This is an old revision of the document!
A few useful links that have nothing to do with science and software resources!
It's very important that you update your phone/office information when you arrive at LSCE, so that other people can find you using the tools above!
Use the following sequence of keys on the Mitel phone in your office:
01 69 08 NN NN
It is important to join the correct mailing lists, if you want to get all the information you need, on time.
When your account is created, your email address should automatically be added to the the all list, that can be used to send mails to all the people working at LSCE. You will also get IPSL information through this list
|firstname.lastname@example.org||Everybody at LSCE|
|email@example.com||People working at Orme|
|firstname.lastname@example.org||People working in Gif|
Mails sent to these lists will reach lots of people. Think well before sending a mail to these lists!
Ask your team leader or Jean-Yves to add you to your team's mailing list
No need to try to connect your laptop to the LSCE wire network, it will not work!
The best you can do is use the eduroam or guest wifi network, if your office is close enough to one of the access points.
Warning! You can't connect directly to the obelix LSCE servers from the wifi network. You first have to connect to
ssh1.lsce.ipsl.fr, and then to
If you try to access the intranet from outside the LSCE network (including eduroam), your browser will open a
password popup window. Use your LSCE login (not your email address!) and password
Intranet web site: https://intranet.lsce.ipsl.fr/
There is a lot of information available on the LSCE intranet, but you can only access it from a computer connected to the LSCE network
Everything about the LSCE servers (and other software and hardware information): https://intranet.lsce.ipsl.fr/informatique/en/orme/index.php
It used to be possible to access the CEA Saclay intranet by just clicking on http://www-saclay.cea.fr/ from any computer on the LSCE network.
This is not possible anymore, now that LSCE is on the Paris-Saclay network (and not on the CEA network)
Use the following steps:
Everybody working for CLIM & ESTIMR gets a computer that can be connected to the LSCE network. Please take the time to read the instructions below, that may help make your life easier
If an application requests administrator's rights to install something or make changes to the computer, and you are sure it's not a virus, use the
.\adminuser account and the
adminuser password you received when your computer was configured, or ask the system administrators.
There are different window managers available, each one with different settings: you should the Cinnamon window manager (xfce is a bit too basic, and Gnome is not very convenient for doing actual work, and uses too much CPU). You can select the window manager by clicking on the little cogwheel below the password field, on the login screen.
This is Linux, you are using it for work, you should be efficient, so you should be able to do most of your work by typing commands in a terminal. The true power is in the correct use of the command-line interfaces, rather than having to spend time finding where to click in the windows. You will find some Linux documentation below.
Depending on what you need to do:
Sorry, you are on your own, but it's soooo easy to use, right?
Just open a terminal and use ssh to connect to the appropriate server
There should be an Obelix shortcut on the left side of your desktop. Double-click on it in order to open a window (e.g. with graphics) environment on one of the obelix servers. Each terminal you will open in this environment will run on the same obelix server. Use ssh to connect another server
If there is not yet an Obelix shortcut, use the VcXsrv XLaunch program to create it
There are lots of things you can do directly on your local Win7/Win10 or Linux desktop (displaying pdf, images, using a text editor, …), rather than on the remote servers. Never forget that your local desktop has access to the remote disks on the Linux servers.
