diff --git a/docs.it4i/anselm/capacity-computing.md b/docs.it4i/anselm/capacity-computing.md
index 71b31ab1f55bc8a407e1f2489b1d9f059d735f65..5057b88ac417857a17154e717fddff52d376b26b 100644
--- a/docs.it4i/anselm/capacity-computing.md
+++ b/docs.it4i/anselm/capacity-computing.md
@@ -9,13 +9,13 @@ However, executing a huge number of jobs via the PBS queue may strain the system
!!! note
Please follow one of the procedures below, in case you wish to schedule more than 100 jobs at a time.
-* Use [Job arrays](anselm/capacity-computing/#job-arrays) when running a huge number of [multithread](anselm/capacity-computing/#shared-jobscript-on-one-node) (bound to one node only) or multinode (multithread across several nodes) jobs
-* Use [GNU parallel](anselm/capacity-computing/#gnu-parallel) when running single core jobs
-* Combine [GNU parallel with Job arrays](anselm/capacity-computing/#job-arrays-and-gnu-parallel) when running huge number of single core jobs
+* Use [Job arrays](/anselm/capacity-computing/#job-arrays) when running a huge number of [multithread](anselm/capacity-computing/#shared-jobscript-on-one-node) (bound to one node only) or multinode (multithread across several nodes) jobs
+* Use [GNU parallel](/anselm/capacity-computing/#gnu-parallel) when running single core jobs
+* Combine [GNU parallel with Job arrays](/anselm/capacity-computing/#job-arrays-and-gnu-parallel) when running huge number of single core jobs
## Policy
-1. A user is allowed to submit at most 100 jobs. Each job may be [a job array](anselm/capacity-computing/#job-arrays).
+1. A user is allowed to submit at most 100 jobs. Each job may be [a job array](/anselm/capacity-computing/#job-arrays).
1. The array size is at most 1000 subjobs.
## Job Arrays
@@ -76,7 +76,7 @@ If running a huge number of parallel multicore (in means of multinode multithrea
### Submit the Job Array
-To submit the job array, use the qsub -J command. The 900 jobs of the [example above](anselm/capacity-computing/#array_example) may be submitted like this:
+To submit the job array, use the qsub -J command. The 900 jobs of the [example above](/anselm/capacity-computing/#array_example) may be submitted like this:
```console
$ qsub -N JOBNAME -J 1-900 jobscript
@@ -207,7 +207,7 @@ In this example, tasks from the tasklist are executed via the GNU parallel. The
### Submit the Job
-To submit the job, use the qsub command. The 101 task job of the [example above](anselm/capacity-computing/#gp_example) may be submitted as follows:
+To submit the job, use the qsub command. The 101 task job of the [example above](/anselm/capacity-computing/#gp_example) may be submitted as follows:
```console
$ qsub -N JOBNAME jobscript
@@ -292,7 +292,7 @@ When deciding this values, keep in mind the following guiding rules:
### Submit the Job Array (-J)
-To submit the job array, use the qsub -J command. The 992 task job of the [example above](anselm/capacity-computing/#combined_example) may be submitted like this:
+To submit the job array, use the qsub -J command. The 992 task job of the [example above](/anselm/capacity-computing/#combined_example) may be submitted like this:
```console
$ qsub -N JOBNAME -J 1-992:32 jobscript
diff --git a/docs.it4i/anselm/compute-nodes.md b/docs.it4i/anselm/compute-nodes.md
index a52810e60eb2dc2daa16b56b9e15e904d1a80018..d27f79303248a745bf3ea3e9b1ae623d0a779254 100644
--- a/docs.it4i/anselm/compute-nodes.md
+++ b/docs.it4i/anselm/compute-nodes.md
@@ -52,7 +52,7 @@ Anselm is cluster of x86-64 Intel based nodes built with Bull Extreme Computing
### Compute Node Summary
-| Node type | Count | Range | Memory | Cores | [Access](general/resources-allocation-policy/) |
+| Node type | Count | Range | Memory | Cores | [Access](/general/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 | qnvidia, qexp |
diff --git a/docs.it4i/anselm/hardware-overview.md b/docs.it4i/anselm/hardware-overview.md
index efcff8068431e648cfa8d0edf6e7c021c9d24153..7dd981ead3348a3fb31dfb4efa030744a1e9f24b 100644
--- a/docs.it4i/anselm/hardware-overview.md
+++ b/docs.it4i/anselm/hardware-overview.md
@@ -17,16 +17,16 @@ There are four types of compute nodes:
* 4 compute nodes with a MIC accelerator - an Intel Xeon Phi 5110P
* 2 fat nodes - equipped with 512 GB of RAM and two 100 GB SSD drives
-[More about Compute nodes](anselm/compute-nodes/).
+[More about Compute nodes](/anselm/compute-nodes/).
-GPU and accelerated nodes are available upon request, see the [Resources Allocation Policy](anselm/resources-allocation-policy/).
+GPU and accelerated nodes are available upon request, see the [Resources Allocation Policy](/anselm/resources-allocation-policy/).
-All of these nodes are interconnected through fast InfiniBand and Ethernet networks. [More about the Network](anselm/network/).
+All of these nodes are interconnected through fast InfiniBand and Ethernet networks. [More about the Network](/anselm/network/).
Every chassis provides an InfiniBand switch, marked **isw**, connecting all nodes in the chassis, as well as connecting the chassis to the upper level switches.
-All of the nodes share a 360 TB /home disk for storage of user files. The 146 TB shared /scratch storage is available for scratch data. These file systems are provided by the Lustre parallel file system. There is also local disk storage available on all compute nodes in /lscratch. [More about Storage](anselm/storage/).
+All of the nodes share a 360 TB /home disk for storage of user files. The 146 TB shared /scratch storage is available for scratch data. These file systems are provided by the Lustre parallel file system. There is also local disk storage available on all compute nodes in /lscratch. [More about Storage](/anselm/storage/).
-User access to the Anselm cluster is provided by two login nodes login1, login2, and data mover node dm1. [More about accessing the cluster.](anselm/shell-and-data-access/)
+User access to the Anselm cluster is provided by two login nodes login1, login2, and data mover node dm1. [More about accessing the cluster.](/anselm/shell-and-data-access/)
The parameters are summarized in the following tables:
@@ -35,7 +35,7 @@ The parameters are summarized in the following tables:
| Primary purpose | High Performance Computing |
| Architecture of compute nodes | x86-64 |
| Operating system | Linux (CentOS) |
-| [**Compute nodes**](anselm/compute-nodes/) | |
+| [**Compute nodes**](/anselm/compute-nodes/) | |
| Total | 209 |
| Processor cores | 16 (2 x 8 cores) |
| RAM | min. 64 GB, min. 4 GB per core |
@@ -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 refer to [Compute nodes](anselm/compute-nodes/), [Storage](anselm/storage/), and [Network](anselm/network/).
+For more details refer to [Compute nodes](/anselm/compute-nodes/), [Storage](anselm/storage/), and [Network](anselm/network/).
diff --git a/docs.it4i/anselm/introduction.md b/docs.it4i/anselm/introduction.md
index 7963784c6dc4cea6838a29c18526d5dc55b343b0..80cf1a4c305d7f5f3d2ee1d1dfe68a002ea37401 100644
--- a/docs.it4i/anselm/introduction.md
+++ b/docs.it4i/anselm/introduction.md
@@ -1,11 +1,11 @@
# Introduction
-Welcome to Anselm supercomputer cluster. The Anselm cluster consists of 209 compute nodes, totalling 3344 compute cores with 15 TB RAM, giving over 94 TFLOP/s theoretical peak performance. Each node is a powerful x86-64 computer, equipped with 16 cores, at least 64 GB of RAM, and a 500 GB hard disk drive. Nodes are interconnected through a fully non-blocking fat-tree InfiniBand network, and are equipped with Intel Sandy Bridge processors. A few nodes are also equipped with NVIDIA Kepler GPU or Intel Xeon Phi MIC accelerators. Read more in [Hardware Overview](anselm/hardware-overview/).
+Welcome to Anselm supercomputer cluster. The Anselm cluster consists of 209 compute nodes, totalling 3344 compute cores with 15 TB RAM, giving over 94 TFLOP/s theoretical peak performance. Each node is a powerful x86-64 computer, equipped with 16 cores, at least 64 GB of RAM, and a 500 GB hard disk drive. Nodes are interconnected through a fully non-blocking fat-tree InfiniBand network, and are equipped with Intel Sandy Bridge processors. A few nodes are also equipped with NVIDIA Kepler GPU or Intel Xeon Phi MIC accelerators. Read more in [Hardware Overview](/anselm/hardware-overview/).
-The cluster runs with an [operating system](software/operating-system/) which is compatible with the RedHat [Linux family.](http://upload.wikimedia.org/wikipedia/commons/1/1b/Linux_Distribution_Timeline.svg) We have installed a wide range of software packages targeted at different scientific domains. These packages are accessible via the [modules environment](environment-and-modules/).
+The cluster runs with an [operating system](/software/operating-system/) which is compatible with the RedHat [Linux family.](http://upload.wikimedia.org/wikipedia/commons/1/1b/Linux_Distribution_Timeline.svg) We have installed a wide range of software packages targeted at different scientific domains. These packages are accessible via the [modules environment](environment-and-modules/).
The user data shared file-system (HOME, 320 TB) and job data shared file-system (SCRATCH, 146 TB) are available to users.
-The PBS Professional workload manager provides [computing resources allocations and job execution](anselm/resources-allocation-policy/).
+The PBS Professional workload manager provides [computing resources allocations and job execution](/anselm/resources-allocation-policy/).
-Read more on how to [apply for resources](general/applying-for-resources/), [obtain login credentials](general/obtaining-login-credentials/obtaining-login-credentials/) and [access the cluster](anselm/shell-and-data-access/).
+Read more on how to [apply for resources](/general/applying-for-resources/), [obtain login credentials](general/obtaining-login-credentials/obtaining-login-credentials/) and [access the cluster](/anselm/shell-and-data-access/).
diff --git a/docs.it4i/anselm/job-submission-and-execution.md b/docs.it4i/anselm/job-submission-and-execution.md
index 008a6c07f9dd9515495636d37612ee1f97ddbf49..9b288b9f4531c58b019dca1a1b8fd7269c63cc92 100644
--- a/docs.it4i/anselm/job-submission-and-execution.md
+++ b/docs.it4i/anselm/job-submission-and-execution.md
@@ -92,9 +92,9 @@ In this example, we allocate 4 nodes, 16 cores per node, selecting only the node
### Placement by IB Switch
-Groups of computational nodes are connected to chassis integrated Infiniband switches. These switches form the leaf switch layer of the [Infiniband network](anselm/network/) fat tree topology. Nodes sharing the leaf switch can communicate most efficiently. Sharing the same switch prevents hops in the network and facilitates unbiased, highly efficient network communication.
+Groups of computational nodes are connected to chassis integrated Infiniband switches. These switches form the leaf switch layer of the [Infiniband network](/anselm/network/) fat tree topology. Nodes sharing the leaf switch can communicate most efficiently. Sharing the same switch prevents hops in the network and facilitates unbiased, highly efficient network communication.
-Nodes sharing the same switch may be selected via the PBS resource attribute ibswitch. Values of this attribute are iswXX, where XX is the switch number. The node-switch mapping can be seen in the [Hardware Overview](anselm/hardware-overview/) section.
+Nodes sharing the same switch may be selected via the PBS resource attribute ibswitch. Values of this attribute are iswXX, where XX is the switch number. The node-switch mapping can be seen in the [Hardware Overview](/anselm/hardware-overview/) section.
We recommend allocating compute nodes to a single switch when best possible computational network performance is required to run the job efficiently:
@@ -373,7 +373,7 @@ exit
In this example, input and executable files are assumed to be preloaded manually in the /scratch/$USER/myjob directory. Note the **mpiprocs** and **ompthreads** qsub options controlling the behavior of the MPI execution. mympiprog.x is executed as one process per node, on all 100 allocated nodes. If mympiprog.x implements OpenMP threads, it will run 16 threads per node.
-More information can be found in the [Running OpenMPI](software/mpi/Running_OpenMPI/) and [Running MPICH2](software/mpi/running-mpich2/)
+More information can be found in the [Running OpenMPI](/software/mpi/Running_OpenMPI/) and [Running MPICH2](software/mpi/running-mpich2/)
sections.
### Example Jobscript for Single Node Calculation
@@ -381,7 +381,7 @@ sections.
!!! note
The local scratch directory is often useful for single node jobs. Local scratch memory will be deleted immediately after the job ends.
-Example jobscript for single node calculation, using [local scratch](anselm/storage/) memory on the node:
+Example jobscript for single node calculation, using [local scratch](/anselm/storage/) memory on the node:
```bash
#!/bin/bash
@@ -407,4 +407,4 @@ In this example, a directory in /home holds the input file input and executable
### Other Jobscript Examples
-Further jobscript examples may be found in the software section and the [Capacity computing](anselm/capacity-computing/) section.
