diff --git a/doc.zih.tu-dresden.de/docs/archive/HardwareAtlas.md b/doc.zih.tu-dresden.de/docs/archive/HardwareAtlas.md
index ec8061e72e58e2910510521edcfbc0dd4ef6086b..184f395bcd3d8ed952ca9dcf26c64a66ed13210b 100644
--- a/doc.zih.tu-dresden.de/docs/archive/HardwareAtlas.md
+++ b/doc.zih.tu-dresden.de/docs/archive/HardwareAtlas.md
@@ -1,5 +1,3 @@
-
-
# MEGWARE PC-Farm Atlas
The PC farm `Atlas` is a heterogenous cluster based on multicore chips
@@ -7,41 +5,42 @@ AMD Opteron 6274 ("Bulldozer"). The nodes are operated by the Linux
operating system SuSE SLES 11 with a 2.6 kernel. Currently, the
following hardware is installed:
-\|CPUs \|AMD Opteron 6274 \| \|number of cores \|5120 \| \|th. peak
-performance\| 45 TFlops\| \|compute nodes \| 4-way nodes *Saxonid* with
-64 cores\| \|nodes with 64 GB RAM \| 48 \| \|nodes with 128 GB RAM \| 12
-\| \|nodes with 512 GB RAM \| 8 \|
-
-\<P>
+| CPUs |AMD Opteron 6274 |
+| number of cores | 5120 |
+|th. peak performance | 45 TFlops |
+|compute nodes | 4-way nodes *Saxonid* with 64 cores |
+|nodes with 64 GB RAM | 48 |
+|nodes with 128 GB RAM | 12 |
+|nodes with 512 GB RAM | 8 |
-Mars and Deimos users: Please read the [migration
-hints](MigrateToAtlas).
+Mars and Deimos users: Please read the [migration hints](MigrateToAtlas.md).
-All nodes share the HOME and `/fastfs/` [file system](FileSystems) with
-our other HPC systems. Each node has 180 GB local disk space for scratch
-mounted on `/tmp` . The jobs for the compute nodes are scheduled by the
-[Platform LSF](Platform LSF) batch system from the login nodes
+All nodes share the `/home` and `/fastfs` file system with our other HPC systems. Each
+node has 180 GB local disk space for scratch mounted on `/tmp` . The jobs for the compute nodes are
+scheduled by the [Platform LSF](PlatformLSF.md) batch system from the login nodes
`atlas.hrsk.tu-dresden.de` .
-A QDR Infiniband interconnect provides the communication and I/O
-infrastructure for low latency / high throughput data traffic.
+A QDR Infiniband interconnect provides the communication and I/O infrastructure for low latency /
+high throughput data traffic.
-Users with a login on the [SGI Altix](HardwareAltix) can access their
-home directory via NFS below the mount point `/hpc_work`.
+Users with a login on the [SGI Altix](HardwareAltix.md) can access their home directory via NFS
+below the mount point `/hpc_work`.
## CPU AMD Opteron 6274
-\| Clock rate \| 2.2 GHz\| \| cores \| 16 \| \| L1 data cache \| 16 KB
-per core \| \| L1 instruction cache \| 64 KB shared in a *module* (i.e.
-2 cores) \| \| L2 cache \| 2 MB per module\| \| L3 cache \| 12 MB total,
-6 MB shared between 4 modules = 8 cores\| \| FP units \| 1 per module
-(supports fused multiply-add)\| \| th. peak performance\| 8.8 GFlops per
-core (w/o turbo) \|
+| Clock rate | 2.2 GHz |
+| cores | 16 |
+| L1 data cache | 16 KB per core |
+| L1 instruction cache | 64 KB shared in a *module* (i.e. 2 cores) |
+| L2 cache | 2 MB per module |
+| L3 cache | 12 MB total, 6 MB shared between 4 modules = 8 cores |
+| FP units | 1 per module (supports fused multiply-add) |
+| th. peak performance | 8.8 GFlops per core (w/o turbo) |
The CPU belongs to the x86_64 family. Since it is fully capable of
running x86-code, one should compare the performances of the 32 and 64
bit versions of the same code.
