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To use the SSM environment on Compute Canada clusters of the Alliance you will first (and only once) have to do the following little "setup". There is nothing to be done on our UQAM servers.
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| You need to follow all of the instructions below! You cannot skip any parts! I strongly suggest to use copy->paste!!! There are dots and spaces that are easy to miss when typing the commands by hand. |
First a little "warning":
By default, the "prompt" (beginning of a command line) on clusters of the Alliance looks like this:
node n%
You first have the name of the login node, followed by the number of you command (which increases by 1 with each command you type), followed by the sign(!) '%'.
For example on narval1 (one of the login nodes on Narval) you might get:
narval1 1%
The '%' here is not a 'percent of setup done' but just a sign to mark the end of the prompt!
1) Rename old bash-profiles
If one or both of the following two files exist remove them or change their name, for example to:
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| mv ~/.bash_profile ~/.bash_profile- mv ~/.bashrc ~/.bashrc- |
On Beluga, to use the old Beluga environment, create the file ~/.modulerc:
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2) Create or link ~/.profile
Then create the file ~/.profile:
On Beluga :
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| cat > ~/.profile <<+ umask 022 type module 2>/dev/null 1>/dev/null || . /etc/profile taskset -cp 0-128 \$\$ module swap intel/2018.3 gcc/7.3.0 2>/dev/null . /home/armnssm/ssm-domains-base/ssm_10.151/etc/ssm.d/profile . env-setup.dot module list 2>&1 | grep '[()]' + |
On Narval :
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First you need to define a space which will get used as the default temporary disk space, ${TMPDIR}: 1) Create a directory which you would like to make your default temporary directory. I suggest you use the default directory of your PI, for example: 2) Create a directory in your home called 'tmp':
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On Rorqual:
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| cd ln -s /home/armnssm/envi/Profile/bin/.profile |
Log out and back in.
3) Link to .group_profile
Then I suggest you create a link to our common '.group_profile'.
This will give you some basic aliases I find quite useful. Have I suggest you have a look at them if you liketo see which ones are available.
I will keep adding aliases and exports to this file.
On Beluga and Narval:
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| ln -s ~winger/.published_profile.d/.group_profile ~/.profile.d/.group_profile |
On Rorqual:
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| ln -s /home/armnssm/envi/Profile/bin/.group_profile ~/.profile.d/.group_profile |
4) Your own personal aliases, exports, etc.
Your own personal aliases, exports, s.ssmuse.dot etc. for interactive use will go into the file
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| ~/.profile.d/.interactive_profile |
which you will have to create.
Then you either log out and back in again or source the new .profiles.
5) Set the core allocation you want your job to run under when submitting it with 'soumet'
When submitting any job on Compute Canada clusters you always need to specify which allocation account should get "billed" for the resources (cores) your job is running on.
Every PI (Principle Investigator - in general your professor) has a certain amount of cores assigned to her/his group which can get used on average(!) throughout the year. They are called "core years". Every PI has a default allocation (def-...) of 50 core years and some PIs also have a research project allocation (rrg-...) or even a contributed allocation (ctb-...), which vary in size from one PI to the next, from one cluster to the next and from one year to the next. To get an rrg-allocation the PI has to fill out an application once a year, describing the projects for which CC resources will get used. To get a ctb-allocation the PI has to buy the hardware.
You can find all the allocation names under which you can run either under your directory:
~/projects
or, depending on the cluster, under:
~/links/projects
Pick the one you want to run your simulations under and write its name into a file (which you have to create) called:
~/.Account
This file has to contain only the account name under which you want to run, nothing else. You can find the accounts names of the different professors in the table below. In general I suggest you put the def-account of your professors as the default account in this file and target the RRG or CTB accounts for certain simulations directly.
| Sponsor | default account | RRG account | CTB account |
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| René Laprise | def-laprise | ||
| Francesco Pausata | def-pausata | rrg-pausata | ctb-pausata (Narval) |
| Julie Thériault | def-jtheriau | rrg-jtheriau | ctb-jtheriau (Narval) |
| Alejandro Di Luca | def-adl561 | rrg-adl561 | |
| Philippe Lucas-Picher | def-picher | rrg-picher | |
| Philippe Gachon | def-gachon | rrg-gachon | |
| Anne de Vernal | def-dev1 | rrg-dev1 |
For example:
$ cat ~/.Account
def-laprise