converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-cfx.md

+ANSYS CFX 
+=========
+
+
+
+
+
+
+
+
+
+[ANSYS
+CFX](http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+CFX)
+software is a high-performance, general purpose fluid dynamics program
+that has been applied to solve wide-ranging fluid flow problems for over
+20 years. At the heart of ANSYS CFX is its advanced solver technology,
+the key to achieving reliable and accurate solutions quickly and
+robustly. The modern, highly parallelized solver is the foundation for
+an abundant choice of physical models to capture virtually any type of
+phenomena related to fluid flow. The solver and its many physical models
+are wrapped in a modern, intuitive, and flexible GUI and user
+environment, with extensive capabilities for customization and
+automation using session files, scripting and a powerful expression
+language.
+
+>To run ANSYS CFX in batch mode you can utilize/modify the default
+cfx.pbs script and execute it via the qsub command.
+
+```
+#!/bin/bash
+#PBS -l nodes=2:ppn=16
+#PBS -q qprod
+#PBS -N $USER-CFX-Project
+#PBS -A XX-YY-ZZ
+
+#! Mail to user when job terminate or abort
+#PBS -m ae
+
+#!change the working directory (default is home directory)
+#cd <working directory> (working directory must exists)
+WORK_DIR="/scratch/$USER/work"
+cd $WORK_DIR
+
+echo Running on host `hostname`
+echo Time is `date`
+echo Directory is `pwd`
+echo This jobs runs on the following processors:
+echo `cat $PBS_NODEFILE`
+
+module load ansys
+
+#### Set number of processors per host listing
+#### (set to 1 as $PBS_NODEFILE lists each node twice if :ppn=2)
+procs_per_host=1
+#### Create host list
+hl=""
+for host in `cat $PBS_NODEFILE`
+do
+ if [ "$hl" = "" ]
+ then hl="$host:$procs_per_host"
+ else hl="${hl}:$host:$procs_per_host"
+ fi
+done
+
+echo Machines: $hl
+
+#-dev input.def includes the input of CFX analysis in DEF format
+#-P the name of prefered license feature (aa_r=ANSYS Academic Research, ane3fl=Multiphysics(commercial))
+/ansys_inc/v145/CFX/bin/cfx5solve -def input.def -size 4 -size-ni 4x -part-large -start-method "Platform MPI Distributed Parallel" -par-dist $hl -P aa_r
+```
+
+Header of the pbs file (above) is common and description can be find
+on [this
+site](../../resource-allocation-and-job-execution/job-submission-and-execution.html).
+SVS FEM recommends to utilize sources by keywords: nodes, ppn. These
+keywords allows to address directly the number of nodes (computers) and
+cores (ppn) which will be utilized in the job. Also the rest of code
+assumes such structure of allocated resources.
+
+Working directory has to be created before sending pbs job into the
+queue. Input file should be in working directory or full path to input
+file has to be specified. >Input file has to be defined by common
+CFX def file which is attached to the cfx solver via parameter
+-def
+
+License** should be selected by parameter -P (Big letter **P**).
+Licensed products are the following: aa_r
+(ANSYS **Academic** Research), ane3fl (ANSYS
+Multiphysics)-**Commercial.**
+[ id="result_box"  More
+ about licensing 
+here](licensing.html)
+
+ 
+
+
+
+

converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-fluent.md

+ANSYS Fluent 
+============
+
+
+
+
+
+
+
+
+
+[ANSYS
+Fluent](http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+Fluent)
+software contains the broad physical modeling capabilities needed to
+model flow, turbulence, heat transfer, and reactions for industrial
+applications ranging from air flow over an aircraft wing to combustion
+in a furnace, from bubble columns to oil platforms, from blood flow to
+semiconductor manufacturing, and from clean room design to wastewater
+treatment plants. Special models that give the software the ability to
+model in-cylinder combustion, aeroacoustics, turbomachinery, and
+multiphase systems have served to broaden its reach.
+
+>1. Common way to run Fluent over pbs file
+------------------------------------------------------
+
+>To run ANSYS Fluent in batch mode you can utilize/modify the
+default fluent.pbs script and execute it via the qsub command.
+
+```
+#!/bin/bash
+#PBS -S /bin/bash
+#PBS -l nodes=2:ppn=16
+#PBS -q qprod
+#PBS -N $USER-Fluent-Project
+#PBS -A XX-YY-ZZ
+
+#! Mail to user when job terminate or abort
+#PBS -m ae
+
+#!change the working directory (default is home directory)
+#cd <working directory> (working directory must exists)
+WORK_DIR="/scratch/$USER/work"
+cd $WORK_DIR
+
+echo Running on host `hostname`
+echo Time is `date`
+echo Directory is `pwd`
+echo This jobs runs on the following processors:
+echo `cat $PBS_NODEFILE`
+
+#### Load ansys module so that we find the cfx5solve command
+module load ansys
+
+# Use following line to specify MPI for message-passing instead
+NCORES=`wc -l $PBS_NODEFILE |awk '{print $1}'`
+
+/ansys_inc/v145/fluent/bin/fluent 3d -t$NCORES -cnf=$PBS_NODEFILE -g -i fluent.jou
+```
+
+Header of the pbs file (above) is common and description can be find
+on [this
+site](../../resource-allocation-and-job-execution/job-submission-and-execution.html).
+[SVS FEM](http://www.svsfem.cz) recommends to utilize
+sources by keywords: nodes, ppn. These keywords allows to address
+directly the number of nodes (computers) and cores (ppn) which will be
+utilized in the job. Also the rest of code assumes such structure of
+allocated resources.
+
+Working directory has to be created before sending pbs job into the
+queue. Input file should be in working directory or full path to input
+file has to be specified. Input file has to be defined by common Fluent
+journal file which is attached to the Fluent solver via parameter -i
+fluent.jou
+
+Journal file with definition of the input geometry and boundary
+conditions and defined process of solution has e.g. the following
+structure:
+
+  /file/read-case aircraft_2m.cas.gz
+  /solve/init
+  init
+  /solve/iterate
+  10
+  /file/write-case-dat aircraft_2m-solution
+  /exit yes
+
+>The appropriate dimension of the problem has to be set by
+parameter (2d/3d). 
+
+>2. Fast way to run Fluent from command line
+--------------------------------------------------------
+
+
+```
+fluent solver_version [FLUENT_options] -i journal_file -pbs
+```
+
+
+This syntax will start the ANSYS FLUENT job under PBS Professional using
+the  qsub command in a batch manner. When
+resources are available, PBS Professional will start the job and return
+a job ID, usually in the form of 
+*job_ID.hostname*. This job ID can then be used
+to query, control, or stop the job using standard PBS Professional
+commands, such as  qstat or 
+qdel. The job will be run out of the current