-For more architectural details, see the [AMD Bulldozer block
-diagram](http://upload.wikimedia.org/wikipedia/commons/e/ec/AMD_Bulldozer_block_diagram_%288_core_CPU%29.PNG)
-and [topology of Atlas compute nodes](%ATTACHURL%/Atlas_Knoten.pdf).
+For more architectural details, see the
+[AMD Bulldozer block diagram](http://upload.wikimedia.org/wikipedia/commons/e/ec/AMD_Bulldozer_block_diagram_%288_core_CPU%29.PNG)
+and [topology of Atlas compute nodes] **todo** %ATTACHURL%/Atlas_Knoten.pdf.
diff --git a/doc.zih.tu-dresden.de/docs/archive/SystemAtlas.md b/doc.zih.tu-dresden.de/docs/archive/SystemAtlas.md
index 13ce0ace2b6d91e07df39d6a83c0ad86fdb7ef9a..59fe0111fbe1052a6b45923128369f703462ea15 100644
--- a/doc.zih.tu-dresden.de/docs/archive/SystemAtlas.md
+++ b/doc.zih.tu-dresden.de/docs/archive/SystemAtlas.md
@@ -1,27 +1,22 @@
# Atlas
-**`%RED%This page is deprecated! Atlas is a former system!%ENDCOLOR%`**
-( [Current hardware](Compendium.Hardware))
+**This page is deprecated! Atlas is a former system!**
-Atlas is a general purpose HPC cluster for jobs using 1 to 128 cores in
-parallel ( [Information on the hardware](HardwareAtlas)).
+Atlas is a general purpose HPC cluster for jobs using 1 to 128 cores in parallel
+([Information on the hardware](HardwareAtlas.md)).
## Compiling Parallel Applications
-When loading a compiler module on Atlas, the module for the MPI
-implementation OpenMPI is also loaded in most cases. If not, you should
-explicitly load the OpenMPI module with `module load openmpi`. This also
-applies when you use the system's (old) GNU compiler. ( [read more about
-Modules](Compendium.RuntimeEnvironment), [read more about
-Compilers](Compendium.Compilers))
+When loading a compiler module on Atlas, the module for the MPI implementation OpenMPI is also
+loaded in most cases. If not, you should explicitly load the OpenMPI module with `module load
+openmpi`. This also applies when you use the system's (old) GNU compiler.
-Use the wrapper commands `mpicc` , `mpiCC` , `mpif77` , or `mpif90` to
-compile MPI source code. They use the currently loaded compiler. To
-reveal the command lines behind the wrappers, use the option `-show`.
+Use the wrapper commands `mpicc` , `mpiCC` , `mpif77` , or `mpif90` to compile MPI source code. They
+use the currently loaded compiler. To reveal the command lines behind the wrappers, use the option
+`-show`.
-For running your code, you have to load the same compiler and MPI module
-as for compiling the program. Please follow te following guiedlines to
-run your parallel program using the batch system.
+For running your code, you have to load the same compiler and MPI module as for compiling the
+program. Please follow te following guiedlines to run your parallel program using the batch system.
## Batch System
@@ -29,45 +24,43 @@ Applications on an HPC system can not be run on the login node. They
have to be submitted to compute nodes with dedicated resources for the
user's job. Normally a job can be submitted with these data:
-- number of CPU cores,
-- requested CPU cores have to belong on one node (OpenMP programs) or
- can distributed (MPI),
-- memory per process,
-- maximum wall clock time (after reaching this limit the process is
- killed automatically),
-- files for redirection of output and error messages,
-- executable and command line parameters.
+- number of CPU cores,
+- requested CPU cores have to belong on one node (OpenMP programs) or
+ can distributed (MPI),
+- memory per process,
+- maximum wall clock time (after reaching this limit the process is
+ killed automatically),
+- files for redirection of output and error messages,
+- executable and command line parameters.
### LSF
-The batch sytem on Atlas is LSF. For general information on LSF, please
-follow [this link](PlatformLSF).
+The batch sytem on Atlas is LSF. For general information on LSF, please follow
+[this link](PlatformLSF.md).