Otherwise, use the appropriate Linux servers. The load balancing system will send you to the server that has currently the smallest load
ssh obelixto get there): never forget that you are sharing these servers with other users! Do not use too much CPU and memory for a long time. Heavy computation should be done on the obelix cluster
$ ssh obelix Last login: Mon Jun 3 08:49:53 2019 from somewhere # You can use one of the following commands if you want to know on which obelix you are >echo $HOST obelix5 >hostname obelix5
It is important to know which shell you are using if you need to configure and tune your Linux account. The shell is basically the program that waits for you to type commands in a terminal and passes them to the computer
If you are not sure which shell is running in your terminals, you can use
echo $SHELL to find out:
# Somewhere with tcsh > echo $SHELL /bin/tcsh # Somewhere else with bash $ echo $SHELL /bin/bash
If the Linux server you are working on seems slow, or if you want to get an idea of the resources you are using, you should use the
jypeter@obelix4 - ...jypeter - 46 >top top - 17:48:51 up 8 days, 23:43, 29 users, load average: 1.22, 1.38, 1.98 Tasks: 324 total, 2 running, 320 sleeping, 2 stopped, 0 zombie Cpu(s): 12.6%us, 0.0%sy, 0.0%ni, 87.4%id, 0.0%wa, 0.0%hi, 0.0%si, 0.0%st Mem: 32877756k total, 14706188k used, 18171568k free, 21372k buffers Swap: 33554428k total, 1628972k used, 31925456k free, 14105940k cached PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND 10193 mpeau 20 0 302m 4336 2272 R 100.0 0.0 7033:08 emacs 16504 mpeau 20 0 110m 2008 1228 S 0.7 0.0 0:00.13 tcsh 26344 dzhu 20 0 1635m 20m 3880 S 0.3 0.1 0:44.90 ipython 1 root 20 0 21448 1108 892 S 0.0 0.0 0:01.61 init [...]
The top lines give you some summary information about the system, but you should monitor the memory usage (
TIME columns. By default,
top will will put the processes using the more CPU at the top (as shown above). You can see above that the
emacs text editor has clearly crashed, because it should not use 100% CPU for such a long time
If you type
M, the processes will be sorted my memory usage, as shown below
PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND 16092 jchang 20 0 8488m 8.1g 7912 R 99.6 25.9 1:41.38 idl 23256 pvait 20 0 232m 70m 2632 S 0.0 0.2 0:01.36 R 26344 dzhu 20 0 1635m 20m 3880 S 0.0 0.1 0:44.87 ipython 10619 astege 20 0 954m 9292 2664 S 0.0 0.0 0:40.67 gedit 1362 nslcd 20 0 442m 6056 2208 S 0.0 0.0 2:13.98 nslcd 16238 twang 20 0 128m 5068 2076 S 0.0 0.0 0:00.05 gconfd-2 10193 mpeau 20 0 302m 4336 2272 R 99.9 0.0 7024:13 emacs [...]
Other useful keys:
|c||Display the command line options of the running processes|
|u||List only the processes of a specific user|
quota -scommand to find out the exact amount)
It is possible to access directly all the disks on the LSCE servers from your local Linux or Windows desktop
ccc_home -hto find out all the available options)
ls -ato see hidden files and directories). Ask your advisor if you should copy somebody else's configuration files
cd(no arguments), and to the home directory of somebody else with
scratch01or a project specific disk)
limit column, and you cannot stay more than 7 days above the limit displayed in the
gracecolumn will display either
None(you cannot write on the disk anymore, unless you get below the
N days(you can use the disk, but you have
N daysto go below the
> quota -s Disk quotas for user jypeter (uid 6369): Filesystem blocks quota limit grace files quota limit grace prolix3:/users/ 4658M 4883M 4981M 23503 0 0
You should store your source codes, scripts, notebooks, manuscripts, reports, figures, on a backed up directory, and only store on the project disks data downloaded from outside, or that you can regenerate with the backed up scripts
Your Linux environment may sometimes stop working correctly because you have exceeded the allowed quota on your disks (check your quotas with
quota -s). You can use the following command to get the size of all the directories and files in the current directory, sorted by size:
du -sh * | sort -rh
jypeter@obelix4 - ...jypeter - 46 >cd /home/scratch01/jypeter /home/scratch01/jypeter jypeter@obelix4 - ...jypeter - 47 >du -sh * | sort -rh 58M GLAC1DHiceF26.nc 47M dashboard 44M GLAC1DdrainagePointerF26ka.nc 15M octcdf 12M 1901.nc 3.2M cmake ...
