From 40c12b02a5d953de2ecb4ef79a18d75ea75cbd1d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Luk=C3=A1=C5=A1=20Krup=C4=8D=C3=ADk?= <lukas.krupcik@vsb.cz>
Date: Wed, 22 Sep 2021 12:42:19 +0200
Subject: [PATCH] Update docs.it4i/software/tools/ansys/ansys-cfx.md,
 docs.it4i/software/tools/ansys/ansys-fluent.md,
 docs.it4i/software/tools/ansys/ansys-ls-dyna.md,
 docs.it4i/software/tools/ansys/ansys-mechanical-apdl.md,
 docs.it4i/software/tools/ansys/licensing.md, mkdocs.yml,
 docs.it4i/software/tools/ansys/setting-license-preferences.md,
 docs.it4i/software/tools/ansys/workbench.md,
 docs.it4i/software/tools/easybuild-images.md,
 docs.it4i/software/tools/spack.md,
 docs.it4i/software/tools/virtualization.md,
 docs.it4i/software/isv_licenses.md, docs.it4i/software/nvidia-cuda.md files
 Deleted docs.it4i/software/tools/ansys/ls-dyna.md

---
 docs.it4i/software/isv_licenses.md            |   2 +-
 docs.it4i/software/nvidia-cuda.md             |  12 +-
 docs.it4i/software/tools/ansys/ansys-cfx.md   |  12 +-
 .../software/tools/ansys/ansys-fluent.md      |  16 +-
 .../software/tools/ansys/ansys-ls-dyna.md     |  14 +-
 .../tools/ansys/ansys-mechanical-apdl.md      |  14 +-
 docs.it4i/software/tools/ansys/licensing.md   |   6 +-
 docs.it4i/software/tools/ansys/ls-dyna.md     |  41 ---
 .../ansys/setting-license-preferences.md      |   2 +-
 docs.it4i/software/tools/ansys/workbench.md   |  11 +-
 docs.it4i/software/tools/easybuild-images.md  |   4 -
 docs.it4i/software/tools/spack.md             | 244 ++++++++++++------
 docs.it4i/software/tools/virtualization.md    |   5 +
 mkdocs.yml                                    |   1 -
 14 files changed, 208 insertions(+), 176 deletions(-)
 delete mode 100644 docs.it4i/software/tools/ansys/ls-dyna.md

diff --git a/docs.it4i/software/isv_licenses.md b/docs.it4i/software/isv_licenses.md
index 28241d491..2fda53070 100644
--- a/docs.it4i/software/isv_licenses.md
+++ b/docs.it4i/software/isv_licenses.md
@@ -79,4 +79,4 @@ The license is used and accounted only with the real usage of the product. So in
 [1]: #Licence
 
 [a]: https://extranet.it4i.cz/rsweb/barbora/licenses
-[b]: http://licelin.it4i.cz/list/
\ No newline at end of file
+[b]: http://licelin.it4i.cz/list/
diff --git a/docs.it4i/software/nvidia-cuda.md b/docs.it4i/software/nvidia-cuda.md
index a55c93487..a78303aac 100644
--- a/docs.it4i/software/nvidia-cuda.md
+++ b/docs.it4i/software/nvidia-cuda.md
@@ -20,13 +20,7 @@ The default programming model for GPU accelerators is NVIDIA CUDA. To set up the
 $ ml CUDA
 ```
 
-If the user code is hybrid and uses both CUDA and MPI, the MPI environment has to be set up as well. One way to do this is to use the `PrgEnv-gnu` module, which sets up the correct combination of the GNU compiler and MPI library:
-
-```console
-$ ml PrgEnv-gnu
-```
-
-CUDA code can be compiled directly on login1 or login2 nodes. The user does not have to use compute nodes with GPU accelerators for compilation. To compile CUDA source code, use the NVCC compiler:
+CUDA code can be compiled directly on login nodes. The user does not have to use compute nodes with GPU accelerators for compilation. To compile CUDA source code, use the NVCC compiler:
 
 ```console
 $ nvcc --version
@@ -37,7 +31,7 @@ The CUDA Toolkit comes with a large number of examples, which can be a helpful r
 ```console
 $ cd ~
 $ mkdir cuda-samples
-$ cp -R /apps/nvidia/cuda/6.5.14/samples/* ~/cuda-samples/
+$ cp -R /apps/nvidia/cuda/VERSION_CUDA/samples/* ~/cuda-samples/
 ```
 
