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@tbrunetti
tbrunetti committed Jan 11, 2018
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38 changes: 21 additions & 17 deletions Nodes_and_Queues.md
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Expand Up @@ -43,18 +43,20 @@ Currently, we have 2 standard compute nodes with SAS licenses or (48 CPU/cores a

__Interactive SAS__
SAS can be run interactively on the Rosalind command line as well by running through the following steps. This is analogous to running SAS in real-time using the SAS command prompt.
1. First request an available SAS node by running the following on the Rosalind command line (note: last character is lowercase L):
*1. First request an available SAS node by running the following on the Rosalind command line (note: last character is lowercase L):*
```
srun --time=60 -p sas -n1 --pty bash -l
```
This will request a single SAS node (-n1) for a total of 1 hour (--time=60).
2. Next, type in the following to execute and start the SAS interactive session:
This will request a single SAS node (-n1) for a total of 1 hour (--time=60).

*2. Next, type in the following to execute and start the SAS interactive session:*
```
/opt/SAS/9.4/SASFoundation/9.4/bin/sas_en -nodmsexp
```
You are now in an interactive SAS session that will automatically terminate in 1 hour. However, it is important to note the following:
__terminating an interactive session earlier than the specified time is a 2 step process!__ If you do not follow the 2 step process, you will be charged for the full time specified regardless if you actually used the reserved node.
3. Terminating an interactive session early:

*3. Terminating an interactive session early:*
* Ctrl-d will terminate SAS
* another ctrl-d will terminate the interactive session on the SAS node or scancel and your jobid which can be found by squeue -u <yourusername>

Expand All @@ -66,18 +68,19 @@ You should see that job that has the sas interactive session has a status of COM


__BATCH SAS__
1. The first step is to specify the batch script should be submitted to a node with a SAS installation. This can be done by adding the following line to the list of #SBATCH headers:
*1. The first step is to specify the batch script should be submitted to a node with a SAS installation. This can be done by adding the following line to the list of #SBATCH headers:*
```
#SBATCH -p sas
```
2. Next, a user may wish to specify the number of SAS nodes they would like to use __(max 2)__ or the number of CPUs/cores they would like to use __(max 24 per node)__. This should be specified in the #SBATCH headers.
*2. Next, a user may wish to specify the number of SAS nodes they would like to use __(max 2)__ or the number of CPUs/cores they would like to use __(max 24 per node)__. This should be specified in the #SBATCH headers.*

3. When running the SAS command call in the sbatch script use the following SAS executable call:

*3. When running the SAS command call in the sbatch script use the following SAS executable call:*
```
/opt/SAS/9.4/SASFoundation/9.4/bin/sas_en <followed by your SAS script>
```

4. Keep in mind if a time is not specified in the batch script header, the job will automatically be killed after 4 hours. However, you can specify a time of up to 1 week for these nodes.
*4. Keep in mind if a time is not specified in the batch script header, the job will automatically be killed after 4 hours. However, you can specify a time of up to 1 week for these nodes.*

<div class="paragraph"><p><br>
<br></p></div>
Expand All @@ -87,20 +90,21 @@ MATLAB access is similar to how one would access the SAS node. Currently, we ha

__Interactive MATLAB__
MATLAB can be run interactively on the Rosalind command line as well by running through the following steps. This is analogous to running MATLAB in real-time using the MATLAB command prompt.
1. First request an available MATLAB node by running the following on the Rosalind command line (note: the character following the bash - is a lowercase L):
*1. First request an available MATLAB node by running the following on the Rosalind command line (note: the character following the bash - is a lowercase L):*
```
srun --time=60 -p matlab -n1 --pty bash -l
```
This will request a single MATLAB node (-n1) for a total of 1 hour (--time=60).
2. Next, type in the following to execute and start the MATLAB interactive session:
This will request a single MATLAB node (-n1) for a total of 1 hour (--time=60).

*2. Next, type in the following to execute and start the MATLAB interactive session:*
```
/opt/MATLAB/R2017b/bin/matlab
```
You are now in an interactive MATLAB session that will automatically terminate in 1 hour. However, it is important to note the following:
__terminating an interactive session earlier than the specified time is a 2 step process!__ If you do not follow the 2 step process, you will be charged for the full time specified regardless if you actually used the reserved node.
3. Terminating an interactive session early:
*3. Terminating an interactive session early:*
* Ctrl-d will terminate MATLAB
* another ctrl-d will terminate the interactive session on the MATLAB node or scancel and your jobid which can be found by squeue -u <yourusername>
* another ctrl-d will terminate the interactive session on the MATLAB node or `scancel` and your jobid which can be found by `squeue -u <yourusername>`

To be sure the session is terminated type:
```
Expand All @@ -110,18 +114,18 @@ You should see that job that has the matlab interactive session has a status of


__BATCH MATLAB__
1. The first step is to specify the batch script should be submitted to a node with a MATLAB installation. This can be done by adding the following line to the list of #SBATCH headers:
*1. The first step is to specify the batch script should be submitted to a node with a MATLAB installation. This can be done by adding the following line to the list of #SBATCH headers:*
```
#SBATCH -p matlab
```
2. Next, a user may wish to specify the number of SAS nodes they would like to use __(max 4)__ or the number of CPUs/cores they would like to use __(max 24 per node)__. This should be specified in the #SBATCH headers.
*2. Next, a user may wish to specify the number of SAS nodes they would like to use __(max 4)__ or the number of CPUs/cores they would like to use __(max 24 per node)__. This should be specified in the #SBATCH headers.*

3. When running the MATLAB command call in the sbatch script use the following MATLAB executable call:
*3. When running the MATLAB command call in the sbatch script use the following MATLAB executable call:*
```
/opt/MATLAB/R2017b/bin/matlab <followed by your MATLAB script>
```

4. Keep in mind if a time is not specified in the batch script header, the job will automatically be killed after 4 hours. However, you can specify a time of up to 1 week for these nodes.
*4. Keep in mind if a time is not specified in the batch script header, the job will automatically be killed after 4 hours. However, you can specify a time of up to 1 week for these nodes.*

<div class="paragraph"><p><br>
<br></p></div>
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