sci-tech on Dreambooker

Points within satellite swath

Tue, 10 Jan 2023 00:00:00 +0000

Selecting points within TROPOMI swath

Self-hosted Staticman on free AWS Lambda

Wed, 21 Dec 2022 00:00:00 +0000

Automating website deployment and supporting Staticman comments

The best reference manager

Thu, 21 Jan 2021 00:00:00 +0000

My favorite reference manager: Zotero

Setting up my Elementary OS

Fri, 04 Dec 2020 00:00:00 +0000

Enjoy the beautiful Linux system: Elementary OS

Integrated Reaction Rates (Part3)

Wed, 02 Dec 2020 00:00:00 +0000

Generate the yaml file of specific mechanism for PERMM

Integrated Reaction Rates (Part2)

Tue, 01 Dec 2020 00:00:00 +0000

Aplication of PERMM for WRF-Chem

Integrated Reaction Rates (Part1)

Mon, 30 Nov 2020 00:00:00 +0000

Useful tool: PERMM

Using the ERA5 O3 data in the WRF initial condition

Mon, 26 Oct 2020 00:00:00 +0000

How to edit the WRF IC

Download FENGYUN data in one script

Fri, 03 Jul 2020 00:00:00 +0000

I can’t stand the official download method any more !!!

Time-lapse images by Raspberry Pi

Wed, 10 Jun 2020 00:00:00 +0000

Time-lapse images using two usb cameras and one Raspberry Pi

Run sublimetext in WSL

Tue, 24 Mar 2020 00:00:00 +0000

Enjoy sublime text in WSL

X11 forwarding Chrome of internal PC

Wed, 11 Mar 2020 00:00:00 +0000

Access the internal resource by proxy

Map MEIC to MOZCART

Tue, 10 Mar 2020 00:00:00 +0000

How to map MEIC emission inventories to MOZART in WRF-Chem

Satpy中英双语简介

Mon, 24 Feb 2020 00:00:00 +0000

Satpy中英双语手册

Plot TROPOMI data using pcolormesh or imshow?

Sat, 22 Feb 2020 00:00:00 +0000

Methods to plot Swath data correctly

Satpy Basic (FY4A)

Thu, 06 Feb 2020 00:00:00 +0000

Using Satpy to read and plot FY4A data

IELTS Notes

Fri, 20 Dec 2019 00:00:00 +0000

How to prepare for IELTS

Initializing the WRF model with ERA5 (pressure level)

Thu, 03 Oct 2019 00:00:00 +0000

Downloading ERA5 pressure level data by Python and initialize WRF model

Hugo+Staticman+Travis

Sat, 17 Aug 2019 00:00:00 +0000

This blog post documents the setup of deploying Hugo with Travis CI to the GitHub Pages.

Prerequisites

GitHub account;
Travis CI account (login with GitHub account);
Installing git, hugo on your local system

Installing libraries and automating WRF-Chem

Thu, 13 Dec 2018 00:00:00 +0000

Backgroud

NETCDF version (netcdf/4.5.0/02-CF-17-par) on TH-2 seems something wrong. This results in error when NETCDF4 of WRF-Chem enabled (NETCDF4=1). So, I decide to compile NETCDF on my own.

Prerequisite

According to NetCDF’s instruction , we need zlib and hdf5 first. For zlib, I use the version zlib/1.2.11-icc17 originally compiled by TH-2.

HDF5

The newest version is 1.10.4.

$ ./configure --prefix=/HOME/nuist_chenq_2/WORKSPACE/xin/software/hdf5-1.10.4 --enable-fortran --enable-static-exec

But, I got this error:

Tricks of TH-2 VPN

Wed, 05 Dec 2018 13:22:09 +0000

Install vpnc

Link

https://pkgs.org/download/vpnc

Edit vpnc config file

/etc/vpnc/default.conf

IPSec gateway vpn2.nscc-gz.cn
IPSec ID VPN
IPSec secret gzcszx@123
#IKE Authmode hybrid
Xauth username vpn_username
Xauth password vpn_password