 To compile examples, change directory to the particular example (here the example used is deviceQuery) and run `make` to start the compilation;
@@ -51,7 +45,7 @@ To run the code, the user can use a PBS interactive session to get access to a n
 
 ```console
 $ qsub -I -q qnvidia -A OPEN-0-0
-$ ml cuda
+$ ml CUDA
 $ ~/cuda-samples/1_Utilities/deviceQuery/deviceQuery
 ```
 
diff --git a/docs.it4i/software/tools/ansys/ansys-cfx.md b/docs.it4i/software/tools/ansys/ansys-cfx.md
index c73546daf..b1411b0a9 100644
--- a/docs.it4i/software/tools/ansys/ansys-cfx.md
+++ b/docs.it4i/software/tools/ansys/ansys-cfx.md
@@ -6,18 +6,16 @@ To run ANSYS CFX in batch mode, you can utilize/modify the default cfx.pbs scrip
 
 ```bash
 #!/bin/bash
-#PBS -l select=5:ncpus=24:mpiprocs=24
+#PBS -l select=5:ncpus=128:mpiprocs=128
 #PBS -q qprod
 #PBS -N ANSYS-test
 #PBS -A XX-YY-ZZ
 
-#! Mail to user when job terminate or abort
-#PBS -m ae
-
 #!change the working directory (default is home directory)
 #cd <working directory> (working directory must exists)
-WORK_DIR="/scratch/$USER/work"
-cd $WORK_DIR
+DIR=/scratch/project/PROJECT_ID/$PBS_JOBID
+mkdir -p "$DIR"
+cd "$DIR" || exit
 
 echo Running on host `hostname`
 echo Time is `date`
@@ -25,7 +23,7 @@ echo Directory is `pwd`
 echo This jobs runs on the following processors:
 echo `cat $PBS_NODEFILE`
 
-ml ANSYS/19.1-intel-2017c
+ml ANSYS/21.1-intel-2018a
 
 #### Set number of processors per host listing
 #### (set to 1 as $PBS_NODEFILE lists each node twice if :ppn=2)
diff --git a/docs.it4i/software/tools/ansys/ansys-fluent.md b/docs.it4i/software/tools/ansys/ansys-fluent.md
index 0d0b20562..378f748b4 100644
--- a/docs.it4i/software/tools/ansys/ansys-fluent.md
+++ b/docs.it4i/software/tools/ansys/ansys-fluent.md
@@ -9,18 +9,16 @@ To run ANSYS Fluent in a batch mode, you can utilize/modify the default fluent.p
 ```bash
 #!/bin/bash
 #PBS -S /bin/bash
-#PBS -l select=5:ncpus=24:mpiprocs=24
+#PBS -l select=5:ncpus=128:mpiprocs=128
 #PBS -q qprod
 #PBS -N ANSYS-test
 #PBS -A XX-YY-ZZ
 
-#! Mail to user when job terminate or abort
-#PBS -m ae
-
 #!change the working directory (default is home directory)
 #cd <working directory> (working directory must exists)
-WORK_DIR="/scratch/$USER/work"
-cd $WORK_DIR
+DIR=/scratch/project/PROJECT_ID/$PBS_JOBID
+mkdir -p "$DIR"
+cd "$DIR" || exit
 
 echo Running on host `hostname`
 echo Time is `date`
@@ -29,7 +27,7 @@ echo This jobs runs on the following processors:
 echo `cat $PBS_NODEFILE`
 
 #### Load ansys module so that we find the cfx5solve command
-ml ANSYS/19.1-intel-2017c
+ml ANSYS/21.1-intel-2018a
 
 # Use following line to specify MPI for message-passing instead
 NCORES=`wc -l $PBS_NODEFILE |awk '{print $1}'`
@@ -91,7 +89,7 @@ To run ANSYS Fluent in batch mode with the user's config file, you can utilize/m
 
 ```bash
 #!/bin/sh
-#PBS -l nodes=2:ppn=4
+#PBS -l nodes=2:mpiprocs=4:ncpus=128
 #PBS -1 qprod
 #PBS -N $USE-Fluent-Project
 #PBS -A XX-YY-ZZ
@@ -135,7 +133,7 @@ To run ANSYS Fluent in batch mode with the user's config file, you can utilize/m
  Fluent arguments: $fluent_args"
 
  #run the solver
- /ansys_inc/v145/fluent/bin/fluent $fluent_args  > $outfile
+ fluent $fluent_args  > $outfile
 ```
 
 It runs the jobs out of the directory from which they are submitted (PBS_O_WORKDIR).
diff --git a/docs.it4i/software/tools/ansys/ansys-ls-dyna.md b/docs.it4i/software/tools/ansys/ansys-ls-dyna.md
index 761ec076b..0c68fd650 100644
--- a/docs.it4i/software/tools/ansys/ansys-ls-dyna.md
+++ b/docs.it4i/software/tools/ansys/ansys-ls-dyna.md
@@ -6,18 +6,16 @@ To run ANSYS LS-DYNA in batch mode, you can utilize/modify the default ansysdyna
 
 ```bash
 #!/bin/bash
-#PBS -l select=5:ncpus=24:mpiprocs=24
+#PBS -l select=5:ncpus=128:mpiprocs=128
 #PBS -q qprod
 #PBS -N ANSYS-test
 #PBS -A XX-YY-ZZ
 
-#! Mail to user when job terminate or abort
-#PBS -m ae
-
 #!change the working directory (default is home directory)
 #cd <working directory>
-WORK_DIR="/scratch/$USER/work"
-cd $WORK_DIR
+DIR=/scratch/project/PROJECT_ID/$PBS_JOBID
+mkdir -p "$DIR"
+cd "$DIR" || exit
 
 echo Running on host `hostname`
 echo Time is `date`
@@ -30,7 +28,7 @@ NPROCS=`wc -l < $PBS_NODEFILE`
 
 echo This job has allocated $NPROCS nodes
 
-ml ANSYS/19.1-intel-2017c
+ml ANSYS/21.1-intel-2018a
 
 #### Set number of processors per host listing
 #### (set to 1 as $PBS_NODEFILE lists each node twice if :ppn=2)
@@ -47,7 +45,7 @@ done
 
 echo Machines: $hl
 
-ansys191 -dis -lsdynampp i=input.k -machines $hl
+ansys211 -dis -lsdynampp i=input.k -machines $hl
 ```
 
