel/jasper/bin/
export PATH=$PATH:/usr/intel/libpng/bin/and these
JASPER=/usr/intel/jasper;export JASPER
JASPERLIB=/usr/intel/jasper/lib/;export JASPERLIB
JASPERINC=/usr/intel/jasper/include/;export JASPERINC
ZLIB=/usr/intel/zlib;export ZLIB
ZLIBLIB=/usr/intel/zlib/lib/;export ZLIBLIB
ZLIBINC=/usr/intel/zlib/include/;export ZLIBINC
export LD_LIBRARY_PATH=/usr/intel/netcdf/lib/:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=/usr/intel/jasper/lib/:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=/usr/intel/libpng/lib/:$LD_LIBRARY_PATH3. Build WRF
Building WRF is relatively easy, once all the libraries have been installed. Here are just some quick note.
1) When choosing the system, go with icc+ifort (serial) first. This will help to check if the dependencies are OK. Once this is done successfully, go with icc+ifort (dmpar).
export EM_CORE=1
export NMM_CORE=0
export WRF_CHEM=1
export WRF_KPP=0NetCDF users note:
This installation of NetCDF supports large file support. To enable large file
support in NetCDF, set the environment variable WRFIO_NCD_LARGE_FILE_SUPPORT
to 1 and run configure again. Set to any other value to avoid this message.
$ export WRFIO_NCD_LARGE_FILE_SUPPORT=1Configure (ver 3.5, here choose option 17 and 1) and
Compile WRF by
nohup ./compile em_real &> compile.log &When I compile the WRF using ./compile em_real, there is an error due to a gcc “bug”: CPP adds extra comments.
/* Copyright (C) 1991-2012 Free Software Foundation, Inc.
1
Error: Invalid character in name at (1)Refer to a similar error post: http://stackoverflow.com/questions/25118052/gcc-e-p-c-adds-extra-comments
Resolve the error by the use of -nostdinc option
vim ./configure.wrf
change the line
CPP = /lib/cpp -C -Pto
CPP = /lib/cpp -C -P -nostdincThen WRF can be compiled smoothly.
Fix another error
tc_em.f90(138): error #6418: This name has already been assigned a data type. [ITMP]
INTEGER :: julyr , julday ,itmp,icnt
vim main/tc_em.F, and change the line
INTEGER :: julyr , julday ,itmp,icnt
to INTEGER :: julyr , julday
Check the exe files
$ ls main/*.exe
main/ndown.exe main/nup.exe main/real.exe main/tc.exe main/wrf.exe
Time for play!
If NEI eimssion inventory is used, convert_emiss.exe will be need to be generated by compilation as below.
./compile emi_conv &>compile.emi.log &convert_emiss.exe will be found in the directory test/em_real/.
I checked and played with the both smpar and dmpar, and here is what I have found:
If we use smpar option, then there is no need to call mpich to run WRF in parallel. Instead, we just need (for real case):
wrf.exe &> log.wrf.txt &A quick reminder is in this mode, do not use mpirun to run your wrf.exe. This just creates two wrf.exe running, but they are all doing the identical thing. Meanwhile, this will create a wrf.exe process that takes up all the CPU resources. In my case I have 12 cores, and they will all be 100% occupied.
Things are a little different with dmpar. With this option, we can run wrf.exe by using:
mpirun -np 8 wrf.exe &> log.wrf.txt &4. Building WPS
WPS can only be built after WRF has been compiled successfully. Follow the instructions in WRF user guide (i.e. a basic source code installation).
$ cd WPS351/
$ ./configure
select the Intel compiler
$ ./compile &> compile.log &Same gcc ‘bug’ error:
wrf_debug.f90(1): error #5082: Syntax error, found '/' when expecting one of: <LABEL> <END-OF-STATEMENT> ; BLOCK PROGRAM BLOCKDATA MODULE INTEGER REAL COMPLEX ...
/* Copyright (C) 1991-2012 Free Software Foundation, Inc.vim configure.wps
change the line CPP = /lib/cpp -C -P -traditional to CPP = /lib/cpp -C -P -traditional -nostdinc
Error2
png.h: No such file or directory
#include <png.h>locate the png.h, then vim configure.wps, find the line
COMPRESSION_INC = -I/data3a/mp/gill/WPS_LIBS/local/include \
and add the libpng include directory
COMPRESSION_INC = -I/data3a/mp/gill/WPS_LIBS/local/include \
-I/usr/intel/libpng/include/
Error3:
enc_png.c: In function ‘enc_png_’:
enc_png.c:101:31: error: ‘voidp’ undeclared (first use in this function)
png_set_write_fn(png_ptr,(voidp)&write_io_ptr,(png_rw_ptr)user_write_data,Solution: change voidp to png_voidp.
