Commit c76730b4 authored by Josef Hrabal's avatar Josef Hrabal
Browse files

Merge branch 'cisteni' into 'master'

Cisteni

Closes #40

See merge request !209
parents ba3ca988 ff2a5b30
......@@ -12,11 +12,6 @@ This is project contain IT4Innovations user documentation source.
* [http://facelessuser.github.io/pymdown-extensions/](http://facelessuser.github.io/pymdown-extensions/)
* [http://squidfunk.github.io/mkdocs-material/](http://squidfunk.github.io/mkdocs-material/)
## Rules
* [spellcheck https://github.com/lukeapage/node-markdown-spellcheck](spellcheck https://github.com/lukeapage/node-markdown-spellcheck)
* [SI units http://physics.nist.gov/cuu/Units/checklist.html](SI units http://physics.nist.gov/cuu/Units/checklist.html)
```
fair-share
InfiniBand
......
......@@ -83,7 +83,7 @@ $ qsub -N JOBNAME -J 1-900 jobscript
12345[].dm2
```
In this example, we submit a job array of 900 subjobs. Each subjob will run on one full node and is assumed to take less than 2 hours (please note the #PBS directives in the beginning of the jobscript file, don't forget to set your valid PROJECT_ID and desired queue).
In this example, we submit a job array of 900 subjobs. Each subjob will run on one full node and is assumed to take less than 2 hours (note the #PBS directives in the beginning of the jobscript file, don't forget to set your valid PROJECT_ID and desired queue).
Sometimes for testing purposes, you may need to submit a one-element only array. This is not allowed by PBSPro, but there's a workaround:
......
......@@ -55,7 +55,7 @@ Anselm is cluster of x86-64 Intel based nodes built with Bull Extreme Computing
| Node type | Count | Range | Memory | Cores | [Access](resources-allocation-policy/) |
| ---------------------------- | ----- | ----------- | ------ | ----------- | -------------------------------------- |
| Nodes without an accelerator | 180 | cn[1-180] | 64GB | 16 @ 2.4GHz | qexp, qprod, qlong, qfree, qprace, qatlas |
| Nodes with a GPU accelerator | 23 | cn[181-203] | 96GB | 16 @ 2.3GHz | qgpu, qexp |
| Nodes with a GPU accelerator | 23 | cn[181-203] | 96GB | 16 @ 2.3GHz | qnvidia, qexp |
| Nodes with a MIC accelerator | 4 | cn[204-207] | 96GB | 16 @ 2.3GHz | qmic, qexp |
| Fat compute nodes | 2 | cn[208-209] | 512GB | 16 @ 2.4GHz | qfat, qexp |
......
......@@ -57,4 +57,4 @@ The parameters are summarized in the following tables:
| MIC accelerated | 2 x Intel Sandy Bridge E5-2470, 2.3 GHz | 96 GB | Intel Xeon Phi 5110P |
| Fat compute node | 2 x Intel Sandy Bridge E5-2665, 2.4 GHz | 512 GB | - |
For more details please refer to [Compute nodes](compute-nodes/), [Storage](storage/), and [Network](network/).
For more details refer to [Compute nodes](compute-nodes/), [Storage](storage/), and [Network](network/).
......@@ -2,7 +2,7 @@
## Job Submission
When allocating computational resources for the job, please specify
When allocating computational resources for the job, specify:
1. a suitable queue for your job (the default is qprod)
1. the number of computational nodes required
......
......@@ -25,14 +25,14 @@ In case of debugging on accelerators:
Load all necessary modules to compile the code. For example:
```bash
$ module load intel
$ module load impi ... or ... module load openmpi/X.X.X-icc
$ ml intel
$ ml impi ... or ... ml openmpi/X.X.X-icc
```
Load the Allinea DDT module:
```bash
$ module load Forge
$ ml Forge
```
Compile the code:
......
......@@ -13,7 +13,7 @@ Our license is limited to 64 MPI processes.