 The header of the PBS file (above) is common and the description can be found on [this site][1]. [SVS FEM][b] recommends to utilize sources by keywords: nodes, ppn. These keywords allows addressing directly the number of nodes (computers) and cores (ppn) utilized in the job. In addition, the rest of the code assumes such structure of allocated resources.
diff --git a/docs.it4i/software/tools/ansys/ansys-mechanical-apdl.md b/docs.it4i/software/tools/ansys/ansys-mechanical-apdl.md
index 1b0e647de..d027f175f 100644
--- a/docs.it4i/software/tools/ansys/ansys-mechanical-apdl.md
+++ b/docs.it4i/software/tools/ansys/ansys-mechanical-apdl.md
@@ -6,18 +6,16 @@ To run ANSYS MAPDL in batch mode you can utilize/modify the default mapdl.pbs sc
 
 ```bash
 #!/bin/bash
-#PBS -l select=5:ncpus=24:mpiprocs=24
+#PBS -l select=5:ncpus=128:mpiprocs=128
 #PBS -q qprod
 #PBS -N ANSYS-test
 #PBS -A XX-YY-ZZ
 
-#! Mail to user when job terminate or abort
-#PBS -m ae
-
 #!change the working directory (default is home directory)
 #cd <working directory> (working directory must exists)
-WORK_DIR="/scratch/$USER/work"
-cd $WORK_DIR
+DIR=/scratch/project/PROJECT_ID/$PBS_JOBID
+mkdir -p "$DIR"
+cd "$DIR" || exit
 
 echo Running on host `hostname`
 echo Time is `date`
@@ -25,7 +23,7 @@ echo Directory is `pwd`
 echo This jobs runs on the following processors:
 echo `cat $PBS_NODEFILE`
 
-ml ANSYS/19.1-intel-2017c
+ml ANSYS/21.1-intel-2018a
 
 #### Set number of processors per host listing
 #### (set to 1 as $PBS_NODEFILE lists each node twice if :ppn=2)
@@ -45,7 +43,7 @@ echo Machines: $hl
 #-i input.dat includes the input of analysis in APDL format
 #-o file.out is output file from ansys where all text outputs will be redirected
 #-p the name of license feature (aa_r=ANSYS Academic Research, ane3fl=Multiphysics(commercial), aa_r_dy=Academic AUTODYN)
-ansys191 -b -dis -p aa_r -i input.dat -o file.out -machines $hl -dir $WORK_DIR
+ansys211 -b -dis -p aa_r -i input.dat -o file.out -machines $hl -dir $WORK_DIR
 ```
 
 The header of the PBS file (above) is common and the description can be found on [this site][1]. [SVS FEM][b] recommends utilizing sources by keywords: nodes, ppn. These keywords allow addressing directly the number of nodes (computers) and cores (ppn) utilized in the job. In, addition the rest of the code assumes such structure of allocated resources.
diff --git a/docs.it4i/software/tools/ansys/licensing.md b/docs.it4i/software/tools/ansys/licensing.md
index 7e2c1dc3e..30b0bf4b9 100644
--- a/docs.it4i/software/tools/ansys/licensing.md
+++ b/docs.it4i/software/tools/ansys/licensing.md
@@ -22,15 +22,13 @@ lic-ansys.vsb.cz / 1055 (2325)
 
