diff --git a/doc.zih.tu-dresden.de/docs/archive/platform_lsf.md b/doc.zih.tu-dresden.de/docs/archive/platform_lsf.md
index 1be15a0a9beb204c188b339e00c487e6ebbd5af0..e0c0b95764618c0585e4eaf07fcac3e1f3bb947e 100644
--- a/doc.zih.tu-dresden.de/docs/archive/platform_lsf.md
+++ b/doc.zih.tu-dresden.de/docs/archive/platform_lsf.md
@@ -1,6 +1,8 @@
# Platform LSF
-**This Page is deprecated!** The current bachsystem on Taurus is [Slurm][../jobs_and_resources/slurm.md]
+!!! warning
+ This Page is deprecated!
+ The current bachsystem on ZIH systems is [Slurm](../jobs_and_resources/slurm.md).
The HRSK-I systems are operated with the batch system LSF running on *Mars*, *Atlas* resp..
@@ -11,26 +13,26 @@ The job submission can be done with the command:
Some options of `bsub` are shown in the following table:
-| bsub option | Description |
-|:-------------------|:---------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| `-n \<N> ` | set number of processors (cores) to N(default=1) |
-| `-W \<hh:mm> ` | set maximum wall clock time to `<hh:mm>` |
-| `-J \<name> ` | assigns the specified name to the job |
-| `-eo \<errfile> ` | writes the standard error output of the job to the specified file (overwriting) |
-| `-o \<outfile> ` | appends the standard output of the job to the specified file |
-| `-R span\[hosts=1\]` | use only one SMP node (automatically set by the batch system) |
-| `-R span\[ptile=2\]` | run 2 tasks per node |
-| `-x ` | disable other jobs to share the node ( Atlas ). |
-| `-m ` | specify hosts to run on ( [see below](#HostList)) |
-| `-M \<M> ` | specify per-process (per-core) memory limit (in MB), the job's memory limit is derived from that number (N proc \* M MB); see examples and [Attn. #2](#AttentionNo2) below |
-| `-P \<project> ` | specifiy project |
+| Bsub Option | Description |
+|:-------------------|:------------|
+| `-n <N>` | set number of processors (cores) to N(default=1) |
+| `-W <hh:mm>` | set maximum wall clock time to `<hh:mm>` |
+| `-J <name>` | assigns the specified name to the job |
+| `-eo <errfile>` | writes the standard error output of the job to the specified file (overwriting) |
+| `-o <outfile>` | appends the standard output of the job to the specified file |
+| `-R span[hosts=1]` | use only one SMP node (automatically set by the batch system) |
+| `-R span[ptile=2]` | run 2 tasks per node |
+| `-x` | disable other jobs to share the node ( Atlas ). |
+| `-m` | specify hosts to run on ( [see below](#host-list)) |
+| `-M <M>` | specify per-process (per-core) memory limit (in MB), the job's memory limit is derived from that number (N proc * M MB); see examples below |
+| `-P <project>` | specify project |
You can use the `%J` -macro to merge the job ID into names.
It might be more convenient to put the options directly in a job file
which you can submit using
-```Bash
+```console
bsub <my_jobfile>
```
@@ -44,7 +46,7 @@ The following example job file shows how you can make use of it:
#BSUB -n 4 # number of processors
#BSUB -M 500 # 500MB per core memory limit
#BSUB -o out.%J # output file
-#BSUB -u name@tu-dresden.de # email address; works ONLY with @tu-dresden.de
+#BSUB -u name@tu-dresden.de # email address; works ONLY with @tu-dresden.de
echo Starting Program
cd $HOME/work
@@ -52,21 +54,21 @@ a.out # e.g. an OpenMP program
echo Finished Program
```
-**Understanding memory limits** The option -M to bsub defines how much
+**Understanding memory limits** The option `-M` to bsub defines how much
memory may be consumed by a single process of the job. The job memory
limit is computed taking this value times the number of processes
-requested (-n). Therefore, having -M 600 and -n 4 results in a job
+requested (`-n`). Therefore, having `-M 600` and `-n 4` results in a job
memory limit of 2400 MB. If any one of your processes consumes more than
600 MB memory OR if all processes belonging to this job consume more
than 2400 MB of memory in sum, then the job will be killed by LSF.
-- For serial programs, the given limit is the same for the process and
- the whole job, e.g. 500 MB `bsub -W 1:00 -n 1 -M 500 myprog`
-- For MPI-parallel programs, the job memory limit is N processes \*
- memory limit, e.g. 32\*800 MB = 25600 MB `bsub -W 8:00 -n 32 -M 800 mympiprog`
-- For OpenMP-parallel programs, the same applies as with MPI-parallel
- programs, e.g. 8\*2000 MB = 16000 MB
- `bsub -W 4:00 -n 8 -M 2000 myompprog`
+- For serial programs, the given limit is the same for the process and
+ the whole job, e.g. 500 MB `bsub -W 1:00 -n 1 -M 500 myprog`
+- For MPI-parallel programs, the job memory limit is N processes \*
+ memory limit, e.g. 32*800 MB = 25600 MB `bsub -W 8:00 -n 32 -M 800 mympiprog`
+- For OpenMP-parallel programs, the same applies as with MPI-parallel
+ programs, e.g. 8*2000 MB = 16000 MB
+ `bsub -W 4:00 -n 8 -M 2000 myompprog`
LSF sets the user environment according to the environment at the time of submission.