Allinea Performance Reports version 6.0 is available
```bash
$ module load PerformanceReports/6.0
$ ml PerformanceReports/6.0
```
The module sets up environment variables, required for using the Allinea Performance Reports. This particular command loads the default module, which is performance reports version 4.2.
......@@ -46,7 +46,7 @@ First, we allocate some nodes via the express queue:
Then we load the modules and run the program the usual way:
```bash
$ module load intel impi allinea-perf-report/4.2
$ ml intel impi allinea-perf-report/4.2
$ mpirun ./mympiprog.x
```
......
......@@ -3,7 +3,7 @@
The Intel compilers version 13.1.1 are available, via module Intel. The compilers include the ICC C and C++ compiler and the IFORT Fortran 77/90/95 compiler.
```bash
$ module load intel
$ ml intel
$ icc -v
$ ifort -v
```
......
......@@ -5,7 +5,7 @@
The intel debugger version 13.0 is available, via module intel. The debugger works for applications compiled with C and C++ compiler and the ifort fortran 77/90/95 compiler. The debugger provides java GUI environment. Use X display for running the GUI.
```bash
$ module load intel
$ ml intel
$ idb
```
......@@ -24,8 +24,8 @@ Example:
qsub: waiting for job 19654.srv11 to start
qsub: job 19654.srv11 ready
$ module load intel
$ module load java
$ ml intel
$ ml java
$ icc -O0 -g myprog.c -o myprog.x
$ idb ./myprog.x
```
......@@ -45,7 +45,7 @@ For debugging small number of MPI ranks, you may execute and debug each rank in
qsub: waiting for job 19654.srv11 to start
qsub: job 19655.srv11 ready
$ module load intel impi
$ ml intel impi
$ mpirun -ppn 1 -hostfile $PBS_NODEFILE --enable-x xterm -e idbc ./mympiprog.x
```
......@@ -60,7 +60,7 @@ Run the idb debugger from within the MPI debug option. This will cause the debug
qsub: waiting for job 19654.srv11 to start
qsub: job 19655.srv11 ready
$ module load intel impi
$ ml intel impi
$ mpirun -n 32 -idb ./mympiprog.x
```
......
......@@ -14,10 +14,10 @@ The Anselm cluster provides several implementations of the MPI library:
MPI libraries are activated via the environment modules.
Look up section modulefiles/mpi in module avail
Look up section modulefiles/mpi in ml av
```bash
$ module avail
$ ml av
------------------------- /opt/modules/modulefiles/mpi -------------------------
bullxmpi/bullxmpi-1.2.4.1 mvapich2/1.9-icc
impi/4.0.3.008 openmpi/1.6.5-gcc(default)
......@@ -44,7 +44,7 @@ There are default compilers associated with any particular MPI implementation. T
Examples:
```bash
$ module load openmpi
$ ml openmpi
```
In this example, we activate the latest openmpi with latest GNU compilers
......@@ -52,8 +52,8 @@ In this example, we activate the latest openmpi with latest GNU compilers
To use openmpi with the intel compiler suite, use
```bash
$ module load intel
$ module load openmpi/1.6.5-icc
$ ml intel
$ ml openmpi/1.6.5-icc
```
In this example, the openmpi 1.6.5 using intel compilers is activated
......
......@@ -10,31 +10,31 @@ Matlab is available in versions R2015a and R2015b. There are always two variants
To load the latest version of Matlab load the module
```bash
$ module load MATLAB
$ ml MATLAB
```
By default the EDU variant is marked as default. If you need other version or variant, load the particular version. To obtain the list of available versions use
```bash
$ module avail MATLAB
$ ml av MATLAB
```
If you need to use the Matlab GUI to prepare your Matlab programs, you can use Matlab directly on the login nodes. But for all computations use Matlab on the compute nodes via PBS Pro scheduler.
If you require the Matlab GUI, please follow the general information about [running graphical applications](../../../general/accessing-the-clusters/graphical-user-interface/x-window-system/).