 ## Available Versions
 
-* 19.1
-* 19.3
+* 21.1
 
 ``` console
 $ ml av ANSYS
 ---------------- /apps/modules/tools -----------------------
-   ANSYS/19.1-intel-2017c (C6)    ANSYS/19.3-intel-2017c (D)
+   ANSYS/21.1-intel-2018a (D)
 
   Where:
-   C6:  Old CentOS6 module
    D:   Default Module
 ```
diff --git a/docs.it4i/software/tools/ansys/ls-dyna.md b/docs.it4i/software/tools/ansys/ls-dyna.md
deleted file mode 100644
index 5ed660201..000000000
--- a/docs.it4i/software/tools/ansys/ls-dyna.md
+++ /dev/null
@@ -1,41 +0,0 @@
-# LS-DYNA
-
-[LS-DYNA][a] is a multi-purpose, explicit and implicit finite element program used to analyze the nonlinear dynamic response of structures. Its fully automated contact analysis capability, a wide range of constitutive models to simulate a whole range of engineering materials (steels, composites, foams, concrete, etc.), error-checking features, and the high scalability have enabled users worldwide to solve successfully many complex problems. Additionally LS-DYNA is extensively used to simulate impacts on structures from drop tests, underwater shock, explosions or high-velocity impacts. Explosive forming, process engineering, accident reconstruction, vehicle dynamics, thermal brake disc analysis, or nuclear safety are further areas in the broad range of possible applications. In leading-edge research, LS-DYNA is used to investigate the behavior of materials like composites, ceramics, concrete, or wood. Moreover, it is used in biomechanics, human modeling, molecular structures, casting, forging, or virtual testing.
-
-!!! Info
-    We provide **1 commercial license of LS-DYNA without HPC** support, now.
-
-To run LS-DYNA in batch mode, you can utilize/modify the default lsdyna.pbs script and execute it via the qsub command:
-
-```bash
-#!/bin/bash
-#PBS -l select=5:ncpus=16:mpiprocs=16
-#PBS -q qprod
-#PBS -N ANSYS-test
-#PBS -A XX-YY-ZZ
-
-#! Mail to user when job terminate or abort
-#PBS -m ae
-
-#!change the working directory (default is home directory)
-#cd <working directory> (working directory must exists)
-WORK_DIR="/scratch/$USER/work"
-cd $WORK_DIR
-
-echo Running on host `hostname`
-echo Time is `date`
-echo Directory is `pwd`
-
-ml lsdyna
-
-/apps/engineering/lsdyna/lsdyna700s i=input.k
-```
-
-The header of the PBS file (above) is common and the description can be found on [this site][1]. [SVS FEM][b] recommends utilizing sources by keywords: nodes, ppn. These keywords allow addressing directly the number of nodes (computers) and cores (ppn) utilized in the job. In addition, the rest of the code assumes such structure of allocated resources.
-
-A working directory has to be created before sending the PBS job into the queue. The input file should be in the working directory or a full path to input file has to be specified. The input file has to be defined by a common LS-DYNA **.k** file which is attached to the LS-DYNA solver via the `i=`  parameter.
-
-[1]: ../../../general/job-submission-and-execution.md
-
-[a]: http://www.lstc.com/
-[b]: http://www.svsfem.cz
diff --git a/docs.it4i/software/tools/ansys/setting-license-preferences.md b/docs.it4i/software/tools/ansys/setting-license-preferences.md
index adafabb19..3c13b571f 100644
--- a/docs.it4i/software/tools/ansys/setting-license-preferences.md
+++ b/docs.it4i/software/tools/ansys/setting-license-preferences.md
@@ -1,6 +1,6 @@
 # Setting License Preferences
 
-Some ANSYS tools allow you to explicitly specify usage of academic or commercial licenses in the command line (e.g. ansys161 -p aa_r to select the Academic Research license). However, we have observed that not all tools obey this option and choose the commercial license.
+Some ANSYS tools allow you to explicitly specify usage of academic or commercial licenses in the command line (e.g. ansys211 -p aa_r to select the Academic Research license). However, we have observed that not all tools obey this option and choose the commercial license.
 
 Thus you need to configure preferred license order with ANSLIC_ADMIN. Follow these steps and move the Academic Research license to the top or bottom of the list accordingly.
 
diff --git a/docs.it4i/software/tools/ansys/workbench.md b/docs.it4i/software/tools/ansys/workbench.md
index b62a4c1d2..e7ef53d93 100644
--- a/docs.it4i/software/tools/ansys/workbench.md
+++ b/docs.it4i/software/tools/ansys/workbench.md
@@ -18,17 +18,16 @@ Now, save the project and close Workbench. We will use this script to launch the
 
 ```bash
     #!/bin/bash
-    #PBS -l select=2:ncpus=24
+    #PBS -l select=2:ncpus=128
     #PBS -q qprod
     #PBS -N test9_mpi_2
     #PBS -A OPEN-0-0
 
-    # Mail to user when job terminate or abort
-    #PBS -m a
 
     # change the working directory
-    WORK_DIR="$PBS_O_WORKDIR"
-    cd $WORK_DIR
+    DIR=/scratch/project/PROJECT_ID/$PBS_JOBID
+    mkdir -p "$DIR"
+    cd "$DIR" || exit
 
     echo Running on host `hostname`
     echo Time is `date`
@@ -36,7 +35,7 @@ Now, save the project and close Workbench. We will use this script to launch the
     echo This jobs runs on the following nodes:
     echo `cat $PBS_NODEFILE`
 
-    ml ANSYS
+    ml ANSYS/21.1-intel-2018a
 
     #### Set number of processors per host listing
     procs_per_host=24
diff --git a/docs.it4i/software/tools/easybuild-images.md b/docs.it4i/software/tools/easybuild-images.md
index cb86b95bf..1efc6d857 100644
--- a/docs.it4i/software/tools/easybuild-images.md
+++ b/docs.it4i/software/tools/easybuild-images.md
@@ -2,10 +2,6 @@
 
 EasyBuild has support for generating container recipes that will use EasyBuild to build and install a specified software stack. In addition, EasyBuild can (optionally) leverage the build tool provided by the container software of choice to create container images.
 
-!!! info
-    The features documented here have been available since **EasyBuild v3.6.0** but are still experimental, which implies they are subject to change in upcoming versions of EasyBuild.
-    To use the features, enable the `--experimental` configuration option.
-
 ## Generating Container Recipes
 
 To generate container recipes, use `eb --containerize`, or `eb -C` for short.
diff --git a/docs.it4i/software/tools/spack.md b/docs.it4i/software/tools/spack.md
index 8084dbe95..b318202b6 100644
--- a/docs.it4i/software/tools/spack.md
+++ b/docs.it4i/software/tools/spack.md
@@ -11,8 +11,7 @@ For more information, see Spack's [documentation][a].
 $ ml av Spack
 
 ---------------------- /apps/modules/devel ------------------------------
-   Spack/default
-
+   Spack/0.16.2 (D)
 ```
 
