structure, script to check paths

docs.it4i/salomon/software/chemistry/molpro.md

-# Molpro
-
-Molpro is a complete system of ab initio programs for molecular electronic structure calculations.
-
-## About Molpro
-
-Molpro is a software package used for accurate ab-initio quantum chemistry calculations. More information can be found at the [official webpage](http://www.molpro.net/).
-
-## License
-
-Molpro software package is available only to users that have a valid license. Please contact support to enable access to Molpro if you have a valid license appropriate for running on our cluster (eg. academic research group licence, parallel execution).
-
-To run Molpro, you need to have a valid license token present in " $HOME/.molpro/token". You can download the token from [Molpro website](https://www.molpro.net/licensee/?portal=licensee).
-
-## Installed Version
-
-Currently on Anselm is installed version 2010.1, patch level 45, parallel version compiled with Intel compilers and Intel MPI.
-
-Compilation parameters are default:
-
-| Parameter                          | Value        |
-| ---------------------------------- | ------------ |
-| max number of atoms                | 200          |
-| max number of valence orbitals     | 300          |
-| max number of basis functions      | 4095         |
-| max number of states per symmmetry | 20           |
-| max number of state symmetries     | 16           |
-| max number of records              | 200          |
-| max number of primitives           | maxbfn x [2] |
-
-## Running
-
-Molpro is compiled for parallel execution using MPI and OpenMP. By default, Molpro reads the number of allocated nodes from PBS and launches a data server on one node. On the remaining allocated nodes, compute processes are launched, one process per node, each with 16 threads. You can modify this behavior by using -n, -t and helper-server options. Please refer to the [Molpro documentation](http://www.molpro.net/info/2010.1/doc/manual/node9.html) for more details.
-
-!!! note
-    The OpenMP parallelization in Molpro is limited and has been observed to produce limited scaling. We therefore recommend to use MPI parallelization only. This can be achieved by passing option mpiprocs=16:ompthreads=1 to PBS.
-
-You are advised to use the -d option to point to a directory in [SCRATCH filesystem](../../storage/storage/). Molpro can produce a large amount of temporary data during its run, and it is important that these are placed in the fast scratch filesystem.
-
-### Example jobscript
-
-```bash
-    #PBS -A IT4I-0-0
-    #PBS -q qprod
-    #PBS -l select=1:ncpus=16:mpiprocs=16:ompthreads=1
-
-    cd $PBS_O_WORKDIR
-
-    # load Molpro module
-    module add molpro
-
-    # create a directory in the SCRATCH filesystem
-    mkdir -p /scratch/$USER/$PBS_JOBID
-
-    # copy an example input
-    cp /apps/chem/molpro/2010.1/molprop_2010_1_Linux_x86_64_i8/examples/caffeine_opt_diis.com .
-
-    # run Molpro with default options
-    molpro -d /scratch/$USER/$PBS_JOBID caffeine_opt_diis.com
-
-    # delete scratch directory
-    rm -rf /scratch/$USER/$PBS_JOBID
-```

docs.it4i/salomon/software/chemistry/nwchem.md

-# NWChem
-
-## Introduction
-
-NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters.
-
-[Homepage](http://www.nwchem-sw.org/index.php/Main_Page)
-
-## Installed Versions
-
-The following versions are currently installed:
-
-* NWChem/6.3.revision2-2013-10-17-Python-2.7.8, current release. Compiled with Intel compilers, MKL and Intel MPI
-* NWChem/6.5.revision26243-intel-2015b-2014-09-10-Python-2.7.8
-
-For a current list of installed versions, execute:
-
-```console
-$ ml av NWChem
-```
-
-The recommend to use version 6.5. Version 6.3 fails on Salomon nodes with accelerator, because it attempts to communicate over scif0 interface. In 6.5 this is avoided by setting ARMCI_OPENIB_DEVICE=mlx4_0, this setting is included in the module.
-
-## Running
-
- NWChem is compiled for parallel MPI execution. Normal procedure for MPI jobs applies. Sample jobscript :
-
-```bash
-    #PBS -A IT4I-0-0
-    #PBS -q qprod
-    #PBS -l select=1:ncpus=24:mpiprocs=24
-
-    cd $PBS_O_WORKDIR
-    module add NWChem/6.5.revision26243-intel-2015b-2014-09-10-Python-2.7.8
-    mpirun nwchem h2o.nw
-```
-
-## Options
-
-Please refer to [the documentation](http://www.nwchem-sw.org/index.php/Release62:Top-level) and in the input file set the following directives :
-
-* MEMORY : controls the amount of memory NWChem will use
-* SCRATCH_DIR : set this to a directory in [SCRATCH filesystem](../../storage/storage/) (or run the calculation completely in a scratch directory). For certain calculations, it might be advisable to reduce I/O by forcing "direct" mode, eg. "scf direct"