If you require the Matlab GUI, follow the general information about [running graphical applications](../../../general/accessing-the-clusters/graphical-user-interface/x-window-system/).
Matlab GUI is quite slow using the X forwarding built in the PBS (qsub -X), so using X11 display redirection either via SSH or directly by xauth (please see the "GUI Applications on Compute Nodes over VNC" part [here](../../../general/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-system/)) is recommended.
Matlab GUI is quite slow using the X forwarding built in the PBS (qsub -X), so using X11 display redirection either via SSH or directly by xauth (see the "GUI Applications on Compute Nodes over VNC" part [here](../../../general/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-system/)) is recommended.
To run Matlab with GUI, use
```bash
$ matlab
$ matlab
```
To run Matlab in text mode, without the Matlab Desktop GUI environment, use
```bash
$ matlab -nodesktop -nosplash
$ matlab -nodesktop -nosplash
```
plots, images, etc... will be still available.
......@@ -72,8 +72,8 @@ With the new mode, MATLAB itself launches the workers via PBS, so you can either
Following example shows how to start interactive session with support for Matlab GUI. For more information about GUI based applications on Anselm see [this page](../../../general/accessing-the-clusters/graphical-user-interface/x-window-system/x-window-system/).
```bash
$ xhost +
$ qsub -I -v DISPLAY=$(uname -n):$(echo $DISPLAY | cut -d ':' -f 2) -A NONE-0-0 -q qexp -l select=1 -l walltime=00:30:00
$ xhost +
$ qsub -I -v DISPLAY=$(uname -n):$(echo $DISPLAY | cut -d ':' -f 2) -A NONE-0-0 -q qexp -l select=1 -l walltime=00:30:00
-l feature__matlab__MATLAB=1
```
......@@ -84,8 +84,8 @@ The second part of the command shows how to request all necessary licenses. In t
Once the access to compute nodes is granted by PBS, user can load following modules and start Matlab:
```bash
r1i0n17$ module load MATLAB/2015b-EDU
r1i0n17$ matlab &
r1i0n17$ ml MATLAB/2015b-EDU
r1i0n17$ matlab &
```
### Parallel Matlab Batch Job in Local Mode
......@@ -93,26 +93,26 @@ Once the access to compute nodes is granted by PBS, user can load following modu
To run matlab in batch mode, write an matlab script, then write a bash jobscript and execute via the qsub command. By default, matlab will execute one matlab worker instance per allocated core.
```bash
#!/bin/bash
#PBS -A PROJECT ID
#PBS -q qprod
#PBS -l select=1:ncpus=16:mpiprocs=16:ompthreads=1
#!/bin/bash
#PBS -A PROJECT ID
#PBS -q qprod
#PBS -l select=1:ncpus=16:mpiprocs=16:ompthreads=1
# change to shared scratch directory
SCR=/scratch/work/user/$USER/$PBS_JOBID
mkdir -p $SCR ; cd $SCR || exit
# change to shared scratch directory
SCR=/scratch/work/user/$USER/$PBS_JOBID
mkdir -p $SCR ; cd $SCR || exit
# copy input file to scratch
cp $PBS_O_WORKDIR/matlabcode.m .
# copy input file to scratch
cp $PBS_O_WORKDIR/matlabcode.m .
# load modules
module load MATLAB/2015a-EDU
# load modules
ml MATLAB/2015a-EDU
# execute the calculation
matlab -nodisplay -r matlabcode > output.out
# execute the calculation
matlab -nodisplay -r matlabcode > output.out
# copy output file to home
cp output.out $PBS_O_WORKDIR/.
# copy output file to home
cp output.out $PBS_O_WORKDIR/.
```
This script may be submitted directly to the PBS workload manager via the qsub command. The inputs and matlab script are in matlabcode.m file, outputs in output.out file. Note the missing .m extension in the matlab -r matlabcodefile call, **the .m must not be included**. Note that the **shared /scratch must be used**. Further, it is **important to include quit** statement at the end of the matlabcode.m script.
