Commit 807e9dc5 authored by Lukáš Krupčík's avatar Lukáš Krupčík
Browse files

This closes #14

parent 373b7a16
Pipeline #1811 passed with stages
in 1 minute and 30 seconds
......@@ -44,4 +44,4 @@ 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"
- 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"
......@@ -20,7 +20,7 @@ Modules
|Application|Version|module|
|---|---|
|**R**|R 3.1.1|R/3.1.1-intel-2015b|
|**Rstudio**|Rstudio 0.97|Rstudio|
|**Rstudio**|Rstudio 0.98.1103|Rstudio|
```bash
$ module load R
......@@ -97,7 +97,7 @@ Download the package [parallell](package-parallel-vignette.pdf) vignette.
The forking is the most simple to use. Forking family of functions provide parallelized, drop in replacement for the serial apply() family of functions.
!!! Note "Note"
!!! warning
Forking via package parallel provides functionality similar to OpenMP construct omp parallel for
Only cores of single node can be utilized this way!
......
......@@ -51,13 +51,201 @@ $ man -M /apps/gentoo/usr/share/man samtools
Listing of bioinformatics applications
--------------------------------------
[gentoo_apps_on_anselm.doc](src/gentoo_apps_on_anselm.doc)
```bash
mmokrejs@login2 ~ $ grep biology /scratch/mmokrejs/gentoo_rap/installed.txt
sci-biology/ANGLE-bin-20080813-r1
sci-biology/AlignGraph-9999
sci-biology/Atlas-Link-0.01-r1
sci-biology/BRANCH-9999
sci-biology/EBARDenovo-1.2.2
sci-biology/FLASH-1.2.9
sci-biology/GAL-0.2.2
sci-biology/Gambit-0.4.145
sci-biology/HTSeq-0.6.1
sci-biology/InterMine-0.98
sci-biology/MochiView-1.45
sci-biology/MuSeqBox-5.4
sci-biology/ONTO-PERL-1.41
sci-biology/ORFcor-20130507
sci-biology/Rcorrector-9999
sci-biology/SSAKE-3.8.2
sci-biology/STAR-9999
sci-biology/YASRA-2.33
sci-biology/abacas-1.3.1
sci-biology/align_to_scf-1.06
sci-biology/assembly-stats-9999
sci-biology/bambus-2.33
sci-biology/bamtools-9999
sci-biology/bcftools-1.2
sci-biology/bedtools-2.22.1
sci-biology/bfast-0.7.0a
sci-biology/biobambam2-9999
sci-biology/bismark-0.13.0
sci-biology/blat-34-r1
sci-biology/blue-1.1.3
sci-biology/bowtie-2.2.9
sci-biology/brat-1.2.4
sci-biology/bwa-0.7.13
sci-biology/bx-python-9999
sci-biology/cast-bin-20080813
sci-biology/cd-hit-4.6.5
sci-biology/cdbfasta-0.1
sci-biology/clover-2011.10.24
sci-biology/clustalw-2.1
sci-biology/cnrun-2.0.3
sci-biology/codonw-1.4.4-r2
sci-biology/conform-gt-1174
sci-biology/conifer-0.2.2
sci-biology/coral-1.4
sci-biology/cross_genome-20140822
sci-biology/cutadapt-9999
sci-biology/dawg-1.1.2
sci-biology/dna2pep-1.1
sci-biology/edena-3.131028
sci-biology/epga-9999
sci-biology/erpin-5.5b
sci-biology/estscan-3.0.3
sci-biology/eugene-4.1d
sci-biology/exonerate-gff3-9999
sci-biology/fastx_toolkit-0.0.14
sci-biology/gemini-9999
sci-biology/geneid-1.4.4
sci-biology/genepop-4.2.1
sci-biology/glimmerhmm-3.0.1-r1
sci-biology/gmap-2015.12.31.5
sci-biology/hexamer-19990330
sci-biology/hts-python-9999
sci-biology/jellyfish-2.1.4
sci-biology/jigsaw-3.2.10
sci-biology/kallisto-9999
sci-biology/karect-1.0.0
sci-biology/lastz-1.03.66
sci-biology/libgtextutils-0.6.1
sci-biology/lucy-1.20
sci-biology/megahit-9999