@@ -78,14 +80,13 @@ of a job placement in a queue is therefore the ratio between used and granted CP
period.
**Attention:** If you do not give the maximum runtime of your program, the
-default runtime for the specified queue is taken. This is way below the
-maximal possible runtime (see table [below](#JobQueues)).
+default runtime for the specified queue is taken.
**Attention 2:** Some systems enforce a limit on how much memory each process and your job as a
-whole may allocate. If your job or any of its processes exceed this limit (N proc.\*limit for the
+whole may allocate. If your job or any of its processes exceed this limit (N proc.*limit for the
job), your job will be killed. If memory limiting is in place, there also exists a default limit
which will be applied to your job if you do not specify one. Please find the limits along with the
-description of the machines' [queues](#JobQueues) below.
+description of the machines' [queues](#job-queues) below.
### Interactive Jobs
@@ -98,52 +99,45 @@ extensive production runs!
Use the bsub options `-Is` for an interactive and, additionally on
*Atlas*, `-XF` for an X11 job like:
-```Bash
+```console
bsub -Is -XF matlab
```
or for an interactive job with a bash use
-```Bash
-bsub -Is -n 2 -W <hh:mm> -P <project> bash
+```console
+bsub -Is -n 2 -W <hh:mm> -P <project> bash
```
You can check the current usage of the system with the command `bhosts`
to estimate the time to schedule.
-## ParallelJobs
-
### Parallel Jobs
-For submitting parallel jobs, a few rules have to be understood and
-followed. In general they depend on the type of parallelization and the
-architecture.
+For submitting parallel jobs, a few rules have to be understood and followed. In general they depend
+on the type of parallelization and the architecture.
#### OpenMP Jobs
-An SMP-parallel job can only run within a node (or a partition), so it
-is necessary to include the option `-R "span[hosts=1]"` . The maximum
-number of processors for an SMP-parallel program is 506 on a large Altix
-partition, and 64 on *Atlas*. A simple example of a job file
-for an OpenMP job can be found above (section [3.4](#LSF-OpenMP)).
+An SMP-parallel job can only run within a node (or a partition), so it is necessary to include the
+option `-R span[hosts=1]` . The maximum number of processors for an SMP-parallel program is 506 on a
+large Altix partition, and 64 on *Atlas*.
#### MPI Jobs
-There are major differences for submitting MPI-parallel jobs on the
-systems at ZIH. Please refer to the HPC systems's section. It is
-essential to use the same modules at compile- and run-time.
+There are major differences for submitting MPI-parallel jobs on the systems at ZIH. Please refer to
+the HPC systems's section. It is essential to use the same modules at compile- and run-time.
### Array Jobs
-Array jobs can be used to create a sequence of jobs that share the same
-executable and resource requirements, but have different input files, to
-be submitted, controlled, and monitored as a single unit.
+Array jobs can be used to create a sequence of jobs that share the same executable and resource
+requirements, but have different input files, to be submitted, controlled, and monitored as a single
+unit.
-After the job array is submitted, LSF independently schedules and
-dispatches the individual jobs. Each job submitted from a job array
-shares the same job ID as the job array and are uniquely referenced
-using an array index. The dimension and structure of a job array is
-defined when the job array is created.
+After the job array is submitted, LSF independently schedules and dispatches the individual jobs.
+Each job submitted from a job array shares the same job ID as the job array and are uniquely
+referenced using an array index. The dimension and structure of a job array is defined when the job
+array is created.
Here is an example how an array job can looks like:
@@ -151,20 +145,19 @@ Here is an example how an array job can looks like:
#!/bin/bash
#BSUB -W 00:10
-#BSUB -n 1
+#BSUB -n 1
#BSUB -J "myTask[1-100:2]" # create job array with 50 tasks
#BSUB -o logs/out.%J.%I # appends the standard output of the job to the specified file that
# contains the job information (%J) and the task information (%I)
-#BSUB -e logs/err.%J.%I # appends the error output of the job to the specified file that
+#BSUB -e logs/err.%J.%I # appends the error output of the job to the specified file that
# contains the job information (%J) and the task information (%I)
echo "Hello Job $LSB_JOBID Task $LSB_JOBINDEX"
```
-Alternatively, you can use the following single command line to submit
-an array job:
+Alternatively, you can use the following single command line to submit an array job:
-```Bash
+```console
bsub -n 1 -W 00:10 -J "myTask[1-100:2]" -o "logs/out.%J.%I" -e "logs/err.%J.%I" "echo Hello Job \$LSB_JOBID Task \$LSB_JOBINDEX"
```
@@ -172,15 +165,13 @@ For further details please read the LSF manual.