+Further jobscript examples may be found in the software section and the [Capacity computing](/anselm/capacity-computing/) section.
diff --git a/docs.it4i/anselm/resources-allocation-policy.md b/docs.it4i/anselm/resources-allocation-policy.md
index ec94c08e2e915010d5a23197fe02875fa904c39f..a60ad4c5e3b493671b7f048ac1a20ae5655c4d77 100644
--- a/docs.it4i/anselm/resources-allocation-policy.md
+++ b/docs.it4i/anselm/resources-allocation-policy.md
@@ -2,7 +2,7 @@
## Job Queue Policies
-The resources are allocated to the job in a fair-share fashion, subject to constraints set by the queue and the resources available to the Project. The Fair-share system of Anselm ensures that individual users may consume approximately equal amounts of resources per week. Detailed information can be found in the [Job scheduling](anselm/job-priority/) section. The resources are accessible via several queues for queueing the jobs. The queues provide prioritized and exclusive access to the computational resources. The following table provides the queue partitioning overview:
+The resources are allocated to the job in a fair-share fashion, subject to constraints set by the queue and the resources available to the Project. The Fair-share system of Anselm ensures that individual users may consume approximately equal amounts of resources per week. Detailed information can be found in the [Job scheduling](/anselm/job-priority/) section. The resources are accessible via several queues for queueing the jobs. The queues provide prioritized and exclusive access to the computational resources. The following table provides the queue partitioning overview:
!!! note
Check the queue status at <https://extranet.it4i.cz/anselm/>
@@ -29,7 +29,7 @@ The resources are allocated to the job in a fair-share fashion, subject to const
## Queue Notes
-The job wall clock time defaults to **half the maximum time**, see the table above. Longer wall time limits can be [set manually, see examples](anselm/job-submission-and-execution/).
+The job wall clock time defaults to **half the maximum time**, see the table above. Longer wall time limits can be [set manually, see examples](/anselm/job-submission-and-execution/).
Jobs that exceed the reserved wall clock time (Req'd Time) get killed automatically. The wall clock time limit can be changed for queuing jobs (state Q) using the qalter command, however it cannot be changed for a running job (state R).
diff --git a/docs.it4i/anselm/shell-and-data-access.md b/docs.it4i/anselm/shell-and-data-access.md
index 6fc1c8f32a1f283313a016d4f5209a3be7984bcb..ab8d2ba3cf1ae7f4c2e26472ce7c633c9a1fe7cb 100644
--- a/docs.it4i/anselm/shell-and-data-access.md
+++ b/docs.it4i/anselm/shell-and-data-access.md
@@ -204,9 +204,9 @@ Now, configure the applications proxy settings to **localhost:6000**. Use port f
## Graphical User Interface
-* The [X Window system](general/accessing-the-clusters/graphical-user-interface/x-window-system/) is the principal way to get GUI access to the clusters.
-* [Virtual Network Computing](general/accessing-the-clusters/graphical-user-interface/vnc/) is a graphical [desktop sharing](http://en.wikipedia.org/wiki/Desktop_sharing) system that uses the [Remote Frame Buffer protocol](http://en.wikipedia.org/wiki/RFB_protocol) to remotely control another [computer](http://en.wikipedia.org/wiki/Computer).
+* The [X Window system](/general/accessing-the-clusters/graphical-user-interface/x-window-system/) is the principal way to get GUI access to the clusters.
+* [Virtual Network Computing](/general/accessing-the-clusters/graphical-user-interface/vnc/) is a graphical [desktop sharing](http://en.wikipedia.org/wiki/Desktop_sharing) system that uses the [Remote Frame Buffer protocol](http://en.wikipedia.org/wiki/RFB_protocol) to remotely control another [computer](http://en.wikipedia.org/wiki/Computer).
## VPN Access
-* Access IT4Innovations internal resources via [VPN](general/accessing-the-clusters/vpn-access/).
+* Access IT4Innovations internal resources via [VPN](/general/accessing-the-clusters/vpn-access/).
diff --git a/docs.it4i/anselm/storage.md b/docs.it4i/anselm/storage.md
index b5b3fb87ba2be0d2d5fdfaa7bc01e6a1535400dd..03869fdc5d9170d7a5523158e723d14f50993be1 100644
--- a/docs.it4i/anselm/storage.md
+++ b/docs.it4i/anselm/storage.md
@@ -105,7 +105,7 @@ The HOME filesystem is mounted in directory /home. Users home directories /home/
The HOME filesystem should not be used to archive data of past Projects or other unrelated data.
-The files on HOME filesystem will not be deleted until end of the [users lifecycle](general/obtaining-login-credentials/obtaining-login-credentials/).
+The files on HOME filesystem will not be deleted until end of the [users lifecycle](/general/obtaining-login-credentials/obtaining-login-credentials/).
The filesystem is backed up, such that it can be restored in case of catasthropic failure resulting in significant data loss. This backup however is not intended to restore old versions of user data or to restore (accidentaly) deleted files.
diff --git a/docs.it4i/environment-and-modules.md b/docs.it4i/environment-and-modules.md
index 632a7574f316c1a43bfd177147ccd0d76e4986b8..77db454c09f4580ebf0ad81c22990270e1df99f9 100644
--- a/docs.it4i/environment-and-modules.md
+++ b/docs.it4i/environment-and-modules.md
@@ -30,7 +30,7 @@ fi
In order to configure your shell for running particular application on clusters we use Module package interface.
-Application modules on clusters are built using [EasyBuild](software/tools/easybuild/). The modules are divided into the following structure:
+Application modules on clusters are built using [EasyBuild](/software/tools/easybuild/). The modules are divided into the following structure:
```
base: Default module class
@@ -61,4 +61,4 @@ Application modules on clusters are built using [EasyBuild](software/tools/easyb
!!! note
The modules set up the application paths, library paths and environment variables for running particular application.
-The modules may be loaded, unloaded and switched, according to momentary needs. For details see [here](software/modules/lmod/).
+The modules may be loaded, unloaded and switched, according to momentary needs. For details see [here](/software/modules/lmod/).
diff --git a/docs.it4i/general/accessing-the-clusters/graphical-user-interface/vnc.md b/docs.it4i/general/accessing-the-clusters/graphical-user-interface/vnc.md
index 864160517d3edcf3d08d73ecef9c1b9efc963d41..1e116b35542990f92042de2afc9897b388b754ca 100644
--- a/docs.it4i/general/accessing-the-clusters/graphical-user-interface/vnc.md
+++ b/docs.it4i/general/accessing-the-clusters/graphical-user-interface/vnc.md
@@ -2,7 +2,7 @@
The **Virtual Network Computing** (**VNC**) is a graphical [desktop sharing](http://en.wikipedia.org/wiki/Desktop_sharing "Desktop sharing") system that uses the [Remote Frame Buffer protocol (RFB)](http://en.wikipedia.org/wiki/RFB_protocol "RFB protocol") to remotely control another [computer](http://en.wikipedia.org/wiki/Computer "Computer"). It transmits the [keyboard](http://en.wikipedia.org/wiki/Computer_keyboard "Computer keyboard") and [mouse](http://en.wikipedia.org/wiki/Computer_mouse") events from one computer to another, relaying the graphical [screen](http://en.wikipedia.org/wiki/Computer_screen "Computer screen") updates back in the other direction, over a [network](http://en.wikipedia.org/wiki/Computer_network "Computer network").
-Vnc-based connections are usually faster (require less network bandwidth) then [X11](general/accessing-the-clusters/graphical-user-interface/x-window-system) applications forwarded directly through ssh.
+Vnc-based connections are usually faster (require less network bandwidth) then [X11](/general/accessing-the-clusters/graphical-user-interface/x-window-system) applications forwarded directly through ssh.
The recommended clients are [TightVNC](http://www.tightvnc.com) or [TigerVNC](http://sourceforge.net/apps/mediawiki/tigervnc/index.php?title=Main_Page) (free, open source, available for almost any platform).
@@ -230,7 +230,7 @@ Allow incoming X11 graphics from the compute nodes at the login node:
$ xhost +
```
-Get an interactive session on a compute node (for more detailed info [look here](anselm/job-submission-and-execution/)). Use the **-v DISPLAY** option to propagate the DISPLAY on the compute node. In this example, we want a complete node (16 cores in this example) from the production queue:
+Get an interactive session on a compute node (for more detailed info [look here](/anselm/job-submission-and-execution/)). Use the **-v DISPLAY** option to propagate the DISPLAY on the compute node. In this example, we want a complete node (16 cores in this example) from the production queue:
```console
$ qsub -I -v DISPLAY=$(uname -n):$(echo $DISPLAY | cut -d ':' -f 2) -A PROJECT_ID -q qprod -l select=1:ncpus=16
diff --git a/docs.it4i/general/accessing-the-clusters/shell-access-and-data-transfer/putty.md b/docs.it4i/general/accessing-the-clusters/shell-access-and-data-transfer/putty.md
index d640530043f4fd23a6586e446653c30cf1345696..1475746ee6ab07e6659eacb5d614b351c4b17d9e 100644
--- a/docs.it4i/general/accessing-the-clusters/shell-access-and-data-transfer/putty.md
+++ b/docs.it4i/general/accessing-the-clusters/shell-access-and-data-transfer/putty.md
@@ -36,7 +36,7 @@ We recommned you to download "**A Windows installer for everything except PuTTYt
* Enter your username if the _Host Name_ input is not in the format "username@salomon.it4i.cz".
-* Enter passphrase for selected [private key](general/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys/) file if Pageant **SSH authentication agent is not used.**
+* Enter passphrase for selected [private key](/general/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys/) file if Pageant **SSH authentication agent is not used.**
## Another PuTTY Settings
@@ -63,7 +63,7 @@ PuTTYgen is the PuTTY key generator. You can load in an existing private key and
You can change the password of your SSH key with "PuTTY Key Generator". Make sure to backup the key.
-* Load your [private key](general/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys/) file with _Load_ button.
+* Load your [private key](/general/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys/) file with _Load_ button.
* Enter your current passphrase.
* Change key passphrase.
* Confirm key passphrase.
@@ -104,4 +104,4 @@ You can generate an additional public/private key pair and insert public key int
* Now you can insert additional public key into authorized_keys file for authentication with your own private key.
- You must log in using ssh key received after registration. Then proceed to [How to add your own key](general/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys/).
+ You must log in using ssh key received after registration. Then proceed to [How to add your own key](/general/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys/).
diff --git a/docs.it4i/general/accessing-the-clusters/vpn-access.md b/docs.it4i/general/accessing-the-clusters/vpn-access.md
index 3275411fcc5d84ecdcf4f153908e3360ddffb0b2..22843534120120dd6291399300194df8aa710a62 100644
--- a/docs.it4i/general/accessing-the-clusters/vpn-access.md
+++ b/docs.it4i/general/accessing-the-clusters/vpn-access.md
@@ -15,7 +15,7 @@ It is impossible to connect to VPN from other operating systems.
## VPN Client Installation
-You can install VPN client from web interface after successful login with [IT4I credentials](general/obtaining-login-credentials/obtaining-login-credentials/#login-credentials) on address [https://vpn.it4i.cz/user](https://vpn.it4i.cz/user)
+You can install VPN client from web interface after successful login with [IT4I credentials](/general/obtaining-login-credentials/obtaining-login-credentials/#login-credentials) on address [https://vpn.it4i.cz/user](https://vpn.it4i.cz/user)
diff --git a/docs.it4i/general/applying-for-resources.md b/docs.it4i/general/applying-for-resources.md
index 40307695f132d810afc7e0d38b75c7443f2400e4..a662320a9d916058f3afbe5cc72393cc6a4395fc 100644
--- a/docs.it4i/general/applying-for-resources.md
+++ b/docs.it4i/general/applying-for-resources.md
@@ -8,4 +8,4 @@ Anyone is welcomed to apply via the [Directors Discretion.](http://www.it4i.cz/o
Foreign (mostly European) users can obtain computational resources via the [PRACE (DECI) program](http://www.prace-ri.eu/DECI-Projects).
-In all cases, IT4Innovations’ access mechanisms are aimed at distributing computational resources while taking into account the development and application of supercomputing methods and their benefits and usefulness for society. The applicants are expected to submit a proposal. In the proposal, the applicants **apply for a particular amount of core-hours** of computational resources. The requested core-hours should be substantiated by scientific excellence of the proposal, its computational maturity and expected impacts. Proposals do undergo a scientific, technical and economic evaluation. The allocation decisions are based on this evaluation. More information at [Computing resources allocation](http://www.it4i.cz/computing-resources-allocation/?lang=en) and [Obtaining Login Credentials](general/obtaining-login-credentials/obtaining-login-credentials/) page.
+In all cases, IT4Innovations’ access mechanisms are aimed at distributing computational resources while taking into account the development and application of supercomputing methods and their benefits and usefulness for society. The applicants are expected to submit a proposal. In the proposal, the applicants **apply for a particular amount of core-hours** of computational resources. The requested core-hours should be substantiated by scientific excellence of the proposal, its computational maturity and expected impacts. Proposals do undergo a scientific, technical and economic evaluation. The allocation decisions are based on this evaluation. More information at [Computing resources allocation](http://www.it4i.cz/computing-resources-allocation/?lang=en) and [Obtaining Login Credentials](/general/obtaining-login-credentials/obtaining-login-credentials/) page.
diff --git a/docs.it4i/general/obtaining-login-credentials/certificates-faq.md b/docs.it4i/general/obtaining-login-credentials/certificates-faq.md
index 6b9f9fbbb15b37f6a4b5fbb93fc13e0d6d98875f..accee6fd3a517b6a74b79a00f091bab5fa0ab3c2 100644
--- a/docs.it4i/general/obtaining-login-credentials/certificates-faq.md
+++ b/docs.it4i/general/obtaining-login-credentials/certificates-faq.md
@@ -17,7 +17,7 @@ However, users need only manage User and CA certificates. Note that your user ce
## Q: Which X.509 Certificates Are Recognised by IT4Innovations?
-[The Certificates for Digital Signatures](general/obtaining-login-credentials/#the-certificates-for-digital-signatures).
+[The Certificates for Digital Signatures](/general/obtaining-login-credentials/#the-certificates-for-digital-signatures).