 !!! note
@@ -27,8 +26,8 @@ $ ml Spack
 == Settings for first use
 Couldn't import dot_parser, loading of dot files will not be possible.
 == temporary log file in case of crash /tmp/eb-wLh1RT/easybuild-54vEn3.log
-== processing EasyBuild easyconfig /apps/easybuild/easyconfigs-it4i/s/Spack/Spack-0.10.0.eb
-== building and installing Spack/0.10.0...
+== processing EasyBuild easyconfig /apps/easybuild/easyconfigs-master/easybuild/easyconfigs/s/Spack/Spack-0.16.2.eb
+== building and installing Spack/0.16.2...
 == fetching files...
 == creating build dir, resetting environment...
 == unpacking...
@@ -46,29 +45,27 @@ Couldn't import dot_parser, loading of dot files will not be possible.
 == permissions...
 == packaging...
 == COMPLETED: Installation ended successfully
-== Results of the build can be found in the log file(s) ~/.local/easybuild/software/Spack/0.10.0/easybuild/easybuild-Spack-0.10.0-20170707.122650.log
+== Results of the build can be found in the log file(s) /home/user/.local/easybuild/software/Spack/0.16.2/easybuild/easybuild-Spack-0.16.2-20210922.123022.log
 == Build succeeded for 1 out of 1
 == Temporary log file(s) /tmp/eb-wLh1RT/easybuild-54vEn3.log* have been removed.
 == Temporary directory /tmp/eb-wLh1RT has been removed.
 == Create folder ~/Spack
 
 The following have been reloaded with a version change:
-  1) Spack/default => Spack/0.10.0
+  1) Spack/default => Spack/0.16.2
 
 $ spack --version
-0.10.0
+0.16.2
 ```
 
 ## Usage Module Spack/Default
 
 ```console
 $ ml Spack
+$ ml
 
-The following have been reloaded with a version change:
-  1) Spack/default => Spack/0.10.0
-
-$ spack --version
-0.10.0
+Currently Loaded Modules:
+  1) Spack/0.16.2
 ```
 
 ## Build Software Package
@@ -107,9 +104,22 @@ To see more available versions of a package, run `spack versions`.
 ```console
 $ spack versions git
 ==> Safe versions (already checksummed):
-  2.11.0  2.9.3  2.9.2  2.9.1  2.9.0  2.8.4  2.8.3  2.8.2  2.8.1  2.8.0  2.7.3  2.7.1
+  2.29.0  2.27.0  2.25.0  2.20.1  2.19.1  2.17.1  2.15.1  2.13.0  2.12.1  2.11.1  2.9.3  2.9.1  2.8.4  2.8.2  2.8.0  2.7.1
+  2.28.0  2.26.0  2.21.0  2.19.2  2.18.0  2.17.0  2.14.1  2.12.2  2.12.0  2.11.0  2.9.2  2.9.0  2.8.3  2.8.1  2.7.3
 ==> Remote versions (not yet checksummed):
-  Found no versions for git
+  2.33.0  2.26.2  2.23.3  2.21.1  2.18.3  2.16.1  2.13.6  2.10.4  2.7.0  2.5.2   2.4.2   2.3.0  2.0.2    1.8.5.2    1.8.3.1
+  2.32.0  2.26.1  2.23.2  2.20.5  2.18.2  2.16.0  2.13.5  2.10.3  2.6.7  2.5.1   2.4.1   2.2.3  2.0.1    1.8.5.1    1.8.3
+  2.31.1  2.25.5  2.23.1  2.20.4  2.18.1  2.15.4  2.13.4  2.10.2  2.6.6  2.5.0   2.4.0   2.2.2  2.0.0    1.8.5      1.8.2.3
+  2.31.0  2.25.4  2.23.0  2.20.3  2.17.6  2.15.3  2.13.3  2.10.1  2.6.5  2.4.12  2.3.10  2.2.1  1.9.5    1.8.4.5    0.7
+  2.30.2  2.25.3  2.22.5  2.20.2  2.17.5  2.15.2  2.13.2  2.10.0  2.6.4  2.4.11  2.3.9   2.2.0  1.9.4    1.8.4.4    0.6
+  2.30.1  2.25.2  2.22.4  2.20.0  2.17.4  2.15.0  2.13.1  2.9.5   2.6.3  2.4.10  2.3.8   2.1.4  1.9.3    1.8.4.3    0.5
+  2.30.0  2.25.1  2.22.3  2.19.6  2.17.3  2.14.6  2.12.5  2.9.4   2.6.2  2.4.9   2.3.7   2.1.3  1.9.2    1.8.4.2    0.04
+  2.29.3  2.24.4  2.22.2  2.19.5  2.17.2  2.14.5  2.12.4  2.8.6   2.6.1  2.4.8   2.3.6   2.1.2  1.9.1    1.8.4.1    0.03
+  2.29.2  2.24.3  2.22.1  2.19.4  2.16.6  2.14.4  2.12.3  2.8.5   2.6.0  2.4.7   2.3.5   2.1.1  1.9.0    1.8.4.rc0  0.02
+  2.29.1  2.24.2  2.22.0  2.19.3  2.16.5  2.14.3  2.11.4  2.7.6   2.5.6  2.4.6   2.3.4   2.1.0  1.8.5.6  1.8.4      0.01
+  2.28.1  2.24.1  2.21.4  2.19.0  2.16.4  2.14.2  2.11.3  2.7.5   2.5.5  2.4.5   2.3.3   2.0.5  1.8.5.5  1.8.3.4
+  2.27.1  2.24.0  2.21.3  2.18.5  2.16.3  2.14.0  2.11.2  2.7.4   2.5.4  2.4.4   2.3.2   2.0.4  1.8.5.4  1.8.3.3
+  2.26.3  2.23.4  2.21.2  2.18.4  2.16.2  2.13.7  2.10.5  2.7.2   2.5.3  2.4.3   2.3.1   2.0.3  1.8.5.3  1.8.3.2
 ```
 
 ## Graph for Software Package
@@ -118,6 +128,7 @@ Spack provides the `spack graph` command to display the dependency graph. By def
 