Speedup WRF-Chem

Sun, 02 Dec 2018 20:58:10 +0000

Background

This is my partial namelist of WRF-Chem:

&time_control
run_days = 147,
&domains
time_step = 72,
time_step_fract_num = 0,
time_step_fract_den = 1,
max_dom = 1,
e_we = 430,
e_sn = 345,
e_vert = 40,
dx = 12000,
dy = 12000,
p_top_requested = 10000,

I used 384 cores to run it and I found the speed of calculation and writing is ~5.45 seconds/step, ~54.5 s/wrfout_file and ~210 s/wrfrst_file. The terrible one is the speed of I/O tasks.

Controlling the exam with Python

Thu, 22 Nov 2018 13:19:33 +0000

Predicaments

We’re asked to learn a library about safety.

However, if the duration is greater than 5 minutes (~300 seconds), we need to click agree to let the timing continue. So, when we finish the learning progress, we’ll click 6*60/5 = 72 times ……..

Trick of binned_statistic_2d

Thu, 22 Nov 2018 09:11:07 +0000

Official example

>>> from scipy import stats

Calculate the counts with explicit bin-edges:

>>> x = [0.1, 0.1, 0.1, 0.6]
>>> y = [2.1, 2.6, 2.1, 2.1]
>>> binx = [0.0, 0.5, 1.0]
>>> biny = [2.0, 2.5, 3.0]
>>> ret = stats.binned_statistic_2d(x, y, None, 'count', bins=[binx,biny])
>>> ret.statistic
array([[ 2., 1.],
[ 1., 0.]])

Send e-mail when file modified

Sun, 18 Nov 2018 22:00:48 +0000

mailx

Download mailx (openSUSE is the distribution of my server) and install it.

$ make PREFIX=/public/home/zhangxin/softwares/mailx SYSCONFDIR=/public/home/zhangxin/softwares/mailx/etc
$ make install UCBINSTALL=/usr/bin/install PREFIX=/public/home/zhangxin/softwares/mailx SYSCONFDIR=/public/home/zhangxin/softwares/mailx/etc

Get your authorization code and edit mailx/etc/nail.rc

set from="363910399@qq.com"
set smtp=smtp.qq.com
set smtp-auth-user="363910399@qq.com"
set smtp-auth-password="authorization_code"
set smtp-auth=login

Set up personal Anaconda mirror

Fri, 16 Nov 2018 10:13:08 +0000

Predicaments

If you encounter any problems as follows, you should try to set up a personal Python(Anaconda) mirror:

Deploy a python environment on servers that have no access to the Internet;
Deploy a python environment which can be used directly by other users on the server;
Internet speed or connection to cloud mirror is slow.

Steps

Installation

Just install Anaconda according to this guide.

Of course, you can download Anaconda installer archive from here.

Download(mirror)

You can use wget to mirror the packages from official Anaconda websites or other mirror websites (TUNA and USTC).

If your server is located in China, I recommend the later one.

I’ll take the later one as example.

Trick of pcolormesh

Wed, 31 Oct 2018 10:40:24 +0000

Reference

http://alex.seeholzer.de/2014/05/fun-with-matplotlib-pcolormesh-getting-data-to-display-in-the-right-position/

Code

Create RAID 5

Mon, 10 Sep 2018 09:25:21 +0000

Reference: https://www.tecmint.com/create-raid-5-in-linux/

Install mdadm and verify drives

yum install mdadm

mdadm -E /dev/sd[b-h]

mdadm: No md superblock detected on /dev/sdc.
mdadm: No md superblock detected on /dev/sdb.
mdadm: No md superblock detected on /dev/sdd.
mdadm: No md superblock detected on /dev/sde.
mdadm: No md superblock detected on /dev/sdf.
mdadm: No md superblock detected on /dev/sdg.
mdadm: No md superblock detected on /dev/sdh.

Partitioning the Disks for RAID

Actually this is optional. If you want to partition first, you should make sure you’re using gpt or others which support larger than 2T.