+working directory, and all output will be written to the file 
+fluent.o> 
+*job_ID*.       
+
+3. Running Fluent via user's config file
+----------------------------------------
+
+
+The sample script uses a configuration file called 
+pbs_fluent.conf  if no command line arguments
+are present. This configuration file should be present in the directory
+from which the jobs are submitted (which is also the directory in which
+the jobs are executed). The following is an example of what the content
+of  pbs_fluent.conf can be:
+
+```
+input="example_small.flin"
+case="Small-1.65m.cas"
+fluent_args="3d -pmyrinet"
+outfile="fluent_test.out"
+mpp="true"
+```
+
+The following is an explanation of the parameters:
+
+
+
+> input is the name of the input
+file.
+
+ case is the name of the 
+.cas file that the input file will utilize.
+
+ fluent_args are extra ANSYS FLUENT
+arguments. As shown in the previous example, you can specify the
+interconnect by using the  -p interconnect
+command. The available interconnects include 
+ethernet (the default), 
+myrinet, class="monospace">
+infiniband,  vendor, 
+altix>, and 
+crayx. The MPI is selected automatically, based
+on the specified interconnect.
+
+ outfile is the name of the file to which
+the standard output will be sent.
+
+ mpp="true" will tell the job script to
+execute the job across multiple processors.               
+
+
+
+
+
+
+
+
+
+
+
+>To run ANSYS Fluent in batch mode with user's config file you can
+utilize/modify the following script and execute it via the qsub
+command.
+
+
+```
+#!/bin/sh
+#PBS -l nodes=2:ppn=4
+#PBS -1 qprod
+#PBS -N $USE-Fluent-Project
+#PBS -A XX-YY-ZZ
+
+ cd $PBS_O_WORKDIR
+ 
+ #We assume that if they didn’t specify arguments then they should use the
+ #config file if [ "xx${input}${case}${mpp}${fluent_args}zz" = "xxzz" ]; then
+ if [ -f pbs_fluent.conf ]; then
+   . pbs_fluent.conf
+ else
+   printf "No command line arguments specified, "
+   printf "and no configuration file found.  Exiting n"
+ fi
+ fi
+ 
+
+ #Augment the ANSYS FLUENT command line arguments case "$mpp" in
+ true)
+   #MPI job execution scenario
+   num_nodes=‘cat $PBS_NODEFILE | sort -u | wc -l‘
+   cpus=‘expr $num_nodes * $NCPUS‘
+   #Default arguments for mpp jobs, these should be changed to suit your
+   #needs.
+   fluent_args="-t${cpus} $fluent_args -cnf=$PBS_NODEFILE"
+   ;;
+ *)
+   #SMP case
+   #Default arguments for smp jobs, should be adjusted to suit your
+   #needs.
+   fluent_args="-t$NCPUS $fluent_args"
+   ;;
+ esac
+ #Default arguments for all jobs
+ fluent_args="-ssh -g -i $input $fluent_args"
+
+ echo "---------- Going to start a fluent job with the following settings:
+ Input: $input
+ Case: $case
+ Output: $outfile
+ Fluent arguments: $fluent_args"
+ 
+ #run the solver
+ /ansys_inc/v145/fluent/bin/fluent $fluent_args> $outfile
+```
+
+
+
+>It runs the jobs out of the directory from which they are
+submitted (PBS_O_WORKDIR).
+
+4. Running Fluent in parralel
+-----------------------------
+
+Fluent could be run in parallel only under Academic Research license. To
+do so this ANSYS Academic Research license must be placed before ANSYS
+CFD license in user preferences. To make this change anslic_admin
+utility should be run
+
+```
+/ansys_inc/shared_les/licensing/lic_admin/anslic_admin
+```
+
+ANSLIC_ADMIN Utility will be run
+
+![](Fluent_Licence_1.jpg)
+
+![](Fluent_Licence_2.jpg)
+
+![](Fluent_Licence_3.jpg)
+
+ 
+
+ANSYS Academic Research license should be moved up to the top of the
+list.
+
+ 
+
+![](Fluent_Licence_4.jpg)
+
+
+
+

converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-ls-dyna.md

+ANSYS LS-DYNA 
+=============
+
+
+
+
+
+
+
+
+
+[ANSYS
+LS-DYNA](http://www.ansys.com/Products/Simulation+Technology/Structural+Mechanics/Explicit+Dynamics/ANSYS+LS-DYNA)
+software provides convenient and easy-to-use access to the
+technology-rich, time-tested explicit solver without the need to contend
+with the complex input requirements of this sophisticated program.
+Introduced in 1996, ANSYS LS-DYNA capabilities have helped customers in
+numerous industries to resolve highly intricate design
+issues. >ANSYS Mechanical users have been able take advantage of
+complex explicit solutions for a long time utilizing the traditional
+ANSYS Parametric Design Language (APDL) environment. >These
+explicit capabilities are available to ANSYS Workbench users as well.
+The Workbench platform is a powerful, comprehensive, easy-to-use
+environment for engineering simulation. CAD import from all sources,
+geometry cleanup, automatic meshing, solution, parametric optimization,
+result visualization and comprehensive report generation are all
+available within a single fully interactive modern  graphical user
+environment.
+
+>To run ANSYS LS-DYNA in batch mode you can utilize/modify the
+default ansysdyna.pbs script and execute it via the qsub command.
+
+```
+#!/bin/bash
+#PBS -l nodes=2:ppn=16
+#PBS -q qprod
+#PBS -N $USER-DYNA-Project
+#PBS -A XX-YY-ZZ
+
+#! Mail to user when job terminate or abort
+#PBS -m ae
+
+#!change the working directory (default is home directory)
+#cd <working directory>
+WORK_DIR="/scratch/$USER/work"
+cd $WORK_DIR
+
+echo Running on host `hostname`
+echo Time is `date`
+echo Directory is `pwd`
+echo This jobs runs on the following processors:
+echo `cat $PBS_NODEFILE`
+
+#! Counts the number of processors
+NPROCS=`wc -l < $PBS_NODEFILE`
+
+echo This job has allocated $NPROCS nodes
+
+module load ansys
+
+#### Set number of processors per host listing
+#### (set to 1 as $PBS_NODEFILE lists each node twice if :ppn=2)
+procs_per_host=1
+#### Create host list
+hl=""
+for host in `cat $PBS_NODEFILE`
+do
+ if [ "$hl" = "" ]
+ then hl="$host:$procs_per_host"
+ else hl="${hl}:$host:$procs_per_host"
+ fi
+done
+
+echo Machines: $hl
+
+/ansys_inc/v145/ansys/bin/ansys145 -dis -lsdynampp i=input.k -machines $hl
+```
+
+>Header of the pbs file (above) is common and description can be
+find on [this
+site](../../resource-allocation-and-job-execution/job-submission-and-execution.html)>.
+[SVS FEM](http://www.svsfem.cz) recommends to utilize
+sources by keywords: nodes, ppn. These keywords allows to address
+directly the number of nodes (computers) and cores (ppn) which will be
+utilized in the job. Also the rest of code assumes such structure of
+allocated resources.
+
+Working directory has to be created before sending pbs job into the
+queue. Input file should be in working directory or full path to input
+file has to be specified. Input file has to be defined by common LS-DYNA
+.**k** file which is attached to the ansys solver via parameter i=
+
+>> 
+
+
+
+

converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl.md

+ANSYS MAPDL 
+===========
+
+
+
+
+
+
+
+
+
+>**[ANSYS
+Multiphysics](http://www.ansys.com/Products/Simulation+Technology/Structural+Mechanics/ANSYS+Multiphysics)**
+software offers a comprehensive product solution for both multiphysics
+and single-physics analysis. The product includes structural, thermal,
+fluid and both high- and low-frequency electromagnetic analysis. The
+product also contains solutions for both direct and sequentially coupled
+physics problems including direct coupled-field elements and the ANSYS
+multi-field solver.
+
+>To run ANSYS MAPDL in batch mode you can utilize/modify the
+default mapdl.pbs script and execute it via the qsub command.
+
+```
+#!/bin/bash
+#PBS -l nodes=2:ppn=16
+#PBS -q qprod
+#PBS -N $USER-ANSYS-Project
+#PBS -A XX-YY-ZZ
+
+#! Mail to user when job terminate or abort
+#PBS -m ae
+
+#!change the working directory (default is home directory)
+#cd <working directory> (working directory must exists)
+WORK_DIR="/scratch/$USER/work"
+cd $WORK_DIR
+
+echo Running on host `hostname`
+echo Time is `date`
+echo Directory is `pwd`
+echo This jobs runs on the following processors:
+echo `cat $PBS_NODEFILE`
+
+module load ansys
+
+#### Set number of processors per host listing
+#### (set to 1 as $PBS_NODEFILE lists each node twice if :ppn=2)
+procs_per_host=1
+#### Create host list
+hl=""
+for host in `cat $PBS_NODEFILE`
+do
+ if [ "$hl" = "" ]
+ then hl="$host:$procs_per_host"
+ else hl="${hl}:$host:$procs_per_host"
+ fi
+done
+
+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)
+/ansys_inc/v145/ansys/bin/ansys145 -b -dis -p aa_r -i input.dat -o file.out -machines $hl -dir $WORK_DIR
+```
+
+Header of the pbs file (above) is common and description can be find on
+[this
+site](../../resource-allocation-and-job-execution/job-submission-and-execution.html).
+[SVS FEM](http://www.svsfem.cz) recommends to utilize
+sources by keywords: nodes, ppn. These keywords allows to address
+directly the number of nodes (computers) and cores (ppn) which will be
+utilized in the job. Also the rest of code assumes such structure of
+allocated resources.
+
+Working directory has to be created before sending pbs job into the
+queue. Input file should be in working directory or full path to input
+file has to be specified. Input file has to be defined by common APDL
+file which is attached to the ansys solver via parameter -i
+
+License** should be selected by parameter -p. Licensed products are
+the following: aa_r (ANSYS **Academic** Research), ane3fl (ANSYS
+Multiphysics)-**Commercial**, aa_r_dy (ANSYS **Academic**
+AUTODYN)>
+[ id="result_box"  More
+ about licensing 
+here](licensing.html)
+
+
+
+
+