 ```console
 $ spack graph git
+==> Warning: gcc@4.8.5 cannot build optimized binaries for "zen2". Using best target possible: "x86_64"
 o  git
 |\
 | |\
@@ -127,45 +138,82 @@ o  git
 | | | | | |\
 | | | | | | |\
 | | | | | | | |\
-| | | | | | | o |  curl
-| |_|_|_|_|_|/| |
-|/| | | |_|_|/ /
-| | | |/| | | |
-| | | o | | | |  openssl
-| |_|/ / / / /
-|/| | | | | |
-| | | | o | |  gettext
-| | | | |\ \ \
-| | | | | |\ \ \
-| | | | | | |\ \ \
-| | | | | | | |\ \ \
-| | | | | | | o | | |  libxml2
-| |_|_|_|_|_|/| | | |
-|/| | | | |_|/| | | |
+| | | | | | | | |\
+| | | | | | | | | |\
+| | | | | | | | | | |\
+| | | | | | | | | | | |\
+| | | | | | | | | | | | |\
+| | | | o | | | | | | | | |  openssh
+| |_|_|/| | | | | | | | | |
+|/| | |/| | | | | | | | | |
+| | | | |\ \ \ \ \ \ \ \ \ \
+| | | | | | | | | | | | o | |  curl
+| |_|_|_|_|_|_|_|_|_|_|/| | |
+|/| | | |_|_|_|_|_|_|_|/| | |
+| | | |/| | | | | |_|_|/ / /
+| | | | | | | | |/| | | | |
+| | | o | | | | | | | | | |  openssl
+| |_|/| | | | | | | | | | |
+|/| |/ / / / / / / / / / /
+| |/| | | | | | | | | | |
+| | | | | | | | | o | | |  gettext
+| | | | |_|_|_|_|/| | | |
+| | | |/| | | | |/| | | |
+| | | | | | | | | |\ \ \ \
+| | | | | | | | | | |\ \ \ \
+| | | | | | | | | | | |\ \ \ \
+| | | | | | | | | | | o | | | |  libxml2
+| |_|_|_|_|_|_|_|_|_|/| | | | |
+|/| | | | | | | | |_|/| | | | |
+| | | | | | | | |/| |/| | | | |
+| | | | | | | | | |/| | | | | |
+o | | | | | | | | | | | | | | |  zlib
+ / / / / / / / / / / / / / / /
+| | | | | | | | o | | | | | |  xz
+| | | | | | | |  / / / / / /
+| | | | | | | | o | | | | |  tar
+| | | | | | | |/ / / / / /
+| | | | | | | | | | | o |  automake
+| |_|_|_|_|_|_|_|_|_|/| |
+|/| | | | | | | | | | | |
+| | | | | | | | | | | |/
+| | | | | | | | | | | o  autoconf
+| |_|_|_|_|_|_|_|_|_|/|
+|/| | | | |_|_|_|_|_|/
 | | | | |/| | | | | |
-o | | | | | | | | | |  zlib
- / / / / / / / / / /
-| | | o | | | | | |  xz
-| | |  / / / / / /
-| | | o | | | | |  tar
-| | |  / / / / /
-| | | | o | | |  pkg-config
-| | | |  / / /
-o | | | | | |  perl
- / / / / / /
-o | | | | |  pcre
- / / / / /
-| o | | |  ncurses
+o | | | | | | | | | |  perl
+|\ \ \ \ \ \ \ \ \ \ \
+o | | | | | | | | | | |  gdbm
+o | | | | | | | | | | |  readline
+| |_|/ / / / / / / / /
+|/| | | | | | | | | |
+| | | o | | | | | | |  libedit
+| |_|/ / / / / / / /
+|/| | | | | | | | |
+o | | | | | | | | |  ncurses
+| |_|_|_|_|_|/ / /
+|/| | | | | | | |
+o | | | | | | | |  pkgconf
+ / / / / / / / /
+| o | | | | | |  pcre2
+|  / / / / / /
+| | o | | | |  libtool
+| |/ / / / /
+| o | | | |  m4
+| | o | | |  libidn2
+| | o | | |  libunistring
+| | |/ / /
+| o | | |  libsigsegv
 |  / / /
-| | | o  autoconf
-| | | o  m4
-| | | o  libsigsegv
-| | |
-o | |  libiconv
- / /
+| | o |  bzip2
+| | o |  diffutils
+| |/ /
+| o |  libiconv
+|  /
 | o  expat
+| o  libbsd
 |
-o  bzip2
+o  berkeley-db
 ```
 
 ### Information for Software Package
@@ -174,45 +222,74 @@ To get more information on a particular package from `spack list`, use `spack in
 