## Q: How Do I Get a User Certificate That Can Be Used With IT4Innovations?
diff --git a/docs.it4i/general/resource_allocation_and_job_execution.md b/docs.it4i/general/resource_allocation_and_job_execution.md
index 2c8594e1da6128d4c2229c050aff27b4f4750d3c..51723a5dfad62ab6f798eb1be722c8f75bc79b6b 100644
--- a/docs.it4i/general/resource_allocation_and_job_execution.md
+++ b/docs.it4i/general/resource_allocation_and_job_execution.md
@@ -1,10 +1,10 @@
# Resource Allocation and Job Execution
-To run a [job](/#terminology-frequently-used-on-these-pages), [computational resources](salomon/resources-allocation-policy/#resource-accounting-policy) for this particular job must be allocated. This is done via the PBS Pro job workload manager software, which distributes workloads across the supercomputer. Extensive information about PBS Pro can be found in the [PBS Pro User's Guide](pbspro).
+To run a [job](/#terminology-frequently-used-on-these-pages), [computational resources](/salomon/resources-allocation-policy/#resource-accounting-policy) for this particular job must be allocated. This is done via the PBS Pro job workload manager software, which distributes workloads across the supercomputer. Extensive information about PBS Pro can be found in the [PBS Pro User's Guide](pbspro).
## Resources Allocation Policy
-The resources are allocated to the job in a fair-share fashion, subject to constraints set by the queue and resources available to the Project. [The Fair-share](salomon/job-priority/#fair-share-priority) ensures that individual users may consume approximately equal amount of resources per week. The resources are accessible via queues for queueing the jobs. The queues provide prioritized and exclusive access to the computational resources. Following queues are are the most important:
+The resources are allocated to the job in a fair-share fashion, subject to constraints set by the queue and resources available to the Project. [The Fair-share](/salomon/job-priority/#fair-share-priority) ensures that individual users may consume approximately equal amount of resources per week. The resources are accessible via queues for queueing the jobs. The queues provide prioritized and exclusive access to the computational resources. Following queues are are the most important:
* **qexp**, the Express queue
* **qprod**, the Production queue
@@ -16,7 +16,7 @@ The resources are allocated to the job in a fair-share fashion, subject to const
!!! note
Check the queue status at [https://extranet.it4i.cz/](https://extranet.it4i.cz/)
-Read more on the [Resource AllocationPolicy](salomon/resources-allocation-policy) page.
+Read more on the [Resource AllocationPolicy](/salomon/resources-allocation-policy) page.
## Job Submission and Execution
@@ -25,7 +25,7 @@ Read more on the [Resource AllocationPolicy](salomon/resources-allocation-policy
The qsub submits the job into the queue. The qsub command creates a request to the PBS Job manager for allocation of specified resources. The **smallest allocation unit is entire node, 16 cores**, with exception of the qexp queue. The resources will be allocated when available, subject to allocation policies and constraints. **After the resources are allocated the jobscript or interactive shell is executed on first of the allocated nodes.**
-Read more on the [Job submission and execution](salomon/job-submission-and-execution) page.
+Read more on the [Job submission and execution](/salomon/job-submission-and-execution) page.
## Capacity Computing
@@ -36,4 +36,4 @@ Use GNU Parallel and/or Job arrays when running (many) single core jobs.
In many cases, it is useful to submit huge (100+) number of computational jobs into the PBS queue system. Huge number of (small) jobs is one of the most effective ways to execute embarrassingly parallel calculations, achieving best runtime, throughput and computer utilization. In this chapter, we discuss the the recommended way to run huge number of jobs, including **ways to run huge number of single core jobs**.
-Read more on [Capacity computing](salomon/capacity-computing) page.
+Read more on [Capacity computing](/salomon/capacity-computing) page.
diff --git a/docs.it4i/index.md b/docs.it4i/index.md
index 784e7b220b5361f9fd518fa8073671ff6a9d31a4..8a892d4fa3affa5e0cfc8c02d557be6669d10f84 100644
--- a/docs.it4i/index.md
+++ b/docs.it4i/index.md
@@ -1,6 +1,6 @@
# Documentation
-Welcome to the IT4Innovations documentation pages. The IT4Innovations national supercomputing center operates the supercomputers [Salomon](salomon/introduction/) and [Anselm](anselm/introduction/). The supercomputers are [available](general/applying-for-resources/) to the academic community within the Czech Republic and Europe, and the industrial community worldwide. The purpose of these pages is to provide comprehensive documentation of the hardware, software and usage of the computers.
+Welcome to the IT4Innovations documentation pages. The IT4Innovations national supercomputing center operates the supercomputers [Salomon](/salomon/introduction/) and [Anselm](/anselm/introduction/). The supercomputers are [available](/general/applying-for-resources/) to the academic community within the Czech Republic and Europe, and the industrial community worldwide. The purpose of these pages is to provide comprehensive documentation of the hardware, software and usage of the computers.
## How to Read the Documentation
@@ -31,7 +31,7 @@ In many cases, you will run your own code on the cluster. In order to fully expl
* **node:** a computer, interconnected via a network to other computers - Computational nodes are powerful computers, designed for, and dedicated to executing demanding scientific computations.
* **core:** a processor core, a unit of processor, executing computations
-* **core-hour:** also normalized core-hour, NCH. A metric of computer utilization, [see definition](salomon/resources-allocation-policy/#normalized-core-hours-nch).
+* **core-hour:** also normalized core-hour, NCH. A metric of computer utilization, [see definition](/salomon/resources-allocation-policy/#normalized-core-hours-nch).
* **job:** a calculation running on the supercomputer - the job allocates and utilizes the resources of the supercomputer for certain time.
* **HPC:** High Performance Computing
* **HPC (computational) resources:** corehours, storage capacity, software licences
diff --git a/docs.it4i/job-features.md b/docs.it4i/job-features.md
index fc7362fd80df3d888916cca844273ca9521a6d14..94200f94c8ffcf1c751bedd24760d83350ba370c 100644
--- a/docs.it4i/job-features.md
+++ b/docs.it4i/job-features.md
@@ -44,7 +44,7 @@ Configure network for virtualization, create interconnect for fast communication
$ qsub ... -l virt_network=true
```
-[See Tap Interconnect](software/tools/virtualization/#tap-interconnect)
+[See Tap Interconnect](/software/tools/virtualization/#tap-interconnect)
## x86 Adapt Support
diff --git a/docs.it4i/prace.md b/docs.it4i/prace.md
index ceb5b53d841121e9ec5fe01935dd52d90f79d8ed..3b9b0893ecd40aa2b84bb98ca0237ea289f50e85 100644
--- a/docs.it4i/prace.md
+++ b/docs.it4i/prace.md
@@ -2,7 +2,7 @@
## Introduction
-PRACE users coming to the TIER-1 systems 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 can lower their comfort, 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.
+PRACE users coming to the TIER-1 systems 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 can lower their comfort, 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 reading the local documentation here.
@@ -10,13 +10,13 @@ All general [PRACE User Documentation](http://www.prace-ri.eu/user-documentation
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.
+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.
## 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 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/).
+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
@@ -147,9 +147,9 @@ $ 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, 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:
+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:
```console
$ gsissh -p 2222 salomon.it4i.cz -L 5961:localhost:5961
@@ -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 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, 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).
@@ -302,7 +302,7 @@ Generally both shared file systems are available through GridFTP:
| /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 [for Salomon here](salomon/storage/) and [for anselm here](anselm/storage).
+More information about the shared file systems is available [for Salomon here](/salomon/storage/) and [for anselm here](/anselm/storage).
!!! hint
`prace` directory is used for PRACE users on the SCRATCH file system.
@@ -318,7 +318,7 @@ Only Salomon cluster /scratch:
There are some limitations for PRACE user 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 be also restrictions obtaining a working license for the commercial software installed on the cluster, mostly because of the license agreement or because of insufficient amount of licenses.
-For production runs always use scratch file systems. The available file systems are described [for Salomon here](salomon/storage/) and [for Anselm here](anselm/storage).
+For production runs always use scratch file systems. The available file systems are described [for Salomon here](/salomon/storage/) and [for Anselm here](/anselm/storage).
### Software, Modules and PRACE Common Production Environment
@@ -332,7 +332,7 @@ $ ml prace
### Resource Allocation and Job Execution
-General information about the resource allocation, job queuing and job execution is in this [section of general documentation for Salomon](salomon/resources-allocation-policy/) and [section of general documentation for Anselm](anselm/resources-allocation-policy/).
+General information about the resource allocation, job queuing and job execution is in this [section of general documentation for Salomon](/salomon/resources-allocation-policy/) and [section of general documentation for Anselm](/anselm/resources-allocation-policy/).
For PRACE users, the default production run queue is "qprace". PRACE users can also use two other queues "qexp" and "qfree".
@@ -356,7 +356,7 @@ For Anselm:
### Accounting & Quota
-The resources that are currently subject to accounting are the core hours. The core hours are accounted on the wall clock basis. 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 [example in the general documentation for Salomon](salomon/resources-allocation-policy/) and [example in the general documentation for Anselm](anselm/resources-allocation-policy/).
+The resources that are currently subject to accounting are the core hours. The core hours are accounted on the wall clock basis. 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 [example in the general documentation for Salomon](/salomon/resources-allocation-policy/) and [example in the general documentation for Anselm](/anselm/resources-allocation-policy/).
PRACE users should check their project accounting using the [PRACE Accounting Tool (DART)](http://www.prace-ri.eu/accounting-report-tool/).
diff --git a/docs.it4i/salomon/capacity-computing.md b/docs.it4i/salomon/capacity-computing.md
index f7be485d1731627aebf9a050a636e68c618cb79c..01ba62296946fa1fecbf48f3373336daaf714fa0 100644
--- a/docs.it4i/salomon/capacity-computing.md
+++ b/docs.it4i/salomon/capacity-computing.md
@@ -147,7 +147,7 @@ Display status information for all user's subjobs.
$ qstat -u $USER -tJ
```
-Read more on job arrays in the [PBSPro Users guide](software/pbspro/).
+Read more on job arrays in the [PBSPro Users guide](/software/pbspro/).
## GNU Parallel
diff --git a/docs.it4i/salomon/compute-nodes.md b/docs.it4i/salomon/compute-nodes.md
index 8eae726d9d194feb4f32f0d035230f24f86b354e..629a85257cb429c1d1650335514af67cb8a52642 100644
--- a/docs.it4i/salomon/compute-nodes.md
+++ b/docs.it4i/salomon/compute-nodes.md
@@ -5,7 +5,7 @@
Salomon is cluster of x86-64 Intel based nodes. The cluster contains two types of compute nodes of the same processor type and memory size.
Compute nodes with MIC accelerator **contains two Intel Xeon Phi 7120P accelerators.**
-[More about schematic representation of the Salomon cluster compute nodes IB topology](salomon/ib-single-plane-topology/).
+[More about schematic representation of the Salomon cluster compute nodes IB topology](/salomon/ib-single-plane-topology/).
### Compute Nodes Without Accelerator
diff --git a/docs.it4i/salomon/hardware-overview.md b/docs.it4i/salomon/hardware-overview.md
index 59c2c42ff0e1785bf3978dc32afd780eb2a52485..4a8e68e10ba20e60010362ff4b8903185e652d9f 100644
--- a/docs.it4i/salomon/hardware-overview.md
+++ b/docs.it4i/salomon/hardware-overview.md
@@ -4,7 +4,7 @@
The Salomon cluster consists of 1008 computational nodes of which 576 are regular compute nodes and 432 accelerated nodes. Each node is a powerful x86-64 computer, equipped with 24 cores (two twelve-core Intel Xeon processors) and 128 GB RAM. The nodes are interlinked by high speed InfiniBand and Ethernet networks. All nodes share 0.5 PB /home NFS disk storage to store the user files. Users may use a DDN Lustre shared storage with capacity of 1.69 PB which is available for the scratch project data. The user access to the Salomon cluster is provided by four login nodes.
-[More about schematic representation of the Salomon cluster compute nodes IB topology](salomon/ib-single-plane-topology/).
+[More about schematic representation of the Salomon cluster compute nodes IB topology](/salomon/ib-single-plane-topology/).
@@ -17,7 +17,7 @@ The parameters are summarized in the following tables:
| Primary purpose | High Performance Computing |
| Architecture of compute nodes | x86-64 |
| Operating system | CentOS 6.x Linux |
-| [**Compute nodes**](salomon/compute-nodes/) | |
+| [**Compute nodes**](/salomon/compute-nodes/) | |
| Totally | 1008 |
| Processor | 2 x Intel Xeon E5-2680v3, 2.5 GHz, 12 cores |
| RAM | 128GB, 5.3 GB per core, DDR4@2133 MHz |
@@ -36,7 +36,7 @@ The parameters are summarized in the following tables:
| w/o accelerator | 576 | 2 x Intel Xeon E5-2680v3, 2.5 GHz | 24 | 128 GB | - |
| MIC accelerated | 432 | 2 x Intel Xeon E5-2680v3, 2.5 GHz | 24 | 128 GB | 2 x Intel Xeon Phi 7120P, 61 cores, 16 GB RAM |
-For more details refer to the [Compute nodes](salomon/compute-nodes/).
+For more details refer to the [Compute nodes](/salomon/compute-nodes/).
## Remote Visualization Nodes
diff --git a/docs.it4i/salomon/ib-single-plane-topology.md b/docs.it4i/salomon/ib-single-plane-topology.md
index ab945605ff0deda9eadc72d15a758dc036e7cdc0..840303416a8e20a62babb5f3b680a34b4d96b6ae 100644
--- a/docs.it4i/salomon/ib-single-plane-topology.md
+++ b/docs.it4i/salomon/ib-single-plane-topology.md
@@ -18,9 +18,9 @@ Each color in each physical IRU represents one dual-switch ASIC switch.
## IB Single-Plane Topology - Accelerated Nodes
-Each of the 3 inter-connected D racks are equivalent to one half of M-Cell rack. 18 x D rack with MIC accelerated nodes [r21-r38] are equivalent to 3 M-Cell racks as shown in a diagram [7D Enhanced Hypercube](salomon/7d-enhanced-hypercube/).