docs.it4i/software/chemistry/INCAR

+  PREC = Accurate
+  IBRION = -1
+  ENCUT = 500
+  EDIFF = 1.0e-08
+  ISMEAR = 0 
+  SIGMA = 0.01
+  IALGO = 38
+  LREAL = .FALSE.
+  ADDGRID = .TRUE.
+  LWAVE = .FALSE.
+  LCHARG = .FALSE.
+  NCORE = 8 
+  KPAR = 8

docs.it4i/software/chemistry/KPOINTS

+Automatic mesh
+0
+Monkhorst Pack
+  3 3 3
+0.5 0.5 0.5
+

docs.it4i/software/chemistry/POSCAR

+ Si
+   1.0
+     5.4335600309153529    0.0000000000000000    0.0000000000000000
+     0.0000000000000000    5.4335600309153529    0.0000000000000000
+     0.0000000000000000    0.0000000000000000    5.4335600309153529
+ Si
+   8
+Direct
+   0.8750000000000000  0.8750000000000000  0.8750000000000000
+   0.8750000000000000  0.3750000000000000  0.3750000000000000
+   0.3750000000000000  0.8750000000000000  0.3750000000000000
+   0.3750000000000000  0.3750000000000000  0.8750000000000000
+   0.1250000000000000  0.1250000000000000  0.1250000000000000
+   0.1250000000000000  0.6250000000000000  0.6250000000000000
+   0.6250000000000000  0.1250000000000000  0.6250000000000000
+   0.6250000000000000  0.6250000000000000  0.1250000000000000

docs.it4i/software/chemistry/gofree-cond1.sh

+#!/bin/bash
+#PBS -A OPEN-6-23
+#PBS -N Si-test1
+#PBS -q qfree 
+#PBS -l select=1:ncpus=24:mpiprocs=24:ompthreads=1
+#PBS -l walltime=01:59:59
+##PBS-l mem=6gb
+#PBS -j oe
+#PBS -S /bin/bash
+module purge
+module load phono3py/0.9.14-ictce-7.3.5-Python-2.7.9
+export OMP_NUM_THREADS=1
+export I_MPI_COMPATIBILITY=4
+##export OMP_STACKSIZE=10gb
+##0	1	2	3	4	10	11	12	13	20	21	22	30	31	40	91	92	93	94	101	102	103	111	112	121	182	183	184	192	193	202	273	274	283	364
+cd $PBS_O_WORKDIR
+phono3py --fc3 --fc2 --dim="2 2 2" --mesh="9 9 9" -c POSCAR  --sigma 0.1 --br --write_gamma --gp="0 1 3 4 10" 
+#phono3py --fc3 --fc2 --dim="2 2 2" --mesh="9 9 9" -c POSCAR  --sigma 0.1 --br --write_gamma --gp="11 12 13 20 21" 
+#phono3py --fc3 --fc2 --dim="2 2 2" --mesh="9 9 9" -c POSCAR  --sigma 0.1 --br --write_gamma --gp="21 22 30 31 40"
+#phono3py --fc3 --fc2 --dim="2 2 2" --mesh="9 9 9" -c POSCAR  --sigma 0.1 --br --write_gamma --gp="91 92 93 94 101"
+#phono3py --fc3 --fc2 --dim="2 2 2" --mesh="9 9 9" -c POSCAR  --sigma 0.1 --br --write_gamma --gp="102 103 111 112 121"
+#phono3py --fc3 --fc2 --dim="2 2 2" --mesh="9 9 9" -c POSCAR  --sigma 0.1 --br --write_gamma --gp="182 183 184 192 193"
+#phono3py --fc3 --fc2 --dim="2 2 2" --mesh="9 9 9" -c POSCAR  --sigma 0.1 --br --write_gamma --gp="202 273 274 283 364"

docs.it4i/software/chemistry/prepare.sh

+#!/bin/bash
+P=`pwd`
+
+# number of displacements
+poc=9
+
+        for i in `seq 1 $poc `;
+        do
+        cd $P
+        mkdir disp-0000"$i"
+        cd disp-0000"$i"   
+        cp ../KPOINTS .
+        cp ../INCAR .
+        cp ../POTCAR .
+        cp ../POSCAR-0000"$i" POSCAR
+                echo $i
+        done 
+
+poc=99
+
+        for i in `seq 10 $poc `;
+        do
+        cd $P
+        mkdir disp-000"$i"
+        cd disp-000"$i"
+        cp ../KPOINTS .
+        cp ../INCAR .
+        cp ../POTCAR .
+        cp ../POSCAR-000"$i" POSCAR
+                echo $i
+        done
+poc=111
+
+        for i in `seq 100 $poc `;
+        do
+        cd $P
+        mkdir disp-00"$i"
+        cd disp-00"$i"
+        cp ../KPOINTS .
+        cp ../INCAR .
+        cp ../POTCAR .
+        cp ../POSCAR-00"$i" POSCAR
+                echo $i
+        done