 ```console
 $ spack info git
-Package:    git
-Homepage:   http://git-scm.com
+AutotoolsPackage:   git
+
+Description:
+    Git is a free and open source distributed version control system
+    designed to handle everything from small to very large projects with
+    speed and efficiency.
+
+Homepage: http://git-scm.com
+
+Tags:
+    None
+
+Preferred version:
+    2.29.0    https://mirrors.edge.kernel.org/pub/software/scm/git/git-2.29.0.tar.gz
 
 Safe versions:
-    2.11.0    https://github.com/git/git/tarball/v2.11.0
-    2.9.3     https://github.com/git/git/tarball/v2.9.3
-    2.9.2     https://github.com/git/git/tarball/v2.9.2
-    2.9.1     https://github.com/git/git/tarball/v2.9.1
-    2.9.0     https://github.com/git/git/tarball/v2.9.0
-    2.8.4     https://github.com/git/git/tarball/v2.8.4
-    2.8.3     https://github.com/git/git/tarball/v2.8.3
-    2.8.2     https://github.com/git/git/tarball/v2.8.2
-    2.8.1     https://github.com/git/git/tarball/v2.8.1
-    2.8.0     https://github.com/git/git/tarball/v2.8.0
-    2.7.3     https://github.com/git/git/tarball/v2.7.3
-    2.7.1     https://github.com/git/git/tarball/v2.7.1
+    2.29.0    https://mirrors.edge.kernel.org/pub/software/scm/git/git-2.29.0.tar.gz
+    2.28.0    https://mirrors.edge.kernel.org/pub/software/scm/git/git-2.28.0.tar.gz
+    2.27.0    https://mirrors.edge.kernel.org/pub/software/scm/git/git-2.27.0.tar.gz
+    2.26.0    https://mirrors.edge.kernel.org/pub/software/scm/git/git-2.26.0.tar.gz
+    2.25.0    https://mirrors.edge.kernel.org/pub/software/scm/git/git-2.25.0.tar.gz
+    2.21.0    https://mirrors.edge.kernel.org/pub/software/scm/git/git-2.21.0.tar.gz
+    2.20.1    https://mirrors.edge.kernel.org/pub/software/scm/git/git-2.20.1.tar.gz
+    2.19.2    https://mirrors.edge.kernel.org/pub/software/scm/git/git-2.19.2.tar.gz
+    2.19.1    https://mirrors.edge.kernel.org/pub/software/scm/git/git-2.19.1.tar.gz
+    2.18.0    https://mirrors.edge.kernel.org/pub/software/scm/git/git-2.18.0.tar.gz
+    2.17.1    https://mirrors.edge.kernel.org/pub/software/scm/git/git-2.17.1.tar.gz
+    2.17.0    https://mirrors.edge.kernel.org/pub/software/scm/git/git-2.17.0.tar.gz
+    2.15.1    https://mirrors.edge.kernel.org/pub/software/scm/git/git-2.15.1.tar.gz
+    2.14.1    https://mirrors.edge.kernel.org/pub/software/scm/git/git-2.14.1.tar.gz
+    2.13.0    https://mirrors.edge.kernel.org/pub/software/scm/git/git-2.13.0.tar.gz
+    2.12.2    https://mirrors.edge.kernel.org/pub/software/scm/git/git-2.12.2.tar.gz
+    2.12.1    https://mirrors.edge.kernel.org/pub/software/scm/git/git-2.12.1.tar.gz
+    2.12.0    https://mirrors.edge.kernel.org/pub/software/scm/git/git-2.12.0.tar.gz
+    2.11.1    https://mirrors.edge.kernel.org/pub/software/scm/git/git-2.11.1.tar.gz
+    2.11.0    https://mirrors.edge.kernel.org/pub/software/scm/git/git-2.11.0.tar.gz
+    2.9.3     https://mirrors.edge.kernel.org/pub/software/scm/git/git-2.9.3.tar.gz
+    2.9.2     https://mirrors.edge.kernel.org/pub/software/scm/git/git-2.9.2.tar.gz
+    2.9.1     https://mirrors.edge.kernel.org/pub/software/scm/git/git-2.9.1.tar.gz
+    2.9.0     https://mirrors.edge.kernel.org/pub/software/scm/git/git-2.9.0.tar.gz
+    2.8.4     https://mirrors.edge.kernel.org/pub/software/scm/git/git-2.8.4.tar.gz
+    2.8.3     https://mirrors.edge.kernel.org/pub/software/scm/git/git-2.8.3.tar.gz
+    2.8.2     https://mirrors.edge.kernel.org/pub/software/scm/git/git-2.8.2.tar.gz
+    2.8.1     https://mirrors.edge.kernel.org/pub/software/scm/git/git-2.8.1.tar.gz
+    2.8.0     https://mirrors.edge.kernel.org/pub/software/scm/git/git-2.8.0.tar.gz
+    2.7.3     https://mirrors.edge.kernel.org/pub/software/scm/git/git-2.7.3.tar.gz
+    2.7.1     https://mirrors.edge.kernel.org/pub/software/scm/git/git-2.7.1.tar.gz
 