converted/docs.it4i.cz/anselm-cluster-documentation/software/ansys/ls-dyna.md

+LS-DYNA 
+=======
+
+
+
+
+
+
+
+
+
+[LS-DYNA](http://www.lstc.com/) 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 behaviour of
+materials like composites, ceramics, concrete, or wood. Moreover, it is
+used in biomechanics, human modelling, molecular structures, casting,
+forging, or virtual testing.
+
+>Anselm provides **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.
+
+```
+#!/bin/bash
+#PBS -l nodes=1:ppn=16
+#PBS -q qprod
+#PBS -N $USER-LSDYNA-Project
+#PBS -A XX-YY-ZZ
+
+#! Mail to user when job terminate or abort
+#PBS -m ae
+
+#!change the working directory (default is home directory)
+#cd <working directory> (working directory must exists)
+WORK_DIR="/scratch/$USER/work"
+cd $WORK_DIR
+
+echo Running on host `hostname`
+echo Time is `date`
+echo Directory is `pwd`
+
+module load lsdyna
+
+/apps/engineering/lsdyna/lsdyna700s i=input.k
+```
+
+Header of the pbs file (above) is common and description can be find
+on [this
+site](../../resource-allocation-and-job-execution/job-submission-and-execution.html).
+[SVS FEM](http://www.svsfem.cz) recommends to utilize
+sources by keywords: nodes, ppn. These keywords allows to address
+directly the number of nodes (computers) and cores (ppn) which will be
+utilized in the job. Also the rest of code assumes such structure of
+allocated resources.
+
+Working directory has to be created before sending pbs job into the
+queue. Input file should be in working directory or full path to input
+file has to be specified. Input file has to be defined by common LS-DYNA
+.k** file which is attached to the LS-DYNA solver via parameter i=
+
+
+
+

converted/docs.it4i.cz/anselm-cluster-documentation/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. 
+
+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.html). 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
+
+  #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 
+
+
+
+

converted/docs.it4i.cz/anselm-cluster-documentation/software/chemistry/nwchem.md

+NWChem 
+======
+
+
+
+
+
+High-Performance Computational Chemistry
+
+
+
+
+
+
+
+
+>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 : 
+
+- 6.1.1, not recommended, problems have been observed with this
+  version
+
+- 6.3-rev2-patch1, current release with QMD patch applied. Compiled
+  with Intel compilers, MKL and Intel MPI
+
+- 6.3-rev2-patch1-openmpi, same as above, but compiled with OpenMPI
+  and NWChem provided BLAS instead of MKL. This version is expected to
+  be slower
+
+- 6.3-rev2-patch1-venus, this version contains only libraries for
+  VENUS interface linking. Does not provide standalone NWChem
+  executable
+
+For a current list of installed versions, execute : 
+
+  module avail nwchem
+
+Running
+-------
+
+NWChem is compiled for parallel MPI execution. Normal procedure for MPI
+jobs applies. Sample jobscript :
+
+  #PBS -A IT4I-0-0
+  #PBS -q qprod
+  #PBS -l select=1:ncpus=16
+
+  module add nwchem/6.3-rev2-patch1
+  mpirun -np 16 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.html#scratch) (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"
+
+
+
+

