Commit 58456136 authored by Lukáš Krupčík's avatar Lukáš Krupčík
Browse files

fix anselm

parent 91301f04
# Environment and Modules
## Environment Customization
After logging in, you may want to configure the environment. Write your preferred path definitions, aliases, functions and module loads in the .bashrc file;
```console
$ cat ./bashrc
# ./bashrc
# Source global definitions
if [ -f /etc/bashrc ]; then
. /etc/bashrc
fi
# User specific aliases and functions
alias qs='qstat -a'
module load PrgEnv-gnu
# Display information to standard output - only in interactive ssh session
if [ -n "$SSH_TTY" ]
then
module list # Display loaded modules
fi
```
!!! note
Do not run commands outputting to standard output (echo, module list, etc) in .bashrc for non-interactive SSH sessions. It breaks the fundamental functionality (scp, PBS) of your account! Consider utilization of SSH session interactivity for such commands as stated in the previous example.
## Application Modules
In order to configure your shell for running a particular application on Anselm we use Module package interface.
!!! note
The modules set up the application paths, library paths, and environment variables for running a particular application.
We can also have a second modules repository. This modules repository is created using a tool called EasyBuild. On the Salomon cluster, all modules are built with this tool. If you want to use software from this modules repository, please follow the instructions in the section [Application Modules Path Expansion](environment-and-modules/#application-modules-path-expansion).
The modules may be loaded, unloaded, and switched as required.
To check available modules use;
```console
$ module avail **or** ml av
```
To load a module, for example the octave module use;
```console
$ module load octave **or** ml octave
```
loading the octave module will set up paths and the environment variables of your active shell such that you are ready to run the octave software.
To check loaded modules use;
```console
$ module list **or** ml
```
To unload a module, for example the octave module use;
```console
$ module unload octave **or** ml -octave
```
Learn more about modules by reading the module man page;
```console
$ man module
```
The following modules set up the development environment;
PrgEnv-gnu sets up the GNU development environment in conjunction with the bullx MPI library.
PrgEnv-intel sets up the INTEL development environment in conjunction with the Intel MPI library.
## Application Modules Path Expansion
All application modules on the Salomon cluster (and further) are built using a tool called [EasyBuild](http://hpcugent.github.io/easybuild/ "EasyBuild"). In the case that you want to use applications that have already been built by EasyBuild, you have to modify your MODULEPATH environment variable.
```console
export MODULEPATH=$MODULEPATH:/apps/easybuild/modules/all/
```
This command expands your searched paths to modules. You can also add this command to the .bashrc file to expand paths permanently. After this command, you can use the same commands to list/add/remove modules as described above.
# PRACE User Support
## Intro
PRACE users coming to Anselm as to TIER-1 system offered through the DECI calls are in general treated as standard users and so most of the general documentation applies to them as well. This section shows the main differences for quicker orientation, but often uses references to the original documentation. PRACE users who don't undergo the full procedure (including signing the IT4I AuP on top of the PRACE AuP) will not have a password and thus access to some services intended for regular users. This is inconvenient, but otherwise they should be able to use the TIER-1 system as intended. Please see the [Obtaining Login Credentials section](../general/obtaining-login-credentials/obtaining-login-credentials/), if the same level of access is required.
All general [PRACE User Documentation](http://www.prace-ri.eu/user-documentation/) should be read before continuing to read the local documentation here.
## Help and Support
If you have any troubles, need information, require support or want to install additional software, please use the [PRACE Helpdesk](http://www.prace-ri.eu/helpdesk-guide264/).
Information about the local services is provided in the [introduction of the general user documentation](introduction/). Please keep in mind, that standard PRACE accounts don't have a password to access the web interface of the local (IT4Innovations) request tracker and thus a new ticket should be created by sending an e-mail to support[at]it4i.cz.
## Obtaining Login Credentials
In general PRACE users already have a PRACE account setup through their HOMESITE (institution from their country) as a result of rewarded PRACE project proposal. This includes signed PRACE AuP, generated and registered certificates, etc.