Create /dev/sdb Partition

Please follow the below instructions to create partition on /dev/sdb drive.

fdisk /dev/sdb

Mount ntfs and start nfs

Tue, 04 Sep 2018 15:01:00 +0000

Mount and start NFS

If the type of disk is ntfs, you need to install ntfs-3g.

mount -t ntfs-3g /dev/??? /new_dir
#start the nfs server service.
service nfsserver start

Exporting Directories on the Server

Set a dark theme in Texstudio

Mon, 03 Sep 2018 14:18:51 +0000

Reference: https://tex.stackexchange.com/questions/108315/how-can-i-set-a-dark-theme-in-texstudio

Original:

Dark:

Steps:

Set decayed tracer for WRF

Tue, 31 Jul 2018 10:09:31 +0000

Because tracer_opt in WRF-Chem support more functions than WRF, we plan to clone and edit it for WRF (which is much quickier than WRF-Chem).

Copy /chem/module_input_tracer_data.F and chem/module_input_tracer.F into /WRFV3/phys.

After compile, I get an error about TRACER_TEST1 not found. It’s related to module_state_description.F

module_state_description.F : ../Registry/$(REGISTRY)
( cd .. ; tools/registry $(ARCHFLAGS) $(ENVCOMPDEFS) -DNEW_BDYS Registry/$(REGISTRY) ) ;

Registry/Registry.EM_COMMON

The cycle of download and move

Wed, 11 Jul 2018 09:27:50 +0000

Download files on node_1 and move all of them to node_2 at intervals.

Install git and oh-my-zsh without root

Thu, 28 Jun 2018 11:57:14 +0000

Git

Check Installing from Source part of the guide.

What I do is a little different from it:

Curl

Since git depend on curl, I installed curl from source according to this guide.

Git

# Download git and uncompress
$ tar -zxf git-2.18.0.tar.gz
$ cd git-2.18.0
$ make configure
# Define CURLDIR=/public/home/zhangxin/softwares/curl if your curl header and library files are # in /public/home/zhangxin/softwares/curl/include and /public/home/zhangxin/softwares/curl/lib # directories.
$ ./configure CURLDIR=/public/home/zhangxin/softwares/curl --prefix=/public/home/zhangxin/softwares/git
# Since we don't need docs actually, just 'make'.
$ make CURLDIR=/public/home/zhangxin/softwares/curl
$ make install CURLDIR=/public/home/zhangxin/softwares/curl

Enable auto-login and auto-networking in Debian 9

Fri, 15 Jun 2018 10:42:48 +0000

sudo nano /usr/share/lightdm/lightdm.conf.d/01_debian.conf

Add these lines below

[SeatDefaults]
autologin-user=username
autologin-user-timeout=0

Auto-networking

Python script

This is the example (python实现校园网自动登录):

Migrate blog to Github(HTTPS) and add continuous integration

Fri, 18 May 2018 17:38:12 +0000

Reference

MARKSZのBlog

Continuous integration

Set Travis-CI account and Token

Sign up Travis-CI and sync your Git-hub account:
Choose your *github.io:

Running Win10 Debian Zsh in Cmder

Sat, 05 May 2018 15:21:53 +0000

References

Running Windows 10 Ubuntu Bash in Cmder

How to Install and Use the Linux Bash Shell on Windows 10

Prerequisites

Bash on Debian on Windows enabled
Cmder.

If you don’t have that, you can simply follow these instructions:

Install Bash On Ubuntu on Windows (the same way to install Debian)

Download and unzip Cmder to a convenient place on your disk. Then start Cmder.exe.

Install (Oh-my-) Zsh on Bash on Ubuntu on Windows

Set up Zsh in Cmder

ssh内网穿透

Sun, 29 Apr 2018 21:20:50 +0000

机房电脑，通过远程端口映射，使得VPS：2222 映射到机房电脑：22：

ssh -N -f -R 2222:127.0.0.1:22 root@vpsIP

VPS则可以ssh到机房电脑:

ssh -p 2222 username@localhost

用ssh代理来浏览内网:

在校外电脑上，通过本地端口映射，使得校外电脑：2222 映射到VPS: 2222

ssh -N -f -L 2222:127.0.0.1:2222 root@vpsIP

Initializing the WRF model with ERA5

Fri, 20 Apr 2018 00:00:00 +0000

Note

This is the tutorial of using WRF with ERA5 model level (138 vertical levels) data.

If you prefer pressure level (38 vertical levels), please check another tutorial.

I recommend the pressure level data, because the download speed is much faster.

If you don’t have cdsapi, please check this official tutorial.

Summarization

Download
Preprocess
Automation
Geogrid
Ungrib
Produce additional intermediate files
Metgrid

BEHR_OMINO2 Guide for non_Berkeley

Sun, 11 Mar 2018 00:00:00 +0000

BEHR_OMINO2 Guide for non_Berkeley

Clone BEHR_Core and other repositories

mkdir BEHR
cd BEHR
git clone https://github.com/CohenBerkeleyLab/BEHR-core.git
cd BEHR-core
./setup.sh # if you want to use develop branch, add --develop

Remarkable - Connecting to a hotspot which supports circumvention

Thu, 18 Jan 2018 00:00:00 +0000

Method 1

Using VPN Hotspot to share the VPN you set on your Android phone.

Method 2

Set up VPN

Initializing the WRF model with ECMWF ERA-Interim reanalysis

Wed, 20 Dec 2017 00:00:00 +0000

Summarization

To summarise, you need three separate data files from the reanalysis data:

Pressure level data (or model levels)

Surface variable data

Fixed data.

WRF-Chem (MOZCART) and WRF_tips

Sun, 10 Dec 2017 00:00:00 +0000

WPS

namelist

i_parent_start and j_parent_start

How to compile WRF-Chem

Mon, 02 Oct 2017 00:00:00 +0000

This is the basic one about WRF-Chem. You can check this one for more information.

sci-tech on Dreambooker

Points within satellite swath

Self-hosted Staticman on free AWS Lambda

The best reference manager

Setting up my Elementary OS

Integrated Reaction Rates (Part3)

Integrated Reaction Rates (Part2)

Integrated Reaction Rates (Part1)

Using the ERA5 O3 data in the WRF initial condition

Download FENGYUN data in one script

Time-lapse images by Raspberry Pi

Run sublimetext in WSL

X11 forwarding Chrome of internal PC

Map MEIC to MOZCART

Satpy中英双语简介

Plot TROPOMI data using pcolormesh or imshow?

Satpy Basic (FY4A)

IELTS Notes

Initializing the WRF model with ERA5 (pressure level)

Hugo+Staticman+Travis

Prerequisites

Installing libraries and automating WRF-Chem

Backgroud

Prerequisite

HDF5

Tricks of TH-2 VPN

Install vpnc

Link

Edit vpnc config file

Speedup WRF-Chem

Background

Controlling the exam with Python

Predicaments

Trick of binned_statistic_2d

Official example

Send e-mail when file modified

mailx

Set up personal Anaconda mirror

Predicaments

Steps

Installation

Download(mirror)

Trick of pcolormesh

Reference

Code

Create RAID 5

Install mdadm and verify drives

Partitioning the Disks for RAID

Create /dev/sdb Partition

Mount ntfs and start nfs

Mount and start NFS

Exporting Directories on the Server

Set a dark theme in Texstudio

Set decayed tracer for WRF

The cycle of download and move

Install git and oh-my-zsh without root

Git

Curl

Git

Enable auto-login and auto-networking in Debian 9

Auto-login

Auto-networking

Python script

Migrate blog to Github(HTTPS) and add continuous integration

Reference

Continuous integration

Set Travis-CI account and Token

Running Win10 Debian Zsh in Cmder

References

Prerequisites

Set up Zsh in Cmder

ssh内网穿透

Initializing the WRF model with ERA5

Note

Summarization

BEHR_OMINO2 Guide for non_Berkeley

BEHR_OMINO2 Guide for non_Berkeley

Clone BEHR_Core and other repositories

Remarkable - Connecting to a hotspot which supports circumvention

Method 1