+Each of the 3 inter-connected D racks are equivalent to one half of M-Cell rack. 18 x D rack with MIC accelerated nodes [r21-r38] are equivalent to 3 M-Cell racks as shown in a diagram [7D Enhanced Hypercube](/salomon/7d-enhanced-hypercube/).
-As shown in a diagram [IB Topology](salomon/7d-enhanced-hypercube/#ib-topology)
+As shown in a diagram [IB Topology](/salomon/7d-enhanced-hypercube/#ib-topology)
* Racks 21, 22, 23, 24, 25, 26 are equivalent to one M-Cell rack.
* Racks 27, 28, 29, 30, 31, 32 are equivalent to one M-Cell rack.
diff --git a/docs.it4i/salomon/introduction.md b/docs.it4i/salomon/introduction.md
index 90625624abbac158466071bd601d69f988c262d5..e8e941d12498243788e7c25fc1442d0010a7ac88 100644
--- a/docs.it4i/salomon/introduction.md
+++ b/docs.it4i/salomon/introduction.md
@@ -1,6 +1,6 @@
# Introduction
-Welcome to Salomon supercomputer cluster. The Salomon cluster consists of 1008 compute nodes, totalling 24192 compute cores with 129 TB RAM and giving over 2 Pflop/s theoretical peak performance. Each node is a powerful x86-64 computer, equipped with 24 cores, and at least 128 GB RAM. Nodes are interconnected through a 7D Enhanced hypercube InfiniBand network and are equipped with Intel Xeon E5-2680v3 processors. The Salomon cluster consists of 576 nodes without accelerators, and 432 nodes equipped with Intel Xeon Phi MIC accelerators. Read more in [Hardware Overview](salomon/hardware-overview/).
+Welcome to Salomon supercomputer cluster. The Salomon cluster consists of 1008 compute nodes, totalling 24192 compute cores with 129 TB RAM and giving over 2 Pflop/s theoretical peak performance. Each node is a powerful x86-64 computer, equipped with 24 cores, and at least 128 GB RAM. Nodes are interconnected through a 7D Enhanced hypercube InfiniBand network and are equipped with Intel Xeon E5-2680v3 processors. The Salomon cluster consists of 576 nodes without accelerators, and 432 nodes equipped with Intel Xeon Phi MIC accelerators. Read more in [Hardware Overview](/salomon/hardware-overview/).
The cluster runs with a [CentOS Linux](http://www.bull.com/bullx-logiciels/systeme-exploitation.html) operating system, which is compatible with the RedHat [Linux family.](http://upload.wikimedia.org/wikipedia/commons/1/1b/Linux_Distribution_Timeline.svg)
diff --git a/docs.it4i/salomon/job-priority.md b/docs.it4i/salomon/job-priority.md
index e4515f3d976991ccc6df6d4e8dfa96b5fedc66fd..906d6753a50ec6074d3b54dbadec7b211b39b5f6 100644
--- a/docs.it4i/salomon/job-priority.md
+++ b/docs.it4i/salomon/job-priority.md
@@ -72,6 +72,6 @@ Specifying more accurate walltime enables better scheduling, better execution ti
### Job Placement
-Job [placement can be controlled by flags during submission](salomon/job-submission-and-execution/#job_placement).
+Job [placement can be controlled by flags during submission](/salomon/job-submission-and-execution/#job_placement).
---8<--- "mathjax.md"
diff --git a/docs.it4i/salomon/job-submission-and-execution.md b/docs.it4i/salomon/job-submission-and-execution.md
index ee87ddcf223ca42c426aabf932a49b677dccc79d..7d4a86a0dbbbe7e3793daff44422a680279fc655 100644
--- a/docs.it4i/salomon/job-submission-and-execution.md
+++ b/docs.it4i/salomon/job-submission-and-execution.md
@@ -102,7 +102,7 @@ exec_vnode = (r21u05n581-mic0:naccelerators=1:ncpus=0)
Per NUMA node allocation.
Jobs are isolated by cpusets.
-The UV2000 (node uv1) offers 3TB of RAM and 104 cores, distributed in 13 NUMA nodes. A NUMA node packs 8 cores and approx. 247GB RAM (with exception, node 11 has only 123GB RAM). In the PBS the UV2000 provides 13 chunks, a chunk per NUMA node (see [Resource allocation policy](salomon/resources-allocation-policy/)). The jobs on UV2000 are isolated from each other by cpusets, so that a job by one user may not utilize CPU or memory allocated to a job by other user. Always, full chunks are allocated, a job may only use resources of the NUMA nodes allocated to itself.
+The UV2000 (node uv1) offers 3TB of RAM and 104 cores, distributed in 13 NUMA nodes. A NUMA node packs 8 cores and approx. 247GB RAM (with exception, node 11 has only 123GB RAM). In the PBS the UV2000 provides 13 chunks, a chunk per NUMA node (see [Resource allocation policy](/salomon/resources-allocation-policy/)). The jobs on UV2000 are isolated from each other by cpusets, so that a job by one user may not utilize CPU or memory allocated to a job by other user. Always, full chunks are allocated, a job may only use resources of the NUMA nodes allocated to itself.
```console
$ qsub -A OPEN-0-0 -q qfat -l select=13 ./myjob
@@ -165,7 +165,7 @@ In this example, we allocate nodes r24u35n680 and r24u36n681, all 24 cores per n
### Placement by Network Location
-Network location of allocated nodes in the [InifiBand network](salomon/network/) influences efficiency of network communication between nodes of job. Nodes on the same InifiBand switch communicate faster with lower latency than distant nodes. To improve communication efficiency of jobs, PBS scheduler on Salomon is configured to allocate nodes - from currently available resources - which are as close as possible in the network topology.
+Network location of allocated nodes in the [InifiBand network](/salomon/network/) influences efficiency of network communication between nodes of job. Nodes on the same InifiBand switch communicate faster with lower latency than distant nodes. To improve communication efficiency of jobs, PBS scheduler on Salomon is configured to allocate nodes - from currently available resources - which are as close as possible in the network topology.
For communication intensive jobs it is possible to set stricter requirement - to require nodes directly connected to the same InifiBand switch or to require nodes located in the same dimension group of the InifiBand network.
@@ -238,7 +238,7 @@ Nodes located in the same dimension group may be allocated using node grouping o
| 6D | ehc_6d | 432,576 |
| 7D | ehc_7d | all |
-In this example, we allocate 16 nodes in the same [hypercube dimension](salomon/7d-enhanced-hypercube/) 1 group.
+In this example, we allocate 16 nodes in the same [hypercube dimension](/salomon/7d-enhanced-hypercube/) 1 group.
```console
$ qsub -A OPEN-0-0 -q qprod -l select=16:ncpus=24 -l place=group=ehc_1d -I
@@ -516,7 +516,7 @@ HTML commented section #2 (examples need to be reworked)
!!! note
Local scratch directory is often useful for single node jobs. Local scratch will be deleted immediately after the job ends. Be very careful, use of RAM disk filesystem is at the expense of operational memory.
-Example jobscript for single node calculation, using [local scratch](salomon/storage/) on the node:
+Example jobscript for single node calculation, using [local scratch](/salomon/storage/) on the node:
```bash
#!/bin/bash
diff --git a/docs.it4i/salomon/network.md b/docs.it4i/salomon/network.md
index 252fe034af4e765d36da76c6e4898264cf4cfd8b..13d5db94c43f9dd423b087f47d1692fa5f69dfc6 100644
--- a/docs.it4i/salomon/network.md
+++ b/docs.it4i/salomon/network.md
@@ -5,10 +5,10 @@ network. Only [InfiniBand](http://en.wikipedia.org/wiki/InfiniBand) network may
## InfiniBand Network
-All compute and login nodes of Salomon are interconnected by 7D Enhanced hypercube [Infiniband](http://en.wikipedia.org/wiki/InfiniBand) network (56 Gbps). The network topology is a [7D Enhanced hypercube](salomon/7d-enhanced-hypercube/).
+All compute and login nodes of Salomon are interconnected by 7D Enhanced hypercube [Infiniband](http://en.wikipedia.org/wiki/InfiniBand) network (56 Gbps). The network topology is a [7D Enhanced hypercube](/salomon/7d-enhanced-hypercube/).
-Read more about schematic representation of the Salomon cluster [IB single-plain topology](salomon/ib-single-plane-topology/)
-([hypercube dimension](salomon/7d-enhanced-hypercube/)).
+Read more about schematic representation of the Salomon cluster [IB single-plain topology](/salomon/ib-single-plane-topology/)
+([hypercube dimension](/salomon/7d-enhanced-hypercube/)).
The compute nodes may be accessed via the Infiniband network using ib0 network interface, in address range 10.17.0.0 (mask 255.255.224.0). The MPI may be used to establish native Infiniband connection among the nodes.
diff --git a/docs.it4i/salomon/resources-allocation-policy.md b/docs.it4i/salomon/resources-allocation-policy.md
index 54a231a945f20ed6a5fea0496d29580db9043230..01b070b25fdf97592ed864e5fc508963205d97a4 100644
--- a/docs.it4i/salomon/resources-allocation-policy.md
+++ b/docs.it4i/salomon/resources-allocation-policy.md
@@ -2,7 +2,7 @@
## Job Queue Policies
-The resources are allocated to the job in a fair-share fashion, subject to constraints set by the queue and resources available to the Project. The fair-share at Anselm ensures that individual users may consume approximately equal amount of resources per week. Detailed information in the [Job scheduling](salomon/job-priority/) section. The resources are accessible via several queues for queueing the jobs. The queues provide prioritized and exclusive access to the computational resources. Following table provides the queue partitioning overview:
+The resources are allocated to the job in a fair-share fashion, subject to constraints set by the queue and resources available to the Project. The fair-share at Anselm ensures that individual users may consume approximately equal amount of resources per week. Detailed information in the [Job scheduling](/salomon/job-priority/) section. The resources are accessible via several queues for queueing the jobs. The queues provide prioritized and exclusive access to the computational resources. Following table provides the queue partitioning overview:
!!! note
Check the queue status at <https://extranet.it4i.cz/rsweb/salomon/>
@@ -35,7 +35,7 @@ The resources are allocated to the job in a fair-share fashion, subject to const
## Queue Notes
-The job wall-clock time defaults to **half the maximum time**, see table above. Longer wall time limits can be [set manually, see examples](salomon/job-submission-and-execution/).
+The job wall-clock time defaults to **half the maximum time**, see table above. Longer wall time limits can be [set manually, see examples](/salomon/job-submission-and-execution/).
Jobs that exceed the reserved wall-clock time (Req'd Time) get killed automatically. Wall-clock time limit can be changed for queuing jobs (state Q) using the qalter command, however can not be changed for a running job (state R).
diff --git a/docs.it4i/salomon/shell-and-data-access.md b/docs.it4i/salomon/shell-and-data-access.md
index e7fd6b57f1ec72877c842ac5dc47aa45e21d6cbe..0183662f0f589a2859d465662ec45f10e6e5303d 100644
--- a/docs.it4i/salomon/shell-and-data-access.md
+++ b/docs.it4i/salomon/shell-and-data-access.md
@@ -65,7 +65,7 @@ Last login: Tue Jul 9 15:57:38 2018 from your-host.example.com
```
!!! note
- The environment is **not** shared between login nodes, except for [shared filesystems](salomon/storage/).
+ The environment is **not** shared between login nodes, except for [shared filesystems](/salomon/storage/).
## Data Transfer
@@ -79,7 +79,7 @@ Data in and out of the system may be transferred by the [scp](http://en.wikipedi
| login3.salomon.it4i.cz | 22 | scp, sftp |
| login4.salomon.it4i.cz | 22 | scp, sftp |
-The authentication is by the [private key](general/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys/)
+The authentication is by the [private key](/general/accessing-the-clusters/shell-access-and-data-transfer/ssh-keys/)
On linux or Mac, use scp or sftp client to transfer the data to Salomon:
@@ -115,7 +115,7 @@ $ man sshfs
On Windows, use [WinSCP client](http://winscp.net/eng/download.php) to transfer the data. The [win-sshfs client](http://code.google.com/p/win-sshfs/) provides a way to mount the Salomon filesystems directly as an external disc.
-More information about the shared file systems is available [here](salomon/storage/).
+More information about the shared file systems is available [here](/salomon/storage/).
## Connection Restrictions
@@ -199,9 +199,9 @@ Now, configure the applications proxy settings to **localhost:6000**. Use port f
## Graphical User Interface
-* The [X Window system](general/accessing-the-clusters/graphical-user-interface/x-window-system/) is a principal way to get GUI access to the clusters.
+* The [X Window system](/general/accessing-the-clusters/graphical-user-interface/x-window-system/) is a principal way to get GUI access to the clusters.
* The [Virtual Network Computing](../general/accessing-the-clusters/graphical-user-interface/vnc/) is a graphical [desktop sharing](http://en.wikipedia.org/wiki/Desktop_sharing) system that uses the [Remote Frame Buffer protocol](http://en.wikipedia.org/wiki/RFB_protocol) to remotely control another [computer](http://en.wikipedia.org/wiki/Computer).
## VPN Access
-* Access to IT4Innovations internal resources via [VPN](general/accessing-the-clusters/vpn-access/).
+* Access to IT4Innovations internal resources via [VPN](/general/accessing-the-clusters/vpn-access/).
diff --git a/docs.it4i/salomon/storage.md b/docs.it4i/salomon/storage.md
index 53336d648a124fe1b0fe8bb5816272bb09e1f374..84506c38e88340b6556429db8f179c8f9e389d0a 100644
--- a/docs.it4i/salomon/storage.md
+++ b/docs.it4i/salomon/storage.md
@@ -235,7 +235,7 @@ Users home directories /home/username reside on HOME file system. Accessible cap
The HOME should not be used to archive data of past Projects or other unrelated data.
-The files on HOME will not be deleted until end of the [users lifecycle](general/obtaining-login-credentials/obtaining-login-credentials/).