If there's a special need a PRACE user can get a standard (local) account at IT4Innovations. To get an account on the Anselm cluster, the user needs to obtain the login credentials. The procedure is the same as for general users of the cluster, so please see the corresponding section of the general documentation here.
## Accessing the Cluster
### Access With GSI-SSH
For all PRACE users, the method for interactive access (login) and data transfer based on grid services from the Globus Toolkit (GSI SSH and GridFTP) is supported.
The user will need a valid certificate and to be present in the PRACE LDAP (please contact your HOME SITE or the primary investigator of your project for LDAP account creation).
Most of the information needed by PRACE users accessing the Anselm TIER-1 system can be found here:
* [General user's FAQ](http://www.prace-ri.eu/Users-General-FAQs)
* [Certificates FAQ](http://www.prace-ri.eu/Certificates-FAQ)
* [Interactive access using GSISSH](http://www.prace-ri.eu/Interactive-Access-Using-gsissh)
* [Data transfer with GridFTP](http://www.prace-ri.eu/Data-Transfer-with-GridFTP-Details)
* [Data transfer with gtransfer](http://www.prace-ri.eu/Data-Transfer-with-gtransfer)
Before you start to use any of the services don't forget to create a proxy certificate from your certificate:
```console
$ grid-proxy-init
```
To check whether your proxy certificate is still valid (by default it's valid for 12 hours), use:
```console
$ grid-proxy-info
```
To access the Anselm cluster, two login nodes running GSI SSH service are available. The service is available publicly on the Internet as well as on the internal PRACE network (only accessible to other PRACE partners).
#### Access From the PRACE Network:
It is recommended to use the single DNS name anselm-prace.it4i.cz which is distributed between the two login nodes. If needed, the user can login directly to one of the login nodes. The addresses are:
| Login address | Port | Protocol | Login node |
| --------------------------- | ---- | -------- | ---------------- |
| anselm-prace.it4i.cz | 2222 | gsissh | login1 or login2 |
| login1-prace.anselm.it4i.cz | 2222 | gsissh | login1 |
| login2-prace.anselm.it4i.cz | 2222 | gsissh | login2 |
```console
$ gsissh -p 2222 anselm-prace.it4i.cz
```
When logging in from another PRACE system, the prace_service script can be used:
```console
$ gsissh `prace_service -i -s anselm`
```
#### Public Access From the Internet:
It is recommended to use the single DNS name anselm.it4i.cz which is distributed between the two login nodes. If needed, the user can login directly to one of the login nodes. The addresses are:
| Login address | Port | Protocol | Login node |
| --------------------- | ---- | -------- | ---------------- |
| anselm.it4i.cz | 2222 | gsissh | login1 or login2 |
| login1.anselm.it4i.cz | 2222 | gsissh | login1 |
| login2.anselm.it4i.cz | 2222 | gsissh | login2 |
```console
$ gsissh -p 2222 anselm.it4i.cz
```
When logging in from another PRACE system, the prace_service script can be used:
```console
$ gsissh `prace_service -e -s anselm`
```
Although the preferred and recommended file transfer mechanism is [using GridFTP](prace/#file-transfers), the GSI SSH implementation on Anselm also supports SCP, so for small files transfer gsiscp can be used:
```console
$ gsiscp -P 2222 _LOCAL_PATH_TO_YOUR_FILE_ anselm.it4i.cz:_ANSELM_PATH_TO_YOUR_FILE_
$ gsiscp -P 2222 anselm.it4i.cz:_ANSELM_PATH_TO_YOUR_FILE_ _LOCAL_PATH_TO_YOUR_FILE_
$ gsiscp -P 2222 _LOCAL_PATH_TO_YOUR_FILE_ anselm-prace.it4i.cz:_ANSELM_PATH_TO_YOUR_FILE_
$ gsiscp -P 2222 anselm-prace.it4i.cz:_ANSELM_PATH_TO_YOUR_FILE_ _LOCAL_PATH_TO_YOUR_FILE_
```
### Access to X11 Applications (VNC)
If the user needs to run an X11 based graphical application and does not have an X11 server, the applications can be run using a VNC service. If the user is using regular SSH based access, please see the relevant section in general documentation.