### Submission of Parallel Jobs
-To run MPI jobs ensure that the same MPI module is loaded as during
-compile-time. In doubt, check you loaded modules with `module list`. If
-you code has been compiled with the standard OpenMPI installation, you
-can load the OpenMPI module via `module load openmpi`.
+To run MPI jobs ensure that the same MPI module is loaded as during compile-time. In doubt, check
+you loaded modules with `module list`. If you code has been compiled with the standard OpenMPI
+installation, you can load the OpenMPI module via `module load openmpi`.
-Please pay attention to the messages you get loading the module. They
-are more up-to-date than this manual. To submit a job the user has to
-use a script or a command-line like this:
+Please pay attention to the messages you get loading the module. They are more up-to-date than this
+manual. To submit a job the user has to use a script or a command-line like this:
- <span class='WYSIWYG_HIDDENWHITESPACE'> </span>bsub -n <N> mpirun <program name><span class='WYSIWYG_HIDDENWHITESPACE'> </span>
+```Bash
+bsub -n <N> mpirun <program name>
+```
### Memory Limits
-**Memory limits are enforced.** This means that jobs which exceed their
-per-node memory limit **may be killed** automatically by the batch
-system.
+**Memory limits are enforced.** This means that jobs which exceed their per-node memory limit **may
+be killed** automatically by the batch system.
-The **default limit** is **300 MB** *per job slot* (bsub -n).
+The **default limit** is **300 MB** *per job slot* (`bsub -n`).
-Atlas has sets of nodes with different amount of installed memory which
-affect where your job may be run. To achieve the shortest possible
-waiting time for your jobs, you should be aware of the limits shown in
-the following table and read through the explanation below.
+Atlas has sets of nodes with different amount of installed memory which affect where your job may be
+run. To achieve the shortest possible waiting time for your jobs, you should be aware of the limits
+shown in the following table and read through the explanation below.
| Nodes | No. of Cores | Avail. Memory per Job Slot | Max. Memory per Job Slot for Oversubscription |
|:-------------|:-------------|:---------------------------|:----------------------------------------------|
@@ -77,14 +70,12 @@ the following table and read through the explanation below.
#### Explanation
-The amount of memory that you request for your job (-M ) restricts to
-which nodes it will be scheduled. Usually, the column **"Avail. Memory
-per Job Slot"** shows the maximum that will be allowed on the respective
-nodes.
+The amount of memory that you request for your job (-M ) restricts to which nodes it will be
+scheduled. Usually, the column **Avail. Memory per Job Slot** shows the maximum that will be
+allowed on the respective nodes.
-However, we allow for **oversubscribing of job slot memory**. This means
-that jobs which use **-n32 or less** may be scheduled to smaller memory
-nodes.
+However, we allow for **oversubscribing of job slot memory**. This means that jobs which use **-n32
+or less** may be scheduled to smaller memory nodes.
Have a look at the **examples below**.
@@ -98,17 +89,17 @@ available for longer running jobs (>10 min).