......@@ -120,7 +120,7 @@ This script may be submitted directly to the PBS workload manager via the qsub c
Submit the jobscript using qsub
```bash
$ qsub ./jobscript
$ qsub ./jobscript
```
### Parallel Matlab Local Mode Program Example
......@@ -128,7 +128,7 @@ Submit the jobscript using qsub
The last part of the configuration is done directly in the user Matlab script before Distributed Computing Toolbox is started.
```bash
cluster = parcluster('local')
cluster = parcluster('local')
```
This script creates scheduler object "cluster" of type "local" that starts workers locally.
......@@ -151,28 +151,28 @@ The last step is to start matlabpool with "cluster" object and correct number of
The complete example showing how to use Distributed Computing Toolbox in local mode is shown here.
```bash
cluster = parcluster('local');
cluster
cluster = parcluster('local');
cluster
parpool(cluster,24);
parpool(cluster,24);
n=2000;
n=2000;
W = rand(n,n);
W = distributed(W);
x = (1:n)';
x = distributed(x);
spmd
[~, name] = system('hostname')
W = rand(n,n);
W = distributed(W);
x = (1:n)';
x = distributed(x);
spmd
[~, name] = system('hostname')
T = W*x; % Calculation performed on labs, in parallel.
% T and W are both codistributed arrays here.
end
T;
whos % T and W are both distributed arrays here.
T = W*x; % Calculation performed on labs, in parallel.
% T and W are both codistributed arrays here.
end
T;
whos % T and W are both distributed arrays here.
parpool close
quit
parpool close
quit
```
You can copy and paste the example in a .m file and execute. Note that the parpool size should correspond to **total number of cores** available on allocated nodes.
......@@ -184,29 +184,29 @@ This mode uses PBS scheduler to launch the parallel pool. It uses the SalomonPBS
This is an example of m-script using PBS mode:
```bash
cluster = parcluster('SalomonPBSPro');
set(cluster, 'SubmitArguments', '-A OPEN-0-0');
set(cluster, 'ResourceTemplate', '-q qprod -l select=10:ncpus=16');
set(cluster, 'NumWorkers', 160);
cluster = parcluster('SalomonPBSPro');
set(cluster, 'SubmitArguments', '-A OPEN-0-0');
set(cluster, 'ResourceTemplate', '-q qprod -l select=10:ncpus=16');
set(cluster, 'NumWorkers', 160);
pool = parpool(cluster, 160);
pool = parpool(cluster, 160);
n=2000;
n=2000;
W = rand(n,n);
W = distributed(W);
x = (1:n)';
x = distributed(x);
spmd
[~, name] = system('hostname')
W = rand(n,n);
W = distributed(W);
x = (1:n)';
x = distributed(x);
spmd
[~, name] = system('hostname')
T = W*x; % Calculation performed on labs, in parallel.
% T and W are both codistributed arrays here.
end
whos % T and W are both distributed arrays here.
T = W*x; % Calculation performed on labs, in parallel.
% T and W are both codistributed arrays here.
end
whos % T and W are both distributed arrays here.
% shut down parallel pool
delete(pool)
% shut down parallel pool
delete(pool)
```
Note that we first construct a cluster object using the imported profile, then set some important options, namely: SubmitArguments, where you need to specify accounting id, and ResourceTemplate, where you need to specify number of nodes to run the job.
......@@ -225,39 +225,39 @@ For this method, you need to use SalomonDirect profile, import it using [the sam
This is an example of m-script using direct mode:
```bash
parallel.importProfile('/apps/all/MATLAB/2015a-EDU/SalomonDirect.settings')
cluster = parcluster('SalomonDirect');
set(cluster, 'NumWorkers', 48);
parallel.importProfile('/apps/all/MATLAB/2015a-EDU/SalomonDirect.settings')
cluster = parcluster('SalomonDirect');
set(cluster, 'NumWorkers', 48);
pool = parpool(cluster, 48);
pool = parpool(cluster, 48);
n=2000;
n=2000;
W = rand(n,n);
W = distributed(W);
x = (1:n)';
x = distributed(x);
spmd
[~, name] = system('hostname')
W = rand(n,n);
W = distributed(W);
x = (1:n)';
x = distributed(x);
spmd
[~, name] = system('hostname')
T = W*x; % Calculation performed on labs, in parallel.