+The files on HOME will not be deleted until end of the [users lifecycle](/general/obtaining-login-credentials/obtaining-login-credentials/).
The workspace is backed up, such that it can be restored in case of catasthropic failure resulting in significant data loss. This backup however is not intended to restore old versions of user data or to restore (accidentaly) deleted files.
diff --git a/docs.it4i/salomon/visualization.md b/docs.it4i/salomon/visualization.md
index 769f7a024cbfe472f174fde2e1dc3d20ab095d96..88a1d5e0e1fd1c1480f5d802953f13e60d0c3b1f 100644
--- a/docs.it4i/salomon/visualization.md
+++ b/docs.it4i/salomon/visualization.md
@@ -14,8 +14,8 @@ Remote visualization with NICE DCV software is availabe on two nodes.
## References
-* [Graphical User Interface](salomon/shell-and-data-access/#graphical-user-interface)
-* [VPN Access](salomon/shell-and-data-access/#vpn-access)
+* [Graphical User Interface](/salomon/shell-and-data-access/#graphical-user-interface)
+* [VPN Access](/salomon/shell-and-data-access/#vpn-access)
## Install and Run
@@ -25,7 +25,7 @@ Remote visualization with NICE DCV software is availabe on two nodes.
* [Linux download](http://www.nice-software.com/storage/nice-dcv/2016.0/endstation/linux/nice-dcv-endstation-2016.0-17066.run)
* [Windows download](http://www.nice-software.com/storage/nice-dcv/2016.0/endstation/win/nice-dcv-endstation-2016.0-17066-Release.msi)
-**Install VPN client** [VPN Access](general/accessing-the-clusters/vpn-access/) (user-computer)
+**Install VPN client** [VPN Access](/general/accessing-the-clusters/vpn-access/) (user-computer)
!!! note
Visualisation server is a compute node. You are not able to SSH with your private key. There are two solutions available to solve login issue.
diff --git a/docs.it4i/software/bio/omics-master/overview.md b/docs.it4i/software/bio/omics-master/overview.md
index c80680308f6b682327ac26819703028e52da2859..0831fc0af141914f89de9aa30f2a6320f4604fd8 100644
--- a/docs.it4i/software/bio/omics-master/overview.md
+++ b/docs.it4i/software/bio/omics-master/overview.md
@@ -165,9 +165,9 @@ Systems biology
We also import systems biology information like interactome information from IntAct (24). Reactome (25) stores pathway and interaction information in BioPAX (26) format. BioPAX data exchange format enables the integration of diverse pathway
resources. We successfully solved the problem of storing data released in BioPAX format into a SQL relational schema, which allowed us importing Reactome in CellBase.
-### [Diagnostic Component (TEAM)](software/bio/omics-master/diagnostic-component-team/)
+### [Diagnostic Component (TEAM)](/software/bio/omics-master/diagnostic-component-team/)
-### [Priorization Component (BiERApp)](software/bio/omics-master/priorization-component-bierapp/)
+### [Priorization Component (BiERApp)](/software/bio/omics-master/priorization-component-bierapp/)
## Usage
@@ -262,7 +262,7 @@ The ped file ( file.ped) contains the following info:
FAM sample_B 0 0 2 2
```
-Now, lets load the NGSPipeline module and copy the sample data to a [scratch directory](salomon/storage/):
+Now, lets load the NGSPipeline module and copy the sample data to a [scratch directory](/salomon/storage/):
```console
$ ml ngsPipeline
@@ -276,7 +276,7 @@ Now, we can launch the pipeline (replace OPEN-0-0 with your Project ID):
$ ngsPipeline -i /scratch/$USER/omics/sample_data/data -o /scratch/$USER/omics/results -p /scratch/$USER/omics/sample_data/data/file.ped --project OPEN-0-0 --queue qprod
```
-This command submits the processing [jobs to the queue](salomon/job-submission-and-execution/).
+This command submits the processing [jobs to the queue](/salomon/job-submission-and-execution/).
If we want to re-launch the pipeline from stage 4 until stage 20 we should use the next command:
diff --git a/docs.it4i/software/cae/comsol/comsol-multiphysics.md b/docs.it4i/software/cae/comsol/comsol-multiphysics.md
index f60a1be857e1806670e0ef808af4b28eb7827f67..efda687f1d7ed7f9b54ec612de22da5eba6427fe 100644
--- a/docs.it4i/software/cae/comsol/comsol-multiphysics.md
+++ b/docs.it4i/software/cae/comsol/comsol-multiphysics.md
@@ -18,7 +18,7 @@ On the clusters COMSOL is available in the latest stable version. There are two
* **Non commercial** or so called **EDU variant**, which can be used for research and educational purposes.
-* **Commercial** or so called **COM variant**, which can used also for commercial activities. **COM variant** has only subset of features compared to the **EDU variant** available. More about licensing [here](software/cae/comsol/licensing-and-available-versions/).
+* **Commercial** or so called **COM variant**, which can used also for commercial activities. **COM variant** has only subset of features compared to the **EDU variant** available. More about licensing [here](/software/cae/comsol/licensing-and-available-versions/).
To load the of COMSOL load the module
@@ -32,7 +32,7 @@ By default the **EDU variant** will be loaded. If user needs other version or va
$ ml av COMSOL
```
-If user needs to prepare COMSOL jobs in the interactive mode it is recommend to use COMSOL on the compute nodes via PBS Pro scheduler. In order run the COMSOL Desktop GUI on Windows is recommended to use the [Virtual Network Computing (VNC)](general/accessing-the-clusters/graphical-user-interface/x-window-system/).
+If user needs to prepare COMSOL jobs in the interactive mode it is recommend to use COMSOL on the compute nodes via PBS Pro scheduler. In order run the COMSOL Desktop GUI on Windows is recommended to use the [Virtual Network Computing (VNC)](/general/accessing-the-clusters/graphical-user-interface/x-window-system/).
Example for Salomon:
@@ -76,7 +76,7 @@ Working directory has to be created before sending the (comsol.pbs) job script i
COMSOL is the software package for the numerical solution of the partial differential equations. LiveLink for MATLAB allows connection to the COMSOL API (Application Programming Interface) with the benefits of the programming language and computing environment of the MATLAB.
-LiveLink for MATLAB is available in both **EDU** and **COM** **variant** of the COMSOL release. On the clusters 1 commercial (**COM**) license and the 5 educational (**EDU**) licenses of LiveLink for MATLAB (see the [ISV Licenses](software/isv_licenses/)) are available. Following example shows how to start COMSOL model from MATLAB via LiveLink in the interactive mode (on Anselm use 16 threads).
+LiveLink for MATLAB is available in both **EDU** and **COM** **variant** of the COMSOL release. On the clusters 1 commercial (**COM**) license and the 5 educational (**EDU**) licenses of LiveLink for MATLAB (see the [ISV Licenses](/software/isv_licenses/)) are available. Following example shows how to start COMSOL model from MATLAB via LiveLink in the interactive mode (on Anselm use 16 threads).
```console
$ xhost +
diff --git a/docs.it4i/software/chemistry/molpro.md b/docs.it4i/software/chemistry/molpro.md
index b6d15716474286f60750fb33a6a9a05076669394..fe3863d67e46b8899b92a89bf5ddc5351030533e 100644
--- a/docs.it4i/software/chemistry/molpro.md
+++ b/docs.it4i/software/chemistry/molpro.md
@@ -35,7 +35,7 @@ Molpro is compiled for parallel execution using MPI and OpenMP. By default, Molp
!!! note
The OpenMP parallelization in Molpro is limited and has been observed to produce limited scaling. We therefore recommend to use MPI parallelization only. This can be achieved by passing option mpiprocs=16:ompthreads=1 to PBS.
-You are advised to use the -d option to point to a directory in [SCRATCH file system - Salomon](salomon/storage/). Molpro can produce a large amount of temporary data during its run, and it is important that these are placed in the fast scratch file system.
+You are advised to use the -d option to point to a directory in [SCRATCH file system - Salomon](/salomon/storage/). Molpro can produce a large amount of temporary data during its run, and it is important that these are placed in the fast scratch file system.
### Example jobscript
diff --git a/docs.it4i/software/chemistry/nwchem.md b/docs.it4i/software/chemistry/nwchem.md
index 3c7a1ca5f9b87881154c61a649d4f046673902bd..1a3e1d9449b7b8247af4a8108cb98e3b6e8f0b16 100644
--- a/docs.it4i/software/chemistry/nwchem.md
+++ b/docs.it4i/software/chemistry/nwchem.md
@@ -33,4 +33,4 @@ mpirun nwchem h2o.nw
Please refer to [the documentation](http://www.nwchem-sw.org/index.php/Release62:Top-level) and in the input file set the following directives :
* MEMORY : controls the amount of memory NWChem will use
-* SCRATCH_DIR : set this to a directory in [SCRATCH filesystem - Salomon](salomon/storage/) (or run the calculation completely in a scratch directory). For certain calculations, it might be advisable to reduce I/O by forcing "direct" mode, eg. "scf direct"
+* SCRATCH_DIR : set this to a directory in [SCRATCH filesystem - Salomon](/salomon/storage/) (or run the calculation completely in a scratch directory). For certain calculations, it might be advisable to reduce I/O by forcing "direct" mode, eg. "scf direct"
diff --git a/docs.it4i/software/compilers.md b/docs.it4i/software/compilers.md
index 0aa3a56c949f62ab8d3543f9f28a77725cb49d6d..baf950b5aa48825b78347ee633dc21087e215f84 100644
--- a/docs.it4i/software/compilers.md
+++ b/docs.it4i/software/compilers.md
@@ -24,7 +24,7 @@ Commercial licenses:
## Intel Compilers
-For information about the usage of Intel Compilers and other Intel products, read the [Intel Parallel studio](software/intel-suite/intel-compilers/) page.
+For information about the usage of Intel Compilers and other Intel products, read the [Intel Parallel studio](/software/intel-suite/intel-compilers/) page.
## PGI Compilers (Only on Salomon)
@@ -187,8 +187,8 @@ For more information see the man pages.
## Java
-For information how to use Java (runtime and/or compiler), read the [Java page](software/java/).
+For information how to use Java (runtime and/or compiler), read the [Java page](/software/java/).
## NVIDIA CUDA
-For information how to work with NVIDIA CUDA, read the [NVIDIA CUDA page](anselm/software/nvidia-cuda/).
+For information how to work with NVIDIA CUDA, read the [NVIDIA CUDA page](/anselm/software/nvidia-cuda/).
diff --git a/docs.it4i/software/debuggers/Introduction.md b/docs.it4i/software/debuggers/Introduction.md
index 947da202b8a84d10927943851019bf88b467a27d..2eaa9033589fe940555d7a57a3a7156f4cc6528a 100644
--- a/docs.it4i/software/debuggers/Introduction.md
+++ b/docs.it4i/software/debuggers/Introduction.md
@@ -15,7 +15,7 @@ $ ml intel
$ idb
```
-Read more at the [Intel Debugger](software/intel/intel-suite/intel-debugger/) page.
+Read more at the [Intel Debugger](/software/intel/intel-suite/intel-debugger/) page.
## Allinea Forge (DDT/MAP)
@@ -26,7 +26,7 @@ $ ml Forge
$ forge
```
-Read more at the [Allinea DDT](software/debuggers/allinea-ddt/) page.
+Read more at the [Allinea DDT](/software/debuggers/allinea-ddt/) page.
## Allinea Performance Reports
@@ -37,7 +37,7 @@ $ ml PerformanceReports/6.0
$ perf-report mpirun -n 64 ./my_application argument01 argument02
```
-Read more at the [Allinea Performance Reports](software/debuggers/allinea-performance-reports/) page.
+Read more at the [Allinea Performance Reports](/software/debuggers/allinea-performance-reports/) page.
## RougeWave Totalview
@@ -48,7 +48,7 @@ $ ml TotalView/8.15.4-6-linux-x86-64
$ totalview
```
-Read more at the [Totalview](software/debuggers/total-view/) page.
+Read more at the [Totalview](/software/debuggers/total-view/) page.
## Vampir Trace Analyzer
@@ -59,4 +59,4 @@ Vampir is a GUI trace analyzer for traces in OTF format.
$ vampir
```
-Read more at the [Vampir](software/debuggers/vampir/) page.
+Read more at the [Vampir](/software/debuggers/vampir/) page.
diff --git a/docs.it4i/software/debuggers/allinea-ddt.md b/docs.it4i/software/debuggers/allinea-ddt.md
index 984091fad44a50bbed454b937488e3d52bfa3a00..67bfdff184ed1244a154848de728d58f4c678c94 100644
--- a/docs.it4i/software/debuggers/allinea-ddt.md
+++ b/docs.it4i/software/debuggers/allinea-ddt.md
@@ -59,7 +59,7 @@ Be sure to log in with an X window forwarding enabled. This could mean using the
$ ssh -X username@anselm.it4i.cz
```
-Other options is to access login node using VNC. Please see the detailed information on how to [use graphic user interface on Anselm](general/accessing-the-clusters/graphical-user-interface/x-window-system/)
+Other options is to access login node using VNC. Please see the detailed information on how to [use graphic user interface on Anselm](/general/accessing-the-clusters/graphical-user-interface/x-window-system/)
From the login node an interactive session **with X windows forwarding** (-X option) can be started by following command:
diff --git a/docs.it4i/software/debuggers/allinea-performance-reports.md b/docs.it4i/software/debuggers/allinea-performance-reports.md
index cc684a10d58bf79a83eca6e0084ee219e87c02f1..6484c1b9d3257dff2265110de829d0f0557f5764 100644
--- a/docs.it4i/software/debuggers/allinea-performance-reports.md
+++ b/docs.it4i/software/debuggers/allinea-performance-reports.md
@@ -22,13 +22,13 @@ The module sets up environment variables, required for using the Allinea Perform
Use the the perf-report wrapper on your (MPI) program.
-Instead of [running your MPI program the usual way](software/mpi/mpi/), use the the perf report wrapper:
+Instead of [running your MPI program the usual way](/software/mpi/mpi/), use the the perf report wrapper:
```console
$ perf-report mpirun ./mympiprog.x
```
-The MPI program will run as usual. The perf-report creates two additional files, in \*.txt and \*.html format, containing the performance report. Note that demanding MPI codes should be run within [the queue system](salomon/job-submission-and-execution/).
+The MPI program will run as usual. The perf-report creates two additional files, in \*.txt and \*.html format, containing the performance report. Note that demanding MPI codes should be run within [the queue system](/salomon/job-submission-and-execution/).
## Example
diff --git a/docs.it4i/software/debuggers/intel-performance-counter-monitor.md b/docs.it4i/software/debuggers/intel-performance-counter-monitor.md
index b5da7bf6061aecd7f6dac2306e63f8a0e9cba7d2..bbc08292b967f5ded59f362f3eebc1584e045dcf 100644
--- a/docs.it4i/software/debuggers/intel-performance-counter-monitor.md
+++ b/docs.it4i/software/debuggers/intel-performance-counter-monitor.md
@@ -2,7 +2,7 @@
## Introduction
-Intel PCM (Performance Counter Monitor) is a tool to monitor performance hardware counters on Intel>® processors, similar to [PAPI](software/debuggers/papi/). The difference between PCM and PAPI is that PCM supports only Intel hardware, but PCM can monitor also uncore metrics, like memory controllers and QuickPath Interconnect links.
+Intel PCM (Performance Counter Monitor) is a tool to monitor performance hardware counters on Intel>® processors, similar to [PAPI](/software/debuggers/papi/). The difference between PCM and PAPI is that PCM supports only Intel hardware, but PCM can monitor also uncore metrics, like memory controllers and QuickPath Interconnect links.
## Installed Version
diff --git a/docs.it4i/software/debuggers/papi.md b/docs.it4i/software/debuggers/papi.md
index 8361776dbe79a274dd7df4b43cef9d27e391e22b..4fcc35a653baf4fd36d11db5985851a90b0db35b 100644
--- a/docs.it4i/software/debuggers/papi.md
+++ b/docs.it4i/software/debuggers/papi.md
@@ -193,7 +193,7 @@ $ ./matrix
!!! note
PAPI currently supports only a subset of counters on the Intel Xeon Phi processor compared to Intel Xeon, for example the floating point operations counter is missing.
-To use PAPI in [Intel Xeon Phi](software/intel/intel-xeon-phi-salomon/) native applications, you need to load module with " -mic" suffix, for example " papi/5.3.2-mic" :
+To use PAPI in [Intel Xeon Phi](/software/intel/intel-xeon-phi-salomon/) native applications, you need to load module with " -mic" suffix, for example " papi/5.3.2-mic" :
```console
$ ml papi/5.3.2-mic
diff --git a/docs.it4i/software/debuggers/scalasca.md b/docs.it4i/software/debuggers/scalasca.md
index 066076b885ddd8f4ba57f08e9f20cc821d399cfe..76286508d32c9d5ffa5a406f11c424638e2f5dc2 100644
--- a/docs.it4i/software/debuggers/scalasca.md
+++ b/docs.it4i/software/debuggers/scalasca.md
@@ -10,8 +10,8 @@ Scalasca supports profiling of MPI, OpenMP and hybrid MPI+OpenMP applications.
There are currently two versions of Scalasca 2.0 [modules](modules-matrix/) installed on Anselm:
-* scalasca2/2.0-gcc-openmpi, for usage with [GNU Compiler](software/compilers/) and [OpenMPI](software/mpi/Running_OpenMPI/),
-* scalasca2/2.0-icc-impi, for usage with [Intel Compiler](software/compilers/) and [Intel MPI](software/mpi/running-mpich2/).
+* scalasca2/2.0-gcc-openmpi, for usage with [GNU Compiler](/software/compilers/) and [OpenMPI](software/mpi/Running_OpenMPI/),
+* scalasca2/2.0-icc-impi, for usage with [Intel Compiler](/software/compilers/) and [Intel MPI](software/mpi/running-mpich2/).
## Usage
@@ -23,7 +23,7 @@ Profiling a parallel application with Scalasca consists of three steps:
### Instrumentation
-Instrumentation via `scalasca -instrument` is discouraged. Use [Score-P instrumentation](software/debuggers/score-p/).
+Instrumentation via `scalasca -instrument` is discouraged. Use [Score-P instrumentation](/software/debuggers/score-p/).
### Runtime Measurement
@@ -43,11 +43,11 @@ Some notable Scalasca options are:
* **-e <directory> Specify a directory to save the collected data to. By default, Scalasca saves the data to a directory with prefix scorep\_, followed by name of the executable and launch configuration.**
!!! note
- Scalasca can generate a huge amount of data, especially if tracing is enabled. Please consider saving the data to a [scratch directory](salomon/storage/).
+ Scalasca can generate a huge amount of data, especially if tracing is enabled. Please consider saving the data to a [scratch directory](/salomon/storage/).
### Analysis of Reports
-For the analysis, you must have [Score-P](software/debuggers/score-p/) and [CUBE](software/debuggers/cube/) modules loaded. The analysis is done in two steps, first, the data is preprocessed and then CUBE GUI tool is launched.
+For the analysis, you must have [Score-P](/software/debuggers/score-p/) and [CUBE](software/debuggers/cube/) modules loaded. The analysis is done in two steps, first, the data is preprocessed and then CUBE GUI tool is launched.
To launch the analysis, run :
@@ -63,7 +63,7 @@ scalasca -examine -s <experiment_directory>
Alternatively you can open CUBE and load the data directly from here. Keep in mind that in that case the pre-processing is not done and not all metrics will be shown in the viewer.
-Refer to [CUBE documentation](software/debuggers/cube/) on usage of the GUI viewer.
+Refer to [CUBE documentation](/software/debuggers/cube/) on usage of the GUI viewer.
## References
diff --git a/docs.it4i/software/debuggers/score-p.md b/docs.it4i/software/debuggers/score-p.md
index afb55bc3be83956c28fb50b2dee7414a2ba1fda1..4fce492a0ce317466b5e7badedd5bdba78e1fb4c 100644
--- a/docs.it4i/software/debuggers/score-p.md
+++ b/docs.it4i/software/debuggers/score-p.md
@@ -4,14 +4,14 @@
The [Score-P measurement infrastructure](http://www.vi-hps.org/projects/score-p/) is a highly scalable and easy-to-use tool suite for profiling, event tracing, and online analysis of HPC applications.
-Score-P can be used as an instrumentation tool for [Scalasca](software/debuggers/scalasca/).
+Score-P can be used as an instrumentation tool for [Scalasca](/software/debuggers/scalasca/).
## Installed Versions
There are currently two versions of Score-P version 1.2.6 [modules](modules-matrix/) installed on Anselm :
-* scorep/1.2.3-gcc-openmpi, for usage with [GNU Compiler](software/compilers/) and [OpenMPI](software/mpi/Running_OpenMPI/)
-* scorep/1.2.3-icc-impi, for usage with [Intel Compiler](software/compilers/)> and [Intel MPI](software/mpi/running-mpich2/)>.
+* scorep/1.2.3-gcc-openmpi, for usage with [GNU Compiler](/software/compilers/) and [OpenMPI](software/mpi/Running_OpenMPI/)
+* scorep/1.2.3-icc-impi, for usage with [Intel Compiler](/software/compilers/)> and [Intel MPI](software/mpi/running-mpich2/)>.
## Instrumentation
diff --git a/docs.it4i/software/debuggers/vampir.md b/docs.it4i/software/debuggers/vampir.md
index 3a1e9c2ee43d07099d2e20f6b4abc2cec947f19f..e1c880f4d6e1a24b46e74c3d4b678b2feaa4bc86 100644
--- a/docs.it4i/software/debuggers/vampir.md
+++ b/docs.it4i/software/debuggers/vampir.md
@@ -1,6 +1,6 @@
# Vampir
-Vampir is a commercial trace analysis and visualization tool. It can work with traces in OTF and OTF2 formats. It does not have the functionality to collect traces, you need to use a trace collection tool (such as [Score-P](software/debuggers/score-p/)) first to collect the traces.
+Vampir is a commercial trace analysis and visualization tool. It can work with traces in OTF and OTF2 formats. It does not have the functionality to collect traces, you need to use a trace collection tool (such as [Score-P](/software/debuggers/score-p/)) first to collect the traces.
diff --git a/docs.it4i/software/intel/intel-suite/intel-debugger.md b/docs.it4i/software/intel/intel-suite/intel-debugger.md
index db236753532b85e4757f2bd8643c5ba1a5475c5b..bbb68a615eb8eddd540454e5cae3c7bc9cfd6e9a 100644
--- a/docs.it4i/software/intel/intel-suite/intel-debugger.md
+++ b/docs.it4i/software/intel/intel-suite/intel-debugger.md
@@ -4,7 +4,7 @@ IDB is no longer available since Intel Parallel Studio 2015
## Debugging Serial Applications
-The intel debugger version is available, via module intel/13.5.192. 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](general/accessing-the-clusters/graphical-user-interface/x-window-system/) for running the GUI.
+The intel debugger version is available, via module intel/13.5.192. 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](/general/accessing-the-clusters/graphical-user-interface/x-window-system/) for running the GUI.
```console
$ ml intel/13.5.192
@@ -18,7 +18,7 @@ The debugger may run in text mode. To debug in text mode, use
$ idbc
```
-To debug on the compute nodes, module intel must be loaded. The GUI on compute nodes may be accessed using the same way as in [the GUI section](general/accessing-the-clusters/graphical-user-interface/x-window-system/)
+To debug on the compute nodes, module intel must be loaded. The GUI on compute nodes may be accessed using the same way as in [the GUI section](/general/accessing-the-clusters/graphical-user-interface/x-window-system/)
Example:
@@ -40,7 +40,7 @@ In this example, we allocate 1 full compute node, compile program myprog.c with
### Small Number of MPI Ranks
-For debugging small number of MPI ranks, you may execute and debug each rank in separate xterm terminal (do not forget the [X display](general/accessing-the-clusters/graphical-user-interface/x-window-system/)). Using Intel MPI, this may be done in following way:
+For debugging small number of MPI ranks, you may execute and debug each rank in separate xterm terminal (do not forget the [X display](/general/accessing-the-clusters/graphical-user-interface/x-window-system/)). Using Intel MPI, this may be done in following way:
```console
$ qsub -q qexp -l select=2:ncpus=24 -X -I
diff --git a/docs.it4i/software/intel/intel-suite/intel-mkl.md b/docs.it4i/software/intel/intel-suite/intel-mkl.md
index cc2a80c55c8b3224b470ad0042562b18078eeeaa..ceff86201db04a39f134f7d58cafb856051c8dc8 100644
--- a/docs.it4i/software/intel/intel-suite/intel-mkl.md
+++ b/docs.it4i/software/intel/intel-suite/intel-mkl.md
@@ -109,7 +109,7 @@ In this example, we compile, link and run the cblas_dgemm example, using LP64 in
## MKL and MIC Accelerators
-The Intel MKL is capable to automatically offload the computations o the MIC accelerator. See section [Intel Xeon Phi](software/intel/intel-xeon-phi-salomon/) for details.
+The Intel MKL is capable to automatically offload the computations o the MIC accelerator. See section [Intel Xeon Phi](/software/intel/intel-xeon-phi-salomon/) for details.
## LAPACKE C Interface
diff --git a/docs.it4i/software/intel/intel-suite/intel-parallel-studio-introduction.md b/docs.it4i/software/intel/intel-suite/intel-parallel-studio-introduction.md
index 264b15e9dbe981c8786157cae3bf4f3e3372e3ab..3306cf687d9cf1382886c81ba1a7c6a5d2edb524 100644
--- a/docs.it4i/software/intel/intel-suite/intel-parallel-studio-introduction.md
+++ b/docs.it4i/software/intel/intel-suite/intel-parallel-studio-introduction.md
@@ -23,7 +23,7 @@ $ icc -v
$ ifort -v
```
-Read more at the [Intel Compilers](software/intel/intel-suite/intel-compilers/) page.
+Read more at the [Intel Compilers](/software/intel/intel-suite/intel-compilers/) page.
## Intel Debugger
@@ -36,7 +36,7 @@ $ ml intel
$ idb
```
-Read more at the [Intel Debugger](software/intel/intel-suite/intel-debugger/) page.
+Read more at the [Intel Debugger](/software/intel/intel-suite/intel-debugger/) page.
## Intel Math Kernel Library
@@ -46,7 +46,7 @@ Intel Math Kernel Library (Intel MKL) is a library of math kernel subroutines, e
$ ml imkl
```
-Read more at the [Intel MKL](software/intel/intel-suite/intel-mkl/) page.
+Read more at the [Intel MKL](/software/intel/intel-suite/intel-mkl/) page.
## Intel Integrated Performance Primitives
@@ -56,7 +56,7 @@ Intel Integrated Performance Primitives, version 7.1.1, compiled for AVX is avai
$ ml ipp
```
-Read more at the [Intel IPP](software/intel/intel-suite/intel-integrated-performance-primitives/) page.
+Read more at the [Intel IPP](/software/intel/intel-suite/intel-integrated-performance-primitives/) page.
## Intel Threading Building Blocks
@@ -66,4 +66,4 @@ Intel Threading Building Blocks (Intel TBB) is a library that supports scalable
$ ml tbb
```
-Read more at the [Intel TBB](software/intel/intel-suite/intel-tbb/) page.
