From 868855d7665dbda7b21b6afff1cc019753522f54 Mon Sep 17 00:00:00 2001 From: tbrunetti Date: Wed, 10 Jan 2018 18:14:31 -0700 Subject: [PATCH] formatting updated --- Nodes_and_Queues.md | 38 +++++++++++++++++++++----------------- 1 file changed, 21 insertions(+), 17 deletions(-) diff --git a/Nodes_and_Queues.md b/Nodes_and_Queues.md index 509dda8..5eaf511 100644 --- a/Nodes_and_Queues.md +++ b/Nodes_and_Queues.md @@ -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 @@ -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 ``` -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.*



@@ -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 + * another ctrl-d will terminate the interactive session on the MATLAB node or `scancel` and your jobid which can be found by `squeue -u ` To be sure the session is terminated type: ``` @@ -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 ``` -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.*