 Variants:
-    None
+    Name [Default]    Allowed values    Description
+    ==============    ==============    ===========================================
+
+    tcltk [off]       on, off           Gitk: provide Tcl/Tk in the run environment
 
 Installation Phases:
-    install
+    autoreconf    configure    build    install
 
 Build Dependencies:
-    autoconf  curl  expat  gettext  libiconv  openssl  pcre  perl  zlib
+    autoconf  automake  curl  expat  gettext  iconv  libidn2  libtool  m4  openssl  pcre  pcre2  perl  tk  zlib
 
 Link Dependencies:
-    curl  expat  gettext  libiconv  openssl  pcre  perl  zlib
+    curl  expat  gettext  iconv  libidn2  openssl  pcre  pcre2  perl  tk  zlib
 
 Run Dependencies:
-    None
+    openssh
 
 Virtual Packages:
     None
-
-Description:
-    Git is a free and open source distributed version control system
-    designed to handle everything from small to very large projects with
-    speed and efficiency.
 ```
 
 ### Install Software Package
@@ -220,10 +297,23 @@ Description:
 `spack install` will install any package shown by `spack list`. For example, to install the latest version of the `git` package, you might type `spack install git` for default version or `spack install git@version` to chose a particular one.
 
 ```console
-$ spack install git@2.11.0
-==> Installing git
-==> Installing pcre
-==> Fetching http://ftp.csx.cam.ac.uk/pub/software/programming/pcre/pcre-8.39.tar.bz2
+$ spack install git@2.29.0
+==> Warning: specifying a "dotkit" module root has no effect [support for "dotkit" has been dropped in v0.13.0]
+==> Warning: gcc@4.8.5 cannot build optimized binaries for "zen2". Using best target possible: "x86_64"
+==> Installing libsigsegv-2.12-lctnabj6w4bmnyxo7q6ct4wewke2bqin
+==> No binary for libsigsegv-2.12-lctnabj6w4bmnyxo7q6ct4wewke2bqin found: installing from source
+==> Fetching https://spack-llnl-mirror.s3-us-west-2.amazonaws.com/_source-cache/archive/3a/3ae1af359eebaa4ffc5896a1aee3568c052c99879316a1ab57f8fe1789c390b6.tar.gz
+######################################################################## 100.0%
+==> libsigsegv: Executing phase: 'autoreconf'
+==> libsigsegv: Executing phase: 'configure'
+==> libsigsegv: Executing phase: 'build'
+==> libsigsegv: Executing phase: 'install'
+[+] /home/kru0052/Spack/opt/spack/linux-centos7-x86_64/gcc-4.8.5/libsigsegv-2.12-lctnabj6w4bmnyxo7q6ct4wewke2bqin
+==> Installing berkeley-db-18.1.40-bwuaqjex546zw3bimt23bgokfctnt46y
+==> No binary for berkeley-db-18.1.40-bwuaqjex546zw3bimt23bgokfctnt46y found: installing from source
+==> Fetching https://spack-llnl-mirror.s3-us-west-2.amazonaws.com/_source-cache/archive/0c/0cecb2ef0c67b166de93732769abdeba0555086d51de1090df325e18ee8da9c8.tar.gz
+######################################################################## 100.0%
+...
 ...
 ```
 
diff --git a/docs.it4i/software/tools/virtualization.md b/docs.it4i/software/tools/virtualization.md
index 3ce3432c2..e4559e6b7 100644
--- a/docs.it4i/software/tools/virtualization.md
+++ b/docs.it4i/software/tools/virtualization.md
@@ -1,5 +1,10 @@
 # Virtualization
 
+<!--
+musime proverit
+-->
+
+
 Running virtual machines on compute nodes.
 
 ## Introduction
diff --git a/mkdocs.yml b/mkdocs.yml
index aded0562e..8c8dd110b 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -206,7 +206,6 @@ nav:
         - ANSYS Fluent: software/tools/ansys/ansys-fluent.md
         - ANSYS LS-DYNA: software/tools/ansys/ansys-ls-dyna.md
         - ANSYS MAPDL: software/tools/ansys/ansys-mechanical-apdl.md
-        - LS-DYNA: software/tools/ansys/ls-dyna.md
         - Workbench: software/tools/ansys/workbench.md
         - Setting License Preferences: software/tools/ansys/licensing.md
         - Licensing and Available Versions: software/tools/ansys/setting-license-preferences.md
-- 
GitLab