+Read more at the [Intel TBB](/software/intel/intel-suite/intel-tbb/) page.
diff --git a/docs.it4i/software/intel/intel-suite/intel-tbb.md b/docs.it4i/software/intel/intel-suite/intel-tbb.md
index d28a92d244539cf04c2b0b349be5a8a421a84d4d..d04d448417c89886fbdbc50ad3f9edc988d3ed37 100644
--- a/docs.it4i/software/intel/intel-suite/intel-tbb.md
+++ b/docs.it4i/software/intel/intel-suite/intel-tbb.md
@@ -2,7 +2,7 @@
## Intel Threading Building Blocks
-Intel Threading Building Blocks (Intel TBB) is a library that supports scalable parallel programming using standard ISO C++ code. It does not require special languages or compilers. To use the library, you specify tasks, not threads, and let the library map tasks onto threads in an efficient manner. The tasks are executed by a runtime scheduler and may be offloaded to [MIC accelerator](software/intel//intel-xeon-phi-salomon/).
+Intel Threading Building Blocks (Intel TBB) is a library that supports scalable parallel programming using standard ISO C++ code. It does not require special languages or compilers. To use the library, you specify tasks, not threads, and let the library map tasks onto threads in an efficient manner. The tasks are executed by a runtime scheduler and may be offloaded to [MIC accelerator](/software/intel//intel-xeon-phi-salomon/).
Intel is available on the cluster.
diff --git a/docs.it4i/software/intel/intel-suite/intel-trace-analyzer-and-collector.md b/docs.it4i/software/intel/intel-suite/intel-trace-analyzer-and-collector.md
index 7a86f2d0a2dc5ad9f2ad5bf3287ca0353ef2cac5..cecfbe09683e12e8a03cb106e07652ad9ec4d8b4 100644
--- a/docs.it4i/software/intel/intel-suite/intel-trace-analyzer-and-collector.md
+++ b/docs.it4i/software/intel/intel-suite/intel-trace-analyzer-and-collector.md
@@ -21,7 +21,7 @@ The trace will be saved in file myapp.stf in the current directory.
## Viewing Traces
-To view and analyze the trace, open ITAC GUI in a [graphical environment](general/accessing-the-clusters/graphical-user-interface/x-window-system/):
+To view and analyze the trace, open ITAC GUI in a [graphical environment](/general/accessing-the-clusters/graphical-user-interface/x-window-system/):
```console
$ ml itac/9.1.2.024
diff --git a/docs.it4i/software/isv_licenses.md b/docs.it4i/software/isv_licenses.md
index d7cbb7cc91d3edc31cbd3f3a1fac145b5749b1cd..ef4e1177ba73682c94e22dbb3cba7eda7bd19733 100644
--- a/docs.it4i/software/isv_licenses.md
+++ b/docs.it4i/software/isv_licenses.md
@@ -68,7 +68,7 @@ Names of applications (APP):
matlab-edu
```
-To get the FEATUREs of a license take a look into the corresponding state file ([see above](software/isv_licenses/#Licence)), or use:
+To get the FEATUREs of a license take a look into the corresponding state file ([see above](/software/isv_licenses/#Licence)), or use:
### Application and List of Provided Features
diff --git a/docs.it4i/software/machine-learning/introduction.md b/docs.it4i/software/machine-learning/introduction.md
index 5c7288676d0a7fd95a282b9b19b8a8bdd2a08a31..4058388d646523034695f0be1ac24b01b634efb4 100644
--- a/docs.it4i/software/machine-learning/introduction.md
+++ b/docs.it4i/software/machine-learning/introduction.md
@@ -16,7 +16,7 @@ Test module:
$ ml Tensorflow
```
-Read more about available versions at the [TensorFlow page](software/machine-learning/tensorflow/).
+Read more about available versions at the [TensorFlow page](/software/machine-learning/tensorflow/).
## Theano
diff --git a/docs.it4i/software/mic/mic_environment.md b/docs.it4i/software/mic/mic_environment.md
index 7f36f256acd7e4511e9ab9c29a29fff4f85a0d53..92a439a2e1ce1f760071e8dab73442dfac9136d5 100644
--- a/docs.it4i/software/mic/mic_environment.md
+++ b/docs.it4i/software/mic/mic_environment.md
@@ -1,12 +1,12 @@
# Intel Xeon Phi Environment
-Intel Xeon Phi (so-called MIC) accelerator can be used in several modes ([Offload](software/intel/intel-xeon-phi-salomon/#offload-mode) and [Native](#native-mode)). The default mode on the cluster is offload mode, but all modes described in this document are supported.
+Intel Xeon Phi (so-called MIC) accelerator can be used in several modes ([Offload](/software/intel/intel-xeon-phi-salomon/#offload-mode) and [Native](#native-mode)). The default mode on the cluster is offload mode, but all modes described in this document are supported.
See sections below for more details.
## Intel Utilities for Xeon Phi
-Continue [here](software/intel/intel-xeon-phi-salomon/)
+Continue [here](/software/intel/intel-xeon-phi-salomon/)
## GCC With [KNC](https://en.wikipedia.org/wiki/Xeon_Phi) Support
@@ -434,4 +434,4 @@ Configure step (for `configure`,`make` and `make install` software)
Modulefile and Lmod
-* Read [Lmod](software/modules/lmod/)
+* Read [Lmod](/software/modules/lmod/)
diff --git a/docs.it4i/software/mpi/mpi.md b/docs.it4i/software/mpi/mpi.md
index b8a61b25e4ec94d8b6616197e23ba445c0ba3c0a..8356521faec784b9a320cc29d2aeaf8a5b9652f8 100644
--- a/docs.it4i/software/mpi/mpi.md
+++ b/docs.it4i/software/mpi/mpi.md
@@ -136,6 +136,6 @@ In the previous two cases with one or two MPI processes per node, the operating
### Running OpenMPI
-The [**OpenMPI 1.8.6**](http://www.open-mpi.org/) is based on OpenMPI. Read more on [how to run OpenMPI](software/mpi/Running_OpenMPI/) based MPI.
+The [**OpenMPI 1.8.6**](http://www.open-mpi.org/) is based on OpenMPI. Read more on [how to run OpenMPI](/software/mpi/Running_OpenMPI/) based MPI.
-The Intel MPI may run on the [Intel Xeon Ph](software/intel/intel-xeon-phi-salomon/) accelerators as well. Read more on [how to run Intel MPI on accelerators](software/intel/intel-xeon-phi-salomon/).
+The Intel MPI may run on the [Intel Xeon Ph](/software/intel/intel-xeon-phi-salomon/) accelerators as well. Read more on [how to run Intel MPI on accelerators](software/intel/intel-xeon-phi-salomon/).
diff --git a/docs.it4i/software/mpi/mpi4py-mpi-for-python.md b/docs.it4i/software/mpi/mpi4py-mpi-for-python.md
index ea39d00485f4e981ee840b6c0f588a4bbb1536f4..b6056fd454487e5756b6e61e24fac9c30dfb8835 100644
--- a/docs.it4i/software/mpi/mpi4py-mpi-for-python.md
+++ b/docs.it4i/software/mpi/mpi4py-mpi-for-python.md
@@ -42,7 +42,7 @@ You need to import MPI to your python program. Include the following line to the
from mpi4py import MPI
```
-The MPI4Py enabled python programs [execute as any other OpenMPI](salomon/mpi/Running_OpenMPI/) code.The simpliest way is to run
+The MPI4Py enabled python programs [execute as any other OpenMPI](/salomon/mpi/Running_OpenMPI/) code.The simpliest way is to run
```console
$ mpiexec python <script>.py
diff --git a/docs.it4i/software/mpi/running-mpich2.md b/docs.it4i/software/mpi/running-mpich2.md
index 35452ed707e80ab5624efa4d582ecd7c0aba9c34..b35d7370cb86b514a988249aa445e463b17ae423 100644
--- a/docs.it4i/software/mpi/running-mpich2.md
+++ b/docs.it4i/software/mpi/running-mpich2.md
@@ -152,4 +152,4 @@ $ mpirun -bindto numa echo $OMP_NUM_THREADS
## Intel MPI on Xeon Phi
-The [MPI section of Intel Xeon Phi chapter](software/intel/intel-xeon-phi-salomon/) provides details on how to run Intel MPI code on Xeon Phi architecture.
+The [MPI section of Intel Xeon Phi chapter](/software/intel/intel-xeon-phi-salomon/) provides details on how to run Intel MPI code on Xeon Phi architecture.
diff --git a/docs.it4i/software/numerical-languages/introduction.md b/docs.it4i/software/numerical-languages/introduction.md
index 50ef104606a5ff3c4c011c3685444be683521189..fa9cf294329593834541c29baa8c1e2b47bef815 100644
--- a/docs.it4i/software/numerical-languages/introduction.md
+++ b/docs.it4i/software/numerical-languages/introduction.md
@@ -15,7 +15,7 @@ $ ml MATLAB
$ matlab
```
-Read more at the [Matlab page](software/numerical-languages/matlab/).
+Read more at the [Matlab page](/software/numerical-languages/matlab/).
## Octave
@@ -26,7 +26,7 @@ $ ml Octave
$ octave
```
-Read more at the [Octave page](software/numerical-languages/octave/).
+Read more at the [Octave page](/software/numerical-languages/octave/).
## R
@@ -37,4 +37,4 @@ $ ml R
$ R
```
-Read more at the [R page](software/numerical-languages/r/).
+Read more at the [R page](/software/numerical-languages/r/).
diff --git a/docs.it4i/software/numerical-languages/matlab.md b/docs.it4i/software/numerical-languages/matlab.md
index 73a283ae903216f0c28b4c08cc7650e3ab5a0d8d..321250b3dc25b565d05149333f35c85b170c59a7 100644
--- a/docs.it4i/software/numerical-languages/matlab.md
+++ b/docs.it4i/software/numerical-languages/matlab.md
@@ -21,9 +21,9 @@ $ 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, 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 (see the "GUI Applications on Compute Nodes over VNC" part [here](general/accessing-the-clusters/graphical-user-interface/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/)) is recommended.
To run Matlab with GUI, use
@@ -68,7 +68,7 @@ With the new mode, MATLAB itself launches the workers via PBS, so you can either
### Parallel Matlab Interactive Session
-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/).
+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/).
```console
$ xhost +
@@ -249,11 +249,11 @@ 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, [look here](software/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](/software/isv_licenses/).
The licensing feature of PBS is currently disabled.
-In case of non-interactive session read the [following information](software/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](/software/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
diff --git a/docs.it4i/software/numerical-languages/matlab_1314.md b/docs.it4i/software/numerical-languages/matlab_1314.md
index 8197edccb9ae71ee180cfedc1d8a47342ac79bef..751e56a5ea810af2644883f7aa43778d67547a1e 100644
--- a/docs.it4i/software/numerical-languages/matlab_1314.md
+++ b/docs.it4i/software/numerical-languages/matlab_1314.md
@@ -3,7 +3,7 @@
## Introduction
!!! note
- This document relates to the old versions R2013 and R2014. For MATLAB 2015 use [this documentation instead](software/numerical-languages/matlab/).
+ This document relates to the old versions R2013 and R2014. For MATLAB 2015 use [this documentation instead](/software/numerical-languages/matlab/).
Matlab is available in the latest stable version. There are always two variants of the release:
@@ -190,9 +190,9 @@ You can copy and paste the example in a .m file and execute. Note that the matla
### 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, [look here](software/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](/software/isv_licenses/).
-In case of non-interactive session read the [following information](software/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](/software/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
diff --git a/docs.it4i/software/numerical-languages/octave.md b/docs.it4i/software/numerical-languages/octave.md
index 5246115022ad5d054876899a943b84ac2af046d7..385724804db00175325c4c8243d2886fade1590d 100644
--- a/docs.it4i/software/numerical-languages/octave.md
+++ b/docs.it4i/software/numerical-languages/octave.md
@@ -60,11 +60,11 @@ Octave may use MPI for interprocess communication This functionality is currentl
## Xeon Phi Support
-Octave may take advantage of the Xeon Phi accelerators. This will only work on the [Intel Xeon Phi](software/intel/intel-xeon-phi-salomon/) [accelerated nodes](salomon/compute-nodes/).
+Octave may take advantage of the Xeon Phi accelerators. This will only work on the [Intel Xeon Phi](/software/intel/intel-xeon-phi-salomon/) [accelerated nodes](/salomon/compute-nodes/).
### Automatic Offload Support
-Octave can accelerate BLAS type operations (in particular the Matrix Matrix multiplications] on the Xeon Phi accelerator, via [Automatic Offload using the MKL library](software/intel/intel-xeon-phi-salomon/)
+Octave can accelerate BLAS type operations (in particular the Matrix Matrix multiplications] on the Xeon Phi accelerator, via [Automatic Offload using the MKL library](/software/intel/intel-xeon-phi-salomon/)
Example
@@ -88,7 +88,7 @@ In this example, the calculation was automatically divided among the CPU cores a
### Native Support
-A version of [native](software/intel/intel-xeon-phi-salomon/) Octave is compiled for Xeon Phi accelerators. Some limitations apply for this version:
+A version of [native](/software/intel/intel-xeon-phi-salomon/) Octave is compiled for Xeon Phi accelerators. Some limitations apply for this version:
* Only command line support. GUI, graph plotting etc. is not supported.
* Command history in interactive mode is not supported.
diff --git a/docs.it4i/software/numerical-languages/r.md b/docs.it4i/software/numerical-languages/r.md
index 81ba42081f1261d525dec8bb4c9bf5c7b17ce842..9081feb843d2a28b0a2d3c19ab290e8e85d6f2d7 100644
--- a/docs.it4i/software/numerical-languages/r.md
+++ b/docs.it4i/software/numerical-languages/r.md
@@ -66,7 +66,7 @@ cp routput.out $PBS_O_WORKDIR/.
exit
```
-This script may be submitted directly to the PBS workload manager via the qsub command. The inputs are in rscript.R file, outputs in routput.out file. See the single node jobscript example in the [Job execution section - Anselm](anselm/job-submission-and-execution/).