sci-biology/merlin-1.1.2
sci-biology/miranda-3.3a
sci-biology/mreps-2.5
sci-biology/mrfast-2.6.0.1
sci-biology/mummer-3.22-r1
sci-biology/muscle-3.8.31
sci-biology/nrcl-110625
sci-biology/nwalign-0.3.1
sci-biology/oases-9999
sci-biology/parafly-20130121
sci-biology/phrap-1.080812-r1
sci-biology/phred-071220
sci-biology/phylip-3.696-r1
sci-biology/plinkseq-0.10
sci-biology/primer3-2.3.7
sci-biology/prinseq-lite-0.20.4
sci-biology/proda-1.0
sci-biology/pybedtools-0.6.9
sci-biology/pysam-0.9.0
sci-biology/pysamstats-0.24.2
sci-biology/quast-2.3
sci-biology/quorum-1.0.0
sci-biology/reaper-15348
sci-biology/repeatmasker-libraries-20150807
sci-biology/reptile-1.1
sci-biology/samstat-20130708
sci-biology/samtools-0.1.20-r2
sci-biology/samtools-1.3-r1
sci-biology/scaffold_builder-20131122-r1
sci-biology/scan_for_matches-20121220
sci-biology/screed-0.7.1
sci-biology/scythe-0.992
sci-biology/seqan-2.1.1
sci-biology/seqtools-4.34.5
sci-biology/sff_dump-1.04
sci-biology/sgp2-1.1
sci-biology/shrimp-2.2.3
sci-biology/sickle-9999
sci-biology/smalt-0.7.6
sci-biology/snpomatic-9999
sci-biology/ssaha2-bin-2.5.5
sci-biology/stampy-1.0.28
sci-biology/stringtie-1.2.2
sci-biology/subread-1.4.6
sci-biology/swissknife-1.72
sci-biology/tagdust-20101028
sci-biology/tclust-110625
sci-biology/tigr-foundation-libs-2.0-r1
sci-biology/trans-abyss-1.4.8
sci-biology/trf-4.07b
sci-biology/uchime-4.2.40
sci-biology/velvet-1.2.10
sci-biology/velvetk-20120606
sci-biology/zmsort-110625
```
```bash
mmokrejs@login2 ~ $ grep sci-libs /scratch/mmokrejs/gentoo_rap/installed.txt
sci-libs/amd-2.3.1
sci-libs/blas-reference-20151113-r1
sci-libs/camd-2.3.1
sci-libs/cbflib-0.9.3.3
sci-libs/ccolamd-2.8.0
sci-libs/cholmod-2.1.2
sci-libs/coinor-cbc-2.8.9
sci-libs/coinor-cgl-0.58.6
sci-libs/coinor-clp-1.15.6-r1
sci-libs/coinor-dylp-1.9.4
sci-libs/coinor-osi-0.106.6
sci-libs/coinor-utils-2.9.11
sci-libs/coinor-vol-1.4.4
sci-libs/colamd-2.8.0
sci-libs/cxsparse-3.1.2
sci-libs/dcmtk-3.6.0
sci-libs/gsl-2.1
sci-libs/hdf5-1.8.15_p1
sci-libs/htslib-1.3
sci-libs/io_lib-1.14.7
sci-libs/lapack-reference-3.6.0-r1
sci-libs/lemon-1.3-r2
sci-libs/libmaus2-9999
sci-libs/qrupdate-1.1.2-r1
sci-libs/scikits-0.1-r1
sci-libs/suitesparseconfig-4.2.1
sci-libs/umfpack-5.6.2
mmokrejs@login2 ~ $
error-correctors
aligners
clusterers
assemblers
scaffolders
motif searching
ORF/gene prediction/genome annotation
genotype/haplotype/popullation genetics
phylogenetics
transcriptome analysis
utilities
GUI
libraries
```
Classification of applications
------------------------------
[gentoo_apps_on_anselm.xls](src/gentoo_apps_on_anselm.xls)
|Applications for bioinformatics at IT4I |
|---|---|
|error-correctors|6|
|aligners|20|
|clusterers|5|
|assemblers|9|
|scaffolders|6|
|motif searching|6|
|ORF/gene prediction/genome annotation|13|
|genotype/haplotype/popullation genetics|3|
|phylogenetics|1|
|transcriptome analysis|2|
|utilities|15|
|GUI|3|
|libraries|4|
|**Total**|**93**|
![graphs](../img/bio-graphs.png)
Other applications available through Gentoo Linux
......
ORCA
====
ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects.
