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--- hpc:applications_and_libraries [2024/02/20 10:17]
Adrien Albert [Gurobi]
+++ hpc:applications_and_libraries [2024/03/25 16:52] (current)
Adrien Albert [Pull an existing image]
@@ Line 431: / Line 431: @@
 </code>
-==== Update Gurobi License ====
-**Last expiration date**: Feb 16, 2025
-**Check the gurobi service on admin1.baobab (By restarting the service we see the license expiration)**:
-<code>
-(baobab)-[root@admin1 ~]$ systemctl restart gurobi
-(baobab)-[root@admin1 ~]$ systemctl status gurobi
-● gurobi.service - Gurobi token server
-   Loaded: loaded (/etc/systemd/system/gurobi.service; enabled; vendor preset: disabled)
-   Active: failed (Result: exit-code) since Tue 2024-02-20 09:52:33 CET; 3s ago
-  Process: 349483 ExecStart=/opt/ebsofts/Gurobi/9.5.0-GCCcore-11.2.0/bin/grb_ts -n (code=exited, status=1/FAILURE)
- Main PID: 349483 (code=exited, status=1/FAILURE)
-Feb 20 09:52:33 admin1.baobab systemd[1]: Started Gurobi token server.
-Feb 20 09:52:33 admin1.baobab grb[349483]: Gurobi Token Server version 9.5.0
-Feb 20 09:52:33 admin1.baobab grb[349483]: Problem with Gurobi license - unable to start token server
-Feb 20 09:52:33 admin1.baobab grb[349483]: Gurobi license file: /opt/ebsofts/licenses/Gurobi/gurobi.lic
-Feb 20 09:52:33 admin1.baobab grb_ts[349483]: Gurobi Token Server version 9.5.0
-Feb 20 09:52:33 admin1.baobab grb_ts[349483]: License expired 2024-02-15
-Feb 20 09:52:33 admin1.baobab grb_ts[349483]: Problem with Gurobi license - unable to start token server
-Feb 20 09:52:33 admin1.baobab grb_ts[349483]: Gurobi license file: /opt/ebsofts/licenses/Gurobi/gurobi.lic
-Feb 20 09:52:33 admin1.baobab systemd[1]: gurobi.service: Main process exited, code=exited, status=1/FAILURE
-Feb 20 09:52:33 admin1.baobab systemd[1]: gurobi.service: Failed with result 'exit-code'.
-</code>
-**Contact Gurobi support to ask an extension:**
-  https://support.gurobi.com/hc/en-us
-**Download the licence file on https://portal.gurobi.com/iam/licenses/list  and copy into the soft directory**:
-  scp gurobi.lic admin1.baobab.hpc.unige.ch:/opt/ebsofts/licenses/Gurobi/gurobi.lic
-**Restart the gurobi service**:
-<code>
-(baobab)-[root@admin1 ~]$ systemctl start gurobi
-(baobab)-[root@admin1 ~]$ systemctl status gurobi
-● gurobi.service - Gurobi token server
-   Loaded: loaded (/etc/systemd/system/gurobi.service; enabled; vendor preset: disabled)
-   Active: active (running) since Tue 2024-02-20 10:00:58 CET; 3s ago
- Main PID: 352723 (grb_ts)
-    Tasks: 1 (limit: 411104)
-   Memory: 7.6M
-   CGroup: /system.slice/gurobi.service
-           └─352723 /opt/ebsofts/Gurobi/9.5.0-GCCcore-11.2.0/bin/grb_ts -n
-Feb 20 10:00:58 admin1.baobab systemd[1]: Started Gurobi token server.
-Feb 20 10:00:58 admin1.baobab grb[352723]: Gurobi Token Server version 9.5.0
-Feb 20 10:00:58 admin1.baobab grb[352723]: Gurobi Token Server version 9.5.0 started: Tue Feb 20 10:00:58 2024
-Feb 20 10:00:58 admin1.baobab grb[352723]: Gurobi license file: /opt/ebsofts/licenses/Gurobi/gurobi.lic
-Feb 20 10:00:58 admin1.baobab grb[352723]: Gurobi Token Server use limit: 4096
-</code>
 ===== Jupyter notebook and Jupyter lab=====
@@ Line 1104: / Line 1054: @@
 ==== Intro ====
-Apptainer is a Docker like for HPC. It is available directly on the OS, not through module.
+Apptainer is a Docker like for HPC. It is available directly on the OS, not through module. \\
+As you don't have root access on Baobab, you cannot build recipe file on Baobab. If you need to do this, you may want to build the image on your own machine and transfer the image to Baobab.\\
+You can download existing images from shub (singularity hub) or from docker (docker public or private registry).\\
+The image will be converted to a read-only squashfs on Baobab disk. It's not possible to have writable images as user. Instead you should build the image as sandbox.\\
-As you don't have root access on Baobab, you cannot build recipe file on Baobab. If you need to do this, you may want to build the image on your own machine and transfer the image to Baobab.
+Apptainer images are immutable, but it is possible to append an overlay, see below.
-You can download existing images from shub (singularity hub) or from docker (docker public or private registry).
+=== Pull an existing image ===
+<WRAP round alert 50%>
+ Do not run the following commands on login node !! It's using too much cpu
+</WRAP>
+Exemple with Rstudio:
-The image will be converted to a read-only squashfs on Baobab disk. It's not possible to have writable images as user. Instead you should build the image as sandbox.
+**Create a project directory and pull the image from compute node:**
+  (baobab)-[alberta@login2 ~]$ MYPROJECT="rocker"
-Apptainer images are immutable, but it is possible to append an overlay, see below.
+  (baobab)-[alberta@login2 ~]$ mkdir -p singularity/$MYPROJECT
+  (baobab)-[alberta@login2 ~]$ cd !$
+  (baobab)-[alberta@login2 rocker]$ salloc --partition=shared-cpu --time=00:30:00 --cpus-per-task 12
+  (baobab)-[alberta@cpu300 rocker]$ apptainer pull docker://rocker/rstudio:4.2
+  (baobab)-[alberta@cpu300 rocker]$ ls
+  rstudio_4.2.sif
+And Voila; I get my sif image rstudio_4.2.sif
 ==== Convert a Docker image ====

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