% T and W are both codistributed arrays here.
end
whos % T and W are both distributed arrays here.
T = W*x; % Calculation performed on labs, in parallel.
% T and W are both codistributed arrays here.
end
whos % T and W are both distributed arrays here.
% shut down parallel pool
delete(pool)
% shut down parallel pool
delete(pool)
```
### Non-Interactive Session and Licenses
If you want to run batch jobs with Matlab, be sure to request appropriate license features with the PBS Pro scheduler, at least the `-l _feature_matlab_MATLAB=1` for EDU variant of Matlab. More information about how to check the license features states and how to request them with PBS Pro, please [look here](../isv_licenses/).
If you want to run batch jobs with Matlab, be sure to request appropriate license features with the PBS Pro scheduler, at least the `-l _feature_matlab_MATLAB=1` for EDU variant of Matlab. More information about how to check the license features states and how to request them with PBS Pro [look here](../isv_licenses/).
In case of non-interactive session please read the [following information](../isv_licenses/) on how to modify the qsub command to test for available licenses prior getting the resource allocation.
In case of non-interactive session read the [following information](../isv_licenses/) on how to modify the qsub command to test for available licenses prior getting the resource allocation.
### Matlab Distributed Computing Engines Start Up Time
Starting Matlab workers is an expensive process that requires certain amount of time. For your information please see the following table:
Starting Matlab workers is an expensive process that requires certain amount of time. For your information see the following table:
| compute nodes | number of workers | start-up time[s] |
| ------------- | ----------------- | ---------------- |
......
......@@ -98,7 +98,7 @@ The architecture of Lustre on Anselm is composed of two metadata servers (MDS) a
### HOME File System
The HOME filesystem is mounted in directory /home. Users home directories /home/username reside on this filesystem. Accessible capacity is 320TB, shared among all users. Individual users are restricted by filesystem usage quotas, set to 250GB per user. If 250GB should prove as insufficient for particular user, please contact [support](https://support.it4i.cz/rt), the quota may be lifted upon request.
The HOME filesystem is mounted in directory /home. Users home directories /home/username reside on this filesystem. Accessible capacity is 320TB, shared among all users. Individual users are restricted by filesystem usage quotas, set to 250GB per user. If 250GB should prove as insufficient for particular user, contact [support](https://support.it4i.cz/rt), the quota may be lifted upon request.
!!! note
The HOME filesystem is intended for preparation, evaluation, processing and storage of data generated by active Projects.
......@@ -127,7 +127,7 @@ Default stripe size is 1MB, stripe count is 1. There are 22 OSTs dedicated for t
### SCRATCH File System
The SCRATCH filesystem is mounted in directory /scratch. Users may freely create subdirectories and files on the filesystem. Accessible capacity is 146TB, shared among all users. Individual users are restricted by filesystem usage quotas, set to 100TB per user. The purpose of this quota is to prevent runaway programs from filling the entire filesystem and deny service to other users. If 100TB should prove as insufficient for particular user, please contact [support](https://support.it4i.cz/rt), the quota may be lifted upon request.
The SCRATCH filesystem is mounted in directory /scratch. Users may freely create subdirectories and files on the filesystem. Accessible capacity is 146TB, shared among all users. Individual users are restricted by filesystem usage quotas, set to 100TB per user. The purpose of this quota is to prevent runaway programs from filling the entire filesystem and deny service to other users. If 100TB should prove as insufficient for particular user, contact [support](https://support.it4i.cz/rt), the quota may be lifted upon request.
!!! note
The Scratch filesystem is intended for temporary scratch data generated during the calculation as well as for high performance access to input and output files. All I/O intensive jobs must use the SCRATCH filesystem as their working directory.