If the user uses GSI SSH based access, then the procedure is similar to the SSH based access, only the port forwarding must be done using GSI SSH:
```console
$ gsissh -p 2222 anselm.it4i.cz -L 5961:localhost:5961
```
### Access With SSH
After successful obtainment of login credentials for the local IT4Innovations account, PRACE users can access the cluster as regular users using SSH. For more information please see the section in general documentation.
## File Transfers
PRACE users can use the same transfer mechanisms as regular users (if they've undergone the full registration procedure). For information about this, please see the relevant section in the general documentation.
Apart from the standard mechanisms, for PRACE users to transfer data to/from the Anselm cluster, a GridFTP server running the Globus Toolkit GridFTP service is available. The service is available publicly over the Internet as well as from the internal PRACE network (accessible only to other PRACE partners).
There is one control server and three backend servers for striping and/or backup in case any of them were to fail.
### Access From the PRACE Network
| Login address | Port | Node role |
| ---------------------------- | ---- | --------------------------- |
| gridftp-prace.anselm.it4i.cz | 2812 | Front end /control server |
| login1-prace.anselm.it4i.cz | 2813 | Backend / data mover server |
| login2-prace.anselm.it4i.cz | 2813 | Backend / data mover server |
| dm1-prace.anselm.it4i.cz | 2813 | Backend / data mover server |
Copy files **to** Anselm by running the following commands on your local machine:
```console
$ globus-url-copy file://_LOCAL_PATH_TO_YOUR_FILE_ gsiftp://gridftp-prace.anselm.it4i.cz:2812/home/prace/_YOUR_ACCOUNT_ON_ANSELM_/_PATH_TO_YOUR_FILE_
```
Or by using the prace_service script:
```console
$ globus-url-copy file://_LOCAL_PATH_TO_YOUR_FILE_ gsiftp://`prace_service -i -f anselm`/home/prace/_YOUR_ACCOUNT_ON_ANSELM_/_PATH_TO_YOUR_FILE_
```
Copy files **from** Anselm with:
```console
$ globus-url-copy gsiftp://gridftp-prace.anselm.it4i.cz:2812/home/prace/_YOUR_ACCOUNT_ON_ANSELM_/_PATH_TO_YOUR_FILE_ file://_LOCAL_PATH_TO_YOUR_FILE_
```
Or by using the prace_service script:
```console
$ globus-url-copy gsiftp://`prace_service -i -f anselm`/home/prace/_YOUR_ACCOUNT_ON_ANSELM_/_PATH_TO_YOUR_FILE_ file://_LOCAL_PATH_TO_YOUR_FILE_
```
### Public Access From the Internet
| Login address | Port | Node role |
| ---------------------- | ---- | --------------------------- |
| gridftp.anselm.it4i.cz | 2812 | Front end /control server |
| login1.anselm.it4i.cz | 2813 | Backend / data mover server |
| login2.anselm.it4i.cz | 2813 | Backend / data mover server |
| dm1.anselm.it4i.cz | 2813 | Backend / data mover server |
Copy files **to** Anselm by running the following commands on your local machine:
```console
$ globus-url-copy file://_LOCAL_PATH_TO_YOUR_FILE_ gsiftp://gridftp.anselm.it4i.cz:2812/home/prace/_YOUR_ACCOUNT_ON_ANSELM_/_PATH_TO_YOUR_FILE_
```
Or by using the prace_service script:
```console
$ globus-url-copy file://_LOCAL_PATH_TO_YOUR_FILE_ gsiftp://`prace_service -e -f anselm`/home/prace/_YOUR_ACCOUNT_ON_ANSELM_/_PATH_TO_YOUR_FILE_
```
Copy files **from** Anselm with:
```console
$ globus-url-copy gsiftp://gridftp.anselm.it4i.cz:2812/home/prace/_YOUR_ACCOUNT_ON_ANSELM_/_PATH_TO_YOUR_FILE_ file://_LOCAL_PATH_TO_YOUR_FILE_
```
Or by using the prace_service script:
```console
$ globus-url-copy gsiftp://`prace_service -e -f anselm`/home/prace/_YOUR_ACCOUNT_ON_ANSELM_/_PATH_TO_YOUR_FILE_ file://_LOCAL_PATH_TO_YOUR_FILE_
```
Generally both shared file systems are available through GridFTP:
| File system mount point | Filesystem | Comment |
| ----------------------- | ---------- | -------------------------------------------------------------- |
| /home | Lustre | Default HOME directories of users in format /home/prace/login/ |
| /scratch | Lustre | Shared SCRATCH mounted on the whole cluster |
More information about the shared file systems is available [here](storage/).
