Merge pull request #404 from uvarc/staging

Staging
uvarc · Jul 18, 2023 · fe2b5da · fe2b5da
2 parents f9d9dbf + 64c152a
commit fe2b5da
Show file tree

Hide file tree

Showing 12 changed files with 29 additions and 10 deletions.
diff --git a/content/post/2023-july-maintenance.md b/content/post/2023-july-maintenance.md
@@ -22,7 +22,13 @@ All systems are expected to return to service by **6 a.m. on Wednesday, July 19*
 
 RC engineers will be installing a new `/scratch` storage filesystem that can be accessed at `/scratch/$USER` after the end of maintenance.
 
-**The current `/scratch` filesystem will be permanently retired on October 17, 2023 and all the data it contains will be deleted.**  We have prepared a sample script for users who wish to transfer files to the new scratch system.  Users should clean up their current `/scratch` directory in preparation, to minimize the load.  The downloadable script will be posted here after maintenance.
+**Modified queue limits will be implemented to provide maximum read/write performance of the new /scratch filesystem.** Users are encouraged to consult our [updated documentation](https://www.rc.virginia.edu/userinfo/rivanna/queues/) and adjust their job scripts accordingly.
+
+**The current `/scratch` filesystem will be permanently retired on October 17, 2023 and all the data it contains will be deleted.**  We have prepared a sample script for users who wish to transfer files to the new scratch system.  Users should clean up their current `/scratch` directory in preparation, to minimize the load.  A sample script is posted below.
+
+**Example script to copy files**
+
+{{< pull-code file="/static/scripts/demo-copy-scratch.slurm" lang="bash" >}}
 
 The script will also be available through the Open OnDemand Job Composer:
 

diff --git a/layouts/shortcodes/code-download.html b/layouts/shortcodes/code-download.html
@@ -0,0 +1,7 @@
+{{ $file := .Get "file" }}
+{{ $lang := .Get "language" }}
+{{ $code :=  readFile $file }}
+{{ (print "```" $lang "\n" $code "\n```") | markdownify }}
+<a href="{{ $file }}" download>
+<i class="fa fa-download" aria-hidden="true"></i>
+</a>
diff --git a/static/scripts/abinit.slurm b/static/scripts/abinit.slurm
@@ -1,7 +1,7 @@
 #!/bin/bash
 #SBATCH --job-name=abinit
 #SBATCH -N 5
-#SBATCH --mem-per-cpu=6000
+#SBATCH --mem-per-cpu=9000
 #SBATCH --ntasks-per-node=20
 #SBATCH -t 10:00:00
 #SBATCH -p parallel

diff --git a/static/scripts/demo-copy-scratch.slurm b/static/scripts/demo-copy-scratch.slurm
@@ -0,0 +1,6 @@
+#!/bin/bash
+#SBATCH -A your_allocation  # to find your allocation, type "allocations"
+#SBATCH -t 12:00:00         # up to 7-00:00:00 (7 days)
+#SBATCH -p standard         
+
+rsync -av /oldscratch/$USER/ /scratch/$USER
diff --git a/static/scripts/gaussian_serial.slurm b/static/scripts/gaussian_serial.slurm
@@ -2,7 +2,7 @@
 #SBATCH --tasks=1
 #SBATCH -t 160:00:00
 #SBATCH -p standard
-#SBATCH --mem=6000
+#SBATCH --mem=9000
 #SBATCH -A mygroup
 
 module load gaussian/g16

diff --git a/static/scripts/mpi_job.slurm b/static/scripts/mpi_job.slurm
@@ -1,6 +1,6 @@
 #!/bin/bash
 #SBATCH --nodes=2
-#SBATCH --ntasks-per-node=16
+#SBATCH --ntasks-per-node=36
 #SBATCH --time=12:00:00
 #SBATCH --output=output_filename
 #SBATCH --partition=parallel

diff --git a/static/scripts/orca_multinode.slurm b/static/scripts/orca_multinode.slurm
@@ -2,7 +2,7 @@
 #SBATCH -A mygroup            # your allocation account
 #SBATCH -p parallel           # partition
 #SBATCH -N 3                  # number of nodes
-#SBATCH --ntasks-per-node=40  # number of tasks
+#SBATCH --ntasks-per-node=36  # number of tasks
 #SBATCH -t 24:00:00           # time
 
 module purge

diff --git a/static/scripts/smrtlink_blasr.slurm b/static/scripts/smrtlink_blasr.slurm
@@ -3,7 +3,7 @@
 #SBATCH --nodes=1
 #SBATCH --ntasks=1
 #SBATCH --cpus-per-task=8
-#SBATCH --mem-per-cpu=6000
+#SBATCH --mem-per-cpu=9000
 #SBATCH --time=06:00:00
 
 module purge

diff --git a/static/scripts/smrtlink_ngmlr.slurm b/static/scripts/smrtlink_ngmlr.slurm
@@ -3,7 +3,7 @@
 #SBATCH --nodes=1
 #SBATCH --ntasks=1
 #SBATCH --cpus-per-task=8
-#SBATCH --mem-per-cpu=6000
+#SBATCH --mem-per-cpu=9000
 #SBATCH --time=06:00:00
 
 module purge

diff --git a/static/scripts/smrtlink_sawriter.slurm b/static/scripts/smrtlink_sawriter.slurm
@@ -3,7 +3,7 @@
 #SBATCH --nodes=1
 #SBATCH --ntasks=1
 #SBATCH --cpus-per-task=1 # multi-threading not supported
-#SBATCH --mem-per-cpu=6000
+#SBATCH --mem-per-cpu=9000
 #SBATCH --time=06:00:00
 
 module purge

diff --git a/static/scripts/spark_multinode.slurm b/static/scripts/spark_multinode.slurm
@@ -3,7 +3,7 @@
 #SBATCH --exclusive   # do not modify
 #SBATCH -A myaccount  # your allocation
 #SBATCH -N 3          # number of nodes
-#SBATCH -c 40         # number of cores per node
+#SBATCH -c 36         # number of cores per node
 #SBATCH -t 3:00:00    # time
 
 module purge

diff --git a/static/scripts/vasp.slurm b/static/scripts/vasp.slurm
@@ -1,7 +1,7 @@
 #!/bin/bash
 #SBATCH --account my_acct
 #SBATCH --nodes=8
-#SBATCH --ntasks-per-node=16
+#SBATCH --ntasks-per-node=36
 #SBATCH --time=3-00:00:00
 #SBATCH --output=thermo.out
 #SBATCH --partition=parallel