......@@ -324,7 +324,7 @@ User of data storage CESNET (DU) association can become organizations or an indi
User may only use data storage CESNET for data transfer and storage which are associated with activities in science, research, development, the spread of education, culture and prosperity. In detail see “Acceptable Use Policy CESNET Large Infrastructure (Acceptable Use Policy, AUP)”.
The service is documented [here](https://du.cesnet.cz/en/start). For special requirements please contact directly CESNET Storage Department via e-mail [du-support(at)cesnet.cz](mailto:du-support@cesnet.cz).
The service is documented [here](https://du.cesnet.cz/en/start). For special requirements contact directly CESNET Storage Department via e-mail [du-support(at)cesnet.cz](mailto:du-support@cesnet.cz).
The procedure to obtain the CESNET access is quick and trouble-free.
......@@ -378,7 +378,7 @@ $ cp -a mydir cesnet/.
$ cp cesnet/myfile .
```
Once done, please remember to unmount the storage
Once done, remember to unmount the storage
```console
$ fusermount -u cesnet
......@@ -386,8 +386,8 @@ $ fusermount -u cesnet
### RSYNC Access
!!! Note "Note"
RSYNC provides delta transfer for best performance, can resume interrupted transfers
!!! info
RSYNC provides delta transfer for best performance, can resume interrupted transfers
RSYNC is a fast and extraordinarily versatile file copying tool. It is famous for its delta-transfer algorithm, which reduces the amount of data sent over the network by sending only the differences between the source files and the existing files in the destination. RSYNC is widely used for backups and mirroring and as an improved copy command for everyday use.
......
......@@ -91,7 +91,7 @@ At your machine, create the tunnel:
local $ ssh -TN -f username@login2.cluster-name.it4i.cz -L 5961:localhost:5961
```
Issue the following command to check the tunnel is established (please note the PID 2022 in the last column, you'll need it for closing the tunnel):
Issue the following command to check the tunnel is established (note the PID 2022 in the last column, you'll need it for closing the tunnel):
```console
local $ netstat -natp | grep 5961
......
......@@ -31,7 +31,7 @@ Yes, provided that the CA which provides this service is also a member of IGTF.
## Q: Does IT4Innovations Support the TERENA Certificate Service?
Yes, ITInnovations supports TERENA eScience personal certificates. For more information, please visit [TCS - Trusted Certificate Service](https://tcs-escience-portal.terena.org/), where you also can find if your organisation/country can use this service
Yes, ITInnovations supports TERENA eScience personal certificates. For more information, visit [TCS - Trusted Certificate Service](https://tcs-escience-portal.terena.org/), where you also can find if your organisation/country can use this service
## Q: What Format Should My Certificate Take?
......@@ -53,7 +53,7 @@ Certification Authority (CA) certificates are used to verify the link between yo
To assist users, SURFsara (a member of PRACE) provides a complete and up-to-date bundle of all the CA certificates that any PRACE user (or IT4Innovations grid services user) will require. Bundle of certificates, in either p12, PEM or JKS formats, are [available here](https://winnetou.surfsara.nl/prace/certs/).
It is worth noting that gsissh-term and DART automatically updates their CA certificates from this SURFsara website. In other cases, if you receive a warning that a server’s certificate can not be validated (not trusted), then please update your CA certificates via the SURFsara website. If this fails, then please contact the IT4Innovations helpdesk.
It is worth noting that gsissh-term and DART automatically updates their CA certificates from this SURFsara website. In other cases, if you receive a warning that a server’s certificate can not be validated (not trusted), then update your CA certificates via the SURFsara website. If this fails, then contact the IT4Innovations helpdesk.
Lastly, if you need the CA certificates for a personal Globus 5 installation, then you can install the CA certificates from a MyProxy server with the following command.
......@@ -104,7 +104,7 @@ To check your certificate (e.g., DN, validity, issuer, public key algorithm, etc
openssl x509 -in usercert.pem -text -noout
```
To download openssl if not pre-installed, [please visit](https://www.openssl.org/source/). On Macintosh Mac OS X computers openssl is already pre-installed and can be used immediately.
