Merge branch 'master' into 'add_soft'

Master

See merge request !170

.gitlab-ci.yml

@@ -6,17 +6,18 @@ stages:
 docs:
   stage: test
   image: davidhrbac/docker-mdcheck:latest
-  allow_failure: true
   script:
-  - mdl -r ~MD013,~MD033,~MD014,~MD026,~MD037 *.md docs.it4i/
+  - mdl -r ~MD013,~MD033,~MD014,~MD026,~MD037 *.md docs.it4i
 
 two spaces:
   stage: test
   image: davidhrbac/docker-mdcheck:latest
   allow_failure: true
-  script:
+  before_script:
   - echo "== Files having more than one space betwee two characters =="
-  - find docs.it4i/ -name '*.md' -exec grep "[[:alpha:]]  [[:alpha:]]" -l {} + || true
+  - find docs.it4i/ -name '*.md' -exec grep "[[:alpha:]]  [[:alpha:]]" {} +
+  script:
+  - find docs.it4i/ -name '*.md' -exec grep "[[:alpha:]]  [[:alpha:]]" -l {} + | grep docs.it4i/ -v
 
 capitalize:
   stage: test
@@ -74,6 +75,8 @@ mkdocs:
     #- bash scripts/clean_json.sh site/mkdocs/search_index.json
     # replace broken links in 404.html
   - sed -i 's,href="" title=",href="/" title=",g' site/404.html
+  - cp site/404.html site/403.html
+  - sed -i 's/404 - Not found/403 - Forbidden/g' site/403.html
     # compress sitemap
   - gzip < site/sitemap.xml > site/sitemap.xml.gz
   artifacts:

docs.it4i/anselm/resources-allocation-policy.md

-## Resources Allocation Policy
+# Resources Allocation Policy
 
-### Job queue policies
+## Job queue policies
 
 The resources are allocated to the job in a fair-share fashion, subject to constraints set by the queue and resources available to the Project. The Fair-share at Anselm ensures that individual users may consume approximately equal amount of resources per week. Detailed information in the [Job scheduling](job-priority/) section. The resources are accessible via several queues for queueing the jobs. The queues provide prioritized and exclusive access to the computational resources. Following table provides the queue partitioning overview:
 
@@ -27,7 +27,7 @@ The resources are allocated to the job in a fair-share fashion, subject to const
 * **qnvidia**, qmic, qfat, the Dedicated queues: The queue qnvidia is dedicated to access the Nvidia accelerated nodes, the qmic to access MIC nodes and qfat the Fat nodes. It is required that active project with nonzero remaining resources is specified to enter these queues. 23 nvidia, 4 mic and 2 fat nodes are included. Full nodes, 16 cores per node are allocated. The queues run with very high priority, the jobs will be scheduled before the jobs coming from the qexp queue. An PI needs explicitly ask [support](https://support.it4i.cz/rt/) for authorization to enter the dedicated queues for all users associated to her/his Project.
 * **qfree**, The Free resource queue: The queue qfree is intended for utilization of free resources, after a Project exhausted all its allocated computational resources (Does not apply to DD projects by default. DD projects have to request for persmission on qfree after exhaustion of computational resources.). It is required that active project is specified to enter the queue, however no remaining resources are required. Consumed resources will be accounted to the Project. Only 178 nodes without accelerator may be accessed from this queue. Full nodes, 16 cores per node are allocated. The queue runs with very low priority and no special authorization is required to use it. The maximum runtime in qfree is 12 hours.
 
-### Queue notes
+## Queue notes
 
 The job wall clock time defaults to **half the maximum time**, see table above. Longer wall time limits can be  [set manually, see examples](job-submission-and-execution/).
 
@@ -35,7 +35,7 @@ Jobs that exceed the reserved wall clock time (Req'd Time) get killed automatica
 
 Anselm users may check current queue configuration at <https://extranet.it4i.cz/anselm/queues>.
 
-### Queue status
+## Queue status
 
 !!! tip
     Check the status of jobs, queues and compute nodes at <https://extranet.it4i.cz/anselm/>

docs.it4i/salomon/resources-allocation-policy.md

-## Resources Allocation Policy
+# Resources Allocation Policy
 
-### Job queue policies
+## Job queue policies
 
 The resources are allocated to the job in a fair-share fashion, subject to constraints set by the queue and resources available to the Project. The fair-share at Anselm ensures that individual users may consume approximately equal amount of resources per week. Detailed information in the [Job scheduling](job-priority/) section. The resources are accessible via several queues for queueing the jobs. The queues provide prioritized and exclusive access to the computational resources. Following table provides the queue partitioning overview:
 
@@ -31,7 +31,7 @@ The resources are allocated to the job in a fair-share fashion, subject to const
 !!! note
     To access node with Xeon Phi co-processor user needs to specify that in [job submission select statement](job-submission-and-execution/).
 