+This script may be submitted directly to the PBS workload manager via the qsub command. The inputs are in rscript.R file, outputs in routput.out file. See the single node jobscript example in the [Job execution section - Anselm](/anselm/job-submission-and-execution/).
## Parallel R
@@ -144,7 +144,7 @@ Every evaluation of the integrad function runs in parallel on different process.
package Rmpi provides an interface (wrapper) to MPI APIs.
-It also provides interactive R slave environment. On the cluster, Rmpi provides interface to the [OpenMPI](software/mpi/Running_OpenMPI/).
+It also provides interactive R slave environment. On the cluster, Rmpi provides interface to the [OpenMPI](/software/mpi/Running_OpenMPI/).
Read more on Rmpi at <http://cran.r-project.org/web/packages/Rmpi/>, reference manual is available at [here](http://cran.r-project.org/web/packages/Rmpi/Rmpi.pdf)
@@ -390,7 +390,7 @@ cp routput.out $PBS_O_WORKDIR/.
exit
```
-For more information about jobscripts and MPI execution refer to the [Job submission](anselm/job-submission-and-execution/) and general [MPI](software/mpi/mpi/) sections.
+For more information about jobscripts and MPI execution refer to the [Job submission](/anselm/job-submission-and-execution/) and general [MPI](/software/mpi/mpi/) sections.
## Xeon Phi Offload
@@ -400,4 +400,4 @@ By leveraging MKL, R can accelerate certain computations, most notably linear al
$ export MKL_MIC_ENABLE=1
```
-[Read more about automatic offload](software/intel/intel-xeon-phi-salomon/)
+[Read more about automatic offload](/software/intel/intel-xeon-phi-salomon/)
diff --git a/docs.it4i/software/numerical-libraries/fftw.md b/docs.it4i/software/numerical-libraries/fftw.md
index 0807bd4d8c9f3b7b3b8b637c623e4f6f4cd80666..9ec5c53604c6fae770ab55a7a1a4f8dbb1abc098 100644
--- a/docs.it4i/software/numerical-libraries/fftw.md
+++ b/docs.it4i/software/numerical-libraries/fftw.md
@@ -68,6 +68,6 @@ $ ml fftw3-mpi
$ mpicc testfftw3mpi.c -o testfftw3mpi.x -Wl,-rpath=$LIBRARY_PATH -lfftw3_mpi
```
-Run the example as [Intel MPI program](software/mpi/running-mpich2/).
+Run the example as [Intel MPI program](/software/mpi/running-mpich2/).
Read more on FFTW usage on the [FFTW website.](http://www.fftw.org/fftw3_doc/)
diff --git a/docs.it4i/software/numerical-libraries/hdf5.md b/docs.it4i/software/numerical-libraries/hdf5.md
index 11cd26da0760918e98d78b76f3a31b9e370bb9fd..e0c6d78800fdb6c197c7c87cb85dae31232c4913 100644
--- a/docs.it4i/software/numerical-libraries/hdf5.md
+++ b/docs.it4i/software/numerical-libraries/hdf5.md
@@ -84,6 +84,6 @@ $ ml hdf5-parallel
$ mpicc hdf5test.c -o hdf5test.x -Wl,-rpath=$LIBRARY_PATH $HDF5_INC $HDF5_SHLIB
```
-Run the example as [Intel MPI program](software/mpi/running-mpich2/).
+Run the example as [Intel MPI program](/software/mpi/running-mpich2/).
For further information, see the website: [http://www.hdfgroup.org/HDF5/](http://www.hdfgroup.org/HDF5/)
diff --git a/docs.it4i/software/numerical-libraries/intel-numerical-libraries.md b/docs.it4i/software/numerical-libraries/intel-numerical-libraries.md
index f25d6edd52ca26f6f9cfd8a71668bc709b398427..dcbe8889418882ae38864369be88c30bc5adacce 100644
--- a/docs.it4i/software/numerical-libraries/intel-numerical-libraries.md
+++ b/docs.it4i/software/numerical-libraries/intel-numerical-libraries.md
@@ -10,7 +10,7 @@ Intel Math Kernel Library (Intel MKL) is a library of math kernel subroutines, e
$ ml mkl **or** ml imkl
```
-Read more at the [Intel MKL](software/intel/intel-suite/intel-mkl/) page.
+Read more at the [Intel MKL](/software/intel/intel-suite/intel-mkl/) page.
## Intel Integrated Performance Primitives
@@ -20,7 +20,7 @@ Intel Integrated Performance Primitives, version 7.1.1, compiled for AVX is avai
$ ml ipp
```
-Read more at the [Intel IPP](software/intel/intel-suite/intel-integrated-performance-primitives/) page.
+Read more at the [Intel IPP](/software/intel/intel-suite/intel-integrated-performance-primitives/) page.
## Intel Threading Building Blocks
@@ -30,4 +30,4 @@ Intel Threading Building Blocks (Intel TBB) is a library that supports scalable
$ ml tbb
```
-Read more at the [Intel TBB](software/intel/intel-suite/intel-tbb/) page.
+Read more at the [Intel TBB](/software/intel/intel-suite/intel-tbb/) page.
diff --git a/docs.it4i/software/tools/ansys/ansys-cfx.md b/docs.it4i/software/tools/ansys/ansys-cfx.md
index 48dac488a1a9cf0215f555a0faa08aec0f5cd86d..49a47327ff7ea82786dd9a4dc2dabce8b295cadd 100644
--- a/docs.it4i/software/tools/ansys/ansys-cfx.md
+++ b/docs.it4i/software/tools/ansys/ansys-cfx.md
@@ -47,7 +47,7 @@ echo Machines: $hl
/ansys_inc/v145/CFX/bin/cfx5solve -def input.def -size 4 -size-ni 4x -part-large -start-method "Platform MPI Distributed Parallel" -par-dist $hl -P aa_r
```
-Header of the PBS file (above) is common and description can be find on [this site](anselm/job-submission-and-execution/). SVS FEM recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.
+Header of the PBS file (above) is common and description can be find on [this site](/anselm/job-submission-and-execution/). SVS FEM recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.
Working directory has to be created before sending PBS job into the queue. Input file should be in working directory or full path to input file has to be specified. >Input file has to be defined by common CFX def file which is attached to the CFX solver via parameter -def
diff --git a/docs.it4i/software/tools/ansys/ansys-fluent.md b/docs.it4i/software/tools/ansys/ansys-fluent.md
index ef50d856c3a5d5070d95cfc3f8d391e35ea44802..63444f88a0a3c984981200af2eaf6e8acbcbb04b 100644
--- a/docs.it4i/software/tools/ansys/ansys-fluent.md
+++ b/docs.it4i/software/tools/ansys/ansys-fluent.md
@@ -38,7 +38,7 @@ NCORES=`wc -l $PBS_NODEFILE |awk '{print $1}'`
/ansys_inc/v145/fluent/bin/fluent 3d -t$NCORES -cnf=$PBS_NODEFILE -g -i fluent.jou
```
-Header of the pbs file (above) is common and description can be find on [this site](salomon/resources-allocation-policy/). [SVS FEM](http://www.svsfem.cz) recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.
+Header of the pbs file (above) is common and description can be find on [this site](/salomon/resources-allocation-policy/). [SVS FEM](http://www.svsfem.cz) recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.
Working directory has to be created before sending pbs job into the queue. Input file should be in working directory or full path to input file has to be specified. Input file has to be defined by common Fluent journal file which is attached to the Fluent solver via parameter -i fluent.jou
diff --git a/docs.it4i/software/tools/ansys/ansys-ls-dyna.md b/docs.it4i/software/tools/ansys/ansys-ls-dyna.md
index cdc14b1f42a86a0888e399a118a7a3bdeea3814f..00328000b323db015b659c8626e38a1b0a7a5eb3 100644
--- a/docs.it4i/software/tools/ansys/ansys-ls-dyna.md
+++ b/docs.it4i/software/tools/ansys/ansys-ls-dyna.md
@@ -50,6 +50,6 @@ echo Machines: $hl
/ansys_inc/v145/ansys/bin/ansys145 -dis -lsdynampp i=input.k -machines $hl
```
-Header of the PBS file (above) is common and description can be find on [this site](anselm/job-submission-and-execution/). [SVS FEM](http://www.svsfem.cz) recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.
+Header of the PBS file (above) is common and description can be find on [this site](/anselm/job-submission-and-execution/). [SVS FEM](http://www.svsfem.cz) recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.
Working directory has to be created before sending PBS job into the queue. Input file should be in working directory or full path to input file has to be specified. Input file has to be defined by common LS-DYNA .**k** file which is attached to the ANSYS solver via parameter i=
diff --git a/docs.it4i/software/tools/ansys/ansys-mechanical-apdl.md b/docs.it4i/software/tools/ansys/ansys-mechanical-apdl.md
index c164437787b1ff777899fc12df7e9867bba96c31..e3e4c9379103bb386cc0b1d500acf60f6eac29cb 100644
--- a/docs.it4i/software/tools/ansys/ansys-mechanical-apdl.md
+++ b/docs.it4i/software/tools/ansys/ansys-mechanical-apdl.md
@@ -49,7 +49,7 @@ echo Machines: $hl
/ansys_inc/v145/ansys/bin/ansys145 -b -dis -p aa_r -i input.dat -o file.out -machines $hl -dir $WORK_DIR
```
-Header of the PBS file (above) is common and description can be found on [this site](anselm/resources-allocation-policy/). [SVS FEM](http://www.svsfem.cz) recommends to utilize sources by keywords: nodes, ppn. These keywords allow to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.
+Header of the PBS file (above) is common and description can be found on [this site](/anselm/resources-allocation-policy/). [SVS FEM](http://www.svsfem.cz) recommends to utilize sources by keywords: nodes, ppn. These keywords allow to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.
Working directory has to be created before sending PBS job into the queue. Input file should be in working directory or full path to input file has to be specified. Input file has to be defined by common APDL file which is attached to the ANSYS solver via parameter -i
diff --git a/docs.it4i/software/tools/ansys/ls-dyna.md b/docs.it4i/software/tools/ansys/ls-dyna.md
index 43c818c2cb0a6460b67a8cdb0da9ccda80671be2..86320a5f106c0ef30daf24bc0f8ca3343340a1d9 100644
--- a/docs.it4i/software/tools/ansys/ls-dyna.md
+++ b/docs.it4i/software/tools/ansys/ls-dyna.md
@@ -30,6 +30,6 @@ ml lsdyna
/apps/engineering/lsdyna/lsdyna700s i=input.k
```
-Header of the PBS file (above) is common and description can be find on [this site](anselm/job-submission-and-execution/). [SVS FEM](http://www.svsfem.cz) recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.
+Header of the PBS file (above) is common and description can be find on [this site](/anselm/job-submission-and-execution/). [SVS FEM](http://www.svsfem.cz) recommends to utilize sources by keywords: nodes, ppn. These keywords allows to address directly the number of nodes (computers) and cores (ppn) which will be utilized in the job. Also the rest of code assumes such structure of allocated resources.
Working directory has to be created before sending PBS job into the queue. Input file should be in working directory or full path to input file has to be specified. Input file has to be defined by common LS-DYNA **.k** file which is attached to the LS-DYNA solver via parameter i=
diff --git a/docs.it4i/software/tools/virtualization.md b/docs.it4i/software/tools/virtualization.md
index 0c88936d692f41678a04ee19826c0689b934c386..22abf7ce9e63286639dd13773721e41836deabab 100644
--- a/docs.it4i/software/tools/virtualization.md
+++ b/docs.it4i/software/tools/virtualization.md
@@ -203,7 +203,7 @@ Run script runs application from shared job directory (mapped as drive z:), proc
### Run Jobs
-Run jobs as usual, see [Resource Allocation and Job Execution](salomon/job-submission-and-execution/). Use only full node allocation for virtualization jobs.
+Run jobs as usual, see [Resource Allocation and Job Execution](/salomon/job-submission-and-execution/). Use only full node allocation for virtualization jobs.
### Running Virtual Machines
diff --git a/docs.it4i/software/viz/openfoam.md b/docs.it4i/software/viz/openfoam.md
index 96e7213a327c2137606e061d915ba3f5270b14b9..34baa15cc3d38f4f75f43687d8d9085b51c48ee7 100644
--- a/docs.it4i/software/viz/openfoam.md
+++ b/docs.it4i/software/viz/openfoam.md
@@ -112,7 +112,7 @@ Job submission (example for Anselm):
$ qsub -A OPEN-0-0 -q qprod -l select=1:ncpus=16,walltime=03:00:00 test.sh
```
-For information about job submission [look here](anselm/job-submission-and-execution/).
+For information about job submission [look here](/anselm/job-submission-and-execution/).
## Running Applications in Parallel
diff --git a/docs.it4i/software/viz/paraview.md b/docs.it4i/software/viz/paraview.md
index f425989b2b331cd7b5794e8f7a7b4c2a8250595e..1678c9bfe6fcc34ff9560b55f017f4ba0ac55eda 100644
--- a/docs.it4i/software/viz/paraview.md
+++ b/docs.it4i/software/viz/paraview.md
@@ -29,7 +29,7 @@ To launch the server, you must first allocate compute nodes, for example
$ qsub -I -q qprod -A OPEN-0-0 -l select=2
```
-to launch an interactive session on 2 nodes. Refer to [Resource Allocation and Job Execution](salomon/job-submission-and-execution/) for details.
+to launch an interactive session on 2 nodes. Refer to [Resource Allocation and Job Execution](/salomon/job-submission-and-execution/) for details.
After the interactive session is opened, load the ParaView module (following examples for Salomon, Anselm instructions in comments):