Your advisor will let you know which (version of which) programs you should use. Some programs are available by default, and you have to use the
module command to access other programs.
At any time, you can use the
which command to determine where a program is located. The option to get the version information of a program may vary (launch the program without arguments, with
> which ncdump /usr/bin/ncdump > ncdump ncdump [-c|-h] [-v ...] [[-b|-f] [c|f]] [-l len] [-n name] [-p n[,n]] [-k] [-x] [-s] [-t|-i] [-g ...] [-w] file [...] netcdf library version 22.214.171.124 of Dec 10 2015 16:44:18 $ > which python /usr/bin/python > python --version Python 2.7.5
module list: list the currently loaded modules
module avail: list the available modules
module load module_a … module_n: load modules (automatically including dependencies)
module load module_a: load default version of module_a
module load module_a/vvv: load
vvvversion of module_a
module purge: remove all modules
> which ncview ncview: Command not found. > module list No Modulefiles Currently Loaded. > module avail [...] batch_env grib_api/1.14.0 netcdf/4 python/3.6 [...] glost/0.3.1 ncview/2.1.7 python/2.7 > module load ncview netcdf/4 > module list Currently Loaded Modulefiles: 1) ncview/2.1.7 2) netcdf/4 > which ncview /usr/local/install/ncview-2.1.7/bin/ncview > which ncdump /usr/local/install/netcdf-4.3.2/bin/ncdump
You can also check the Les fondamentaux du pôle de modélisation du climat de l'IPSL wiki page
ncdump -h some_climate_data_file.nc
Send a mail to help-lsce
When you need help from the administrators or other people, it will save a lot of time if you describe your problem as accurately as possible (do not just report XXXXX is not working as expected !)
You can copy-paste the error message(s). Finding the error log file(s) of the program/system (when available), or using the verbose mode of a program will make the problem resolution much easier and faster. The example below shows how to use the verbose mode of
>ssh -v obelix OpenSSH_7.4p1, OpenSSL 1.0.2k-fips 26 Jan 2017 debug1: Reading configuration data /home/users/jypeter/.ssh/config debug1: Reading configuration data /etc/ssh/ssh_config debug1: /etc/ssh/ssh_config line 58: Applying options for * debug1: Connecting to obelix [126.96.36.199] port 22. debug1: Connection established. debug1: key_load_public: No such file or directory debug1: identity file /home/users/jypeter/.ssh/id_rsa type -1 [...] debug1: Entering interactive session. debug1: pledge: exec debug1: client_input_global_request: rtype email@example.com want_reply 0 debug1: Requesting X11 forwarding with authentication spoofing. debug1: Sending environment. debug1: Sending env LANG = en_US Last login: Thu Mar 1 15:52:44 2018 from lsce4078.lsce.ipsl.fr Disk quotas for user jypeter (uid 6369): Filesystem space quota limit grace files quota limit grace prolix3:/users 4558M 9766M 10743M 23741 0 0 jypeter@obelix3 - ...jypeter - 41 >
Sometimes, it may also help to send a picture of what is wrong!
On Windows, you can use the Capture screen option of XnView
The only way to access the LSCE servers from outside LSCE is to connect first to the ssh1.lsce.ipsl.fr gateway server.
sshto connect to ssh1
ssh -A -X firstname.lastname@example.org
ssh -A -X email@example.com -t ssh -A obelix
ssh -A -X firstname.lastname@example.org -t ssh -A email@example.com
alias sobelix 'ssh -A -X firstname.lastname@example.org -t ssh -A obelix'
alias sobelix='ssh -A -X email@example.com -t ssh -A obelix'
If you need to transfer files to/from LSCE, use
scp (on Linux and Windows 10), or a graphical scp client such as WinSCP (on Windows) between your computer and
scp -p file_on_your_computer_outside_lsce firstname.lastname@example.org:/home/scratch01/your_lsce_login/
scp -pr directory_on_your_computer_outside_lsce email@example.com:/home/scratch01/your_lsce_login/