converted/docs.it4i.cz/anselm-cluster-documentation/software/compilers.md

+Compilers 
+=========
+
+
+
+
+
+Available compilers, including GNU, INTEL and UPC compilers
+
+
+
+
+
+
+
+
+
+
+
+
+Currently there are several compilers for different programming
+languages available on the Anselm cluster:
+
+- C/C++
+- Fortran 77/90/95
+- Unified Parallel C
+- Java
+- nVidia CUDA
+
+ 
+
+The C/C++ and Fortran compilers are divided into two main groups GNU and
+Intel.
+
+Intel Compilers
+---------------
+
+For information about the usage of Intel Compilers and other Intel
+products, please read the [Intel Parallel
+studio](intel-suite.html) page.
+
+GNU C/C++ and Fortran Compilers
+-------------------------------
+
+For compatibility reasons there are still available the original (old
+4.4.6-4) versions of GNU compilers as part of the OS. These are
+accessible in the search path  by default.
+
+It is strongly recommended to use the up to date version (4.8.1) which
+comes with the module gcc:
+
+  $ module load gcc
+  $ gcc -v
+  $ g++ -v
+  $ gfortran -v
+
+With the module loaded two environment variables are predefined. One for
+maximum optimizations on the Anselm cluster architecture, and the other
+for debugging purposes:
+
+  $ echo $OPTFLAGS
+  -O3 -march=corei7-avx
+
+  $ echo $DEBUGFLAGS
+  -O0 -g
+
+For more informations about the possibilities of the compilers, please
+see the man pages.
+
+Unified Parallel C
+------------------
+
+UPC is supported by two compiler/runtime implementations:
+
+- GNU - SMP/multi-threading support only
+- Berkley - multi-node support as well as SMP/multi-threading support
+
+### GNU UPC Compiler
+
+To use the GNU UPC compiler and run the compiled binaries use the module
+gupc
+
+  $ module add gupc
+  $ gupc -v
+  $ g++ -v
+
+Simple program to test the compiler
+
+  $ cat count.upc 
+
+  /* hello.upc - a simple UPC example */
+  #include <upc.h>
+  #include <stdio.h>
+
+  int main() {
+    if (MYTHREAD == 0) {
+      printf("Welcome to GNU UPC!!!n");
+    }
+    upc_barrier;
+    printf(" - Hello from thread %in", MYTHREAD);
+    return 0;
+  } 
+
+To compile the example use
+
+  $ gupc -o count.upc.x count.upc
+
+To run the example with 5 threads issue
+
+  $ ./count.upc.x -fupc-threads-5
+
+For more informations see the man pages.
+
+### Berkley UPC Compiler
+
+To use the Berkley UPC compiler and runtime environment to run the
+binaries use the module bupc
+
+  $ module add bupc
+  $ upcc -version
+
+As default UPC network the "smp" is used. This is very quick and easy
+way for testing/debugging, but limited to one node only.
+
+For production runs, it is recommended to use the native Infiband
+implementation of UPC network "ibv". For testing/debugging using
+multiple nodes, the "mpi" UPC network is recommended. Please note, that
+the selection of the network is done at the compile time** and not at
+runtime (as expected)!
+
+Example UPC code:
+
+  $ cat hello.upc 
+
+  /* hello.upc - a simple UPC example */
+  #include <upc.h>
+  #include <stdio.h>
+
+  int main() {
+    if (MYTHREAD == 0) {
+      printf("Welcome to Berkeley UPC!!!n");
+    }
+    upc_barrier;
+    printf(" - Hello from thread %in", MYTHREAD);
+    return 0;
+  } 
+
+To compile the example with the "ibv" UPC network use
+
+  $ upcc -network=ibv -o hello.upc.x hello.upc 
+
+To run the example with 5 threads issue
+
+  $ upcrun -n 5 ./hello.upc.x
+
+To run the example on two compute nodes using all 32 cores, with 32
+threads, issue
+
+  $ qsub -I -q qprod -A PROJECT_ID -l select=2:ncpus=16 
+  $ module add bupc
+  $ upcrun -n 32 ./hello.upc.x
+
+ For more informations see the man pages.
+
+Java
+----
+
+For information how to use Java (runtime and/or compiler), please read
+the [Java page](java.html).
+
+nVidia CUDA
+-----------
+
+For information how to work with nVidia CUDA, please read the [nVidia
+CUDA page](nvidia-cuda.html).
+
+
+
+