To download openssl if not pre-installed, see [here](https://www.openssl.org/source/). On Macintosh Mac OS X computers openssl is already pre-installed and can be used immediately.
## Q: How Do I Create and Then Manage a Keystore?
......@@ -134,7 +134,7 @@ Most grid services require the use of your certificate; however, the format of y
If employing the PRACE version of GSISSH-term (also a Java Web Start Application), you may use either the PEM or p12 formats. Note that this service automatically installs up-to-date PRACE CA certificates.
If the grid service is UNICORE, then you bind your certificate, in either the p12 format or JKS, to UNICORE during the installation of the client on your local machine. For more information, please visit [UNICORE6 in PRACE](http://www.prace-ri.eu/UNICORE6-in-PRACE)
If the grid service is UNICORE, then you bind your certificate, in either the p12 format or JKS, to UNICORE during the installation of the client on your local machine. For more information visit [UNICORE6 in PRACE](http://www.prace-ri.eu/UNICORE6-in-PRACE)
If the grid service is part of Globus, such as GSI-SSH, GriFTP or GRAM5, then the certificates can be in either p12 or PEM format and must reside in the "$HOME/.globus" directory for Linux and Mac users or %HOMEPATH%.globus for Windows users. (Windows users will have to use the DOS command ’cmd’ to create a directory which starts with a ’.’). Further, user certificates should be named either "usercred.p12" or "usercert.pem" and "userkey.pem", and the CA certificates must be kept in a pre-specified directory as follows. For Linux and Mac users, this directory is either $HOME/.globus/certificates or /etc/grid-security/certificates. For Windows users, this directory is %HOMEPATH%.globuscertificates. (If you are using GSISSH-Term from prace-ri.eu then you do not have to create the .globus directory nor install CA certificates to use this tool alone).
......@@ -156,7 +156,7 @@ A proxy certificate is a short-lived certificate which may be employed by UNICOR
## Q: Someone May Have Copied or Had Access to the Private Key of My Certificate Either in a Separate File or in the Browser. What Should I Do?
Please ask the CA that issued your certificate to revoke this certificate and to supply you with a new one. In addition, please report this to IT4Innovations by contacting [the support team](https://support.it4i.cz/rt).
Please ask the CA that issued your certificate to revoke this certificate and to supply you with a new one. In addition, report this to IT4Innovations by contacting [the support team](https://support.it4i.cz/rt).
## Q: My Certificate Expired. What Should I Do?
......
......@@ -117,13 +117,13 @@ Certificate generation process for academic purposes, utilizing the CESNET certi
!!! note
Certificate file can be installed into your email client. Web-based email interfaces cannot be used for secure communication, external application, such as Thunderbird or Outlook must be used. This way, your new credentials will be visible only in applications, that have access to your certificate.
If you are not able to obtain certificate from any of the respected certification authorities, please follow the Alternative Way bellow.
If you are not able to obtain certificate from any of the respected certification authorities, follow the Alternative Way bellow.
A FAQ about certificates can be found here: [Certificates FAQ](certificates-faq/).
## Alternative Way to Personal Certificate
Follow these steps **only** if you can not obtain your certificate in a standard way. In case you choose this procedure, please attach a **scan of photo ID** (personal ID or passport or drivers license) when applying for login credentials.
Follow these steps **only** if you can not obtain your certificate in a standard way. In case you choose this procedure, attach a **scan of photo ID** (personal ID or passport or drivers license) when applying for login credentials.
!!! warning
Please use Firefox (clone) for following steps. Other browsers, like Chrome, are not compatible.
......
......@@ -60,7 +60,7 @@ local $
## Errors
Although we have taken every care to ensure the accuracy of the content, mistakes do happen.
If you find an inconsistency or error, please report it by visiting <http://support.it4i.cz/rt>, creating a new ticket, and entering the details.