| Job Spec. | Nodes Allowed | Remark |
|:--------------------------------------------------------------------------------------|:--------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------|
-| `bsub %GREEN%-n 1 -M 500%ENDCOLOR%` | `All nodes` | \<= 940 Fits everywhere |
-| `bsub %GREEN%-n 64 -M 700%ENDCOLOR%` | `All nodes` | \<= 940 Fits everywhere |
-| `bsub %GREEN%-n 4 -M 1800%ENDCOLOR%` | `All nodes` | Is allowed to oversubscribe on small nodes n\[001-047\] |
-| `bsub %GREEN%-n 64 -M 1800%ENDCOLOR%` | `n[049-092]` | 64\*1800 will not fit onto a single small node and is therefore restricted to running on medium and large nodes |
-| \<span>bsub \<span style`"color: #eecc22;">-n 4 -M 2000</span></span> | =n[049-092]` | Over limit for oversubscribing on small nodes n\[001-047\], but may still go to medium nodes | |
-| \<span>bsub \<span style`"color: #eecc22;">-n 32 -M 2000</span></span> | =n[049-092]` | Same as above | |
-| `bsub %GREEN%-n 32 -M 1880%ENDCOLOR%` | `All nodes` | Using max. 1880 MB, the job is eligible for running on any node |
-| \<span>bsub \<span style`"color: #eecc22;">-n 64 -M 2000</span></span> | =n[085-092]` | Maximum for medium nodes is 1950 per slot - does the job **really** need **2000 MB** per process? | |
-| `bsub %GREEN%-n 64 -M 1950%ENDCOLOR%` | `n[049-092]` | When using 1950 as maximum, it will fit to the medium nodes |
-| `bsub -n 32 -M 16000` | `n[085-092]` | Wait time might be **very long** |
-| `bsub %RED%-n 64 -M 16000%ENDCOLOR%` | `n[085-092]` | Memory request cannot be satisfied (64\*16 MB = 1024 GB), **%RED%cannot schedule job%ENDCOLOR%** |
+| `bsub -n 1 -M 500` | All nodes | <= 940 Fits everywhere |
+| `bsub -n 64 -M 700` | All nodes | <= 940 Fits everywhere |
+| `bsub -n 4 -M 1800` | All nodes | Is allowed to oversubscribe on small nodes n\[001-047\] |
+| `bsub -n 64 -M 1800` | `n[049-092]` | 64\*1800 will not fit onto a single small node and is therefore restricted to running on medium and large nodes |
+| `bsub -n 4 -M 2000` | `-n[049-092]` | Over limit for oversubscribing on small nodes `n[001-047]`, but may still go to medium nodes |
+| `bsub -n 32 -M 2000` | `-n[049-092]` | Same as above |
+| `bsub -n 32 -M 1880` | All nodes | Using max. 1880 MB, the job is eligible for running on any node |
+| `bsub -n 64 -M 2000` | `-n[085-092]` | Maximum for medium nodes is 1950 per slot - does the job **really** need **2000 MB** per process? |
+| `bsub -n 64 -M 1950` | `n[049-092]` | When using 1950 as maximum, it will fit to the medium nodes |
+| `bsub -n 32 -M 16000` | `n[085-092]` | Wait time might be **very long** |
+| `bsub -n 64 -M 16000` | `n[085-092]` | Memory request cannot be satisfied (64\*16 MB = 1024 GB), **cannot schedule job** |
### Batch Queues
@@ -117,10 +108,10 @@ scheduling policy prefers short running jobs over long running ones.
This means that **short jobs get higher priorities** and are usually
started earlier than long running jobs.
-| Batch Queue | Admitted Users | Max. Cores | Default Runtime | \<div style="text-align: right;">Max. Runtime\</div> |
-|:--------------|:---------------|:---------------------------------------------|:--------------------------------------------------|:-----------------------------------------------------|
-| `interactive` | `all` | \<div style="text-align: right;">n/a\</div> | \<div style="text-align: right;">12h 00min\</div> | \<div style="text-align: right;">12h 00min\</div> |
-| `short` | `all` | \<div style="text-align: right;">1024\</div> | \<div style="text-align: right;">1h 00min\</div> | \<div style="text-align: right;">24h 00min\</div> |
-| `medium` | `all` | \<div style="text-align: right;">1024\</div> | \<div style="text-align: right;">24h 01min\</div> | \<div style="text-align: right;">72h 00min\</div> |
-| `long` | `all` | \<div style="text-align: right;">1024\</div> | \<div style="text-align: right;">72h 01min\</div> | \<div style="text-align: right;">120h 00min\</div> |
-| `rtc` | `on request` | \<div style="text-align: right;">4\</div> | \<div style="text-align: right;">12h 00min\</div> | \<div style="text-align: right;">300h 00min\</div> |
+| Batch Queue | Admitted Users | Max. Cores | Default Runtime | Max. Runtime |
+|:--------------|:---------------|:----------------------------------|:-------------------|:-------------|
+| `interactive` | `all` | n/a | 12h 00min | 12h 00min |
+| `short` | `all` | 1024 | 1h 00min | 24h 00min |
+| `medium` | `all` | 1024 | 24h 01min | 72h 00min |
+| `long` | `all` | 1024 | 72h 01min | 120h 00min |
+| `rtc` | `on request` | 4 | 12h 00min | 300h 00min |