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Wind extinguishes a candle but energizes fire.-
Ubuntu下用parted分区4TB硬盘
Orion要用来做天池比赛的服务器啦，安多一块硬盘用来存雷达数据。放上后需要用parted做分区，然后mkfs格式化，过程和CentOS差不多。这里做一下记录：
lzhenn@thinkstation:~$ sudo parted /dev/sdb (parted) mklabel GPT (parted) mkpart primary 0% 100% (parted) print Model: ATA HGST HUS724040AL (scsi) Disk /dev/sdb: 4001GB Sector size (logical/physical): 512B/4096B Partition Table: gpt Disk Flags: Number Start End Size File system Name Flags 1 1049kB 4001GB 4001GB primary (parted) quit lzhenn@thinkstation:~$ partprobe # let the core know the partation lzhenn@thinkstation:~$ mkfs.ext4 /dev/sdb1 # formatformat后，建立fstab并mount -a即可。与CentOS完全一致。
Updated 2018-06-05
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Change CESM/CLM Surface to Pure Bare Ground
In our hierarchy experiments, we hope to make the NO_TOPO series experiments as simple as possible. Thus, it would be great if there is no vegetation on the ground. In the CLM, we expect there is an external forcing data to control the surface type of ground/vegetation. Then I found this in
lnd_infilefsurdat = '/users/yangsong3/CESM/input/lnd/clm2/surfdata/surfdata_1.9x2.5_simyr2000_c091005.nc'If you
ncdumpthat file, you will see this variable:double PCT_PFT(lsmpft, lsmlat, lsmlon) ; PCT_PFT:long_name = "percent plant functional type of gridcell" ; PCT_PFT:units = "unitless" ;The first dimension show the corresponding PFT (Plant Functional Types), which define the types and fraction of different landcovers a certain grid (Mosaic method). There is the code table:
Thus, the only thing we need to do is to create a new file with change only in PCT_PFT(0,:,:)=100.0.
Updated 2018-06-05
When we tried to run the model, we got several errors.
surfrd_wtxy_veg_all ERROR: sum(pct) over numpft+1 is not = 100. 490 100.106661159475 0.106661159474527 4473According to the error, it seems that the sum of pft is not 100. After checking the data, we found several variables:
pct_list=(/"PCT_LAKE", "PCT_WETLAND", "PCT_GLACIER", "PCT_URBAN"/)So I remain all the pct about water, urban, and glacier, and make the bare ground equal to
100-sum(pct_list).Note that after changing all the landuse pct, the default CLM initial condition cannot satisfy the model, so we need to “cold” start the model. Use
env_run.xmlto set it.<entry id="CLM_FORCE_COLDSTART" value="on" />Updated 2018-06-06
Some issues happened after 10+ years integration. In no_topo experiment, the model exit with error in 0013-03, with Error message:
(shr_sys_abort) ERROR: remap transport: bad departure points (shr_sys_abort) WARNING: calling shr_mpi_abort() and stopping Warning: Departure points out of bounds in remap my_task, i, j = 31 20 13 application called MPI_Abort(MPI_COMM_WORLD, 1001) - process 0 dpx, dpy = -28367.4880120091 54137.9986747345 HTN(i,j), HTN(i+1,j) = 30148.1831506031 30030.4921250813 HTE(i,j), HTE(i,j+1) = 46470.5086842257 46750.9484318852 istep1, my_task, iblk = 1310809 31 2 Global block: 241 Global i and j: 19 372After searching, it seems that the CICE model encountered a CFL violation problem:
This is essentially a CFL violation in the CICE model. You would need to reduce the timestep. In the CESM, the CICE timestep is tied to the coupling interval with the atmosphere. Have a look at ATM_NCPL and ICE_NCPL. Try doubling ATM_NCPL and this should help. For high resolution (0.1-degree) you can use xndt_dyn or ndtd depending on the version of the code. This allows you to take multiple dynamic timesteps per thermodynamic timestep.
I found ATM_NCPL in env_run.xml:
<!--"base period associated with NCPL coupling frequency, valid values: hour,day,year,decade (char) " --> <entry id="NCPL_BASE_PERIOD" value="day" /> <!--"number of atm coupling intervals per NCPL_BASE_PERIOD (integer) (char) " --> <entry id="ATM_NCPL" value="48" />Since the atm run in
dtime=1800s, double theATM_NCPLis meaningless.Another strategy is to double the CICE dynamic timesteps per thermodynamic timestep.
The dynamics timestep should be reduced to integrate past this problem. Set
xndt_dyn = 2in the namelist and restart the model. When the job completes set the value back to 1.That is quite interesting, set it back when pass the unstable point? How could there be this operation?!
Still confused, then I turned to
NO_TOPO_SCONand found another similar error happened in the ocean model:POP Exiting... POP_SolversChronGear: solver not converged POP_SolverRun: error in ChronGear POP_BarotropicDriver: error in solver Step: error in barotropicAnd I searched and found the POP FAQ:
If your case has been running successfully for a period of time, but then the ocean model suddenly fails to converge, you might have encountered a time-stepping instability. If so, you will need to decrease the ocean timestep and restart your case. We recommend you back up at least one month prior to the time of nonconvergence, decrease the ocean-model timestep by about 15-20%, and then restart your case.
And the method to change the timestep:
To change the size of the POP2 timestep, you simply change the value of dt_count in your $CASE/user_nl_pop2 file.
To decrease the POP2 timestep, you must increase the POP2 time_manager_nml namelist variable dt_count.
For example, if the ocean grid in your case is gx1v6, then the default value for dt_count is 23. In order decrease the timestep by roughly 15%, you would increase dt_count to 26. To do this, put the following line in your
$CASE/user_nl_pop2file:dt_count = 26You do not need to rebuild the executable in order to change dt_count.Considering doubling the CICE dynamic timesteps will significantly increase the integration time. I tried the following method:
- In
user_nl_pop2:
dt_count=26- Turn off cold start of the CLM and use 5-day clm2.r file to remap a new file with bare ground.
According to the paleo FAQ:
However, if you have changed your land cover in your new simulation (for example, if you have changed your land ice distribution), you will first need to create a new clm2.r file that conforms to the new land cover assignments in your modified surface datafile. Creating a new clm2.r file is a two step process. Step 1: Run a short (e.g., 5 day) startup simulation with arbitrary initial conditions and your new surface dataset. The 5 day simulation will produce a restart file that is consistent with the ice distribution in your new surface dataset, which is different from the original experiment that you wish to branch from. Use the tool, interpinic, to re-map the restart data from the original simulation to the new restart file created by the 5-day run.
I used to cold start the model, it seems this can be a big problem:
CLM4 does not require an initial condition file and can be initialized with arbitrary initialization (finidat=” “). However, arbitrary initialization starts the model from essentially bare ground, with vegetation, soil carbon, soil nitrogen, and soil moisture set to zero. The land model will spin up all variables at once, but will therefore require many hundreds of years to come into equilibrium.
Following the instruction, we first startup a
NO_TOPOexperiment with 5 day integration and our own bare ground surface data. Then, useinterpinicto remap aREAL_WORLDrestart file to our 5-day restart file: Path:/users/yangsong3/CESM/cesm1_2_2/models/lnd/clm/tools/clm4_0/interpinic./interpinic -i /users/yangsong3/L_Zealot/B/B20f19-realworld/exe/B20f19-realworld.clm2.r.0021-01-01-00000.nc -o /users/yangsong3/L_Zealot/B/B20f19-topo/clm.r/B20f19-topo.clm2.r.interpinic.ncAfter that, I thought for a while and tried to comment out the pop timestep change, turn off CLM cold start, and use frequent restart file output (10 year).
References
- https://bb.cgd.ucar.edu/error-remap-transport-bad-departure-points
- http://www.cesm.ucar.edu/models/cesm1.0/cice/doc/node35.html
- http://www.cesm.ucar.edu/models/paleo/faq/#lnd
Updated 2018-06-11
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我TM又病了
两个月烧了三次，我都想给自己跪下了。真是哔了狗了，怀疑第一次感冒联合几种耐药菌感染，上次支气管炎抗生素又没吃够疗程，丫就潜伏下来了，这次劳累过后，再次烧了起来，扁桃体痛如刀割，左右陆续溃疡，随后又不得不取消了AOGS的行程，其实出发在周日，我当成了周六，今天周六已经基本恢复，票却也退了，残念就残念吧，想想咳咳咳还要做报告，不折腾也挺好，免得再复发。过程记录如下：
date record 5.28 午休后，下午再办逐渐感觉劳累，晚上回宿舍后开始低烧，全身酸痛 5.29 0点体温37.7，8点37.4，随后去校医，拿了5天量头孢，回宿舍，低烧，全身酸痛 5.30 凌晨3点，37.2，早晨7:46，37.4；晚上19:15 37.5, 依然低烧 5.31 早晨起感觉略有退烧，下午到办公室，还是觉得冷，不舒适，看到老板不去，并且推了报告给我，决定取消夏威夷行程 6.1 退烧，咳嗽加重，去校医复查，又拿了五天抗生素，还有止咳药孟鲁斯特钠，这货感觉奇效。 6.2 基本恢复，但是夏威夷残念了。 坚持一个周抗生素，然后慢慢调节肠道菌落吧，诶。后面悠着点，不能太累。
May the luck be with me.
再次复发！症状要轻很多，感觉可能是某些没想到的病症，后来查到跳蚤可以传播立克次体为病原体的疾病，比如战壕热，Q热什么的，这种反复发作有点类似战壕热，只不过症状基本为上感，发热也轻很多。希望这是最后一次了。
date record 6.18 端午，本科同学聚会，有劳累不适感 6.19 出现肠胃症状，略有腹痛不适，前往省局开会，期间开始流涕。 6.20 流涕，偶尔有黄绿色脓涕，但基本以透明粘稠状为主。 6.21 开始有轻微咳嗽，没有发热症状，但是会某些时候畏寒，疲乏 6.22 助教，有畏寒，疲乏，手脚发热感，咳嗽略有加重 6.23 团队活动，手脚发热显著，依然咳嗽 6.24 咳嗽好转，开始大量咳痰，没有畏寒和手脚发热感 6.25 轻微咳嗽，没有发热畏寒，好转。 Updated 2018-06-02
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