### Chain Jobs
-You can use chain jobs to create dependencies between jobs. This is
-often the case if a job relies on the result of one or more preceding
-jobs. Chain jobs can also be used if the runtime limit of the batch
-queues is not sufficient for your job.
+You can use chain jobs to create dependencies between jobs. This is often the case if a job relies
+on the result of one or more preceding jobs. Chain jobs can also be used if the runtime limit of the
+batch queues is not sufficient for your job.
-To create dependencies between jobs you have to use the option `-w`.
-Since `-w` relies on the job id or the job name it is advisable to use
-the option `-J` to create a user specified name for a single job. For
-detailed information see the man pages of bsub with `man bsub`.
+To create dependencies between jobs you have to use the option `-w`. Since `-w` relies on the job
+id or the job name it is advisable to use the option `-J` to create a user specified name for a
+single job. For detailed information see the man pages of bsub with `man bsub`.
Here is an example how a chain job can looks like:
@@ -217,52 +208,47 @@ done
## Job Queues
-With the command `bqueues [-l <queue name>]` you can get information
-about available queues. With `bqueues -l` you get a detailed listing of
-the queue properties.
+With the command `bqueues [-l <queue name>]` you can get information about available queues. With
+`bqueues -l` you get a detailed listing of the queue properties.
-`Attention`: The queue `interactive` is the only one to accept
-interactive jobs!
+**Attention:** The queue `interactive` is the only one to accept interactive jobs!
## Job Monitoring
-You can check the current usage of the system with the command `bhosts`
-to estimate the time to schedule. Or to get an overview on *Atlas*,
-lsfview shows the current usage of the system.
+You can check the current usage of the system with the command `bhosts` to estimate the time to
+schedule. Or to get an overview on *Atlas*, lsfview shows the current usage of the system.
The command `bhosts` shows the load on the hosts.
-For a more convenient overview the command `lsfshowjobs` displays
-information on the LSF status like this:
+For a more convenient overview the command `lsfshowjobs` displays information on the LSF status like
+this:
-```Bash
+```console
You have 1 running job using 64 cores
You have 1 pending job
```
-and the command `lsfnodestat` displays the node and core status of
-machine like this:
+and the command `lsfnodestat` displays the node and core status of machine like this:
-```Bash
+```console
# -------------------------------------------
nodes available: 714/714 nodes damaged: 0
# -------------------------------------------
-jobs running: 1797 \| cores closed (exclusive jobs): 94 jobs wait: 3361
-\| cores closed by ADMIN: 129 jobs suspend: 0 \| cores working: 2068
-jobs damaged: 0 \|
+jobs running: 1797 | cores closed (exclusive jobs): 94 jobs wait: 3361
+| cores closed by ADMIN: 129 jobs suspend: 0 | cores working: 2068
+jobs damaged: 0 |
# -------------------------------------------
normal working cores: 2556 cores free for jobs: 265
```
-The command `bjobs` allows to monitor your running jobs. It has the
-following options:
+The command `bjobs` allows to monitor your running jobs. It has the following options:
-| bjobs option | Description |
+| Bjobs Option | Description |
|:--------------|:----------------------------------------------------------------------------------------------------------------------------------|
| `-r` | Displays running jobs. |
| `-s` | Displays suspended jobs, together with the suspending reason that caused each job to become suspended. |
@@ -270,26 +256,24 @@ following options:
| `-a` | Displays information on jobs in all states, including finished jobs that finished recently. |
| `-l [job_id]` | Displays detailed information for each job or for a particular job. |
-## Checking the progress of your jobs
+## Checking the Progress of Your Jobs
-If you run code that regularily emits status or progress messages, using
-the command
+If you run code that regularly emits status or progress messages, using the command
-```Bash
+```console
watch -n10 tail -n2 '*out'
```
-in your `$HOME/.lsbatch` directory is a very handy way to keep yourself
-informed. Note that this only works if you did not use the `-o` option
-of `bsub`, If you used `-o`, replace `*out` with the list of file names
-you passed to this very option.
+in your `$HOME/.lsbatch` directory is a very handy way to keep yourself informed. Note that this
+only works if you did not use the `-o` option of `bsub`, If you used `-o`, replace `*out` with the
+list of file names you passed to this very option.
## Host List
-The `bsub` option `-m` can be used to specify a list of hosts for
-execution. This is especially useful for memory intensive computations.
+The `bsub` option `-m` can be used to specify a list of hosts for execution. This is especially
+useful for memory intensive computations.
### Altix
-Jupiter, saturn, and uranus have 4 GB RAM per core, mars only 1GB. So it
-makes sense to specify '-m "jupiter saturn uranus".
+Jupiter, Saturn, and Uranus have 4 GB RAM per core, mars only 1 GB. So it makes sense to specify
+`-m "jupiter saturn uranus"`.