## Usage of the Cluster
There are some limitations for PRACE users when using the cluster. By default PRACE users aren't allowed to access special queues in the PBS Pro to have high priority or exclusive access to some special equipment like accelerated nodes and high memory (fat) nodes. There may also be restrictions when obtaining a working license for the commercial software installed on the cluster, mostly because of the license agreement or because of insufficient amounts of licenses.
For production runs always use the scratch file systems, either the global shared or the local ones. The available file systems are described [here](hardware-overview/).
### Software, Modules, and the PRACE Common Production Environment
All system wide installed software on the cluster is made available to users via the modules. The information about environment and module usage is in this [section of general documentation](environment-and-modules/).
PRACE users, via the "prace" module, can use the [PRACE Common Production Environment](http://www.prace-ri.eu/prace-common-production-environment/);
```console
$ module load prace
```
### Resource Allocation and Job Execution
General information about the resource allocation, job queuing and job execution is in this [section of general documentation](resources-allocation-policy/).
For PRACE users, the default production run queue is "qprace". PRACE users can also use two other queues "qexp" and "qfree".
| queue | Active project | Project resources | Nodes | priority | authorization | walltime |
| ----------------------------- | -------------- | ----------------- | ------------------- | -------- | ------------- | --------- |
| **qexp** Express queue | no | none required | 2 reserved, 8 total | high | no | 1 / 1h |
| **qprace** Production queue | yes | > 0 | 178 w/o accelerator | medium | no | 24 / 48 h |
| **qfree** Free resource queue | yes | none required | 178 w/o accelerator | very low | no | 12 / 12 h |
**qprace**, the PRACE queue: This queue is intended for normal production runs. It is required that an active project with nonzero remaining resources is specified to enter the qprace. The queue runs with medium priority and no special authorization is required to use it. The maximum runtime in qprace is 12 hours. If the job needs a longer time, it must use checkpoint/restart functionality.
### Accounting & Quota
The resources that are currently subject to accounting are the core hours. The core hours are accounted on the basis of wall clock time. The accounting runs whenever the computational cores are allocated or blocked via the PBS Pro workload manager (the qsub command), regardless of whether the cores are actually used for any calculation. See the [example in the general documentation](resources-allocation-policy/).
PRACE users should check their project accounting using the [PRACE Accounting Tool (DART)](http://www.prace-ri.eu/accounting-report-tool/).
Users who have undergone the full local registration procedure (including signing the IT4Innovations Acceptable Use Policy) and who have received a local password may check at any time, how many core-hours have been consumed by themselves and their projects using the command "it4ifree".
!!! note
You need to know your user password to use the command. Displayed core hours are "system core hours" which differ from PRACE "standardized core hours".
!!! hint
The **it4ifree** command is a part of it4i.portal.clients package, [located here](https://pypi.python.org/pypi/it4i.portal.clients).
```console
$ it4ifree
Password:
PID Total Used ...by me Free
-------- ------- ------ -------- -------
OPEN-0-0 1500000 400644 225265 1099356
DD-13-1 10000 2606 2606 7394
```
By default a file system quota is applied. To check the current status of the quota use;
```console
$ lfs quota -u USER_LOGIN /home
$ lfs quota -u USER_LOGIN /scratch
```
If the quota is insufficient, please contact the [support](prace/#help-and-support) and request an increase.
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