Error4:
dec_png.c: In function ‘dec_png_’:
dec_png.c:101:30: error: ‘voidp’ undeclared (first use in this function)
png_set_read_fn(png_ptr,(voidp)&read_io_ptr,(png_rw_ptr)user_read_data);Solution: change voidp to png_voidp.
Error 5:
ld: cannot find -ljasper
ld: cannot find -lpng12
ld: cannot find -lpngvim configure.wps, change
COMPRESSION_LIBS = -L/data3a/mp/gill/WPS_LIBS/local/lib
-ljasper -lpng12 -lpng -lzto
COMPRESSION_LIBS = -L/data3a/mp/gill/WPS_LIBS/local/lib \
-L/usr/intel/jasper/lib \
-L/usr/intel/libpng/lib \
-ljasper -lpng16 -lpng -lzError 6:
ld: cannot find -lncarg
ld: cannot find -lncarg_gks
ld: cannot find -lncarg_c
ld: cannot find -lX11After NCL installed, the first 3 errors gone. Now deal with the last one.
Try to change the line
-L/usr/X11R6/lib -lX11to
-L/usr/lib -lX11No luck…. but seems the exe files are generated and perform well. Test confirmed.
5. Building RIP4
5.1 Install NCL
RIP4 relies on NCL (NCAR Command Language). I did not install it, but just installed a pre-compiled binary file. Download the file from here. I went with “ncl_ncarg-6.3.0.Linux_RHEL6.4_x86_64_nodap_intel1215.tar.gz”.
Find the install file from the page https://www.ncl.ucar.edu/Download/install.shtml
tar -zxf ncl_ncarg-6.3.0.Linux_RHEL6.4_x86_64_nodap_intel1215.tar.gz
sudo mkdir /usr/intel/ncl
sudo cp -r bin include lib /usr/intel/ncl/Before running NCL, make sure the following environment variables are set.
export NCARG_ROOT=/usr/intel/ncl
export PATH="$NCARG_ROOT/bin:$PATH"
export LD_LIBRARY_PATH="/opt/intel/composer_xe_2015.6.233/compiler/lib/intel64:$LD_LIBRARY_PATH"Now you can try you luck with
ng4ex gsun01n -cleanIf NCL was installed successfully, you will get several plots.
5.2 Install RIP4
(This part is skipped)
First set RIP_ROOT as your RIP4 directory. Then configure it, as always. But you may get several problems when compiling it. Here are the solutions for my problems.
Basically it cannot find several lib files. They are not installed by default in CentOS 7, so we need to get them and modify the configure.rip4 file:
1) For NetCDF issues, change “NETCDFLIB=-L${NETCDF}/lib -lnetcdf” into “NETCDFLIB=-L${NETCDF}/lib -lnetcdff -lnetcdf”. Note “-netcdff” must comes before “-netcdf”. “-lnetcdf” means the netcdf-C libraries, but the program is also looking for netcdf-Fortran libraries, so we use “-lnetcdff”. Similarly, “-lnetcdf_c++” is for netcdf-C++ libraries.
2) For “cairo”/”freetype” issues, instal cairo-devel and freetype-devel, and modify “NCARGLIBS=-L${NCARG_ROOT}/lib -lncarg -lcgm -lncarg_gks -lncarg_c -lX11 -lm”. Here is what you should do:
First use “locate” to find out the library location:
$ locate libcairo.so
/usr/lib64/libcairo.soThen add “-L/usr/lib64 -lcairo” to NCARGLIBS. Similarly, for freetype libs, add “-L -lfreetype” to NCARGLIBS.
Now a basic WRF setup is done. We can start playing with it, and be our “god of weather”!
6. WRF/Chem Test.
An error occur: “wrf Segmentation fault (core dumped)”
Solution:
Refer to http://forum.wrfforum.com/viewtopic.php?f=6&t=4391,
“Early segmentation faults often are a simple memory issue.
Did you try the command “ulimit -s unlimited” before running WRF? ”
After typing the command, the wrf/chem worked.
[1] 用CentOS 7打造合适的科研环境 http://seisman.info/linux-environment-for-seismology-research.html
[2] Installing WRF on CentOS 7 https://wolfscie.wordpress.com/2015/04/23/installing-wrf-on-centos-7/
[3] [netCDF #JZT-105309]: neCDF 4.3.0 installation issue - Can’t find or link to the hdf5 library https://www.unidata.ucar.edu/support/help/MailArchives/netcdf/msg11947.html
[4] Building the netCDF-4.2 and later Fortran libraries
http://www.unidata.ucar.edu/software/netcdf/docs/netcdf-fortran-install.html
[5] WRF official website
http://www.wrf-model.org/index.php
[6] A tutorial on how to compile WRF
http://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php