diff --git a/_sources/docs/biohpc/slurm-quick-start.md b/_sources/docs/biohpc/slurm-quick-start.md index ea49b25..efaef1b 100644 --- a/_sources/docs/biohpc/slurm-quick-start.md +++ b/_sources/docs/biohpc/slurm-quick-start.md @@ -15,10 +15,15 @@ From a command line, run the following lines, logout, then back in, and hencefor ```bash echo 'export SLURM_CLUSTERS="cbsueccosl01"' >> $HOME/.bash_profile +``` + +In the following, replace `netid` with your actual NetID. + + +```bash echo netid@cornell.edu >> $HOME/.forward ``` -(replace your `netid` in the second command). ### Enabling software via `module` @@ -59,6 +64,28 @@ If you need a specific node, use srun -w cbsueccoXX --pty bash -l ``` +## Interactive GUI jobs + +You should be able to get interactive GUI jobs (Stata, MATLAB) to work as follows: + +```bash +salloc -N 1 +ssh -X $SLURM_NODELIST /usr/local/stata18/xstata +``` + +or + +```bash +salloc -N 1 +ssh -X $SLURM_NODELIST /local/opt/MATLAB/R2023a/bin/matlab +``` + +:::{warning} + +It is technically feasible to login to each node without using SLURM. However, this confuses the job scheduler. Do not abuse this, exclusion from use of the cluster may be the consequence. + +::: + ## To see running jobs ``` @@ -77,4 +104,4 @@ where the ID can be gleaned from the `squeue` command. ## Additional information -- [https://biohpc.cornell.edu/lab/SLURM-on-demand.htm](https://biohpc.cornell.edu/lab/SLURM-on-demand.htm) \ No newline at end of file +- [https://biohpc.cornell.edu/lab/SLURM-on-demand.htm](https://biohpc.cornell.edu/lab/SLURM-on-demand.htm) diff --git a/docs/biohpc/slurm-quick-start.html b/docs/biohpc/slurm-quick-start.html index 9af123d..bf63dbc 100644 --- a/docs/biohpc/slurm-quick-start.html +++ b/docs/biohpc/slurm-quick-start.html @@ -439,6 +439,7 @@

Contents

  • Submitting jobs
  • Interactive shell
    • +
  • Interactive GUI jobs
  • To see running jobs
  • To cancel a running job
  • Additional information
    • @@ -465,10 +466,12 @@

    Command line#

    From a command line, run the following lines, logout, then back in, and henceforth you can skip the --cluster cbsueccosl01 option:

    echo 'export SLURM_CLUSTERS="cbsueccosl01"' >> $HOME/.bash_profile
-echo netid@cornell.edu >> $HOME/.forward
    -

    (replace your netid in the second command).

    +

    In the following, replace netid with your actual NetID.

    +
    echo netid@cornell.edu >> $HOME/.forward
+
    +

    Enabling software via module#

    @@ -502,6 +505,23 @@

    Interactive shell +

    Interactive GUI jobs#

    +

    You should be able to get interactive GUI jobs (Stata, MATLAB) to work as follows:

    +
    salloc -N 1 
+ssh -X $SLURM_NODELIST /usr/local/stata18/xstata
+
    +
    +

    or

    +
    salloc -N 1 
+ssh -X $SLURM_NODELIST /local/opt/MATLAB/R2023a/bin/matlab
+
    +
    +
    +

    Warning

    +

    It is technically feasible to login to each node without using SLURM. However, this confuses the job scheduler. Do not abuse this, exclusion from use of the cluster may be the consequence.

    +
    +

    To see running jobs#

    squeue
@@ -596,6 +616,7 @@ 
    Additional information
 
  • Submitting jobs
    • 
 
  • Interactive shell
    • 
+
  • Interactive GUI jobs
    • 
 
  • To see running jobs
    • 
 
  • To cancel a running job
    • 
 
  • Additional information
    • 
diff --git a/docs/biohpc/slurm.html b/docs/biohpc/slurm.html
index 943ee94..4b9ffef 100644
--- a/docs/biohpc/slurm.html
+++ b/docs/biohpc/slurm.html
@@ -463,7 +463,7 @@ 
     Contents 
    
 
    
 
-
    
+
    
@@ -484,7 +484,7 @@ 
     Contents