-### Queue notes
+## Queue notes
 
 The job wall-clock time defaults to **half the maximum time**, see table above. Longer wall time limits can be  [set manually, see examples](job-submission-and-execution/).
 
@@ -39,7 +39,7 @@ Jobs that exceed the reserved wall-clock time (Req'd Time) get killed automatica
 
 Salomon users may check current queue configuration at <https://extranet.it4i.cz/rsweb/salomon/queues>.
 
-### Queue Status
+## Queue Status
 
 !!! note
     Check the status of jobs, queues and compute nodes at [https://extranet.it4i.cz/rsweb/salomon/](https://extranet.it4i.cz/rsweb/salomon)

docs.it4i/snippets/resource_accounting.md

-## Resource Accounting Policy
+# Resource Accounting Policy
 
-### Wall-clock Core-Hours WCH
+## Wall-clock Core-Hours WCH
 
 The wall-clock core-hours (WCH) are the basic metric of computer utilization time.
 1 wall-clock core-hour is defined as 1 processor core allocated for 1 hour of wall-clock time. Allocating a full node (16 cores Anselm,  24 cores Salomon)
 for 1 hour amounts to 16 wall-clock core-hours (Anselm) or 24 wall-clock core-hours (Salomon).
 
-### Normalized Core-Hours NCH
+## Normalized Core-Hours NCH
 
 The resources subject to accounting are the normalized core-hours (NCH).
 The normalized core-hours are obtained from WCH by applying a normalization factor:
@@ -37,7 +37,7 @@ In future, the factors F will be updated, as new systems are installed. Factors
 
 See examples in the [Job submission and execution](job-submission-and-execution/) section.
 
-### Consumed Resources
+## Consumed Resources
 
 Check how many core-hours have been consumed. The command it4ifree is available on cluster login nodes.
 

docs.it4i/software/lang/csc.md

@@ -72,6 +72,7 @@ false
 ```
 
 Show all files modified in last 5 days:
+
 ```csc
 csharp> using System.IO;
 csharp> from f in Directory.GetFiles ("mydirectory")

docs.it4i/software/lang/java.md

@@ -23,3 +23,64 @@ $ which javac
 ```
 
 Java applications may use MPI for inter-process communication, in conjunction with Open MPI. Read more on <http://www.open-mpi.org/faq/?category=java>. This functionality is currently not supported on Anselm cluster. In case you require the java interface to MPI, please contact [cluster support](https://support.it4i.cz/rt/).
+
+## Java with OpenMPI
+
+Because there is an increasing interest in using Java for HPC. Also, MPI can benefit from Java because its widespread use makes it likely to find new uses beyond traditional HPC applications.
+
+The Java bindings are integrated into Open MPI starting from the v1.7 series. Beginning with the v2.0 series, the Java bindings include coverage of MPI-3.1.
+
+### Example (Hello.java)
+
+```java
+import mpi.*;
+
+class Hello {
+    static public void main(String[] args) throws MPIException {
+
+
+        MPI.Init(args);
+
+        int myrank = MPI.COMM_WORLD.getRank();
+        int size = MPI.COMM_WORLD.getSize() ;
+        System.out.println("Hello world from rank " + myrank + " of " + size);
+
+        MPI.Finalize();
+    }
+}
+```
+
+```console
+$ ml Java/1.8.0_144
+$ ml OpenMPI/1.8.0_144
+$ mpijavac Hello.java
+$ mpirun java Hello
+Hello world from rank 23 of 28
+Hello world from rank 25 of 28
+Hello world from rank 0 of 28
+Hello world from rank 4 of 28
+Hello world from rank 7 of 28
+Hello world from rank 8 of 28
+Hello world from rank 11 of 28
+Hello world from rank 12 of 28
+Hello world from rank 13 of 28
+Hello world from rank 18 of 28
+Hello world from rank 17 of 28
+Hello world from rank 24 of 28
+Hello world from rank 27 of 28
+Hello world from rank 2 of 28
+Hello world from rank 3 of 28
+Hello world from rank 1 of 28
+Hello world from rank 10 of 28
+Hello world from rank 14 of 28
+Hello world from rank 16 of 28
+Hello world from rank 19 of 28
+Hello world from rank 26 of 28
+Hello world from rank 6 of 28
+Hello world from rank 9 of 28
+Hello world from rank 15 of 28
+Hello world from rank 20 of 28
+Hello world from rank 5 of 28
+Hello world from rank 21 of 28
+Hello world from rank 22 of 28
+```
\ No newline at end of file

docs.it4i/software/tools/spack.md

@@ -239,7 +239,7 @@ $ spack edit git
 ```
 
 !!! note
-    To change source link (ftp:// to http://) use `spack create URL -f` to regenerates rules.
+    To change source link (`ftp://` to `http://`) use `spack create URL -f` to regenerates rules.
 