converted/docs.it4i.cz/anselm-cluster-documentation/software/debuggers.md

+Debuggers and profilers summary 
+===============================
+
+
+
+
+
+
+
+
+
+
+
+
+
+Introduction
+------------
+
+We provide state of the art programms and tools to develop, profile and
+debug HPC codes at IT4Innovations.
+On these pages, we provide an overview of the profiling and debugging
+tools available on Anslem at IT4I.
+
+Intel debugger
+--------------
+
+The intel debugger version 13.0 is available, via module intel. The
+debugger works for applications compiled with C and C++ compiler and the
+ifort fortran 77/90/95 compiler. The debugger provides java GUI
+environment. Use [X
+display](https://docs.it4i.cz/anselm-cluster-documentation/software/debuggers/resolveuid/11e53ad0d2fd4c5187537f4baeedff33)
+for running the GUI.
+
+  $ module load intel
+  $ idb
+
+Read more at the [Intel
+Debugger](intel-suite/intel-debugger.html) page.
+
+Allinea Forge (DDT/MAP)
+-----------------------
+
+Allinea DDT, is a commercial debugger primarily for debugging parallel
+MPI or OpenMP programs. It also has a support for GPU (CUDA) and Intel
+Xeon Phi accelerators. DDT provides all the standard debugging features
+(stack trace, breakpoints, watches, view variables, threads etc.) for
+every thread running as part of your program, or for every process -
+even if these processes are distributed across a cluster using an MPI
+implementation.
+
+  $ module load Forge
+  $ forge
+
+Read more at the [Allinea
+DDT](debuggers/allinea-ddt.html) page.
+
+Allinea Performance Reports
+---------------------------
+
+Allinea Performance Reports characterize the performance of HPC
+application runs. After executing your application through the tool, a
+synthetic HTML report is generated automatically, containing information
+about several metrics along with clear behavior statements and hints to
+help you improve the efficiency of your runs. Our license is limited to
+64 MPI processes.
+
+  $ module load PerformanceReports/6.0 
+  $ perf-report mpirun -n 64 ./my_application argument01 argument02
+
+Read more at the [Allinea Performance
+Reports](debuggers/allinea-performance-reports.html)
+page.
+
+RougeWave Totalview
+-------------------
+
+TotalView is a source- and machine-level debugger for multi-process,
+multi-threaded programs. Its wide range of tools provides ways to
+analyze, organize, and test programs, making it easy to isolate and
+identify problems in individual threads and processes in programs of
+great complexity.
+
+  $ module load totalview
+  $ totalview
+
+Read more at the [Totalview](debuggers/total-view.html)
+page.
+
+Vampir trace analyzer
+---------------------
+
+Vampir is a GUI trace analyzer for traces in OTF format.
+
+  $ module load Vampir/8.5.0
+  $ vampir
+
+Read more at
+the [Vampir](../../salomon/software/debuggers/vampir.html) page.
+
+
+
+