docs.it4i/software/chemistry/run.sh

+#!/bin/bash
+#PBS -A IT4I-9-11
+#PBS -N Si-test
+#PBS -q qprod 
+#PBS -l select=8:ncpus=16:mpiprocs=16:ompthreads=1
+#PBS -l walltime=23:59:59
+##PBS-l mem=6gb
+#PBS -j oe
+#PBS -S /bin/bash
+module load impi/4.1.1.036 intel/13.5.192 fftw3-mpi/3.3.3-icc
+export OMP_NUM_THREADS=1
+export I_MPI_COMPATIBILITY=4
+##export OMP_STACKSIZE=10gb
+b=`basename $PBS_O_WORKDIR`
+echo $b >log.vasp
+SCRDIR=/scratch/$USER/$b
+mkdir -p $SCRDIR
+cd $SCRDIR || exit
+
+# copy input file to scratch 
+cp $PBS_O_WORKDIR/* .
+
+mpirun ~/bin/vasp5.4.1 > log.exc
+
+# copy output file to home
+cp * $PBS_O_WORKDIR/. && cd ..
+
+rm -rf "$SCRDIR"
+
+#exit
+exit

docs.it4i/software/chemistry/submit.sh

+#!/bin/bash
+P=`pwd`
+
+# number of displacements
+poc=9
+
+        for i in `seq 1 $poc `;
+        do
+        cd $P
+        cd disp-0000"$i"   
+        cp ../run.sh .
+        qsub run.sh
+                echo $i
+        done 
+
+poc=99
+
+        for i in `seq 10 $poc `;
+        do
+        cd $P
+        cd disp-000"$i"
+        cp ../run.sh .
+        qsub run.sh
+                echo $i
+        done
+poc=111
+
+        for i in `seq 100 $poc `;
+        do
+        cd $P
+        cd disp-00"$i"
+        cp ../run.sh .
+        qsub run.sh
+                echo $i
+        done

docs.it4i/software/comsol/comsol-multiphysics.md

@@ -18,7 +18,7 @@ On the clusters COMSOL is available in the latest stable version. There are two
 
 * **Non commercial** or so called **EDU variant**, which can be used for research and educational purposes.
 
-* **Commercial** or so called **COM variant**, which can used also for commercial activities. **COM variant** has only subset of features compared to the **EDU variant** available. More about licensing [here](licensing-and-available-versions).
+* **Commercial** or so called **COM variant**, which can used also for commercial activities. **COM variant** has only subset of features compared to the **EDU variant** available. More about licensing [here](licensing-and-available-versions/).
 
 To load the of COMSOL load the module
 

docs.it4i/software/numerical-languages/r.md

@@ -146,7 +146,7 @@ Every evaluation of the integrad function runs in parallel on different process.
 
 package Rmpi provides an interface (wrapper) to MPI APIs.
 
-It also provides interactive R slave environment. On the cluster, Rmpi provides interface to the [OpenMPI](../mpi/Running_OpenMPI/).
+It also provides interactive R slave environment. On the cluster, Rmpi provides interface to the [OpenMPI](../../anselm/software/mpi/Running_OpenMPI/).
 
 Read more on Rmpi at <http://cran.r-project.org/web/packages/Rmpi/>, reference manual is available at <http://cran.r-project.org/web/packages/Rmpi/Rmpi.pdf>
 

pathcheck.sh

+#!/bin/bash
+
+
+
+
+for file in $@; do
+check=$(cat $file | grep -Eo "\[.*?\]\([^ ]*\)" | grep -v "#" | grep -vE "http|www|ftp|none" | sed 's/\[.*\]//g' | sed 's/[()]//g' | sed 's/\/$/.md/g')
+if [ ! -z "$check" ]; then
+#	echo "\n+++++ $file +++++\n"
+
+wrong=0
+for line in $check; do
+#echo $line
+
+pathtocheck=$(dirname $file)/$line
+
+
+if [ -f $(dirname $file)/$line ]; then
+	:
+	#echo "ok $pathtocheck"
+else
+	if [ $wrong -eq "0" ]; then
+		echo ""
+		echo "\n+++++ $file +++++\n"
+	fi
+	wrong=1
+	echo "wrong link in $pathtocheck"
+fi
+done
+fi
+done
+echo ""

todelete

+docs.it4i/anselm/software/numerical-languages/introduction.md
+docs.it4i/anselm/software/numerical-languages/matlab.md
+docs.it4i/anselm/software/numerical-languages/matlab_1314.md
+docs.it4i/anselm/software/numerical-languages/octave.md
+docs.it4i/anselm/software/numerical-languages/r.md
+docs.it4i/salomon/software/comsol/licensing-and-available-versions.md
+docs.it4i/salomon/software/java.md
+docs.it4i/salomon/software/numerical-languages/introduction.md
+docs.it4i/salomon/software/numerical-languages/matlab.md
+docs.it4i/salomon/software/numerical-languages/octave.md
+docs.it4i/salomon/software/numerical-languages/opencoarrays.md
+docs.it4i/salomon/software/numerical-languages/r.md