If you find an inconsistency or error, report it by visiting <http://support.it4i.cz/rt>, creating a new ticket, and entering the details.
By doing so, you can save other readers from frustration and help us improve.
!!! tip
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......@@ -8,7 +8,7 @@ All general [PRACE User Documentation](http://www.prace-ri.eu/user-documentation
## Help and Support
If you have any troubles, need information, request support or want to install additional software, please use [PRACE Helpdesk](http://www.prace-ri.eu/helpdesk-guide264/).
If you have any troubles, need information, request support or want to install additional software, use [PRACE Helpdesk](http://www.prace-ri.eu/helpdesk-guide264/).
Information about the local services are provided in the [introduction of general user documentation Salomon](salomon/introduction/) and [introduction of general user documentation Anselm](anselm/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.
......@@ -16,7 +16,7 @@ Information about the local services are provided in the [introduction of genera
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 a 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](general/obtaining-login-credentials/obtaining-login-credentials/).
If there's a special need a PRACE user can get a standard (local) account at IT4Innovations. To get an account on a cluster, the user needs to obtain the login credentials. The procedure is the same as for general users of the cluster, so see the corresponding [section of the general documentation here](general/obtaining-login-credentials/obtaining-login-credentials/).
## Accessing the Cluster
......@@ -24,7 +24,7 @@ If there's a special need a PRACE user can get a standard (local) account at IT4
For all PRACE users the method for interactive access (login) and data transfer based on grid services from 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).
The user will need a valid certificate and to be present in the PRACE LDAP (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 TIER-1 systems can be found here:
......@@ -147,7 +147,7 @@ $ gsiscp -P 2222 anselm-prace.it4i.cz:_ANSELM_PATH_TO_YOUR_FILE_ _LOCAL_PATH_TO_
### Access to X11 Applications (VNC)
If the user needs to run X11 based graphical application and does not have a X11 server, the applications can be run using VNC service. If the user is using regular SSH based access, please see the [section in general documentation](general/accessing-the-clusters/graphical-user-interface/x-window-system/).
If the user needs to run X11 based graphical application and does not have a X11 server, the applications can be run using VNC service. If the user is using regular SSH based access, see the [section in general documentation](general/accessing-the-clusters/graphical-user-interface/x-window-system/).
If the user uses GSI SSH based access, then the procedure is similar to the SSH based access ([look here](general/accessing-the-clusters/graphical-user-interface/x-window-system/)), only the port forwarding must be done using GSI SSH:
......@@ -157,11 +157,11 @@ $ gsissh -p 2222 salomon.it4i.cz -L 5961:localhost:5961
### Access With SSH
After successful obtainment of login credentials for the local IT4Innovations account, the PRACE users can access the cluster as regular users using SSH. For more information please see [the section in general documentation for Salomon](salomon/shell-and-data-access/) and [the section in general documentation for Anselm](anselm/shell-and-data-access/).
After successful obtainment of login credentials for the local IT4Innovations account, the PRACE users can access the cluster as regular users using SSH. For more information see [the section in general documentation for Salomon](salomon/shell-and-data-access/) and [the section in general documentation for Anselm](anselm/shell-and-data-access/).
## 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 section in the general documentation for Salomon](salomon/shell-and-data-access/) and [the section in general documentation for Anselm](anselm/shell-and-data-access/).
PRACE users can use the same transfer mechanisms as regular users (if they've undergone the full registration procedure). For information about this, see [the section in the general documentation for Salomon](salomon/shell-and-data-access/) and [the section in general documentation for Anselm](anselm/shell-and-data-access/).
Apart from the standard mechanisms, for PRACE users to transfer data to/from Salomon cluster, a GridFTP server running Globus Toolkit GridFTP service is available. The service is available from public Internet as well as from the internal PRACE network (accessible only from other PRACE partners).
......@@ -381,4 +381,4 @@ $ quota
$ lfs quota -u USER_LOGIN /scratch
```
If the quota is insufficient, please contact the [support](