 #### **Example**
 

docs.it4i/src/css.css

+.md-icon--edit:before {
+    content: "edit";
+}
+
+.md-icon--check:before {
+    content: "check";
+}
+
+.md-icon--help:before {
+    content: "help";
+}
+
 a:not([href*="//"]) {
     /* CSS for internal links */
 }
@@ -6,7 +18,7 @@ a.md-footer-social__link.fa.fa-globe {
     !background: none;
 }
 
-a[href*="//"]:not( [href*='gitlab.it4i.cz'] ):not( [href*='code.it4i.cz'] ):not( [href*='https://www.it4i.cz'] )  {
+a[href*="//"]:not( [href*='gitlab.it4i.cz'] ):not( [href*='code.it4i.cz'] ):not( [href*='https://www.it4i.cz'] ):not( [href*='https://support.it4i.cz'] )  {
     /*CSS for external links */
     background: transparent url("/img/external.png") no-repeat right 0px top 1px;
     background-size: 12px;

material/partials/language.html

@@ -4,5 +4,5 @@
   "footer.next": "Next",
   "search.placeholder": "Search",
   "source.link.title": "Go to repository",
-  "toc.title": "Table of contents"
+  "toc.title": "On this page"
 }[key] }}{% endmacro %}

material/partials/toc.html

@@ -4,6 +4,38 @@
   {% if toc_ | first is defined and "\x3ch1 id=" in page.content %}
     {% set toc_ = (toc_ | first).children %}
   {% endif %}
+  {% if page.abs_url.rstrip('index.html').rstrip('/') == '' %}
+    {% set it4i_link = config.repo_url + '/edit/master/docs.it4i/index.md' %}
+    {% set it4i_page = '/index.md' %}
+    {% set it4i_url = 'https://docs.it4i.cz' %}
+  {% else %}
+    {% set it4i_link = config.repo_url + '/edit/master/docs.it4i' + page.abs_url.rstrip('index.html').rstrip('/') + '.md' %}
+    {% set it4i_page = page.abs_url.rstrip('index.html').rstrip('/') + '.md' %}
+    {% set it4i_url = 'https://docs.it4i.cz' +  page.abs_url %}
+  {% endif %}
+  <ul class="md-nav__list" data-md-scrollfix>
+    <li class="md-nav__item">
+      <a href="{{ it4i_link }}" title="Edit This Page" class="md-nav__link" target="_blank">
+	<i class="md-icon md-icon--edit">
+	</i>
+	Edit This Page
+      </a>
+    </li>
+    <li class="md-nav__item">
+      <a href="https://code.it4i.cz/sccs/docs.it4i.cz/issues/new?issue%5Bdescription%5D=Requested change in page [{{ it4i_page }}]({{ it4i_url }}) /cc @hrb33 @kru0052" title="Request Change" class="md-nav__link" target="_blank">
+	<i class="md-icon md-icon--check">
+	</i>
+	Request Change
+      </a>
+    </li>
+    <li class="md-nav__item">
+      <a href="https://support.it4i.cz/rt" title="Get Support" class="md-nav__link" target="_blank">
+	<i class="md-icon md-icon--help">
+	</i>
+	Get Support
+      </a>
+    </li>
+  </ul>
   {% if toc_ | first is defined %}
   <label class="md-nav__title" for="toc">{{ lang.t('toc.title') }}</label>
   <ul class="md-nav__list" data-md-scrollfix>

mkdocs.yml

@@ -25,7 +25,7 @@ pages:
       - X Window System: general/accessing-the-clusters/graphical-user-interface/x-window-system.md
       - VNC: general/accessing-the-clusters/graphical-user-interface/vnc.md
       - VPN Access: general/accessing-the-clusters/vpn-access.md
-    - Resource allocation and job execution: general/resource_allocation_and_job_execution.md
+    - Resource Allocation and Job Execution: general/resource_allocation_and_job_execution.md
   - Salomon Cluster:
     - Introduction: salomon/introduction.md
     - Hardware Overview: salomon/hardware-overview.md