Making orca available
---------------------
The following module command makes the latest version of orca available to your session
```bash
$ module load ORCA/3_0_3-linux_x86-64
```
**Dependency**
```bash
$ module list
Currently Loaded Modulefiles:
1) /opt/modules/modulefiles/oscar-modules/1.0.3(default)
2) GCC/4.9.3-binutils-2.25
3) binutils/2.25-GCC-4.9.3-binutils-2.25
4) GNU/4.9.3-2.25
5) icc/2015.3.187-GNU-4.9.3-2.25
6) ifort/2015.3.187-GNU-4.9.3-2.25
7) iccifort/2015.3.187-GNU-4.9.3-2.25
8) numactl/2.0.10-iccifort-2015.3.187-GNU-4.9.3-2.25
9) hwloc/1.11.1-iccifort-2015.3.187-GNU-4.9.3-2.25
10) OpenMPI/1.8.8-iccifort-2015.3.187-GNU-4.9.3-2.25
11) ORCA/3_0_3-linux_x86-64
```
Example single core job
-----------------------
Create a file called orca_serial.inp that contains the following orca commands
```
# My first ORCA calculation :-)
#
# Taken from the Orca manual
# https://orcaforum.cec.mpg.de/OrcaManual.pdf
! HF SVP
* xyz 0 1
C 0 0 0
O 0 0 1.13
*
```
Create a Sun Grid Engine submission file called submit_serial.sh that looks like this
```bash
!/bin/bash
module load ORCA/3_0_3-linux_x86-64
orca orca_serial.inp
```
Submit the job to the queue with the command
```bash
$ qsub -q qexp -I -l select=1
qsub: waiting for job 196821.isrv5 to start
qsub: job 196821.isrv5 ready
[username@r37u04n944 ~]$ ./submit_serial.sh
*****************
* O R C A *
*****************
--- An Ab Initio, DFT and Semiempirical electronic structure package ---
#######################################################
# -***- #
# Department of molecular theory and spectroscopy #
# Directorship: Frank Neese #
# Max Planck Institute for Chemical Energy Conversion #
# D-45470 Muelheim/Ruhr #
# Germany #
# #
# All rights reserved #
# -***- #
#######################################################
...
****ORCA TERMINATED NORMALLY****
TOTAL RUN TIME: 0 days 0 hours 0 minutes 2 seconds 796 msec
[username@r37u04n944 orca]$ logout
qsub: job 196821.isrv5 completed
```
Register as a user
------------------
You are encouraged to register as a user of Orca at [Here](https://orcaforum.cec.mpg.de/) in order to take advantage of updates, announcements and also of the users forum.
Documentation
-------------
A comprehensive [.pdf](https://orcaforum.cec.mpg.de/OrcaManual.pdf) manual is available online.
,kru0052,kru0052,24.01.2017 06:58,file:///home/kru0052/.config/libreoffice/4;
\ No newline at end of file
......@@ -53,7 +53,7 @@ pages:
- ANSYS MAPDL: anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl.md
- LS-DYNA: anselm-cluster-documentation/software/ansys/ls-dyna.md
- 'Bioinformatics':
- Bioinformatics Applications: anselm-cluster-documentation/software/bio-gentoo.md
- Bioinformatics Applications: software/bio-gentoo.md
- 'Debuggers':
- Allinea Forge (DDT,MAP): anselm-cluster-documentation/software/debuggers/allinea-ddt.md
- Allinea Performance Reports: anselm-cluster-documentation/software/debuggers/allinea-performance-reports.md
......@@ -70,6 +70,7 @@ pages:
- 'Chemistry':
- Molpro: anselm-cluster-documentation/software/chemistry/molpro.md
- NWChem: anselm-cluster-documentation/software/chemistry/nwchem.md
- ORCA: software/orca.md
- COMSOL: anselm-cluster-documentation/software/comsol-multiphysics.md
- Compilers: anselm-cluster-documentation/software/compilers.md
- GPI-2: anselm-cluster-documentation/software/gpi2.md
......@@ -138,10 +139,13 @@ pages:
- Workbench: salomon/software/ansys/workbench.md
- Setting License Preferences: salomon/software/ansys/licensing.md
- Licensing and Available Versions: salomon/software/ansys/setting-license-preferences.md
- 'Bioinformatics':
- Bioinformatics Applications: software/bio-gentoo.md
- 'Chemistry':
- Molpro: salomon/software/chemistry/molpro.md
- NWChem: salomon/software/chemistry/nwchem.md
- Phono3py: salomon/software/chemistry/phono3py.md
- ORCA: software/orca.md
- Compilers: salomon/software/compilers.md
- 'COMSOL':
- COMSOL: salomon/software/comsol/comsol-multiphysics.md
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment